Coffin-Siris syndrome

Mendelian MONDO:0015452 Pathograph 41 Show in embeddings browser chromatin remodeling disorder neurodevelopmental disorder

Coffin-Siris syndrome is a genetically heterogeneous autosomal dominant neurodevelopmental disorder caused by pathogenic variants in genes encoding subunits of the BAF/SWI-SNF chromatin remodeling complex. Core manifestations include developmental delay or intellectual disability, coarse facial features, hypoplasia or aplasia of the fifth digit nails or distal phalanges, hypotonia, feeding difficulties, hypertrichosis, sparse scalp hair, short stature, and additional congenital anomalies including cardiac, renal, and brain malformations. Epilepsy and hearing impairment are frequent complications.

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Classifications

ISDS Skeletal Nosology

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Inheritance

Autosomal dominant inheritance HP:0000006

Coffin-Siris syndrome is usually inherited in an autosomal dominant manner, and many molecularly confirmed cases are de novo.

Autosomal dominant inheritance

Show evidence (2 references)

PMID:38790056 SUPPORT Human Clinical

"Coffin-Siris syndrome (CSS) is a rare autosomal dominant inheritance disorder characterized by distinctive facial features, hypoplasia of the distal phalanx or nail of the fifth and additional digits, developmental or cognitive delay of varying degree, hypotonia, hirsutism/hypertrichosis, sparse..."

This directly supports autosomal dominant inheritance for CSS.

PMID:23815551 SUPPORT Human Clinical

"By examining available parental samples, we ascertained that 17 occurred de novo."

This supports the statement that many CSS cases arise de novo.

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Subtypes

Coffin-Siris syndrome 4 (SMARCA4-related) MONDO:0013821

SMARCA4 hgnc:11100 Autosomal dominant inheritance

The SMARCA4-related form of Coffin-Siris syndrome, corresponding to OMIM 614609. SMARCA4 encodes BRG1, the catalytic ATPase subunit of the BAF/PBAF chromatin-remodelling complex - so this is the subtype in which the motor of the complex is damaged rather than one of its scaffolding or targeting subunits. The subtype carries two names for one concept, and the second name is the informative one. MONDO's primary label is "intellectual disability, autosomal dominant 16" (MRD16); its synonyms include "Coffin-Siris syndrome 4" and "SMARCA4-related BAFopathy"; and its definition is explicitly "any Coffin-Siris syndrome in which the cause of the disease is a mutation in the SMARCA4 gene". The MRD16 label exists because a substantial fraction of SMARCA4 patients come to attention as non-syndromic intellectual disability or autism rather than as classic Coffin-Siris syndrome: in one series of eight children with novel SMARCA4 missense variants, all had moderate to severe intellectual disability and seven had autistic or likely-autistic features, while being *less* likely than published Coffin-Siris patients to show the craniofacial or finger and toe anomalies. Reading MRD16 as a separate disease from Coffin-Siris syndrome would split one gene's phenotypic range in two along an ascertainment line. Genotype-phenotype, stated with the hedge the sources put on it. SMARCA4 variants in Coffin-Siris syndrome were originally all non-truncating - missense or in-frame deletion - which is the variant class this subtype was defined on, and which distinguishes it from the germline loss-of-function SMARCA4 alleles that cause rhabdoid tumour predisposition syndrome 2. That distinction has since softened: a 15-patient SMARCA4 registry cohort included two individuals with nonsense variants who had milder learning and behavioural differences and no organ-system involvement. At the level of gene families rather than individual alleles, SMARC-related Coffin-Siris patients have been proposed to have more severe organ-related complications than ARID-related patients - but the same study that reports that correlation concludes that everyone with a BAF-related condition is at risk of most of the phenotype and that surveillance should be broad. The correlation is a tendency, not a triage rule.

Show evidence (9 references)

PMID:23556151 SUPPORT DIRECT Human Clinical

"The diagnosis of CSS is established in a proband with suggestive findings and a heterozygous pathogenic variant in one of the following 14 known genes identified by molecular genetic testing: ARID1A, ARID1B, ARID2, BICRA, DPF2, PHF6, SMARCA2, SMARCA4, SMARCB1, SMARCC2, SMARCD1, SMARCE1, SOX4, or SOX11."

GeneReviews establishes the diagnosis of Coffin-Siris syndrome on a variant in any of fourteen genes including SMARCA4, which is what makes the gene a subtype axis within this disease rather than a disease boundary.

PMID:23815551 SUPPORT DIRECT Human Clinical

"All mutations in SMARCB1 and SMARCA4 were non-truncating (missense or in-frame deletion) whereas those in ARID1B were all truncating (nonsense or frameshift deletion/insertion)"

The non-truncating variant class on which this subtype was originally defined, and the feature that separated it from loss-of-function SMARCA4 disease.

PMID:34813034 SUPPORT DIRECT Human Clinical

"All eight patients had moderate to severe intellectual disability, and seven showed autistic/likely autistic features."

The neurodevelopmental pole of the SMARCA4 phenotype, which is why MONDO's primary label for this concept is an intellectual-disability term rather than a Coffin-Siris one.

+ 6 more references

Coffin-Siris syndrome 6 (ARID2-related) MONDO:0033492

ARID2 hgnc:18037 Autosomal dominant inheritance

The ARID2-related form of Coffin-Siris syndrome, corresponding to OMIM 617808. ARID2 is a PBAF-specific subunit - an intrinsic component of the polybromo brahma-associated factor SWI/SNF subcomplex - so this is a subtype in which a targeting subunit of the complex is damaged rather than its catalytic ATPase, which is the CSS4 lesion. The mechanism is loss of function through truncating variants, mostly de novo. ARID2 is already curated in this entry's `genetic:` block, where it is recorded as a less frequent CSS gene with a somewhat milder but still recognisably classic phenotype and a higher rate of hip dysplasia; this row adds the MONDO subtype identity that the gene record did not carry. ClinGen classifies the gene-disease relationship as Definitive against Coffin-Siris syndrome itself (MONDO:0015452).

Show evidence (5 references)

CGGV:assertion_ae1a697f-8dcd-4edf-a25b-e5e0593e7e61-2022-12-06T230000.000Z SUPPORT Other

ClinGen curates the ARID2 gene-disease relationship against Coffin-Siris syndrome, which is the basis for placing this subtype row on this entry rather than under a non-syndromic parent.

CGGV:assertion_ae1a697f-8dcd-4edf-a25b-e5e0593e7e61-2022-12-06T230000.000Z SUPPORT Other

"ARID2 was first reported in relation to autosomal dominant Coffin-Siris syndrome in 2015 by Shang et al . (PMID: 26238514), who reported four individuals with truncating variants."

The founding report of the ARID2-Coffin-Siris relationship, and the source of the truncating-variant mechanism recorded above.

CGGV:assertion_ae1a697f-8dcd-4edf-a25b-e5e0593e7e61-2022-12-06T230000.000Z SUPPORT Other

"ARID2 is an intrinsic component of polybromo brahma-associated factor (PBAF), a SWI/SNF subcomplex involved in chromatin remodeling."

Places ARID2 in the PBAF subcomplex, the basis for contrasting this subtype with the SMARCA4 catalytic-ATPase lesion of CSS4.

+ 2 more references

Coffin-Siris syndrome 1 (ARID1B-related) MONDO:0007617

ARID1B hgnc:18040 Autosomal dominant inheritance

The numbered form caused by heterozygous ARID1B variants, and the largest single group within molecularly confirmed Coffin-Siris syndrome. Most variants are truncating and act through haploinsufficiency; a subset of non-truncating variants act instead through protein aggregation, which the pathophysiology section models as a separate node.

Show evidence (2 references)

PMID:24674232 SUPPORT Human Clinical

"ARID1B mutations have been identified as the predominant cause of Coffin-Siris syndrome and have also been shown to be a frequent cause of nonsyndromic intellectual disability."

Supports ARID1B as the predominant cause, which is why this numbered form is the largest group.

CGGV:assertion_d487e6c4-9727-4315-90a2-11338128a8e5-2019-12-04T200734.569Z SUPPORT Other

ClinGen classifies the relationship as Definitive under autosomal dominant inheritance, which is the mode recorded on this subtype.

Coffin-Siris syndrome 2 (ARID1A-related; MONDO label "intellectual disability, autosomal dominant 14") MONDO:0013819

ARID1A hgnc:11110 Autosomal dominant inheritance

The numbered form caused by heterozygous ARID1A variants, one of the six SWI/SNF subunit genes in the founding 2012 series. MONDO's primary label for this concept is "intellectual disability, autosomal dominant 14" rather than a Coffin-Siris name, which is why the display name records both.

Show evidence (2 references)

PMID:22426308 SUPPORT Human Clinical

"Twenty affected individuals (87%) each had a germline mutation in one of six SWI/SNF subunit genes, including SMARCB1, SMARCA4, SMARCA2, SMARCE1, ARID1A and ARID1B."

Identifies ARID1A as one of the six original Coffin-Siris SWI/SNF genes.

CGGV:assertion_aaf6d47a-656a-49ca-ba9e-169f25bf03e7-2021-07-07T160000.000Z SUPPORT Other

ClinGen classifies the relationship as Definitive under autosomal dominant inheritance.

Coffin-Siris syndrome 3 (SMARCB1-related; MONDO label "intellectual disability, autosomal dominant 15") MONDO:0013820

SMARCB1 hgnc:11103 Autosomal dominant inheritance

The numbered form caused by heterozygous SMARCB1 variants. Unlike ARID1B, the Coffin-Siris-associated SMARCB1 variants are non-truncating, which is the distinction the cited cohort drew. MONDO's primary label is "intellectual disability, autosomal dominant 15". SMARCB1 is separately a tumour-predisposition gene; this subtype records only the germline neurodevelopmental disorder.

Show evidence (2 references)

PMID:23815551 SUPPORT Human Clinical

"All mutations in SMARCB1 and SMARCA4 were non-truncating (missense or in-frame deletion) whereas those in ARID1B were all truncating (nonsense or frameshift deletion/insertion)"

Supports the non-truncating variant class recorded in this subtype's description.

CGGV:assertion_ea554e80-81d2-4100-8d0e-b762ea38fe23-2023-08-15T040000.000Z SUPPORT Other

ClinGen classifies the relationship as Definitive under autosomal dominant inheritance.

Coffin-Siris syndrome 5 (SMARCE1-related) MONDO:0014838

SMARCE1 hgnc:11109 Autosomal dominant inheritance

The numbered form caused by heterozygous SMARCE1 variants. SMARCE1 was one of the six SWI/SNF subunit genes identified in the founding 2012 series.

Show evidence (2 references)

PMID:22426308 SUPPORT Human Clinical

"Twenty affected individuals (87%) each had a germline mutation in one of six SWI/SNF subunit genes, including SMARCB1, SMARCA4, SMARCA2, SMARCE1, ARID1A and ARID1B."

Identifies SMARCE1 as one of the six original Coffin-Siris SWI/SNF genes.

CGGV:assertion_877f5e0f-5b30-4a4f-87c3-cb6b87caa1e4-2024-09-18T190000.000Z SUPPORT Other

ClinGen classifies the relationship as Definitive under autosomal dominant inheritance.

Coffin-Siris syndrome 7 (DPF2-related) MONDO:0054831

DPF2 hgnc:9964 Autosomal dominant inheritance

The numbered form caused by de novo DPF2 variants, for which the founding report proposes a dominant-negative mechanism rather than simple haploinsufficiency.

Show evidence (2 references)

PMID:29429572 SUPPORT Human Clinical

"Altogether, we provide compelling evidence that de novo variants in DPF2 cause Coffin-Siris syndrome and propose a dominant-negative mechanism of pathogenicity."

Supports both the de novo variant class and the dominant-negative mechanism recorded in this subtype's description.

CGGV:assertion_cc8c072e-7b8d-4a94-97fe-c15c91759f0f-2023-08-15T020000.000Z SUPPORT Other

ClinGen classifies the relationship as Definitive under autosomal dominant inheritance.

Coffin-Siris syndrome 8 (SMARCC2-related) MONDO:0032702

SMARCC2 hgnc:11105 Autosomal dominant inheritance

The numbered form caused by heterozygous SMARCC2 variants. SMARCC2 is among the BAF-complex genes whose pathogenic variants cause this disease.

Show evidence (2 references)

PMID:41291750 SUPPORT Human Clinical

"Coffin-Siris Syndrome 8 (CSS8; MIM# 618362) is a rare neurodevelopmental disorder caused by heterozygous variants in the SMARCC2 gene."

Names the numbered form and its causal gene, which is the identity this subtype binds.

CGGV:assertion_aa645aa6-3a03-4ab7-9d09-b17be3184259-2025-09-17T100000.000Z SUPPORT Other

ClinGen classifies the relationship as Definitive under autosomal dominant inheritance.

Coffin-Siris syndrome 10 (SOX4-related; reported as CSS-like rather than classic CSS) MONDO:0032791

SOX4 hgnc:11200 Autosomal dominant inheritance

The form caused by de novo SOX4 variants clustering in the HMG DNA-binding domain, which abolish SOX4 transcriptional activity in vitro. SOX4 is a SOXC transcription factor rather than a BAF subunit, and it reaches the shared skeletal mechanism through the SOXC paralogue programme that the pathophysiology section models. The MONDO label numbers this as Coffin-Siris syndrome 10, but the largest published cohort is explicit that these patients resemble Coffin-Siris syndrome while lacking its most specific features, and concludes that the entity is a fairly non-specific neurodevelopmental syndrome due to SOX4 haploinsufficiency. It is curated here as a subtype because the gene sits in the same developmental programme as SOX11 and is routinely reported in the BAF/Coffin-Siris gene panel, but the phenotype distinction should not be lost.

Show evidence (2 references)

PMID:30661772 SUPPORT Human Clinical

"Using trio-based exome sequencing, we here identify de novo SOX4 heterozygous missense variants in four children who share developmental delay, intellectual disability, and mild facial and digital morphological abnormalities."

Establishes de novo heterozygous SOX4 variants and the dominant inheritance recorded on this subtype.

PMID:35232796 SUPPORT Human Clinical

"They resembled patients with other neurodevelopmental diseases, including the SOX11-related and Coffin-Siris (CSS) syndromes, but lacked the most specific features of CSS."

Supports the caveat recorded above: the largest cohort places SOX4 disease next to Coffin-Siris syndrome rather than inside it.

Coffin-Siris syndrome 11 (SMARCD1-related) MONDO:0032912

SMARCD1 hgnc:11106 Autosomal dominant inheritance

The numbered form caused by de novo SMARCD1 variants. SMARCD1 is a core SWI/SNF subunit, so the mechanism is the shared BAF-complex dysfunction. As with SOX4, the founding series notes that these individuals overlap the BAF-related syndromes clinically but lack their typical facial dysmorphisms, so the numbered Coffin-Siris label is broader than the reported phenotype.

Show evidence (2 references)

PMID:30879640 SUPPORT Human Clinical

"Here, we report on five individuals with mutations in SMARCD1; the individuals present with developmental delay, intellectual disability, hypotonia, feeding difficulties, and small hands and feet."

Establishes SMARCD1 as the causal gene and gives the reported phenotype.

PMID:30879640 SUPPORT Human Clinical

"Although the individuals presented here have dysmorphisms and some clinical overlap with these syndromes, they lack their typical facial dysmorphisms."

Supports the phenotype caveat recorded above.

Coffin-Siris syndrome 12 (BICRA-related, non-canonical BAF) MONDO:0025699

BICRA hgnc:4332 Autosomal dominant inheritance

The numbered form caused by haploinsufficiency of BICRA (also GLTSCR1), which encodes a subunit of the non-canonical BAF (ncBAF) complex rather than of canonical BAF. Most reported individuals lack fifth digit or nail hypoplasia, which is otherwise the signature feature of this disease group, so the phenotype is recognisably a SWI/SNF-related disorder without the Coffin-Siris hand finding.

Show evidence (4 references)

PMID:33232675 SUPPORT Human Clinical

"We have identified 12 individuals with rare variants (10 loss-of-function, 2 missense) in the BICRA (BRD4 interacting chromatin remodeling complex-associated protein) gene, also known as GLTSCR1, which encodes a subunit of the non-canonical BAF (ncBAF) complex."

Establishes BICRA as causal in 12 individuals and places it in the non-canonical BAF complex, which is the distinction recorded in this subtype's description.

PMID:33232675 SUPPORT Human Clinical

"Notably, the majority of individuals lack the fifth digit/nail hypoplasia phenotype, a hallmark of most SSRIDDs."

Supports the absence of the signature hand finding recorded above.

PMID:36437209 SUPPORT Human Clinical

"Pathogenic heterozygous variants in BICRA have recently been identified in patients with SWI/SNF-related intellectual disability (SSRIDD) - Coffin-Siris syndrome 12."

Names the numbered Coffin-Siris syndrome 12 designation for BICRA disease, which is the identity this subtype binds.

+ 1 more reference

SOX11-related neurodevelopmental disorder (mild Coffin-Siris phenotype)

SOX11 hgnc:11191 Autosomal dominant inheritance

The form caused by de novo SOX11 variants. Like SOX4, SOX11 is a SOXC transcription factor rather than a BAF subunit, and the phenotype is reported as a mild Coffin-Siris syndrome. No subtype_term is bound. MONDO gives this concept no Coffin-Siris number; its class is MONDO:0014376, whose primary label names intellectual developmental disorder with microcephaly and with or without ocular malformations or hypogonadotropic hypogonadism, and that class is already the disease_term of the SOX11-Related_Neurodevelopmental_Disorder entry. This row carries the gene for the parent pathograph rather than claiming the same identifier a second time.

Show evidence (2 references)

PMID:30661772 SUPPORT BACKGROUND Human Clinical

"De novo SOX11 heterozygous mutations have been shown to cause intellectual disability, growth deficiency, and dysmorphic features compatible with mild Coffin-Siris syndrome."

States the mild Coffin-Siris reading of SOX11 disease that this subtype records. Marked BACKGROUND because the sentence is the cited SOX4 paper's framing of prior work on SOX11, not its own result.

PMID:39501269 SUPPORT Human Clinical

"The combination of clinical presentation and genetic testing results supports that the patient suffers from Coffin-Siris syndrome due to a genetic variant in the SOX11 gene."

An independent case report diagnosing Coffin-Siris syndrome on the basis of a SOX11 variant.

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Pathophysiology

BAF/SWI-SNF chromatin remodeling dysfunction

Pathogenic variants in BAF-complex genes reduce or alter ATP-dependent chromatin remodeling, disturbing transcriptional programs required for embryonic patterning and neurodevelopment. CSS therefore behaves as a BAFopathy in which disruption of one of several chromatin-remodeling subunits converges on abnormal developmental gene regulation.

neural progenitor cell CL:0011020

ARID1A hgnc:11110 ARID1B hgnc:18040 ARID2 hgnc:18037 DPF2 hgnc:9964 SMARCA2 hgnc:11098 SMARCA4 hgnc:11100 SMARCB1 hgnc:11103 SMARCE1 hgnc:11109 SMARCC2 hgnc:11105 SMARCD1 hgnc:11106

BAF complex GO:0016514

chromatin remodeling GO:0006338 regulation of transcription by RNA polymerase II GO:0006357 nervous system development GO:0007399

brain UBERON:0000955

Downstream

Altered developmental transcription programs Reduced BAF activity perturbs expression programs needed for normal tissue differentiation.

Global developmental delay Multisystem dysregulation of developmental gene expression manifests clinically as near-universal global developmental delay.

Intellectual disability Disrupted BAF-dependent regulation of neuronal gene programs underlies the universal cognitive impairment of CSS.

Show evidence (5 references)

PMID:23815551 SUPPORT Human Clinical

"Our data further support that CSS is a SWI/SNF complex disorder."

This explicitly supports CSS as a SWI/SNF complex disorder.

PMID:30276971 SUPPORT Human Clinical

"Coffin-Siris syndrome (CSS; MIM 135900) is a multisystem congenital anomaly syndrome caused by mutations in the genes in the Brg-1 associated factors (BAF) complex."

This independently confirms BAF-complex dysfunction as the central disease mechanism.

PMID:22426308 SUPPORT Human Clinical

"Twenty affected individuals (87%) each had a germline mutation in one of six SWI/SNF subunit genes, including SMARCB1, SMARCA4, SMARCA2, SMARCE1, ARID1A and ARID1B."

The landmark 2012 study showing high diagnostic yield of SWI/SNF mutations in CSS.

+ 2 more references

Cortical interneuron deficiency from ARID1B haploinsufficiency

ARID1B haploinsufficiency reduces GABAergic interneuron numbers in the cerebral cortex through impaired proliferation and increased apoptosis of interneuron progenitors in the ganglionic eminence, creating an excitatory-inhibitory imbalance that underlies cognitive and behavioral abnormalities.

GABAergic interneuron CL:0000617 neural progenitor cell CL:0011020

ARID1B hgnc:18040

GABAergic neuron differentiation GO:0097154 regulation of neuron apoptotic process GO:0043523

cerebral cortex UBERON:0000956

Downstream

Excitatory-inhibitory imbalance Reduced cortical GABAergic interneurons create an imbalance between excitatory and inhibitory synaptic transmission, contributing to cognitive dysfunction and autism-like behaviors.

Intellectual disability Loss of cortical inhibitory interneurons and the resulting cortical excitation-inhibition imbalance contribute to cognitive impairment; conditional deletion of Arid1b in ventral (interneuron) progenitors specifically produces ID- and ASD-like behavior in mice.

Seizures Reduced cortical GABAergic inhibition and resulting excitatory-inhibitory imbalance provide a mechanistic basis for the increased seizure susceptibility seen in CSS.

Show evidence (2 references)

PMID:29184203 SUPPORT Model Organism

"Arid1b-heterozygous mice showed a decreased number of cortical GABAergic interneurons and reduced proliferation of interneuron progenitors in the ganglionic eminence."

Direct evidence from an Arid1b haploinsufficiency mouse model showing reduced cortical interneurons.

PMID:29184203 SUPPORT Model Organism

"Arid1b haploinsufficiency suppressed histone H3 lysine 9 acetylation (H3K9ac) overall and particularly reduced H3K9ac of the Pvalb promoter, resulting in decreased transcription."

This provides the epigenetic mechanism linking Arid1b loss to reduced parvalbumin interneuron differentiation.

Altered cell-cycle dynamics from ARID1B haploinsufficiency

ARID1B haploinsufficiency causes delayed cell-cycle re-entry in patient-derived cells, indicating that abnormal proliferation dynamics contribute to CSS pathogenesis and likely impair tissue growth and developmental progression.

fibroblast CL:0000057

ARID1B hgnc:18040

regulation of cell cycle process GO:0010564

Downstream

Reduced proliferative capacity Delayed cell-cycle re-entry limits normal expansion of developing cell populations.

Microcephaly Reduced proliferation of cortical neural progenitors limits cortical neuron output and brain volume; ARID1B-deficient cortical and ventral neural progenitors show decreased proliferation and increased cell death.

Short stature Reduced proliferative capacity of mesenchymal/somatic cells and ARID1B-dependent IGF1/GH axis dysregulation jointly produce growth restriction and short stature.

Show evidence (2 references)

PMID:24674232 SUPPORT In Vitro

"Analysis of both patient-derived and ARID1B knockdown fibroblasts after serum starvation demonstrated delayed cell cycle re-entry associated with reduced cell number in the S1 phase."

This provides direct functional evidence that ARID1B haploinsufficiency alters cell-cycle dynamics.

PMID:24674232 SUPPORT In Vitro

"We present the first direct evidence in patient-derived cells that alterations in cell cycle contribute to the underlying pathogenesis of syndromes associated with ARID1B haploinsufficiency."

This explicitly connects altered cell-cycle control to CSS pathogenesis.

Protein misfolding and aggregation of non-truncating ARID1B variants

A subset of ARID1B missense variants cause CSS by provoking protein misfolding and aggregate formation rather than classical nonsense-mediated decay, thereby reducing functional nuclear BAF activity through an alternative loss-of-function mechanism.

ARID1B hgnc:18040

protein folding GO:0006457

Downstream

Reduced functional ARID1B availability Aggregated ARID1B fails to contribute normally to BAF-complex function.

Show evidence (2 references)

PMID:39028335 SUPPORT In Vitro

"The present study substantiates the pathogenesis of ARID1B non-truncating/NMD-escaping variants located in the SMARCA4-interacting EHD2 and DNA-binding ARID domains. Overexpression assays in cell lines revealed that the majority of EHD2 variants lead to protein misfolding and formation of..."

This supports protein misfolding and aggregation as a pathogenic mechanism for a subset of ARID1B variants in CSS.

PMID:39028335 SUPPORT Human Clinical

"Genome-wide transcriptome and methylation analysis in affected individuals revealed expression and methylome patterns consistent with those of the pathogenic haploinsufficiency ARID1B alterations in CSS cases."

This shows that aggregation-prone ARID1B variants converge on the same downstream molecular state as haploinsufficient CSS.

Cranial neural crest specification defect from ARID1A-BAF/ZIC2 axis

ARID1A haploinsufficiency impairs ARID1A-BAF binding at enhancers of epithelial-to-mesenchymal transition (EMT) genes, disrupts ZIC2 occupancy at these enhancers, and impairs delamination/migration of cranial neural crest cells. Conserved BAF complex activity (via BAF155/BAF170) is also required during murine neural crest development for correct craniofacial, pharyngeal arch and outflow tract formation. Failure of cranial neural crest specification underlies coarse facial dysmorphism, micrognathism, and other craniofacial features of CSS.

cranial neural crest cell CL:0000008 migratory neural crest cell CL:0000333

ARID1A hgnc:11110 SMARCA4 hgnc:11100

BAF complex GO:0016514

neural crest cell migration GO:0001755 epithelial to mesenchymal transition GO:0001837

neural tube UBERON:0001049

Downstream

Coarse facial features Impaired cranial neural crest delamination and migration disrupts development of facial mesenchyme and the craniofacial skeleton, producing the coarse and dysmorphic facial features that are a defining clinical feature of CSS.

Microcephaly Neural crest contributions to the cranial vault, plus broader BAF requirements during forebrain development, link cranial NCC and BAF dysfunction to reduced cranial growth.

Show evidence (4 references)

PMID:39226899 SUPPORT In Vitro

"Using CSS-patient-derived ARID1A+/- induced pluripotent stem cells to model CNCC specification, we discovered that ARID1A-haploinsufficiency impairs epithelial-to-mesenchymal transition (EMT), a process necessary for CNCC delamination and migration from the neural tube."

Directly demonstrates that ARID1A haploinsufficiency in CSS-patient iPSCs impairs cranial neural crest EMT and delamination.

PMID:39226899 SUPPORT In Vitro

"ARID1A-BAF binding at these enhancers is impaired in heterozygotes while binding at promoters is unaffected."

Mechanistically supports loss of ARID1A-BAF activity at EMT enhancers as the molecular event upstream of cranial NCC failure.

PMID:33750945 SUPPORT Model Organism

"Neural crest-specific deletion of BAF155/BAF170 leads to embryonic lethality due to a wide range of developmental defects including craniofacial, pharyngeal arch artery, and OFT defects."

Independent in vivo evidence that the BAF complex is required for craniofacial neural crest development.

+ 1 more reference

Cardiac neural crest dysregulation from BAF dysfunction

Brg1 (SMARCA4)/BAF activity in neural crest cells is required for outflow tract septation, pharyngeal arch artery patterning, and cardiomyocyte differentiation. CSS-causing variants in SMARCA4 and other BAF subunits disrupt the cardiac neural crest gene program, producing the spectrum of congenital heart defects (including septal defects, hypoplastic left heart, truncus arteriosus, and outflow tract anomalies) seen in CSS, particularly in prenatal and ARID1A-related cases.

cardiac neural crest cell CL:0000333

SMARCA4 hgnc:11100 ARID1A hgnc:11110 SMARCB1 hgnc:11103

BAF complex GO:0016514

outflow tract morphogenesis GO:0003151 neural crest cell migration GO:0001755

heart UBERON:0000948

Downstream

Congenital heart defects Disrupted Brg1/BAF activity in cardiac neural crest leads to outflow tract shortening, abnormal pharyngeal arch artery patterning and defective cardiogenic gene programs, producing structural cardiac defects ranging from septal defects to severe prenatal cardiovascular malformations.

Show evidence (2 references)

PMID:23319608 SUPPORT Model Organism

"Brahma-related gene 1 (Brg1), an ATPase subunit of the Brg1/Brahma-associated factor (BAF) chromatin-remodeling complex, is required in NCCs to direct cardiovascular development."

Establishes Brg1/SMARCA4 as required in cardiac neural crest, the cell population implicated in CSS cardiac malformations.

PMID:30814119 SUPPORT Model Organism

"the catalytic subunit gene Brg1 has a specific role in cardiac precursors (CPs) to initiate cardiac gene expression programs and repress non-cardiac expression."

Provides the mechanistic role of Brg1/BAF in cardiac precursors, complementing the neural-crest pathway.

Corpus callosum projection neuron axonogenesis defect from ARID1B haploinsufficiency

ARID1B haploinsufficiency impairs maturation of SATB2+ callosal projection neurons by reducing chromatin accessibility at TCF/NFI/ARID-bound regulatory regions controlling corpus callosum (CC) genes, leading to underdeveloped long-range axonal projections and structural underconnectivity. This cell-autonomous axonogenesis defect explains the high frequency of agenesis or hypoplasia of the corpus callosum (~50% in some cohorts) seen in CSS.

callosal projection neuron CL:0000540

ARID1B hgnc:18040

axonogenesis GO:0007409 regulation of transcription by RNA polymerase II GO:0006357

corpus callosum UBERON:0002336

Downstream

Agenesis of corpus callosum Impaired maturation and axon outgrowth of SATB2+ callosal projection neurons leads to absent or hypoplastic corpus callosum.

Intellectual disability Loss of long-range interhemispheric connectivity and dysregulated callosal axonogenesis programs contribute to cognitive impairment in CSS independent of the cortical interneuron deficit.

Show evidence (3 references)

PMID:38718796 SUPPORT In Vitro

"neurons expressing SATB2, a determinant of callosal projection neuron (CPN) identity, show impaired maturation in ARID1B+/- neural organoids."

Functionally identifies the cell-autonomous defect in SATB2+ neurons as the proximate cause of CC agenesis in ARID1B haploinsufficiency.

PMID:38718796 SUPPORT In Vitro

"a reduction in chromatin accessibility of genomic regions targeted by TCF-like, NFI-like, and ARID-like transcription factors drives the differential expression of genes required for corpus callosum (CC) development."

Provides the chromatin-accessibility/transcriptomic mechanism connecting ARID1B haploinsufficiency to CC dysgenesis.

PMID:34706719 SUPPORT Human Clinical

"Agenesis or hypoplasia of the corpus callosum was observed in half of the patients (6/12)."

Cohort-level confirmation that corpus callosum dysgenesis is a frequent CSS phenotype consistent with this mechanism.

Midline brain glia aberrations from SMARCB1 dysfunction

Heterozygous nervous-system-restricted partial loss of SMARCB1 produces brain midline abnormalities including agenesis of the corpus callosum through defective midline glia development. This pathway provides a SMARCB1-specific mechanism for the brain midline phenotype that overlaps with the ARID1B-axonogenesis pathway above.

glial cell CL:0000125

SMARCB1 hgnc:11103

glial cell development GO:0021782

corpus callosum UBERON:0002336 forebrain UBERON:0001890

Downstream

Agenesis of corpus callosum Defective midline glia development in Smarcb1 mutant mice causes corpus callosum agenesis recapitulating the brain midline phenotype seen in SMARCB1 (and other BAF) CSS patients.

Show evidence (1 reference)

PMID:31273213 SUPPORT Model Organism

"These Smarcb1 mutant mice show various brain midline abnormalities that are also found in individuals with Coffin-Siris syndrome (CSS) caused by SMARCB1, SMARCE1, and ARID1B mutations and in SMARCB1-related intellectual disability (ID) with choroid plexus hyperplasia (CPH)."

Provides the disease-model linkage for the SMARCB1 brain midline mechanism in CSS.

IGF1/GH axis dysregulation in ARID1B haploinsufficiency

ARID1B haploinsufficiency in mice produces growth impairment driven by insulin-like growth factor 1 (IGF1) deficiency with inadequate compensation by GHRH and GH. Growth hormone supplementation rescued growth retardation and muscle weakness, identifying a reversible endocrine axis underlying the short stature and contributing to hypotonia in CSS.

ARID1B hgnc:18040

insulin-like growth factor receptor signaling pathway GO:0048009 growth hormone secretion GO:0030252

Downstream

Short stature IGF1 deficiency with inadequate GHRH/GH compensation produces postnatal growth retardation; growth hormone supplementation corrected this in Arid1b heterozygous mice.

Hypotonia Reduced IGF1/GH signaling impairs muscle development and contributes to the muscle weakness/hypotonia phenotype seen in CSS; GH supplementation rescued muscle weakness in the Arid1b mouse model.

Show evidence (1 reference)

PMID:28695822 SUPPORT Model Organism

"We generated Arid1b heterozygous mice, which showed social behavior impairment, altered vocalization, anxiety-like behavior, neuroanatomical abnormalities, and growth impairment."

Establishes the Arid1b haploinsufficiency mouse model that recapitulates ARID1B-CSS growth phenotypes.

Mesenchymal stem cell quiescence loss and tooth root progenitor defects

ARID1B normally maintains GLI1+ mesenchymal stem cell quiescence by suppressing BCL11B-driven non-canonical Activin signaling. Loss of ARID1B drives MSCs out of quiescence into ectopic proliferation. In parallel, Arid1a controls a Plagl1-Hedgehog signaling axis required for the differentiation-associated cell-cycle arrest of tooth root progenitors; Arid1a loss causes shortened tooth roots and odontoblast differentiation defects. Together, these BAF-dependent MSC and odontogenic mechanisms underlie dental anomalies in CSS.

mesenchymal stem cell CL:0000134 odontoblast CL:0000060

ARID1B hgnc:18040 ARID1A hgnc:11110

stem cell maintenance GO:0019827 smoothened signaling pathway GO:0007224

Downstream

Dental anomalies ARID1B-MSC and ARID1A-Plagl1-Hh defects in odontogenic progenitors produce abnormal odontoblast differentiation and shortened tooth roots, contributing to the dental hypoplasia/abnormal dental morphology seen in CSS.

Show evidence (2 references)

PMID:38816354 SUPPORT Model Organism

"loss of Arid1b in the GLI1+ MSC lineage disturbs MSCs' quiescence and leads to their proliferation due to the ectopic activation of non-canonical Activin signaling via p-ERK."

Establishes ARID1B as a regulator of MSC quiescence in the craniofacial/dental lineage relevant to CSS.

PMID:33826897 SUPPORT Model Organism

"loss of Arid1a leads to increased expression of Arid1b, which is also indispensable for odontoblast differentiation but is not involved in regulation of Hh signaling."

Shows BAF-paralog (ARID1A/ARID1B) interdependence is required for odontoblast differentiation, supporting the dental phenotype mechanism.

Limb skeletal patterning defect from SOXC and BAF dysfunction

SOX11 and its SOXC paralogs (SOX4/SOX12) are required in limb mesenchyme for growth plate formation and skeletal elongation through noncanonical Wnt/PCP signaling. SoxC deletion in limb bud skeletogenic mesenchyme abolishes growth plate formation and produces severely shortened skeletal elements. SOX11 also positively regulates GDF5 in the joint interzone, contributing to joint and digit development. CSS-causing SOX11 variants therefore plausibly underlie the signature distal phalanx and fifth-digit hypoplasia, complementing the broader BAF-complex requirement for skeletal differentiation.

chondrocyte CL:0000138 skeletal mesenchymal cell CL:0000134

SOX11 hgnc:11191 SOX4 hgnc:11200

skeletal system development GO:0001501 chondrocyte differentiation GO:0002062 planar cell polarity pathway involved in axis elongation GO:0060071

limb UBERON:0002101

Downstream

Hypoplastic fifth fingernail Disrupted SOXC-driven growth plate formation and joint patterning, combined with BAF-dependent skeletal differentiation defects, plausibly underlie the distal phalangeal hypoplasia and fifth-digit nail anomalies that are the signature physical feature of CSS.

Show evidence (2 references)

PMID:25761772 SUPPORT Model Organism

"SoxC genes were necessary in perichondrocytes for expression of Wnt5a, which encodes a noncanonical WNT ligand required for growth plate formation, and in chondrocytes and perichondrocytes for expression of Fzd3 and Csnk1e, which encode a WNT receptor and casein kinase-1 subunit mediating planar..."

Establishes the SOXC -> noncanonical Wnt/PCP -> growth plate axis required for limb skeletal development.

PMID:23356643 SUPPORT Model Organism

"Sox11 is initially expressed broadly in the murine cartilage condensations at early stages of skeletal development, but its expression is specifically increased in the forming joint interzone as is forms."

SOX11 expression and GDF5 regulation in joint interzones link SOX11 dysfunction to digit/joint development relevant to the CSS fifth-digit phenotype.

⬡

Pathograph

Use the checkboxes to hide or show graph categories. Hover nodes for evidence and cross-linked metadata.

Referential integrity issues (4):

Target 'Altered developmental transcription programs' (from 'BAF/SWI-SNF chromatin remodeling dysfunction') not found in named elements
Target 'Excitatory-inhibitory imbalance' (from 'Cortical interneuron deficiency from ARID1B haploinsufficiency') not found in named elements
Target 'Reduced proliferative capacity' (from 'Altered cell-cycle dynamics from ARID1B haploinsufficiency') not found in named elements
Target 'Reduced functional ARID1B availability' (from 'Protein misfolding and aggregation of non-truncating ARID1B variants') not found in named elements

●

Phenotypes

Cardiovascular 1

Congenital heart defects Abnormal heart morphology HP:0001627

Show evidence (2 references)

PMID:38243407 SUPPORT Human Clinical

"hip dysplasia appears to occur more often than with other genes, however more severe medical challenges such as significant brain and cardiac malformations are rarer"

This confirms that cardiac malformations are part of the CSS phenotypic spectrum, though they occur less frequently in ARID2-associated cases.

PMID:38790056 SUPPORT Human Clinical

"patent foramen ovale"

This case report documents a cardiac anomaly (patent foramen ovale) in a CSS patient.

Digestive 1

Feeding difficulties in infancy HP:0008872

Show evidence (1 reference)

PMID:38243407 SUPPORT Human Clinical

"Individuals with CSS have a spectrum of various medical challenges, most often evident at birth, including feeding difficulties, hypotonia, organ-system anomalies, and learning and developmental differences."

This supports infant feeding difficulties as a common clinical issue in CSS.

Ear 1

Hearing impairment HP:0000365

Show evidence (1 reference)

PMID:38790056 SUPPORT Human Clinical

"moderate hearing loss"

This case report documents hearing loss as part of the ARID1B-associated CSS phenotype.

Eye 1

Microphthalmia HP:0000568

Show evidence (1 reference)

PMID:28608987 SUPPORT Human Clinical

"our case supports the dual role of chromatin remodellers in developmental disorders and cancer, as well as the involvement of SMARCA4 in microphthalmia, confirming previous findings in mouse models and the DECIPHER database."

Establishes SMARCA4-related microphthalmia within the CSS phenotypic spectrum.

Genitourinary 1

Renal anomalies Abnormality of the kidney HP:0000077

Show evidence (2 references)

PMID:38790056 SUPPORT Human Clinical

"bilateral renal cysts"

This case report documents bilateral renal cysts in a CSS patient.

PMID:35579625 SUPPORT Human Clinical

"Prenatal anomalies that were frequently observed in our cohort include hydrocephalus, agenesis of the corpus callosum, hypoplastic left heart syndrome, persistent left vena cava, diaphragmatic hernia, renal agenesis, and intrauterine growth restriction."

44-patient prenatal CSS cohort confirms renal anomalies (including renal agenesis) as a recognized fetal phenotype.

Head and Neck 4

Coarse facial features HP:0000280

Show evidence (2 references)

PMID:30276971 SUPPORT Human Clinical

"Other physical features seen include growth restriction, coarse facial features, hypertrichosis or hirsutism, sparse scalp hair, dental anomalies, and other organ-system abnormalities."

This supports coarse facial features as one of the major physical findings in CSS.

PMID:38182156 SUPPORT Human Clinical

"Coffin-Siris syndrome (CSS) is a rare congenital disorder characterized by coarse facial features, intellectual disability or developmental delay, and aplasia or hypoplasia of the tips of the fifth finger and/or toes."

This independently confirms coarse facial features as a defining clinical characteristic.

Sparse scalp hair HP:0002209

Show evidence (1 reference)

PMID:30276971 SUPPORT Human Clinical

"Other physical features seen include growth restriction, coarse facial features, hypertrichosis or hirsutism, sparse scalp hair, dental anomalies, and other organ-system abnormalities."

This supports sparse scalp hair as a characteristic ectodermal feature of CSS.

Microcephaly HP:0000252

Show evidence (1 reference)

PMID:23815551 SUPPORT Human Clinical

"Coffin-Siris syndrome (CSS) is a congenital disorder characterized by intellectual disability, growth deficiency, microcephaly, coarse facial features, and hypoplastic or absent fifth fingernails and/or toenails."

Microcephaly is listed as a defining characteristic of CSS.

Dental anomalies Abnormal dental morphology HP:0006482

Show evidence (2 references)

PMID:30276971 SUPPORT Human Clinical

"Other physical features seen include growth restriction, coarse facial features, hypertrichosis or hirsutism, sparse scalp hair, dental anomalies, and other organ-system abnormalities."

Dental anomalies are listed among the physical features of CSS.

PMID:38790056 SUPPORT Human Clinical

"dental hypoplasia"

This case report documents dental hypoplasia in an ARID1B-associated CSS patient.

Integument 2

Hypoplastic fifth fingernail HP:0008398

Show evidence (1 reference)

PMID:30276971 SUPPORT Human Clinical

"Classically, individuals with CSS have been described with hypo- or aplasia of the fifth digit nails or phalanges (hence the term "fifth digit syndrome")."

This directly supports the classic fifth-digit nail/phalangeal hypoplasia phenotype in CSS.

Hypertrichosis HP:0000998

Show evidence (2 references)

PMID:30276971 SUPPORT Human Clinical

"Other physical features seen include growth restriction, coarse facial features, hypertrichosis or hirsutism, sparse scalp hair, dental anomalies, and other organ-system abnormalities."

This supports hypertrichosis as a recurring physical feature in CSS.

PMID:34205270 SUPPORT Human Clinical

"hypotonia, hypertrichosis, sparse scalp hair, and hypoplasia of the distal phalanx are still some of the most common features."

208-individual registry data identify hypertrichosis among the most common CSS features.

Musculoskeletal 1

Hypotonia HP:0001252

Show evidence (3 references)

PMID:38243407 SUPPORT Human Clinical

This supports hypotonia as a frequent early-life manifestation of CSS.

PMID:38790056 SUPPORT Human Clinical

This independently lists hypotonia as a characteristic feature of CSS.

PMID:34205270 SUPPORT Human Clinical

"hypotonia, hypertrichosis, sparse scalp hair, and hypoplasia of the distal phalanx are still some of the most common features."

208-individual CSS/BAF complex registry confirms hypotonia is among the most common features across all CSS genotypes.

Nervous System 7

Global developmental delay HP:0001263

Show evidence (1 reference)

PMID:30276971 SUPPORT Human Clinical

"Varying degrees of developmental and intellectual delay are universal."

This supports global developmental delay as a near-universal feature of CSS.

Intellectual disability HP:0001249

Show evidence (2 references)

PMID:30276971 SUPPORT Human Clinical

"Varying degrees of developmental and intellectual delay are universal."

This directly supports intellectual disability as a core clinical feature of CSS.

PMID:23815551 SUPPORT Human Clinical

This confirms intellectual disability as a defining feature of CSS.

Seizures HP:0001250

Frequency intentionally omitted from the structured field because the available registry-vs-literature estimates differ (7.2% caregiver-reported in a 334-patient registry vs ~26-28% in literature reviews) per the project's frequency-evidence guidelines.

Show evidence (3 references)

PMID:29184203 SUPPORT Model Organism

"Arid1b haploinsufficiency also led to an imbalance between excitatory and inhibitory synapses in the cerebral cortex."

The excitatory-inhibitory imbalance from Arid1b haploinsufficiency provides a mechanistic basis for seizure susceptibility in CSS.

PMID:36177969 SUPPORT Human Clinical

"The literature review yielded 311 unique CSS patients, 82 of which (26.4%) carried diagnoses of seizures or epilepsy."

International CSS registry literature review quantifies epilepsy prevalence at ~26% of published CSS patients.

PMID:36177969 SUPPORT Human Clinical

"Seventeen patients (5.1%) reported EEG abnormalities, the majority of which were described as focal or multifocal (87.5%)."

Documents the focal/multifocal character of seizures consistent with the predicted cortical interneuron-deficit substrate.

Hydrocephalus HP:0000238

Show evidence (2 references)

PMID:35579625 SUPPORT Human Clinical

Confirms hydrocephalus as a frequent prenatal CSS phenotype across 44 fetal cases.

PMID:28867767 SUPPORT Model Organism

"Hydrocephalus was present in 5 of 91 hKO mice, while it was not observed in wild-type littermates (0 of 188)."

Arid1b haploinsufficient mouse model recapitulates hydrocephalus seen in CSS patients.

Agenesis of corpus callosum HP:0001274

Show evidence (3 references)

PMID:34706719 SUPPORT Human Clinical

"Agenesis or hypoplasia of the corpus callosum was observed in half of the patients (6/12)."

Cohort-level frequency of CC agenesis/hypoplasia among Korean SSRIDD patients (predominantly CSS).

PMID:38718796 SUPPORT In Vitro

"The most common structural abnormality in the brain of ARID1B patients is agenesis of the corpus callosum (ACC), characterized by the absence of an interhemispheric white matter tract that connects distant cortical regions."

Identifies CC agenesis as the most common structural brain abnormality in ARID1B-related CSS.

PMID:31273213 SUPPORT Human Clinical

Confirms that brain midline abnormalities (including CC agenesis) are seen in CSS patients with multiple BAF gene variants.

Speech and language delay Delayed speech and language development HP:0000750

Show evidence (1 reference)

PMID:34706719 SUPPORT Human Clinical

"Developmental delay was observed in all patients, and profound speech delay was also characteristic."

Direct cohort-level evidence that profound speech delay is a defining CSS feature.

Autistic behavior HP:0000729

Show evidence (2 references)

PMID:37692302 SUPPORT Human Clinical

"An 8-year-old boy with ASD, congenital anomalies, and neurological problems had been diagnosed with Coffin-Siris syndrome after genetic testing."

Case-level documentation of CSS-ASD comorbidity in an ARID1B variant carrier.

PMID:28867767 SUPPORT Model Organism

"Arid1b heterozygous knockout (hKO) mice exhibited ASD-like traits related to social behavior, anxiety, and perseveration"

Mouse model evidence linking ARID1B haploinsufficiency to autism-like phenotypes.

Growth 1

Short stature HP:0004322

Show evidence (2 references)

PMID:38243407 SUPPORT Human Clinical

"Although individuals with ARID2 have been reported to have classic features of CSS including hypertrichosis, coarse facial features, short stature, and fifth digit anomalies, as with many of the other CSS genes, there appears to be a spectrum of phenotypes."

This supports short stature as part of the recognized CSS phenotype spectrum.

PMID:23815551 SUPPORT Human Clinical

Growth deficiency supports the short stature phenotype in CSS.

🧬

Genetic Associations

ARID1B (Causative)

Gene: ARID1B hgnc:18040 gene page

Show evidence (4 references)

PMID:24674232 SUPPORT Human Clinical

"ARID1B mutations have been identified as the predominant cause of Coffin-Siris syndrome and have also been shown to be a frequent cause of nonsyndromic intellectual disability."

This supports ARID1B as the predominant causative gene in CSS.

PMID:39028335 SUPPORT Human Clinical

"ARID1B is the most frequently mutated gene in Coffin-Siris syndrome (CSS)."

This independently confirms ARID1B as the most common CSS gene.

PMID:39028335 SUPPORT Human Clinical

"To date, the vast majority of causative variants reported in ARID1B are truncating, leading to nonsense-mediated mRNA decay."

This supports the haploinsufficiency mechanism for most ARID1B variants.

+ 1 more reference

SMARCA4 (Causative)

Gene: SMARCA4 hgnc:11100 gene page

Show evidence (3 references)

PMID:23815551 SUPPORT Human Clinical

"We found that SMARCB1, SMARCA4, or ARID1B were mutated in 20 patients."

This supports SMARCA4 as one of the causative CSS genes.

PMID:23815551 SUPPORT Human Clinical

"All mutations in SMARCB1 and SMARCA4 were non-truncating (missense or in-frame deletion) whereas those in ARID1B were all truncating (nonsense or frameshift deletion/insertion)"

This establishes the distinctive non-truncating variant pattern for SMARCA4 in CSS.

CGGV:assertion_61d29c73-9a30-4664-9df2-2f5831219221-2025-06-08T220000.000Z SUPPORT Other

ClinGen classifies the SMARCA4-Coffin-Siris syndrome gene-disease relationship as definitive with autosomal dominant inheritance.

SMARCB1 (Causative)

Gene: SMARCB1 hgnc:11103 gene page

Show evidence (3 references)

PMID:22426308 SUPPORT Human Clinical

"we found de novo SMARCB1 mutations in two of five individuals with typical Coffin-Siris syndrome"

The original 2012 identification of SMARCB1 as a CSS gene.

PMID:23815551 SUPPORT Human Clinical

"All mutations in SMARCB1 and SMARCA4 were non-truncating (missense or in-frame deletion) whereas those in ARID1B were all truncating (nonsense or frameshift deletion/insertion)"

This establishes the non-truncating variant pattern for SMARCB1 in CSS.

CGGV:assertion_ea554e80-81d2-4100-8d0e-b762ea38fe23-2023-08-15T040000.000Z SUPPORT Other

ClinGen classifies the SMARCB1-Coffin-Siris syndrome gene-disease relationship as definitive with autosomal dominant inheritance.

SMARCE1 (Causative)

Gene: SMARCE1 hgnc:11109

Show evidence (2 references)

PMID:22426308 SUPPORT Human Clinical

"Twenty affected individuals (87%) each had a germline mutation in one of six SWI/SNF subunit genes, including SMARCB1, SMARCA4, SMARCA2, SMARCE1, ARID1A and ARID1B."

SMARCE1 is identified as one of the six CSS-causing SWI/SNF genes.

CGGV:assertion_877f5e0f-5b30-4a4f-87c3-cb6b87caa1e4-2024-09-18T190000.000Z SUPPORT Other

ClinGen classifies the SMARCE1-Coffin-Siris syndrome gene-disease relationship as definitive with autosomal dominant inheritance.

ARID1A (Causative)

Gene: ARID1A hgnc:11110 gene page

Show evidence (2 references)

PMID:22426308 SUPPORT Human Clinical

"Twenty affected individuals (87%) each had a germline mutation in one of six SWI/SNF subunit genes, including SMARCB1, SMARCA4, SMARCA2, SMARCE1, ARID1A and ARID1B."

ARID1A is identified as one of the six CSS-causing SWI/SNF genes.

CGGV:assertion_aaf6d47a-656a-49ca-ba9e-169f25bf03e7-2021-07-07T160000.000Z SUPPORT Other

ClinGen classifies the ARID1A-Coffin-Siris syndrome gene-disease relationship as definitive with autosomal dominant inheritance.

DPF2 (Causative)

Gene: DPF2 hgnc:9964

Show evidence (2 references)

PMID:29429572 SUPPORT Human Clinical

"Altogether, we provide compelling evidence that de novo variants in DPF2 cause Coffin-Siris syndrome and propose a dominant-negative mechanism of pathogenicity."

This supports DPF2 as a causative CSS gene with a dominant-negative mechanism.

CGGV:assertion_cc8c072e-7b8d-4a94-97fe-c15c91759f0f-2023-08-15T020000.000Z SUPPORT Other

ClinGen classifies the DPF2-Coffin-Siris syndrome gene-disease relationship as definitive with autosomal dominant inheritance.

ARID2 (Causative)

Gene: ARID2 hgnc:18037

Show evidence (3 references)

PMID:38243407 SUPPORT Human Clinical

This supports ARID2 as a recognized CSS gene with a variable phenotype spectrum.

PMID:38243407 SUPPORT Human Clinical

"hip dysplasia appears to occur more often than with other genes, however more severe medical challenges such as significant brain and cardiac malformations are rarer"

This highlights the distinctive and generally milder ARID2-associated phenotype.

CGGV:assertion_ae1a697f-8dcd-4edf-a25b-e5e0593e7e61-2022-12-06T230000.000Z SUPPORT Other

ClinGen classifies the ARID2-Coffin-Siris syndrome gene-disease relationship as definitive with autosomal dominant inheritance.

SOX11 (Causative)

Gene: SOX11 hgnc:11191 gene page

Show evidence (1 reference)

PMID:39501269 SUPPORT Human Clinical

"The combination of clinical presentation and genetic testing results supports that the patient suffers from Coffin-Siris syndrome due to a genetic variant in the SOX11 gene."

A case report confirming SOX11 as a causative CSS gene.

SMARCC2 (Causative)

Gene: SMARCC2 hgnc:11105

Show evidence (2 references)

PMID:41291750 SUPPORT Human Clinical

"Coffin-Siris Syndrome 8 (CSS8; MIM# 618362) is a rare neurodevelopmental disorder caused by heterozygous variants in the SMARCC2 gene."

This directly supports SMARCC2 as a causative CSS gene.

CGGV:assertion_aa645aa6-3a03-4ab7-9d09-b17be3184259-2025-09-17T100000.000Z SUPPORT Other

ClinGen classifies the SMARCC2-Coffin-Siris syndrome gene-disease relationship as definitive with autosomal dominant inheritance.

SMARCA2 (Causative)

Gene: SMARCA2 hgnc:11098 gene page

Show evidence (1 reference)

PMID:22426308 SUPPORT Human Clinical

"Twenty affected individuals (87%) each had a germline mutation in one of six SWI/SNF subunit genes, including SMARCB1, SMARCA4, SMARCA2, SMARCE1, ARID1A and ARID1B."

SMARCA2 is identified as one of the six original CSS-causing SWI/SNF genes.

BICRA (Causative)

Gene: BICRA hgnc:4332

Show evidence (2 references)

PMID:38243407 SUPPORT Human Clinical

"SMARCC2, DPF2, and more recently, BICRA"

BICRA is listed as a recently identified CSS gene in this ARID2 cohort study. Note that the same sentence erroneously expands BAF as "Bromocriptine activating factor" rather than the correct "BRG1/BRM-Associated Factors."

CGGV:assertion_2dcc8864-4487-4c5c-b541-cfd972767269-2024-11-20T170000.000Z SUPPORT Other

ClinGen classifies the BICRA-Coffin-Siris syndrome gene-disease relationship as definitive with autosomal dominant inheritance.

SOX4 (Causative)

Gene: SOX4 hgnc:11200

Show evidence (2 references)

PMID:30661772 SUPPORT Human Clinical

"Taken together, these findings point to specific SOX4 HMG-domain missense variants as the cause of a characteristic human neurodevelopmental disorder associated with mild facial and digital dysmorphism."

Establishes SOX4 HMG-domain missense variants as causative, and names the mild facial and digital dysmorphism that brings the phenotype into this disease group.

PMID:35232796 SUPPORT Human Clinical

"These findings consolidate evidence of a fairly non-specific neurodevelopmental syndrome due to SOX4 haploinsufficiency in neurogenesis and multiple other developmental processes."

Establishes haploinsufficiency as the mechanism and records the cohort's judgement that the syndrome is non-specific, which is the caveat in the notes above.

SMARCD1 (Causative)

Gene: SMARCD1 hgnc:11106

Show evidence (2 references)

PMID:30879640 SUPPORT Human Clinical

"Here, we report on five individuals with mutations in SMARCD1; the individuals present with developmental delay, intellectual disability, hypotonia, feeding difficulties, and small hands and feet."

Establishes SMARCD1 as a causative gene in five individuals with a neurodevelopmental phenotype.

PMID:30879640 SUPPORT Human Clinical

"Mutations in several genes encoding components of the SWI/SNF chromatin remodeling complex cause neurodevelopmental disorders (NDDs)."

Places SMARCD1 disease within the SWI/SNF component group, which is the basis for binding the gene to the shared BAF-complex node.

💊

Medical Actions

Multidisciplinary supportive care and surveillance

Action: supportive care Ontology label: Supportive Care NCIT:C15747

CSS management is primarily supportive and multidisciplinary, with attention to feeding, development, hypotonia, organ-system anomalies, and longitudinal surveillance for complications.

Show evidence (1 reference)

PMID:30276971 SUPPORT Human Clinical

"In addition, we offer surveillance and management recommendations based on the medical issues encountered in this cohort to help guide physicians and patients' families."

This supports structured supportive management and surveillance as the main treatment approach for CSS.

Speech and language therapy

Action: speech and language therapy Ontology label: Speech Language Therapy NCIT:C159273

Platform: Behavioral / lifestyle

Speech and language therapy addresses the universal speech and language delays in CSS.

Show evidence (1 reference)

PMID:30276971 SUPPORT Human Clinical

"Varying degrees of developmental and intellectual delay are universal."

Universal developmental delay supports the need for speech and language therapy as part of CSS management.

Genetic counseling

Action: Genetic Counseling NCIT:C15240

Genetic counseling is recommended for affected individuals and families given the autosomal dominant inheritance and high rate of de novo mutations.

Show evidence (1 reference)

PMID:23815551 SUPPORT Human Clinical

"By examining available parental samples, we ascertained that 17 occurred de novo."

The high rate of de novo mutations in CSS supports the importance of genetic counseling for recurrence risk assessment.

Physical therapy

Action: physical therapy Ontology label: Physical Therapy NCIT:C15302

Platform: Behavioral / lifestyle

Physical therapy targets hypotonia and motor delays to improve functional mobility and developmental milestones.

Target Phenotypes: Hypotonia HP:0001252

Show evidence (1 reference)

PMID:38243407 SUPPORT Human Clinical

"Feeding difficulties, hypotonia, and short stature occur often"

The high frequency of hypotonia supports physical therapy as part of CSS management.

Antiseizure medication

Action: Pharmacotherapy NCIT:C15986

Most CSS patients with epilepsy achieve seizure control on antiseizure medications; in the international CSS registry, all but one of the patients with seizures were controlled on ASMs.

Mechanism Target:

Cortical interneuron deficiency from ARID1B haploinsufficiency — ASMs counteract the cortical excitatory-inhibitory imbalance arising from reduced GABAergic interneuron numbers.

Show evidence (1 reference)

PMID:29184203 SUPPORT Model Organism

"Arid1b-heterozygous mice exhibited abnormal cognitive and social behaviors, which were rescued by treatment with a positive allosteric GABAA receptor modulator."

Mouse-model rescue with a GABAA-receptor positive allosteric modulator provides indirect support that pharmacologic enhancement of inhibitory transmission targets the interneuron-deficit mechanism that drives CSS seizures.

Target Phenotypes: Seizures HP:0001250

Show evidence (1 reference)

PMID:36177969 SUPPORT Human Clinical

"In all but one patient, seizures were controlled on antiseizure medications (ASMs)."

Registry data support standard ASM therapy as the operative epilepsy management for CSS patients.

Growth hormone supplementation (investigational)

Action: Pharmacotherapy NCIT:C15986

Agent: somatropin NCIT:C837

In the Arid1b haploinsufficient mouse model, growth hormone supplementation rescued growth retardation and muscle weakness, identifying a mechanistically rational therapeutic strategy for the IGF1/GH axis dysregulation underlying CSS short stature. Clinical use of GH in CSS is investigational and would require individualized endocrine assessment.

Mechanism Target:

RESTORES IGF1/GH axis dysregulation in ARID1B haploinsufficiency — GH supplementation directly restores IGF1 signaling that is reduced in ARID1B haploinsufficiency.

Show evidence (1 reference)

PMID:28695822 SUPPORT Model Organism

"A focus on reversible mechanisms identified Insulin-like growth factor (IGF1) deficiency with inadequate compensation by Growth hormone-releasing hormone (GHRH) and Growth hormone (GH), underappreciated findings in ARID1B patients."

Same study identifies IGF1/GH axis deficiency as the mechanistic target restored by exogenous GH supplementation.

Target Phenotypes: Short stature HP:0004322

Show evidence (1 reference)

PMID:28695822 SUPPORT Model Organism

"Therapeutically, GH supplementation was able to correct growth retardation and muscle weakness."

Mouse-model evidence that GH supplementation can rescue ARID1B haploinsufficiency-driven growth and muscle phenotypes.

🔬

Diagnosis

Molecular genetic testing

Diagnosis is established by identification of a heterozygous pathogenic variant in a CSS-associated BAF complex gene via multigene panel or exome/genome sequencing. Approximately 87% of clinically typical CSS individuals have identifiable mutations in SWI/SNF subunit genes.

Show evidence (1 reference)

PMID:22426308 SUPPORT Human Clinical

"Twenty affected individuals (87%) each had a germline mutation in one of six SWI/SNF subunit genes, including SMARCB1, SMARCA4, SMARCA2, SMARCE1, ARID1A and ARID1B."

This establishes the high diagnostic yield of molecular testing in CSS.

DNA methylation episignature

A disorder-specific peripheral-blood DNA methylation signature is now an established diagnostic adjunct for CSS and other BAFopathies. A machine-learning classifier trained on the methylation profile can resolve ambiguous clinical cases, reclassify variants of unknown significance, and even identify previously undiagnosed individuals through targeted screening. The CSS/Nicolaides-Baraitser episignatures show overlap consistent with a shared functional basis as BAFopathies.

Show evidence (3 references)

PMID:30459321 SUPPORT Human Clinical

"We report overlapping peripheral blood DNA methylation epi-signatures in individuals with various subtypes of CSS (ARID1B, SMARCB1, and SMARCA4) and NCBRS (SMARCA2)."

Establishes the existence of CSS-specific peripheral blood methylation episignatures across multiple BAF subunits.

PMID:30459321 SUPPORT Human Clinical

"We demonstrate that a machine-learning model trained on this DNA methylation profile can resolve ambiguous clinical cases, reclassify those with variants of unknown significance, and identify previously undiagnosed subjects through targeted population screening."

Documents the diagnostic utility of the CSS episignature, including VUS reclassification.

PMID:39028335 SUPPORT Human Clinical

Supports the use of methylation episignatures for CSS variant classification, including aggregation-prone non-truncating variants.

📊

Prevalence

Published literature cohorts

Point Prevalence 1.0–10.0 per 100,000 1–9 per 100,000

Robust population prevalence estimates are not established in PubMed abstracts, but Coffin-Siris syndrome remains ultra-rare in the clinical literature. By 2018, approximately 200 individuals had been described, and a 2024 case report cites an estimated incidence of 1:10,000-1:100,000.

Show evidence (2 references)

PMID:30276971 SUPPORT Human Clinical

"To date, approximately 200 individuals have been described in the literature."

This registry paper provides the clearest PubMed-abstract estimate of how many Coffin-Siris syndrome cases had been described in the literature.

PMID:38790056 SUPPORT Human Clinical

"Coffin-Siris syndrome (CSS) is a rare autosomal dominant inheritance disorder"

This recent clinical report supports the interpretation of Coffin-Siris syndrome as an ultra-rare disorder in current clinical practice.

{ }

Source YAML

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name: Coffin-Siris syndrome
creation_date: "2026-03-15T23:04:34Z"
category: Mendelian
description: >-
  Coffin-Siris syndrome is a genetically heterogeneous autosomal dominant
  neurodevelopmental disorder caused by pathogenic variants in genes encoding
  subunits of the BAF/SWI-SNF chromatin remodeling complex. Core manifestations
  include developmental delay or intellectual disability, coarse facial
  features, hypoplasia or aplasia of the fifth digit nails or distal phalanges,
  hypotonia, feeding difficulties, hypertrichosis, sparse scalp hair, short
  stature, and additional congenital anomalies including cardiac, renal, and
  brain malformations. Epilepsy and hearing impairment are frequent
  complications.
disease_term:
  preferred_term: Coffin-Siris syndrome
  term:
    id: MONDO:0015452
    label: Coffin-Siris syndrome
parents:
- chromatin remodeling disorder
- neurodevelopmental disorder
notes: >-
  Series enumeration and lump/split decisions from a genetics pass over the
  gene-defined MONDO subtypes of this disease. Enumerating the descendants of
  MONDO:0015452 in the local MONDO build returned eleven classes besides the root,
  and each now has a has_subtypes row here: CSS1 (MONDO:0007617, ARID1B), CSS2
  (MONDO:0013819, ARID1A), CSS3 (MONDO:0013820, SMARCB1), CSS4 (MONDO:0013821,
  SMARCA4), CSS5 (MONDO:0014838, SMARCE1), CSS7 (MONDO:0054831, DPF2), CSS8
  (MONDO:0032702, SMARCC2), CSS10 (MONDO:0032791, SOX4), CSS11 (MONDO:0032912,
  SMARCD1), CSS12 (MONDO:0025699, BICRA), and the SOX11 class MONDO:0014376. No
  class numbered Coffin-Siris syndrome 9 appears among them. Ten of the eleven
  rows bind the MONDO class as their subtype_term; the SOX11 row does not,
  because MONDO:0014376 is already the disease_term of the
  SOX11-Related_Neurodevelopmental_Disorder entry, and that row carries the gene
  for the parent pathograph instead.

  The CSS6 row (MONDO:0033492, ARID2) is a twelfth gene-defined row and is not in
  that descendant set: MONDO asserts the class under autosomal dominant
  non-syndromic intellectual disability instead, which the
  Autosomal_Dominant_Non-Syndromic_Intellectual_Disability entry's notes already
  record as a MONDO defect. It is curated here because MONDO's own textual
  definition of the class names Coffin-Siris syndrome and ClinGen curates ARID2
  against Coffin-Siris syndrome.

  MONDO's primary labels for four of these do not name Coffin-Siris syndrome at
  all: CSS2, CSS3 and CSS4 are labelled "intellectual disability, autosomal
  dominant 14", "15" and "16", and the SOX11 class is labelled "intellectual
  developmental disorder with microcephaly and with or without ocular
  malformations or hypogonadotropic hypogonadism". The display_name on each row
  records both readings so a curator searching for a Coffin-Siris number can find
  the row.

  Two rows carry a phenotype caveat rather than a clean equivalence, and it is
  recorded in the row rather than only here. For SOX4 (CSS10), the largest
  published cohort states that these patients resemble Coffin-Siris syndrome but
  lack its most specific features, and calls the entity a fairly non-specific
  neurodevelopmental syndrome. For SMARCD1 (CSS11), the founding series reports
  clinical overlap with the BAF-related syndromes without their typical facial
  dysmorphisms. Both are curated as subtypes because the genes sit in the same
  developmental programmes as the rest of the series and are reported on the same
  gene panel, but the MONDO numbering is broader than the reported phenotypes.

  SMARCA2 is deliberately left without a subtype row. It is retained as a
  genetic record because it was one of the six SWI/SNF genes in the founding
  2012 Coffin-Siris series, but SMARCA2 variants principally cause
  Nicolaides-Baraitser syndrome, which is a separate disease with its own entry
  (Nicolaides-Baraitser_Syndrome, MONDO:0011053), and no descendant of
  MONDO:0015452 is defined by SMARCA2. SMARCB1 and SMARCA4 are also
  tumour-predisposition genes; the CSS3 and CSS4 rows record only the germline
  neurodevelopmental disorder, and any somatic role belongs in the relevant
  tumour entries.
classifications:
  isds_skeletal_category:
  - classification_value: brachydactyly_with_extraskeletal_manifestations
    notes: >-
      ISDS Nosology and Classification of Genetic Skeletal Disorders, 2019
      revision (Mortier et al., PMID:31633310), Table 1 group 38 "Brachydactylies
      (with extraskeletal manifestations)"; listed as "Coffin-Siris syndrome".
has_subtypes:
- name: CSS4
  display_name: Coffin-Siris syndrome 4 (SMARCA4-related)
  subtype_term:
    preferred_term: intellectual disability, autosomal dominant 16
    term:
      id: MONDO:0013821
      label: intellectual disability, autosomal dominant 16
  genes:
  - preferred_term: SMARCA4
    term:
      id: hgnc:11100
      label: SMARCA4
  inheritance:
  - name: Autosomal dominant inheritance
    inheritance_term:
      preferred_term: Autosomal dominant inheritance
      term:
        id: HP:0000006
        label: Autosomal dominant inheritance
  description: >-
    The SMARCA4-related form of Coffin-Siris syndrome, corresponding to OMIM
    614609. SMARCA4 encodes BRG1, the catalytic ATPase subunit of the BAF/PBAF
    chromatin-remodelling complex - so this is the subtype in which the motor of
    the complex is damaged rather than one of its scaffolding or targeting
    subunits.

    The subtype carries two names for one concept, and the second name is the
    informative one. MONDO's primary label is "intellectual disability,
    autosomal dominant 16" (MRD16); its synonyms include "Coffin-Siris syndrome
    4" and "SMARCA4-related BAFopathy"; and its definition is explicitly "any
    Coffin-Siris syndrome in which the cause of the disease is a mutation in the
    SMARCA4 gene". The MRD16 label exists because a substantial fraction of
    SMARCA4 patients come to attention as non-syndromic intellectual disability
    or autism rather than as classic Coffin-Siris syndrome: in one series of
    eight children with novel SMARCA4 missense variants, all had moderate to
    severe intellectual disability and seven had autistic or likely-autistic
    features, while being *less* likely than published Coffin-Siris patients to
    show the craniofacial or finger and toe anomalies. Reading MRD16 as a
    separate disease from Coffin-Siris syndrome would split one gene's
    phenotypic range in two along an ascertainment line.

    Genotype-phenotype, stated with the hedge the sources put on it. SMARCA4
    variants in Coffin-Siris syndrome were originally all non-truncating -
    missense or in-frame deletion - which is the variant class this subtype was
    defined on, and which distinguishes it from the germline loss-of-function
    SMARCA4 alleles that cause rhabdoid tumour predisposition syndrome 2. That
    distinction has since softened: a 15-patient SMARCA4 registry cohort
    included two individuals with nonsense variants who had milder learning and
    behavioural differences and no organ-system involvement. At the level of
    gene families rather than individual alleles, SMARC-related Coffin-Siris
    patients have been proposed to have more severe organ-related complications
    than ARID-related patients - but the same study that reports that
    correlation concludes that everyone with a BAF-related condition is at risk
    of most of the phenotype and that surveillance should be broad. The
    correlation is a tendency, not a triage rule.
  review_notes: >-
    Scope of this addition, recorded so the single-subtype list is not misread.
    Coffin-Siris syndrome is caused by variants in fourteen genes, and each of
    the numbered CSS types has its own OMIM and MONDO identity. This entry now
    carries one of them, CSS4, because that is the concept the curation request
    covered; the absence of CSS1 through CSS3 and CSS5 onward from this list
    reflects what has been curated, not a claim that SMARCA4 is the only
    subtype. A later pass adding the rest would be a straightforward and useful
    piece of work.

    Deep research. A falcon report was run for this concept with a
    disambiguating query and is committed alongside this edit;
    `just preflight-dr` PASSed against MONDO:0013821, with SMARCA4 mentioned 57
    times and the report's OMIM number matching MONDO's. It independently
    reaches the framing used here, including the CSS4-versus-RTPS2 allele-class
    distinction and the point that rare nonsense variants and whole-gene
    deletions create a genuine boundary zone between them. Several of its
    findings are recorded as uncited leads rather than curated, because they
    come from cohort tables rather than from quotable abstract text: in a
    15-person SMARCA4 cohort, 11 of 12 missense variants fell in or near the
    helicase/ATPase domains between residues 761 and 1243 and 10 of 12 were
    confirmed de novo; a 12-person parent-reported registry subset gives
    per-feature frequencies and developmental-milestone medians; and the 2025
    GeneReviews update assigns dominant-negative or gain-of-function effects to
    typical CSS4 alleles while allowing haploinsufficiency for the truncating
    and deletion cases. A curator with those tables should curate them properly.

    Lump/split reasoning. MONDO:0013821 was curated as a `has_subtypes` entry
    here rather than as a standalone `kb/disorders/` entry for three reasons.
    MONDO defines it as a Coffin-Siris syndrome, not as a sibling of one.
    GeneReviews establishes the diagnosis of Coffin-Siris syndrome by a
    heterozygous pathogenic variant in any one of the fourteen genes, which
    makes the gene the subtype axis rather than the disease axis. And this
    knowledge base already curates SMARCA4 in this entry's `genetic:` block with
    its own evidence, so a standalone entry would have duplicated the whole
    BAF-complex pathograph to hold one gene that is already here. Note the
    contrast with Nicolaides-Baraitser syndrome (SMARCA2) and rhabdoid tumour
    predisposition syndrome 2 (SMARCA4 loss-of-function), both of which are
    curated as separate entries in this knowledge base because they are separate
    clinical entities rather than gene-defined slices of this one.
  evidence:
  - reference: PMID:23556151
    reference_title: Coffin-Siris Syndrome.
    supports: SUPPORT
    evidence_source: HUMAN_CLINICAL
    directness: DIRECT
    snippet: >-
      The diagnosis of CSS is established in a proband with suggestive findings
      and a heterozygous pathogenic variant in one of the following 14 known
      genes identified by molecular genetic testing: ARID1A, ARID1B, ARID2,
      BICRA, DPF2, PHF6, SMARCA2, SMARCA4, SMARCB1, SMARCC2, SMARCD1, SMARCE1,
      SOX4, or SOX11.
    explanation: >-
      GeneReviews establishes the diagnosis of Coffin-Siris syndrome on a
      variant in any of fourteen genes including SMARCA4, which is what makes
      the gene a subtype axis within this disease rather than a disease
      boundary.
  - reference: PMID:23815551
    reference_title: "Coffin-Siris syndrome is a SWI/SNF complex disorder."
    supports: SUPPORT
    evidence_source: HUMAN_CLINICAL
    directness: DIRECT
    snippet: "All mutations in SMARCB1 and SMARCA4 were non-truncating (missense or in-frame deletion) whereas those in ARID1B were all truncating (nonsense or frameshift deletion/insertion)"
    explanation: >-
      The non-truncating variant class on which this subtype was originally
      defined, and the feature that separated it from loss-of-function SMARCA4
      disease.
  - reference: PMID:34813034
    reference_title: "Novel Variants of the SMARCA4 Gene Associated with Autistic Features Rather Than Typical Coffin-Siris Syndrome in Eight Chinese Pediatric Patients."
    supports: SUPPORT
    evidence_source: HUMAN_CLINICAL
    directness: DIRECT
    snippet: >-
      All eight patients had moderate to severe intellectual disability, and
      seven showed autistic/likely autistic features.
    explanation: >-
      The neurodevelopmental pole of the SMARCA4 phenotype, which is why MONDO's
      primary label for this concept is an intellectual-disability term rather
      than a Coffin-Siris one.
  - reference: PMID:34813034
    reference_title: "Novel Variants of the SMARCA4 Gene Associated with Autistic Features Rather Than Typical Coffin-Siris Syndrome in Eight Chinese Pediatric Patients."
    supports: SUPPORT
    evidence_source: HUMAN_CLINICAL
    directness: DIRECT
    snippet: >-
      Compared with the patients reported in the literature, our patients were
      less likely to show craniofacial or finger/toe anomalies.
    explanation: >-
      Documents that SMARCA4 patients can lack the classic Coffin-Siris physical
      features, which is the ascertainment difference the MRD16 name encodes.
  - reference: PMID:32686290
    reference_title: "The variability of SMARCA4-related Coffin-Siris syndrome: Do nonsense candidate variants add to milder phenotypes?"
    supports: SUPPORT
    evidence_source: HUMAN_CLINICAL
    directness: DIRECT
    snippet: >-
      We describe here a cohort of 15 unrelated individuals with SMARCA4
      variants from the Coffin-Siris syndrome/BAF pathway disorders registry who
      further display variability in severity and degrees of learning impairment
      and health issues.
    explanation: >-
      The largest dedicated SMARCA4-Coffin-Siris cohort, and its central finding
      of phenotypic variability within the subtype.
  - reference: PMID:32686290
    reference_title: "The variability of SMARCA4-related Coffin-Siris syndrome: Do nonsense candidate variants add to milder phenotypes?"
    supports: SUPPORT
    evidence_source: HUMAN_CLINICAL
    directness: DIRECT
    snippet: >-
      Within this cohort, we also report two individuals with novel nonsense
      variants who appear to have a phenotype of milder learning/behavioral
      differences and no organ-system involvement.
    explanation: >-
      Softens the non-truncating rule the subtype was defined on: nonsense
      SMARCA4 variants can also give a Coffin-Siris-spectrum phenotype, at the
      mild end.
  - reference: PMID:34205270
    reference_title: "Genotype-Phenotype Correlations in 208 Individuals with Coffin-Siris Syndrome."
    supports: SUPPORT
    evidence_source: HUMAN_CLINICAL
    directness: DIRECT
    snippet: >-
      It has been previously proposed that individuals with ARID-related
      variants are thought to have more learning and developmental struggles,
      and individuals with SMARC-related variants, while they also have
      developmental delay, tend to have more severe organ-related complications.
    explanation: >-
      The gene-family-level genotype-phenotype tendency that places SMARC
      subtypes, including this one, toward the organ-anomaly end.
  - reference: PMID:34205270
    reference_title: "Genotype-Phenotype Correlations in 208 Individuals with Coffin-Siris Syndrome."
    supports: SUPPORT
    evidence_source: HUMAN_CLINICAL
    directness: DIRECT
    snippet: >-
      we have found that all individuals with BAF-related conditions are at risk
      of many aspects of the phenotype, and management and surveillance should
      be broad
    explanation: >-
      The authors' own limit on the correlation above. Cited alongside it so the
      tendency is not read as a management rule.
  - reference: CGGV:assertion_61d29c73-9a30-4664-9df2-2f5831219221-2025-06-08T220000.000Z
    reference_title: "SMARCA4 / Coffin-Siris syndrome (Definitive)"
    supports: SUPPORT
    evidence_source: OTHER
    directness: DIRECT
    snippet: "SMARCA4 | HGNC:11100 | Coffin-Siris syndrome | MONDO:0015452 | AD | Definitive"
    explanation: >-
      ClinGen asserts the SMARCA4 gene-disease relationship against Coffin-Siris
      syndrome itself, at definitive strength - a second authority treating
      SMARCA4 as a cause of this disease rather than of a separate one.
- name: CSS6
  display_name: Coffin-Siris syndrome 6 (ARID2-related)
  subtype_term:
    preferred_term: ARID2-related Coffin-Siris syndrome
    term:
      id: MONDO:0033492
      label: Coffin-Siris syndrome 6
  genes:
  - preferred_term: ARID2
    term:
      id: hgnc:18037
      label: ARID2
  inheritance:
  - name: Autosomal dominant inheritance
    inheritance_term:
      preferred_term: Autosomal dominant inheritance
      term:
        id: HP:0000006
        label: Autosomal dominant inheritance
  description: >-
    The ARID2-related form of Coffin-Siris syndrome, corresponding to
    OMIM 617808. ARID2 is a PBAF-specific subunit - an intrinsic
    component of the polybromo brahma-associated factor SWI/SNF
    subcomplex - so this is a subtype in which a targeting subunit of
    the complex is damaged rather than its catalytic ATPase, which is
    the CSS4 lesion. The mechanism is loss of function through
    truncating variants, mostly de novo. ARID2 is already curated in
    this entry's `genetic:` block, where it is recorded as a less
    frequent CSS gene with a somewhat milder but still recognisably
    classic phenotype and a higher rate of hip dysplasia; this row adds
    the MONDO subtype identity that the gene record did not carry.
    ClinGen classifies the gene-disease relationship as Definitive
    against Coffin-Siris syndrome itself (MONDO:0015452).
  review_notes: >-
    Why this row is here rather than on the autosomal dominant
    non-syndromic intellectual disability entry. MONDO asserts
    MONDO:0033492 as a direct subclass of `autosomal dominant
    non-syndromic intellectual disability` (MONDO:0015802) and of
    `BAFopathy`, and not as a subclass of `Coffin-Siris syndrome`
    (MONDO:0015452) - yet its own textual definition reads `any
    Coffin-Siris syndrome in which the cause of the disease is a
    mutation in the ARID2 gene`, so MONDO's asserted hierarchy
    contradicts its own definition. Coffin-Siris syndrome is a syndromic
    disorder by definition, and ClinGen curates ARID2 against
    Coffin-Siris syndrome, so the definition is the side to follow. The
    concept reached this knowledge base through issue 12226, a pass
    enumerating gene-defined subtypes under MONDO:0015802; it was
    declined there and routed here instead. This also closes part of the
    gap the CSS4 review_notes above records: CSS1 to CSS3 and CSS5
    onward other than CSS6 are still absent, and that remains a
    statement about what has been curated rather than about the gene
    set.
  evidence:
  - reference: CGGV:assertion_ae1a697f-8dcd-4edf-a25b-e5e0593e7e61-2022-12-06T230000.000Z
    reference_title: "ARID2 / Coffin-Siris syndrome (Definitive)"
    supports: SUPPORT
    evidence_source: OTHER
    snippet: >-
      ARID2 | HGNC:18037 | Coffin-Siris syndrome | MONDO:0015452 | AD
      | Definitive | SOP9 | Intellectual Disability and Autism Gene
      Curation Expert Panel
    explanation: >-
      ClinGen curates the ARID2 gene-disease relationship against
      Coffin-Siris syndrome, which is the basis for placing this
      subtype row on this entry rather than under a non-syndromic
      parent.
  - reference: CGGV:assertion_ae1a697f-8dcd-4edf-a25b-e5e0593e7e61-2022-12-06T230000.000Z
    reference_title: "ARID2 / Coffin-Siris syndrome (Definitive)"
    supports: SUPPORT
    evidence_source: OTHER
    snippet: >-
      ARID2 was first reported in relation to autosomal dominant
      Coffin-Siris syndrome in 2015 by Shang et al . (PMID: 26238514),
      who reported four individuals with truncating variants.
    explanation: >-
      The founding report of the ARID2-Coffin-Siris relationship, and
      the source of the truncating-variant mechanism recorded above.
  - reference: CGGV:assertion_ae1a697f-8dcd-4edf-a25b-e5e0593e7e61-2022-12-06T230000.000Z
    reference_title: "ARID2 / Coffin-Siris syndrome (Definitive)"
    supports: SUPPORT
    evidence_source: OTHER
    snippet: >-
      ARID2 is an intrinsic component of polybromo brahma-associated
      factor (PBAF), a SWI/SNF subcomplex involved in chromatin
      remodeling.
    explanation: >-
      Places ARID2 in the PBAF subcomplex, the basis for contrasting
      this subtype with the SMARCA4 catalytic-ATPase lesion of CSS4.
  - reference: CGGV:assertion_ae1a697f-8dcd-4edf-a25b-e5e0593e7e61-2022-12-06T230000.000Z
    reference_title: "ARID2 / Coffin-Siris syndrome (Definitive)"
    supports: SUPPORT
    evidence_source: OTHER
    snippet: >-
      The mechanism of pathogenicity is loss of function, supported by
      a pLI score of 1 (gnomAD v2.1.1).
    explanation: >-
      Source for the loss-of-function mechanism stated in this row's
      description.
  - reference: CGGV:assertion_ae1a697f-8dcd-4edf-a25b-e5e0593e7e61-2022-12-06T230000.000Z
    reference_title: "ARID2 / Coffin-Siris syndrome (Definitive)"
    supports: SUPPORT
    evidence_source: OTHER
    snippet: >-
      The majority of variants are de novo , although in at least one
      individual the variant was inherited from a mildly affected
      mother (PMID: 35813374).
    explanation: >-
      Source for the statement that the variants are mostly de novo,
      and records the transmitted exception.
- name: CSS1
  display_name: Coffin-Siris syndrome 1 (ARID1B-related)
  subtype_term:
    preferred_term: Coffin-Siris syndrome 1
    term:
      id: MONDO:0007617
      label: Coffin-Siris syndrome 1
  description: >-
    The numbered form caused by heterozygous ARID1B variants, and the largest
    single group within molecularly confirmed Coffin-Siris syndrome. Most
    variants are truncating and act through haploinsufficiency; a subset of
    non-truncating variants act instead through protein aggregation, which the
    pathophysiology section models as a separate node.
  inheritance:
  - name: Autosomal dominant inheritance
    inheritance_term:
      preferred_term: Autosomal dominant inheritance
      term:
        id: HP:0000006
        label: Autosomal dominant inheritance
  genes:
  - preferred_term: ARID1B
    term:
      id: hgnc:18040
      label: ARID1B
  evidence:
  - reference: PMID:24674232
    reference_title: "Expanding the phenotypic spectrum of ARID1B-mediated disorders and identification of altered cell-cycle dynamics due to ARID1B haploinsufficiency."
    supports: SUPPORT
    evidence_source: HUMAN_CLINICAL
    snippet: "ARID1B mutations have been identified as the predominant cause of Coffin-Siris syndrome and have also been shown to be a frequent cause of nonsyndromic intellectual disability."
    explanation: >-
      Supports ARID1B as the predominant cause, which is why this numbered form is the
      largest group.
  - reference: CGGV:assertion_d487e6c4-9727-4315-90a2-11338128a8e5-2019-12-04T200734.569Z
    reference_title: "ARID1B / Coffin-Siris syndrome (Definitive)"
    supports: SUPPORT
    evidence_source: OTHER
    snippet: "ARID1B | HGNC:18040 | Coffin-Siris syndrome | MONDO:0015452 | AD | Definitive"
    explanation: >-
      ClinGen classifies the relationship as Definitive under autosomal dominant
      inheritance, which is the mode recorded on this subtype.
- name: CSS2
  display_name: Coffin-Siris syndrome 2 (ARID1A-related; MONDO label "intellectual disability, autosomal dominant 14")
  subtype_term:
    preferred_term: intellectual disability, autosomal dominant 14
    term:
      id: MONDO:0013819
      label: intellectual disability, autosomal dominant 14
  description: >-
    The numbered form caused by heterozygous ARID1A variants, one of the six
    SWI/SNF subunit genes in the founding 2012 series. MONDO's primary label for
    this concept is
    "intellectual disability, autosomal dominant 14" rather than a Coffin-Siris
    name, which is why the display name records both.
  inheritance:
  - name: Autosomal dominant inheritance
    inheritance_term:
      preferred_term: Autosomal dominant inheritance
      term:
        id: HP:0000006
        label: Autosomal dominant inheritance
  genes:
  - preferred_term: ARID1A
    term:
      id: hgnc:11110
      label: ARID1A
  evidence:
  - reference: PMID:22426308
    reference_title: "Mutations affecting components of the SWI/SNF complex cause Coffin-Siris syndrome."
    supports: SUPPORT
    evidence_source: HUMAN_CLINICAL
    snippet: "Twenty affected individuals (87%) each had a germline mutation in one of six SWI/SNF subunit genes, including SMARCB1, SMARCA4, SMARCA2, SMARCE1, ARID1A and ARID1B."
    explanation: >-
      Identifies ARID1A as one of the six original Coffin-Siris SWI/SNF genes.
  - reference: CGGV:assertion_aaf6d47a-656a-49ca-ba9e-169f25bf03e7-2021-07-07T160000.000Z
    reference_title: "ARID1A / Coffin-Siris syndrome (Definitive)"
    supports: SUPPORT
    evidence_source: OTHER
    snippet: "ARID1A | HGNC:11110 | Coffin-Siris syndrome | MONDO:0015452 | AD | Definitive"
    explanation: >-
      ClinGen classifies the relationship as Definitive under autosomal dominant
      inheritance.
- name: CSS3
  display_name: Coffin-Siris syndrome 3 (SMARCB1-related; MONDO label "intellectual disability, autosomal dominant 15")
  subtype_term:
    preferred_term: intellectual disability, autosomal dominant 15
    term:
      id: MONDO:0013820
      label: intellectual disability, autosomal dominant 15
  description: >-
    The numbered form caused by heterozygous SMARCB1 variants. Unlike ARID1B,
    the Coffin-Siris-associated SMARCB1 variants are non-truncating, which is
    the distinction the cited cohort drew. MONDO's primary label is
    "intellectual disability,
    autosomal dominant 15". SMARCB1 is separately a tumour-predisposition gene;
    this subtype records only the germline neurodevelopmental disorder.
  inheritance:
  - name: Autosomal dominant inheritance
    inheritance_term:
      preferred_term: Autosomal dominant inheritance
      term:
        id: HP:0000006
        label: Autosomal dominant inheritance
  genes:
  - preferred_term: SMARCB1
    term:
      id: hgnc:11103
      label: SMARCB1
  evidence:
  - reference: PMID:23815551
    reference_title: "Coffin-Siris syndrome is a SWI/SNF complex disorder."
    supports: SUPPORT
    evidence_source: HUMAN_CLINICAL
    snippet: "All mutations in SMARCB1 and SMARCA4 were non-truncating (missense or in-frame deletion) whereas those in ARID1B were all truncating (nonsense or frameshift deletion/insertion)"
    explanation: >-
      Supports the non-truncating variant class recorded in this subtype's description.
  - reference: CGGV:assertion_ea554e80-81d2-4100-8d0e-b762ea38fe23-2023-08-15T040000.000Z
    reference_title: "SMARCB1 / Coffin-Siris syndrome (Definitive)"
    supports: SUPPORT
    evidence_source: OTHER
    snippet: "SMARCB1 | HGNC:11103 | Coffin-Siris syndrome | MONDO:0015452 | AD | Definitive"
    explanation: >-
      ClinGen classifies the relationship as Definitive under autosomal dominant
      inheritance.
- name: CSS5
  display_name: Coffin-Siris syndrome 5 (SMARCE1-related)
  subtype_term:
    preferred_term: Coffin-Siris syndrome 5
    term:
      id: MONDO:0014838
      label: Coffin-Siris syndrome 5
  description: >-
    The numbered form caused by heterozygous SMARCE1 variants. SMARCE1 was one of
    the six SWI/SNF subunit genes identified in the founding 2012 series.
  inheritance:
  - name: Autosomal dominant inheritance
    inheritance_term:
      preferred_term: Autosomal dominant inheritance
      term:
        id: HP:0000006
        label: Autosomal dominant inheritance
  genes:
  - preferred_term: SMARCE1
    term:
      id: hgnc:11109
      label: SMARCE1
  evidence:
  - reference: PMID:22426308
    reference_title: "Mutations affecting components of the SWI/SNF complex cause Coffin-Siris syndrome."
    supports: SUPPORT
    evidence_source: HUMAN_CLINICAL
    snippet: "Twenty affected individuals (87%) each had a germline mutation in one of six SWI/SNF subunit genes, including SMARCB1, SMARCA4, SMARCA2, SMARCE1, ARID1A and ARID1B."
    explanation: >-
      Identifies SMARCE1 as one of the six original Coffin-Siris SWI/SNF genes.
  - reference: CGGV:assertion_877f5e0f-5b30-4a4f-87c3-cb6b87caa1e4-2024-09-18T190000.000Z
    reference_title: "SMARCE1 / Coffin-Siris syndrome (Definitive)"
    supports: SUPPORT
    evidence_source: OTHER
    snippet: "SMARCE1 | HGNC:11109 | Coffin-Siris syndrome | MONDO:0015452 | AD | Definitive"
    explanation: >-
      ClinGen classifies the relationship as Definitive under autosomal dominant
      inheritance.
- name: CSS7
  display_name: Coffin-Siris syndrome 7 (DPF2-related)
  subtype_term:
    preferred_term: Coffin-Siris syndrome 7
    term:
      id: MONDO:0054831
      label: Coffin-Siris syndrome 7
  description: >-
    The numbered form caused by de novo DPF2 variants, for which the founding
    report proposes a dominant-negative mechanism rather than simple
    haploinsufficiency.
  inheritance:
  - name: Autosomal dominant inheritance
    inheritance_term:
      preferred_term: Autosomal dominant inheritance
      term:
        id: HP:0000006
        label: Autosomal dominant inheritance
  genes:
  - preferred_term: DPF2
    term:
      id: hgnc:9964
      label: DPF2
  evidence:
  - reference: PMID:29429572
    reference_title: "Mutations in the BAF-Complex Subunit DPF2 Are Associated with Coffin-Siris Syndrome."
    supports: SUPPORT
    evidence_source: HUMAN_CLINICAL
    snippet: "Altogether, we provide compelling evidence that de novo variants in DPF2 cause Coffin-Siris syndrome and propose a dominant-negative mechanism of pathogenicity."
    explanation: >-
      Supports both the de novo variant class and the dominant-negative mechanism
      recorded in this subtype's description.
  - reference: CGGV:assertion_cc8c072e-7b8d-4a94-97fe-c15c91759f0f-2023-08-15T020000.000Z
    reference_title: "DPF2 / Coffin-Siris syndrome (Definitive)"
    supports: SUPPORT
    evidence_source: OTHER
    snippet: "DPF2 | HGNC:9964 | Coffin-Siris syndrome | MONDO:0015452 | AD | Definitive"
    explanation: >-
      ClinGen classifies the relationship as Definitive under autosomal dominant
      inheritance.
- name: CSS8
  display_name: Coffin-Siris syndrome 8 (SMARCC2-related)
  subtype_term:
    preferred_term: Coffin-Siris syndrome 8
    term:
      id: MONDO:0032702
      label: Coffin-Siris syndrome 8
  description: >-
    The numbered form caused by heterozygous SMARCC2 variants. SMARCC2 is among
    the BAF-complex genes whose pathogenic variants cause this disease.
  inheritance:
  - name: Autosomal dominant inheritance
    inheritance_term:
      preferred_term: Autosomal dominant inheritance
      term:
        id: HP:0000006
        label: Autosomal dominant inheritance
  genes:
  - preferred_term: SMARCC2
    term:
      id: hgnc:11105
      label: SMARCC2
  evidence:
  - reference: PMID:41291750
    reference_title: "Long-read sequencing identifies a novel de novo inversion in SMARCC2 in a pediatric patient with Coffin-siris syndrome 8: a case report."
    supports: SUPPORT
    evidence_source: HUMAN_CLINICAL
    snippet: "Coffin-Siris Syndrome 8 (CSS8; MIM# 618362) is a rare neurodevelopmental disorder caused by heterozygous variants in the SMARCC2 gene."
    explanation: >-
      Names the numbered form and its causal gene, which is the identity this subtype
      binds.
  - reference: CGGV:assertion_aa645aa6-3a03-4ab7-9d09-b17be3184259-2025-09-17T100000.000Z
    reference_title: "SMARCC2 / Coffin-Siris syndrome (Definitive)"
    supports: SUPPORT
    evidence_source: OTHER
    snippet: "SMARCC2 | HGNC:11105 | Coffin-Siris syndrome | MONDO:0015452 | AD | Definitive"
    explanation: >-
      ClinGen classifies the relationship as Definitive under autosomal dominant
      inheritance.
- name: CSS10
  display_name: Coffin-Siris syndrome 10 (SOX4-related; reported as CSS-like rather than classic CSS)
  subtype_term:
    preferred_term: Coffin-Siris syndrome 10
    term:
      id: MONDO:0032791
      label: Coffin-Siris syndrome 10
  description: >-
    The form caused by de novo SOX4 variants clustering in the HMG DNA-binding
    domain, which abolish SOX4 transcriptional activity in vitro. SOX4 is a SOXC
    transcription factor rather than a BAF subunit, and it reaches the shared
    skeletal mechanism through the SOXC paralogue programme that the
    pathophysiology section models.

    The MONDO label numbers this as Coffin-Siris syndrome 10, but the largest
    published cohort is explicit that these patients resemble Coffin-Siris
    syndrome while lacking its most specific features, and concludes that the
    entity is a fairly non-specific neurodevelopmental syndrome due to SOX4
    haploinsufficiency. It is curated here as a subtype because the gene sits in
    the same developmental programme as SOX11 and is routinely reported in the
    BAF/Coffin-Siris gene panel, but the phenotype distinction should not be lost.
  inheritance:
  - name: Autosomal dominant inheritance
    inheritance_term:
      preferred_term: Autosomal dominant inheritance
      term:
        id: HP:0000006
        label: Autosomal dominant inheritance
  genes:
  - preferred_term: SOX4
    term:
      id: hgnc:11200
      label: SOX4
  evidence:
  - reference: PMID:30661772
    reference_title: De Novo SOX4 Variants Cause a Neurodevelopmental Disease Associated with Mild Dysmorphism.
    supports: SUPPORT
    evidence_source: HUMAN_CLINICAL
    snippet: >-
      Using trio-based exome sequencing, we here identify de novo SOX4
      heterozygous missense variants in four children who share developmental
      delay, intellectual disability, and mild facial and digital morphological
      abnormalities.
    explanation: >-
      Establishes de novo heterozygous SOX4 variants and the dominant inheritance
      recorded on this subtype.
  - reference: PMID:35232796
    reference_title: Consolidation of the clinical and genetic definition of a SOX4-related neurodevelopmental syndrome.
    supports: SUPPORT
    evidence_source: HUMAN_CLINICAL
    snippet: >-
      They resembled patients with other neurodevelopmental diseases, including
      the SOX11-related and Coffin-Siris (CSS) syndromes, but lacked the most
      specific features of CSS.
    explanation: >-
      Supports the caveat recorded above: the largest cohort places SOX4 disease next to
      Coffin-Siris syndrome rather than inside it.
- name: CSS11
  display_name: Coffin-Siris syndrome 11 (SMARCD1-related)
  subtype_term:
    preferred_term: Coffin-Siris syndrome 11
    term:
      id: MONDO:0032912
      label: Coffin-Siris syndrome 11
  description: >-
    The numbered form caused by de novo SMARCD1 variants. SMARCD1 is a core
    SWI/SNF subunit, so the mechanism is the shared BAF-complex dysfunction. As
    with SOX4, the founding series notes that these individuals overlap the
    BAF-related syndromes clinically but lack their typical facial dysmorphisms,
    so the numbered Coffin-Siris label is broader than the reported phenotype.
  inheritance:
  - name: Autosomal dominant inheritance
    inheritance_term:
      preferred_term: Autosomal dominant inheritance
      term:
        id: HP:0000006
        label: Autosomal dominant inheritance
  genes:
  - preferred_term: SMARCD1
    term:
      id: hgnc:11106
      label: SMARCD1
  evidence:
  - reference: PMID:30879640
    reference_title: "A Syndromic Neurodevelopmental Disorder Caused by Mutations in SMARCD1, a Core SWI/SNF Subunit Needed for Context-Dependent Neuronal Gene Regulation in Flies."
    supports: SUPPORT
    evidence_source: HUMAN_CLINICAL
    snippet: >-
      Here, we report on five individuals with mutations in SMARCD1; the
      individuals present with developmental delay, intellectual disability,
      hypotonia, feeding difficulties, and small hands and feet.
    explanation: >-
      Establishes SMARCD1 as the causal gene and gives the reported phenotype.
  - reference: PMID:30879640
    reference_title: "A Syndromic Neurodevelopmental Disorder Caused by Mutations in SMARCD1, a Core SWI/SNF Subunit Needed for Context-Dependent Neuronal Gene Regulation in Flies."
    supports: SUPPORT
    evidence_source: HUMAN_CLINICAL
    snippet: >-
      Although the individuals presented here have dysmorphisms and some clinical
      overlap with these syndromes, they lack their typical facial dysmorphisms.
    explanation: >-
      Supports the phenotype caveat recorded above.
- name: CSS12
  display_name: Coffin-Siris syndrome 12 (BICRA-related, non-canonical BAF)
  subtype_term:
    preferred_term: Coffin-Siris syndrome 12
    term:
      id: MONDO:0025699
      label: Coffin-Siris syndrome 12
  description: >-
    The numbered form caused by haploinsufficiency of BICRA (also GLTSCR1), which
    encodes a subunit of the non-canonical BAF (ncBAF) complex rather than of
    canonical BAF. Most reported individuals lack fifth digit or nail hypoplasia,
    which is otherwise the signature feature of this disease group, so the
    phenotype is recognisably a SWI/SNF-related disorder without the Coffin-Siris
    hand finding.
  inheritance:
  - name: Autosomal dominant inheritance
    inheritance_term:
      preferred_term: Autosomal dominant inheritance
      term:
        id: HP:0000006
        label: Autosomal dominant inheritance
  genes:
  - preferred_term: BICRA
    term:
      id: hgnc:4332
      label: BICRA
  evidence:
  - reference: PMID:33232675
    reference_title: "BICRA, a SWI/SNF Complex Member, Is Associated with BAF-Disorder Related Phenotypes in Humans and Model Organisms."
    supports: SUPPORT
    evidence_source: HUMAN_CLINICAL
    snippet: >-
      We have identified 12 individuals with rare variants (10 loss-of-function,
      2 missense) in the BICRA (BRD4 interacting chromatin remodeling
      complex-associated protein) gene, also known as GLTSCR1, which encodes a
      subunit of the non-canonical BAF (ncBAF) complex.
    explanation: >-
      Establishes BICRA as causal in 12 individuals and places it in the non-canonical BAF
      complex, which is the distinction recorded in this subtype's description.
  - reference: PMID:33232675
    reference_title: "BICRA, a SWI/SNF Complex Member, Is Associated with BAF-Disorder Related Phenotypes in Humans and Model Organisms."
    supports: SUPPORT
    evidence_source: HUMAN_CLINICAL
    snippet: >-
      Notably, the majority of individuals lack the fifth digit/nail hypoplasia
      phenotype, a hallmark of most SSRIDDs.
    explanation: >-
      Supports the absence of the signature hand finding recorded above.
  - reference: PMID:36437209
    reference_title: Identification of a novel BICRA variant leading to the newly described Coffin-Siris syndrome 12.
    supports: SUPPORT
    evidence_source: HUMAN_CLINICAL
    snippet: "Pathogenic heterozygous variants in BICRA have recently been identified in patients with SWI/SNF-related intellectual disability (SSRIDD) - Coffin-Siris syndrome 12."
    explanation: >-
      Names the numbered Coffin-Siris syndrome 12 designation for BICRA disease, which is
      the identity this subtype binds.
  - reference: CGGV:assertion_2dcc8864-4487-4c5c-b541-cfd972767269-2024-11-20T170000.000Z
    reference_title: "BICRA / Coffin-Siris syndrome (Definitive)"
    supports: SUPPORT
    evidence_source: OTHER
    snippet: "BICRA | HGNC:4332 | Coffin-Siris syndrome | MONDO:0015452 | AD | Definitive"
    explanation: >-
      ClinGen classifies the relationship as Definitive under autosomal dominant
      inheritance.
- name: SOX11
  display_name: SOX11-related neurodevelopmental disorder (mild Coffin-Siris phenotype)
  description: >-
    The form caused by de novo SOX11 variants. Like SOX4, SOX11 is a SOXC
    transcription factor rather than a BAF subunit, and the phenotype is reported
    as a mild Coffin-Siris syndrome.

    No subtype_term is bound. MONDO gives this concept no Coffin-Siris number;
    its class is MONDO:0014376, whose primary label names intellectual
    developmental disorder with microcephaly and with or without ocular
    malformations or hypogonadotropic hypogonadism, and that class is already the
    disease_term of the SOX11-Related_Neurodevelopmental_Disorder entry. This row
    carries the gene for the parent pathograph rather than claiming the same
    identifier a second time.
  inheritance:
  - name: Autosomal dominant inheritance
    inheritance_term:
      preferred_term: Autosomal dominant inheritance
      term:
        id: HP:0000006
        label: Autosomal dominant inheritance
  genes:
  - preferred_term: SOX11
    term:
      id: hgnc:11191
      label: SOX11
  evidence:
  - reference: PMID:30661772
    reference_title: De Novo SOX4 Variants Cause a Neurodevelopmental Disease Associated with Mild Dysmorphism.
    supports: SUPPORT
    evidence_source: HUMAN_CLINICAL
    quote_role: BACKGROUND
    snippet: >-
      De novo SOX11 heterozygous mutations have been shown to cause intellectual
      disability, growth deficiency, and dysmorphic features compatible with mild
      Coffin-Siris syndrome.
    explanation: >-
      States the mild Coffin-Siris reading of SOX11 disease that this subtype records.
      Marked BACKGROUND because the sentence is the cited SOX4 paper's framing of prior
      work on SOX11, not its own result.
  - reference: PMID:39501269
    reference_title: "A rare Coffin-Siris syndrome induced by SOX11: a de novo nonsense variant of short stature."
    supports: SUPPORT
    evidence_source: HUMAN_CLINICAL
    snippet: "The combination of clinical presentation and genetic testing results supports that the patient suffers from Coffin-Siris syndrome due to a genetic variant in the SOX11 gene."
    explanation: >-
      An independent case report diagnosing Coffin-Siris syndrome on the basis of a SOX11
      variant.

prevalence:
- population: Published literature cohorts
  measure_type: POINT_PREVALENCE
  prevalence_class: BAND_1_9_PER_100000
  rate_low: 1.0
  rate_high: 10.0
  percentage: approximately 1:10,000 to 1:100,000
  notes: >-
    Robust population prevalence estimates are not established in PubMed
    abstracts, but Coffin-Siris syndrome remains ultra-rare in the clinical
    literature. By 2018, approximately 200 individuals had been described, and
    a 2024 case report cites an estimated incidence of 1:10,000-1:100,000.
  evidence:
  - reference: PMID:30276971
    reference_title: "First data from a parent-reported registry of 81 individuals with Coffin-Siris syndrome: Natural history and management recommendations."
    supports: SUPPORT
    evidence_source: HUMAN_CLINICAL
    snippet: "To date, approximately 200 individuals have been described in the literature."
    explanation: This registry paper provides the clearest PubMed-abstract estimate of how many Coffin-Siris syndrome cases had been described in the literature.
  - reference: PMID:38790056
    reference_title: "De novo variation in ARID1B gene causes Coffin-Siris syndrome 1 in a Chinese family with excessive early-onset high myopia."
    supports: SUPPORT
    evidence_source: HUMAN_CLINICAL
    snippet: "Coffin-Siris syndrome (CSS) is a rare autosomal dominant inheritance disorder"
    explanation: This recent clinical report supports the interpretation of Coffin-Siris syndrome as an ultra-rare disorder in current clinical practice.
inheritance:
- name: Autosomal dominant inheritance
  inheritance_term:
    preferred_term: Autosomal dominant inheritance
    term:
      id: HP:0000006
      label: Autosomal dominant inheritance
  description: >-
    Coffin-Siris syndrome is usually inherited in an autosomal dominant manner,
    and many molecularly confirmed cases are de novo.
  evidence:
  - reference: PMID:38790056
    reference_title: "De novo variation in ARID1B gene causes Coffin-Siris syndrome 1 in a Chinese family with excessive early-onset high myopia."
    supports: SUPPORT
    evidence_source: HUMAN_CLINICAL
    snippet: "Coffin-Siris syndrome (CSS) is a rare autosomal dominant inheritance disorder characterized by distinctive facial features, hypoplasia of the distal phalanx or nail of the fifth and additional digits, developmental or cognitive delay of varying degree, hypotonia, hirsutism/hypertrichosis, sparse scalp hair and varying kind of congenital anomalies."
    explanation: This directly supports autosomal dominant inheritance for CSS.
  - reference: PMID:23815551
    reference_title: "Coffin-Siris syndrome is a SWI/SNF complex disorder."
    supports: SUPPORT
    evidence_source: HUMAN_CLINICAL
    snippet: "By examining available parental samples, we ascertained that 17 occurred de novo."
    explanation: This supports the statement that many CSS cases arise de novo.
pathophysiology:
- name: BAF/SWI-SNF chromatin remodeling dysfunction
  conforms_to: "epigenetic_machinery_neurodevelopmental_dysregulation#Epigenetic Machinery Component Haploinsufficiency"
  description: >-
    Pathogenic variants in BAF-complex genes reduce or alter ATP-dependent
    chromatin remodeling, disturbing transcriptional programs required for
    embryonic patterning and neurodevelopment. CSS therefore behaves as a
    BAFopathy in which disruption of one of several chromatin-remodeling
    subunits converges on abnormal developmental gene regulation.
  genes:
  - preferred_term: ARID1A
    term:
      id: hgnc:11110
      label: ARID1A
  - preferred_term: ARID1B
    term:
      id: hgnc:18040
      label: ARID1B
  - preferred_term: ARID2
    term:
      id: hgnc:18037
      label: ARID2
  - preferred_term: DPF2
    term:
      id: hgnc:9964
      label: DPF2
  - preferred_term: SMARCA2
    term:
      id: hgnc:11098
      label: SMARCA2
  - preferred_term: SMARCA4
    term:
      id: hgnc:11100
      label: SMARCA4
  - preferred_term: SMARCB1
    term:
      id: hgnc:11103
      label: SMARCB1
  - preferred_term: SMARCE1
    term:
      id: hgnc:11109
      label: SMARCE1
  - preferred_term: SMARCC2
    term:
      id: hgnc:11105
      label: SMARCC2
  - preferred_term: SMARCD1
    term:
      id: hgnc:11106
      label: SMARCD1
  protein_complexes:
  - preferred_term: BAF complex
    term:
      id: GO:0016514
      label: SWI/SNF complex
  cell_types:
  - preferred_term: neural progenitor cell
    term:
      id: CL:0011020
      label: neural progenitor cell
  locations:
  - preferred_term: brain
    term:
      id: UBERON:0000955
      label: brain
  biological_processes:
  - preferred_term: chromatin remodeling
    term:
      id: GO:0006338
      label: chromatin remodeling
  - preferred_term: regulation of transcription by RNA polymerase II
    term:
      id: GO:0006357
      label: regulation of transcription by RNA polymerase II
  - preferred_term: nervous system development
    term:
      id: GO:0007399
      label: nervous system development
  downstream:
  - target: Altered developmental transcription programs
    description: Reduced BAF activity perturbs expression programs needed for normal tissue differentiation.
    causal_link_type: DIRECT
    evidence:
    - reference: PMID:23815551
      reference_title: "Coffin-Siris syndrome is a SWI/SNF complex disorder."
      supports: SUPPORT
      evidence_source: HUMAN_CLINICAL
      snippet: "We previously reported that five genes are mutated in CSS, all of which encode subunits of the switch/sucrose non-fermenting (SWI/SNF) ATP-dependent chromatin-remodeling complex: SMARCB1, SMARCA4, SMARCE1, ARID1A, and ARID1B."
      explanation: Because CSS genes encode an ATP-dependent chromatin-remodeling complex, this supports the inferred downstream consequence of altered developmental transcriptional control.
  - target: Global developmental delay
    description: Multisystem dysregulation of developmental gene expression manifests clinically as near-universal global developmental delay.
    causal_link_type: INDIRECT_KNOWN_INTERMEDIATES
    intermediate_mechanisms:
    - Altered developmental transcription programs
    - Impaired neurogenesis and neuronal maturation
    evidence:
    - reference: PMID:30276971
      reference_title: "First data from a parent-reported registry of 81 individuals with Coffin-Siris syndrome: Natural history and management recommendations."
      supports: SUPPORT
      evidence_source: HUMAN_CLINICAL
      snippet: "Varying degrees of developmental and intellectual delay are universal."
      explanation: This supports the downstream consequence of neurodevelopmental impairment following BAF-complex dysfunction.
  - target: Intellectual disability
    description: Disrupted BAF-dependent regulation of neuronal gene programs underlies the universal cognitive impairment of CSS.
    causal_link_type: INDIRECT_KNOWN_INTERMEDIATES
    intermediate_mechanisms:
    - Altered developmental transcription programs
    evidence:
    - reference: PMID:34205270
      reference_title: "Genotype-Phenotype Correlations in 208 Individuals with Coffin-Siris Syndrome."
      supports: SUPPORT
      evidence_source: HUMAN_CLINICAL
      snippet: "Coffin-Siris syndrome (CSS, MIM 135900) is a multi-system intellectual disability syndrome characterized by classic dysmorphic features, developmental delays, and organ system anomalies."
      explanation: Direct registry-level evidence that intellectual disability is a defining downstream phenotype of CSS BAF dysfunction.
  evidence:
  - reference: PMID:23815551
    reference_title: "Coffin-Siris syndrome is a SWI/SNF complex disorder."
    supports: SUPPORT
    evidence_source: HUMAN_CLINICAL
    snippet: "Our data further support that CSS is a SWI/SNF complex disorder."
    explanation: This explicitly supports CSS as a SWI/SNF complex disorder.
  - reference: PMID:30276971
    reference_title: "First data from a parent-reported registry of 81 individuals with Coffin-Siris syndrome: Natural history and management recommendations."
    supports: SUPPORT
    evidence_source: HUMAN_CLINICAL
    snippet: "Coffin-Siris syndrome (CSS; MIM 135900) is a multisystem congenital anomaly syndrome caused by mutations in the genes in the Brg-1 associated factors (BAF) complex."
    explanation: This independently confirms BAF-complex dysfunction as the central disease mechanism.
  - reference: PMID:22426308
    reference_title: "Mutations affecting components of the SWI/SNF complex cause Coffin-Siris syndrome."
    supports: SUPPORT
    evidence_source: HUMAN_CLINICAL
    snippet: "Twenty affected individuals (87%) each had a germline mutation in one of six SWI/SNF subunit genes, including SMARCB1, SMARCA4, SMARCA2, SMARCE1, ARID1A and ARID1B."
    explanation: The landmark 2012 study showing high diagnostic yield of SWI/SNF mutations in CSS.
  - reference: PMID:38243407
    reference_title: "ARID2, a milder cause of Coffin-Siris Syndrome? Broadening the phenotype with 17 additional individuals."
    supports: SUPPORT
    evidence_source: HUMAN_CLINICAL
    snippet: >-
      Coffin-Siris Syndrome (CSS, MIM 135900) is now a well-described genetic
      condition caused by pathogenic variants in the Bromocriptine activating
      factor (BAF) complex, including ARID1B, ARID1A, ARID2, SMARCA4, SMARCE1,
      SMARCB1, SOX11, SMARCC2, DPF2, and more recently, BICRA.
    explanation: >-
      Supports binding SMARCC2 to this node by naming it among the BAF-complex genes whose
      variants cause the disease. As recorded on the BICRA genetic record, this sentence
      erroneously expands BAF as "Bromocriptine activating factor"; the correct expansion
      is BRG1/BRM-Associated Factors.
  - reference: PMID:30879640
    reference_title: "A Syndromic Neurodevelopmental Disorder Caused by Mutations in SMARCD1, a Core SWI/SNF Subunit Needed for Context-Dependent Neuronal Gene Regulation in Flies."
    supports: SUPPORT
    evidence_source: HUMAN_CLINICAL
    snippet: >-
      Mutations in several genes encoding components of the SWI/SNF chromatin
      remodeling complex cause neurodevelopmental disorders (NDDs). Here, we
      report on five individuals with mutations in SMARCD1; the individuals
      present with developmental delay, intellectual disability, hypotonia,
      feeding difficulties, and small hands and feet.
    explanation: >-
      Supports binding SMARCD1 to this node: the paper reports it as a SWI/SNF component
      gene whose mutation produces a neurodevelopmental disorder.
- name: Cortical interneuron deficiency from ARID1B haploinsufficiency
  description: >-
    ARID1B haploinsufficiency reduces GABAergic interneuron numbers in the
    cerebral cortex through impaired proliferation and increased apoptosis of
    interneuron progenitors in the ganglionic eminence, creating an
    excitatory-inhibitory imbalance that underlies cognitive and behavioral
    abnormalities.
  genes:
  - preferred_term: ARID1B
    term:
      id: hgnc:18040
      label: ARID1B
  cell_types:
  - preferred_term: GABAergic interneuron
    term:
      id: CL:0000617
      label: GABAergic neuron
  - preferred_term: neural progenitor cell
    term:
      id: CL:0011020
      label: neural progenitor cell
  locations:
  - preferred_term: cerebral cortex
    term:
      id: UBERON:0000956
      label: cerebral cortex
  biological_processes:
  - preferred_term: GABAergic neuron differentiation
    term:
      id: GO:0097154
      label: GABAergic neuron differentiation
  - preferred_term: regulation of neuron apoptotic process
    term:
      id: GO:0043523
      label: regulation of neuron apoptotic process
  downstream:
  - target: Excitatory-inhibitory imbalance
    description: >-
      Reduced cortical GABAergic interneurons create an imbalance between
      excitatory and inhibitory synaptic transmission, contributing to
      cognitive dysfunction and autism-like behaviors.
    causal_link_type: DIRECT
    evidence:
    - reference: PMID:29184203
      reference_title: "Arid1b haploinsufficiency disrupts cortical interneuron development and mouse behavior."
      supports: SUPPORT
      evidence_source: MODEL_ORGANISM
      snippet: "Arid1b haploinsufficiency also led to an imbalance between excitatory and inhibitory synapses in the cerebral cortex."
      explanation: Mouse model demonstrates the excitatory-inhibitory imbalance resulting from Arid1b haploinsufficiency.
  - target: Intellectual disability
    description: >-
      Loss of cortical inhibitory interneurons and the resulting cortical
      excitation-inhibition imbalance contribute to cognitive impairment;
      conditional deletion of Arid1b in ventral (interneuron) progenitors
      specifically produces ID- and ASD-like behavior in mice.
    causal_link_type: INDIRECT_KNOWN_INTERMEDIATES
    intermediate_mechanisms:
    - Excitatory-inhibitory imbalance
    evidence:
    - reference: PMID:33594090
      reference_title: "Differential roles of ARID1B in excitatory and inhibitory neural progenitors in the developing cortex."
      supports: SUPPORT
      evidence_source: MODEL_ORGANISM
      snippet: "Conditional homozygous deletion of Arid1b in ventral neural progenitors led to pronounced ID- and ASD-like behaviors in mice, whereas the deletion in cortical neural progenitors resulted in minor cognitive deficits."
      explanation: Conditional knockout in inhibitory progenitors recapitulates intellectual disability, anchoring the interneuron-deficit -> ID path.
  - target: Seizures
    description: >-
      Reduced cortical GABAergic inhibition and resulting excitatory-inhibitory
      imbalance provide a mechanistic basis for the increased seizure
      susceptibility seen in CSS.
    causal_link_type: INDIRECT_KNOWN_INTERMEDIATES
    intermediate_mechanisms:
    - Excitatory-inhibitory imbalance
    evidence:
    - reference: PMID:29184203
      reference_title: "Arid1b haploinsufficiency disrupts cortical interneuron development and mouse behavior."
      supports: SUPPORT
      evidence_source: MODEL_ORGANISM
      snippet: "Arid1b haploinsufficiency also led to an imbalance between excitatory and inhibitory synapses in the cerebral cortex."
      explanation: Excitatory-inhibitory imbalance from Arid1b haploinsufficiency provides the cellular substrate for the elevated seizure risk in CSS patients.
  evidence:
  - reference: PMID:29184203
    reference_title: "Arid1b haploinsufficiency disrupts cortical interneuron development and mouse behavior."
    supports: SUPPORT
    evidence_source: MODEL_ORGANISM
    snippet: "Arid1b-heterozygous mice showed a decreased number of cortical GABAergic interneurons and reduced proliferation of interneuron progenitors in the ganglionic eminence."
    explanation: Direct evidence from an Arid1b haploinsufficiency mouse model showing reduced cortical interneurons.
  - reference: PMID:29184203
    reference_title: "Arid1b haploinsufficiency disrupts cortical interneuron development and mouse behavior."
    supports: SUPPORT
    evidence_source: MODEL_ORGANISM
    snippet: "Arid1b haploinsufficiency suppressed histone H3 lysine 9 acetylation (H3K9ac) overall and particularly reduced H3K9ac of the Pvalb promoter, resulting in decreased transcription."
    explanation: This provides the epigenetic mechanism linking Arid1b loss to reduced parvalbumin interneuron differentiation.
- name: Altered cell-cycle dynamics from ARID1B haploinsufficiency
  description: >-
    ARID1B haploinsufficiency causes delayed cell-cycle re-entry in patient-derived
    cells, indicating that abnormal proliferation dynamics contribute to CSS
    pathogenesis and likely impair tissue growth and developmental progression.
  genes:
  - preferred_term: ARID1B
    term:
      id: hgnc:18040
      label: ARID1B
  cell_types:
  - preferred_term: fibroblast
    term:
      id: CL:0000057
      label: fibroblast
  biological_processes:
  - preferred_term: regulation of cell cycle process
    term:
      id: GO:0010564
      label: regulation of cell cycle process
  downstream:
  - target: Reduced proliferative capacity
    description: Delayed cell-cycle re-entry limits normal expansion of developing cell populations.
    causal_link_type: DIRECT
    evidence:
    - reference: PMID:24674232
      reference_title: "Expanding the phenotypic spectrum of ARID1B-mediated disorders and identification of altered cell-cycle dynamics due to ARID1B haploinsufficiency."
      supports: SUPPORT
      evidence_source: IN_VITRO
      snippet: "Analysis of both patient-derived and ARID1B knockdown fibroblasts after serum starvation demonstrated delayed cell cycle re-entry associated with reduced cell number in the S1 phase."
      explanation: This directly supports reduced proliferative capacity as the downstream consequence of altered ARID1B-dependent cell-cycle control.
  - target: Microcephaly
    description: >-
      Reduced proliferation of cortical neural progenitors limits cortical
      neuron output and brain volume; ARID1B-deficient cortical and ventral
      neural progenitors show decreased proliferation and increased cell death.
    causal_link_type: INDIRECT_KNOWN_INTERMEDIATES
    intermediate_mechanisms:
    - Reduced proliferative capacity
    - Decreased neural progenitor proliferation and survival
    evidence:
    - reference: PMID:33594090
      reference_title: "Differential roles of ARID1B in excitatory and inhibitory neural progenitors in the developing cortex."
      supports: SUPPORT
      evidence_source: MODEL_ORGANISM
      snippet: "We detected an overall decrease in the proliferation of cortical and ventral neural progenitors following homozygous deletion of Arid1b, as well as altered cell cycle regulation and increased cell death."
      explanation: Reduced progenitor proliferation and increased apoptosis in ARID1B-deficient cortex provide the cellular basis for microcephaly observed in CSS.
  - target: Short stature
    description: >-
      Reduced proliferative capacity of mesenchymal/somatic cells and ARID1B-dependent
      IGF1/GH axis dysregulation jointly produce growth restriction
      and short stature.
    causal_link_type: INDIRECT_KNOWN_INTERMEDIATES
    intermediate_mechanisms:
    - Reduced proliferative capacity
    - IGF1/GH axis dysregulation
    evidence:
    - reference: PMID:28695822
      reference_title: "Arid1b haploinsufficient mice reveal neuropsychiatric phenotypes and reversible causes of growth impairment."
      supports: SUPPORT
      evidence_source: MODEL_ORGANISM
      snippet: "Sequencing studies have implicated haploinsufficiency of ARID1B, a SWI/SNF chromatin-remodeling subunit, in short stature"
      explanation: ARID1B haploinsufficiency is mechanistically and clinically linked to short stature in human and mouse data.
  evidence:
  - reference: PMID:24674232
    reference_title: "Expanding the phenotypic spectrum of ARID1B-mediated disorders and identification of altered cell-cycle dynamics due to ARID1B haploinsufficiency."
    supports: SUPPORT
    evidence_source: IN_VITRO
    snippet: "Analysis of both patient-derived and ARID1B knockdown fibroblasts after serum starvation demonstrated delayed cell cycle re-entry associated with reduced cell number in the S1 phase."
    explanation: This provides direct functional evidence that ARID1B haploinsufficiency alters cell-cycle dynamics.
  - reference: PMID:24674232
    reference_title: "Expanding the phenotypic spectrum of ARID1B-mediated disorders and identification of altered cell-cycle dynamics due to ARID1B haploinsufficiency."
    supports: SUPPORT
    evidence_source: IN_VITRO
    snippet: "We present the first direct evidence in patient-derived cells that alterations in cell cycle contribute to the underlying pathogenesis of syndromes associated with ARID1B haploinsufficiency."
    explanation: This explicitly connects altered cell-cycle control to CSS pathogenesis.
- name: Protein misfolding and aggregation of non-truncating ARID1B variants
  description: >-
    A subset of ARID1B missense variants cause CSS by provoking protein
    misfolding and aggregate formation rather than classical nonsense-mediated
    decay, thereby reducing functional nuclear BAF activity through an
    alternative loss-of-function mechanism.
  genes:
  - preferred_term: ARID1B
    term:
      id: hgnc:18040
      label: ARID1B
  biological_processes:
  - preferred_term: protein folding
    term:
      id: GO:0006457
      label: protein folding
  downstream:
  - target: Reduced functional ARID1B availability
    description: Aggregated ARID1B fails to contribute normally to BAF-complex function.
    evidence:
    - reference: PMID:39028335
      reference_title: "The missing link: ARID1B non-truncating variants causing Coffin-Siris syndrome due to protein aggregation."
      supports: SUPPORT
      evidence_source: IN_VITRO
      snippet: "The present study substantiates the pathogenesis of ARID1B non-truncating/NMD-escaping variants located in the SMARCA4-interacting EHD2 and DNA-binding ARID domains. Overexpression assays in cell lines revealed that the majority of EHD2 variants lead to protein misfolding and formation of cytoplasmic aggresomes surrounded by vimentin cage-like structures and co-localizing with the microtubule organisation center."
      explanation: This supports aggregation-mediated loss of functional ARID1B availability as a downstream consequence of non-truncating variants.
  evidence:
  - reference: PMID:39028335
    reference_title: "The missing link: ARID1B non-truncating variants causing Coffin-Siris syndrome due to protein aggregation."
    supports: SUPPORT
    evidence_source: IN_VITRO
    snippet: "The present study substantiates the pathogenesis of ARID1B non-truncating/NMD-escaping variants located in the SMARCA4-interacting EHD2 and DNA-binding ARID domains. Overexpression assays in cell lines revealed that the majority of EHD2 variants lead to protein misfolding and formation of cytoplasmic aggresomes surrounded by vimentin cage-like structures and co-localizing with the microtubule organisation center."
    explanation: This supports protein misfolding and aggregation as a pathogenic mechanism for a subset of ARID1B variants in CSS.
  - reference: PMID:39028335
    reference_title: "The missing link: ARID1B non-truncating variants causing Coffin-Siris syndrome due to protein aggregation."
    supports: SUPPORT
    evidence_source: HUMAN_CLINICAL
    snippet: "Genome-wide transcriptome and methylation analysis in affected individuals revealed expression and methylome patterns consistent with those of the pathogenic haploinsufficiency ARID1B alterations in CSS cases."
    explanation: This shows that aggregation-prone ARID1B variants converge on the same downstream molecular state as haploinsufficient CSS.
- name: Cranial neural crest specification defect from ARID1A-BAF/ZIC2 axis
  description: >-
    ARID1A haploinsufficiency impairs ARID1A-BAF binding at enhancers of
    epithelial-to-mesenchymal transition (EMT) genes, disrupts ZIC2 occupancy
    at these enhancers, and impairs delamination/migration of cranial neural
    crest cells. Conserved BAF complex activity (via BAF155/BAF170) is also
    required during murine neural crest development for correct craniofacial,
    pharyngeal arch and outflow tract formation. Failure of cranial neural
    crest specification underlies coarse facial dysmorphism, micrognathism, and
    other craniofacial features of CSS.
  genes:
  - preferred_term: ARID1A
    term:
      id: hgnc:11110
      label: ARID1A
  - preferred_term: SMARCA4
    term:
      id: hgnc:11100
      label: SMARCA4
  protein_complexes:
  - preferred_term: BAF complex
    term:
      id: GO:0016514
      label: SWI/SNF complex
  cell_types:
  - preferred_term: cranial neural crest cell
    term:
      id: CL:0000008
      label: migratory cranial neural crest cell
  - preferred_term: migratory neural crest cell
    term:
      id: CL:0000333
      label: migratory neural crest cell
  locations:
  - preferred_term: neural tube
    term:
      id: UBERON:0001049
      label: neural tube
  biological_processes:
  - preferred_term: neural crest cell migration
    term:
      id: GO:0001755
      label: neural crest cell migration
  - preferred_term: epithelial to mesenchymal transition
    term:
      id: GO:0001837
      label: epithelial to mesenchymal transition
  downstream:
  - target: Coarse facial features
    description: >-
      Impaired cranial neural crest delamination and migration disrupts
      development of facial mesenchyme and the craniofacial skeleton, producing
      the coarse and dysmorphic facial features that are a defining clinical
      feature of CSS.
    causal_link_type: INDIRECT_KNOWN_INTERMEDIATES
    intermediate_mechanisms:
    - Impaired EMT and delamination of cranial neural crest
    - Disrupted ARID1A-ZIC2 enhancer regulation
    evidence:
    - reference: PMID:39226899
      reference_title: "ARID1A-BAF coordinates ZIC2 genomic occupancy for epithelial-to-mesenchymal transition in cranial neural crest specification."
      supports: SUPPORT
      evidence_source: IN_VITRO
      snippet: "Variants in BAF subunits cause Coffin-Siris syndrome (CSS), a congenital disorder characterized by coarse craniofacial features and intellectual disability."
      explanation: Connects CSS coarse facial features directly to BAF-dependent cranial neural crest specification.
  - target: Microcephaly
    description: >-
      Neural crest contributions to the cranial vault, plus broader BAF
      requirements during forebrain development, link cranial NCC and BAF
      dysfunction to reduced cranial growth.
    causal_link_type: INDIRECT_KNOWN_INTERMEDIATES
    intermediate_mechanisms:
    - Impaired cranial neural crest specification
    - Impaired forebrain neural progenitor proliferation
    evidence:
    - reference: PMID:33750945
      reference_title: "Critical role of the BAF chromatin remodeling complex during murine neural crest development."
      supports: SUPPORT
      evidence_source: MODEL_ORGANISM
      snippet: "Neural crest-specific deletion of BAF155/BAF170 leads to embryonic lethality due to a wide range of developmental defects including craniofacial, pharyngeal arch artery, and OFT defects."
      explanation: BAF complex is required for craniofacial development from neural crest, supporting the link to reduced craniofacial/cranial growth.
  evidence:
  - reference: PMID:39226899
    reference_title: "ARID1A-BAF coordinates ZIC2 genomic occupancy for epithelial-to-mesenchymal transition in cranial neural crest specification."
    supports: SUPPORT
    evidence_source: IN_VITRO
    snippet: "Using CSS-patient-derived ARID1A+/- induced pluripotent stem cells to model CNCC specification, we discovered that ARID1A-haploinsufficiency impairs epithelial-to-mesenchymal transition (EMT), a process necessary for CNCC delamination and migration from the neural tube."
    explanation: Directly demonstrates that ARID1A haploinsufficiency in CSS-patient iPSCs impairs cranial neural crest EMT and delamination.
  - reference: PMID:39226899
    reference_title: "ARID1A-BAF coordinates ZIC2 genomic occupancy for epithelial-to-mesenchymal transition in cranial neural crest specification."
    supports: SUPPORT
    evidence_source: IN_VITRO
    snippet: "ARID1A-BAF binding at these enhancers is impaired in heterozygotes while binding at promoters is unaffected."
    explanation: Mechanistically supports loss of ARID1A-BAF activity at EMT enhancers as the molecular event upstream of cranial NCC failure.
  - reference: PMID:33750945
    reference_title: "Critical role of the BAF chromatin remodeling complex during murine neural crest development."
    supports: SUPPORT
    evidence_source: MODEL_ORGANISM
    snippet: "Neural crest-specific deletion of BAF155/BAF170 leads to embryonic lethality due to a wide range of developmental defects including craniofacial, pharyngeal arch artery, and OFT defects."
    explanation: Independent in vivo evidence that the BAF complex is required for craniofacial neural crest development.
  - reference: PMID:37624665
    reference_title: "The SWI/SNF Complex in Neural Crest Cell Development and Disease."
    supports: SUPPORT
    evidence_source: MODEL_ORGANISM
    snippet: "Two mammalian paralogs of the SWI/SNF (switch/sucrose nonfermentable) chromatin-remodeling complexes, BAF (Brg1-associated factors) and PBAF (polybromo-associated BAF), are critical for neural crest specification during normal mammalian development."
    explanation: Review-level summary establishing BAF/PBAF as essential for neural crest specification, supporting the CSS pathograph branch.
- name: Cardiac neural crest dysregulation from BAF dysfunction
  description: >-
    Brg1 (SMARCA4)/BAF activity in neural crest cells is required for outflow
    tract septation, pharyngeal arch artery patterning, and cardiomyocyte
    differentiation. CSS-causing variants in SMARCA4 and other BAF subunits
    disrupt the cardiac neural crest gene program, producing the spectrum of
    congenital heart defects (including septal defects, hypoplastic left
    heart, truncus arteriosus, and outflow tract anomalies) seen in CSS,
    particularly in prenatal and ARID1A-related cases.
  genes:
  - preferred_term: SMARCA4
    term:
      id: hgnc:11100
      label: SMARCA4
  - preferred_term: ARID1A
    term:
      id: hgnc:11110
      label: ARID1A
  - preferred_term: SMARCB1
    term:
      id: hgnc:11103
      label: SMARCB1
  protein_complexes:
  - preferred_term: BAF complex
    term:
      id: GO:0016514
      label: SWI/SNF complex
  cell_types:
  - preferred_term: cardiac neural crest cell
    term:
      id: CL:0000333
      label: migratory neural crest cell
  locations:
  - preferred_term: heart
    term:
      id: UBERON:0000948
      label: heart
  biological_processes:
  - preferred_term: outflow tract morphogenesis
    term:
      id: GO:0003151
      label: outflow tract morphogenesis
  - preferred_term: neural crest cell migration
    term:
      id: GO:0001755
      label: neural crest cell migration
  downstream:
  - target: Congenital heart defects
    description: >-
      Disrupted Brg1/BAF activity in cardiac neural crest leads to outflow
      tract shortening, abnormal pharyngeal arch artery patterning and
      defective cardiogenic gene programs, producing structural cardiac
      defects ranging from septal defects to severe prenatal cardiovascular
      malformations.
    causal_link_type: INDIRECT_KNOWN_INTERMEDIATES
    intermediate_mechanisms:
    - Impaired cardiac neural crest migration and proliferation
    - Disrupted Brg1-driven cardiac gene expression program
    evidence:
    - reference: PMID:23319608
      reference_title: "Brg1 governs distinct pathways to direct multiple aspects of mammalian neural crest cell development."
      supports: SUPPORT
      evidence_source: MODEL_ORGANISM
      snippet: "Mouse embryos lacking Brg1 in NCCs display immature cerebral vessels, aberrant PAA patterning, and shortened OFT."
      explanation: Direct mouse evidence that NCC-specific loss of the SMARCA4/Brg1 ATPase produces the same cardiovascular malformations seen in CSS.
    - reference: PMID:37981638
      reference_title: "Prenatal Coffin-Siris Syndrome: Expanding the Phenotypic and Genotypic Spectrum of the Disease."
      supports: SUPPORT
      evidence_source: HUMAN_CLINICAL
      snippet: "severely hypoplastic right ventricle with VSD and truncus arteriosus type III"
      explanation: Human prenatal CSS phenotypes match the cardiac neural crest / outflow tract phenotype predicted by BAF dysfunction.
  evidence:
  - reference: PMID:23319608
    reference_title: "Brg1 governs distinct pathways to direct multiple aspects of mammalian neural crest cell development."
    supports: SUPPORT
    evidence_source: MODEL_ORGANISM
    snippet: "Brahma-related gene 1 (Brg1), an ATPase subunit of the Brg1/Brahma-associated factor (BAF) chromatin-remodeling complex, is required in NCCs to direct cardiovascular development."
    explanation: Establishes Brg1/SMARCA4 as required in cardiac neural crest, the cell population implicated in CSS cardiac malformations.
  - reference: PMID:30814119
    reference_title: "Dynamic BAF chromatin remodeling complex subunit inclusion promotes temporally distinct gene expression programs in cardiogenesis."
    supports: SUPPORT
    evidence_source: MODEL_ORGANISM
    snippet: "the catalytic subunit gene Brg1 has a specific role in cardiac precursors (CPs) to initiate cardiac gene expression programs and repress non-cardiac expression."
    explanation: Provides the mechanistic role of Brg1/BAF in cardiac precursors, complementing the neural-crest pathway.
- name: Corpus callosum projection neuron axonogenesis defect from ARID1B haploinsufficiency
  description: >-
    ARID1B haploinsufficiency impairs maturation of SATB2+ callosal projection
    neurons by reducing chromatin accessibility at TCF/NFI/ARID-bound regulatory
    regions controlling corpus callosum (CC) genes, leading to underdeveloped
    long-range axonal projections and structural underconnectivity. This
    cell-autonomous axonogenesis defect explains the high frequency of agenesis
    or hypoplasia of the corpus callosum (~50% in some cohorts) seen in CSS.
  conforms_to: "projection_neuron_subtype_specification#Mis-specified Long-Range Axon Target Selection"
  genes:
  - preferred_term: ARID1B
    term:
      id: hgnc:18040
      label: ARID1B
  cell_types:
  - preferred_term: callosal projection neuron
    term:
      id: CL:0000540
      label: neuron
  locations:
  - preferred_term: corpus callosum
    term:
      id: UBERON:0002336
      label: corpus callosum
  biological_processes:
  - preferred_term: axonogenesis
    term:
      id: GO:0007409
      label: axonogenesis
  - preferred_term: regulation of transcription by RNA polymerase II
    term:
      id: GO:0006357
      label: regulation of transcription by RNA polymerase II
  downstream:
  - target: Agenesis of corpus callosum
    description: >-
      Impaired maturation and axon outgrowth of SATB2+ callosal projection
      neurons leads to absent or hypoplastic corpus callosum.
    causal_link_type: DIRECT
    evidence:
    - reference: PMID:38718796
      reference_title: "ARID1B controls transcriptional programs of axon projection in an organoid model of the human corpus callosum."
      supports: SUPPORT
      evidence_source: IN_VITRO
      snippet: "The most common structural abnormality in the brain of ARID1B patients is agenesis of the corpus callosum (ACC), characterized by the absence of an interhemispheric white matter tract that connects distant cortical regions."
      explanation: Directly anchors agenesis of the corpus callosum as the structural phenotype produced by this ARID1B-driven mechanism.
  - target: Intellectual disability
    description: >-
      Loss of long-range interhemispheric connectivity and dysregulated
      callosal axonogenesis programs contribute to cognitive impairment in CSS
      independent of the cortical interneuron deficit.
    causal_link_type: INDIRECT_KNOWN_INTERMEDIATES
    intermediate_mechanisms:
    - Impaired callosal axon outgrowth
    - Cortical interhemispheric underconnectivity
    evidence:
    - reference: PMID:38718796
      reference_title: "ARID1B controls transcriptional programs of axon projection in an organoid model of the human corpus callosum."
      supports: SUPPORT
      evidence_source: IN_VITRO
      snippet: "this transcriptional dysregulation impairs the formation of long-range axonal projections, causing structural underconnectivity."
      explanation: Structural underconnectivity is a plausible substrate for the cognitive deficit phenotype in ARID1B CSS.
  evidence:
  - reference: PMID:38718796
    reference_title: "ARID1B controls transcriptional programs of axon projection in an organoid model of the human corpus callosum."
    supports: SUPPORT
    evidence_source: IN_VITRO
    snippet: "neurons expressing SATB2, a determinant of callosal projection neuron (CPN) identity, show impaired maturation in ARID1B+/- neural organoids."
    explanation: Functionally identifies the cell-autonomous defect in SATB2+ neurons as the proximate cause of CC agenesis in ARID1B haploinsufficiency.
  - reference: PMID:38718796
    reference_title: "ARID1B controls transcriptional programs of axon projection in an organoid model of the human corpus callosum."
    supports: SUPPORT
    evidence_source: IN_VITRO
    snippet: "a reduction in chromatin accessibility of genomic regions targeted by TCF-like, NFI-like, and ARID-like transcription factors drives the differential expression of genes required for corpus callosum (CC) development."
    explanation: Provides the chromatin-accessibility/transcriptomic mechanism connecting ARID1B haploinsufficiency to CC dysgenesis.
  - reference: PMID:34706719
    reference_title: "Phenotypic and molecular spectra of patients with switch/sucrose nonfermenting complex-related intellectual disability disorders in Korea."
    supports: SUPPORT
    evidence_source: HUMAN_CLINICAL
    snippet: "Agenesis or hypoplasia of the corpus callosum was observed in half of the patients (6/12)."
    explanation: Cohort-level confirmation that corpus callosum dysgenesis is a frequent CSS phenotype consistent with this mechanism.
- name: Midline brain glia aberrations from SMARCB1 dysfunction
  description: >-
    Heterozygous nervous-system-restricted partial loss of SMARCB1 produces
    brain midline abnormalities including agenesis of the corpus callosum
    through defective midline glia development. This pathway provides a
    SMARCB1-specific mechanism for the brain midline phenotype that overlaps
    with the ARID1B-axonogenesis pathway above.
  genes:
  - preferred_term: SMARCB1
    term:
      id: hgnc:11103
      label: SMARCB1
  cell_types:
  - preferred_term: glial cell
    term:
      id: CL:0000125
      label: glial cell
  locations:
  - preferred_term: corpus callosum
    term:
      id: UBERON:0002336
      label: corpus callosum
  - preferred_term: forebrain
    term:
      id: UBERON:0001890
      label: forebrain
  biological_processes:
  - preferred_term: glial cell development
    term:
      id: GO:0021782
      label: glial cell development
  downstream:
  - target: Agenesis of corpus callosum
    description: >-
      Defective midline glia development in Smarcb1 mutant mice causes corpus
      callosum agenesis recapitulating the brain midline phenotype seen in
      SMARCB1 (and other BAF) CSS patients.
    causal_link_type: DIRECT
    evidence:
    - reference: PMID:31273213
      reference_title: "Mutations in SMARCB1 and in other Coffin-Siris syndrome genes lead to various brain midline defects."
      supports: SUPPORT
      evidence_source: MODEL_ORGANISM
      snippet: "Analyses of the Smarcb1 mutant animals indicate that one prominent midline abnormality, corpus callosum agenesis, is due to midline glia aberrations."
      explanation: Directly establishes the SMARCB1 -> midline glia -> CC agenesis path.
  evidence:
  - reference: PMID:31273213
    reference_title: "Mutations in SMARCB1 and in other Coffin-Siris syndrome genes lead to various brain midline defects."
    supports: SUPPORT
    evidence_source: MODEL_ORGANISM
    snippet: "These Smarcb1 mutant mice show various brain midline abnormalities that are also found in individuals with Coffin-Siris syndrome (CSS) caused by SMARCB1, SMARCE1, and ARID1B mutations and in SMARCB1-related intellectual disability (ID) with choroid plexus hyperplasia (CPH)."
    explanation: Provides the disease-model linkage for the SMARCB1 brain midline mechanism in CSS.
- name: IGF1/GH axis dysregulation in ARID1B haploinsufficiency
  description: >-
    ARID1B haploinsufficiency in mice produces growth impairment driven by
    insulin-like growth factor 1 (IGF1) deficiency with inadequate compensation
    by GHRH and GH. Growth hormone supplementation rescued growth retardation
    and muscle weakness, identifying a reversible endocrine axis underlying the
    short stature and contributing to hypotonia in CSS.
  genes:
  - preferred_term: ARID1B
    term:
      id: hgnc:18040
      label: ARID1B
  biological_processes:
  - preferred_term: insulin-like growth factor receptor signaling pathway
    term:
      id: GO:0048009
      label: insulin-like growth factor receptor signaling pathway
  - preferred_term: growth hormone secretion
    term:
      id: GO:0030252
      label: growth hormone secretion
  downstream:
  - target: Short stature
    description: >-
      IGF1 deficiency with inadequate GHRH/GH compensation produces postnatal
      growth retardation; growth hormone supplementation corrected this in
      Arid1b heterozygous mice.
    causal_link_type: DIRECT
    evidence:
    - reference: PMID:28695822
      reference_title: "Arid1b haploinsufficient mice reveal neuropsychiatric phenotypes and reversible causes of growth impairment."
      supports: SUPPORT
      evidence_source: MODEL_ORGANISM
      snippet: "A focus on reversible mechanisms identified Insulin-like growth factor (IGF1) deficiency with inadequate compensation by Growth hormone-releasing hormone (GHRH) and Growth hormone (GH), underappreciated findings in ARID1B patients."
      explanation: Direct mouse-model evidence that IGF1/GH axis deficiency is the upstream driver of ARID1B-related short stature.
    - reference: PMID:28695822
      reference_title: "Arid1b haploinsufficient mice reveal neuropsychiatric phenotypes and reversible causes of growth impairment."
      supports: SUPPORT
      evidence_source: MODEL_ORGANISM
      snippet: "Therapeutically, GH supplementation was able to correct growth retardation and muscle weakness."
      explanation: Reversibility of growth retardation by GH supplementation cements IGF1/GH dysregulation as the operative mechanism for short stature.
  - target: Hypotonia
    description: >-
      Reduced IGF1/GH signaling impairs muscle development and contributes to
      the muscle weakness/hypotonia phenotype seen in CSS; GH supplementation
      rescued muscle weakness in the Arid1b mouse model.
    causal_link_type: INDIRECT_KNOWN_INTERMEDIATES
    intermediate_mechanisms:
    - IGF1/GH axis dysregulation
    - Impaired muscle growth and tone
    evidence:
    - reference: PMID:28695822
      reference_title: "Arid1b haploinsufficient mice reveal neuropsychiatric phenotypes and reversible causes of growth impairment."
      supports: SUPPORT
      evidence_source: MODEL_ORGANISM
      snippet: "Therapeutically, GH supplementation was able to correct growth retardation and muscle weakness."
      explanation: Demonstrates muscle weakness (a major correlate of clinical hypotonia) is GH-axis-dependent in the Arid1b model.
  evidence:
  - reference: PMID:28695822
    reference_title: "Arid1b haploinsufficient mice reveal neuropsychiatric phenotypes and reversible causes of growth impairment."
    supports: SUPPORT
    evidence_source: MODEL_ORGANISM
    snippet: "We generated Arid1b heterozygous mice, which showed social behavior impairment, altered vocalization, anxiety-like behavior, neuroanatomical abnormalities, and growth impairment."
    explanation: Establishes the Arid1b haploinsufficiency mouse model that recapitulates ARID1B-CSS growth phenotypes.
- name: Mesenchymal stem cell quiescence loss and tooth root progenitor defects
  description: >-
    ARID1B normally maintains GLI1+ mesenchymal stem cell quiescence by
    suppressing BCL11B-driven non-canonical Activin signaling. Loss of ARID1B
    drives MSCs out of quiescence into ectopic proliferation. In parallel,
    Arid1a controls a Plagl1-Hedgehog signaling axis required for the
    differentiation-associated cell-cycle arrest of tooth root progenitors;
    Arid1a loss causes shortened tooth roots and odontoblast differentiation
    defects. Together, these BAF-dependent MSC and odontogenic mechanisms
    underlie dental anomalies in CSS.
  genes:
  - preferred_term: ARID1B
    term:
      id: hgnc:18040
      label: ARID1B
  - preferred_term: ARID1A
    term:
      id: hgnc:11110
      label: ARID1A
  cell_types:
  - preferred_term: mesenchymal stem cell
    term:
      id: CL:0000134
      label: mesenchymal stem cell
  - preferred_term: odontoblast
    term:
      id: CL:0000060
      label: odontoblast
  biological_processes:
  - preferred_term: stem cell maintenance
    term:
      id: GO:0019827
      label: stem cell population maintenance
  - preferred_term: smoothened signaling pathway
    term:
      id: GO:0007224
      label: smoothened signaling pathway
  downstream:
  - target: Dental anomalies
    description: >-
      ARID1B-MSC and ARID1A-Plagl1-Hh defects in odontogenic progenitors
      produce abnormal odontoblast differentiation and shortened tooth roots,
      contributing to the dental hypoplasia/abnormal dental morphology seen in
      CSS.
    causal_link_type: INDIRECT_KNOWN_INTERMEDIATES
    intermediate_mechanisms:
    - Loss of MSC quiescence
    - Impaired odontoblast differentiation
    evidence:
    - reference: PMID:33826897
      reference_title: "Arid1a-Plagl1-Hh signaling is indispensable for differentiation-associated cell cycle arrest of tooth root progenitors."
      supports: SUPPORT
      evidence_source: MODEL_ORGANISM
      snippet: "loss of Arid1a impairs the differentiation-associated cell cycle arrest of tooth root progenitors through Hedgehog (Hh) signaling regulation, leading to shortened roots."
      explanation: Direct mouse evidence linking BAF (Arid1a) loss to odontogenic defects, providing a mechanistic basis for CSS dental anomalies.
  evidence:
  - reference: PMID:38816354
    reference_title: "ARID1B maintains mesenchymal stem cell quiescence via inhibition of BCL11B-mediated non-canonical Activin signaling."
    supports: SUPPORT
    evidence_source: MODEL_ORGANISM
    snippet: "loss of Arid1b in the GLI1+ MSC lineage disturbs MSCs' quiescence and leads to their proliferation due to the ectopic activation of non-canonical Activin signaling via p-ERK."
    explanation: Establishes ARID1B as a regulator of MSC quiescence in the craniofacial/dental lineage relevant to CSS.
  - reference: PMID:33826897
    reference_title: "Arid1a-Plagl1-Hh signaling is indispensable for differentiation-associated cell cycle arrest of tooth root progenitors."
    supports: SUPPORT
    evidence_source: MODEL_ORGANISM
    snippet: "loss of Arid1a leads to increased expression of Arid1b, which is also indispensable for odontoblast differentiation but is not involved in regulation of Hh signaling."
    explanation: Shows BAF-paralog (ARID1A/ARID1B) interdependence is required for odontoblast differentiation, supporting the dental phenotype mechanism.
- name: Limb skeletal patterning defect from SOXC and BAF dysfunction
  description: >-
    SOX11 and its SOXC paralogs (SOX4/SOX12) are required in limb mesenchyme
    for growth plate formation and skeletal elongation through noncanonical
    Wnt/PCP signaling. SoxC deletion in limb bud skeletogenic mesenchyme
    abolishes growth plate formation and produces severely shortened skeletal
    elements. SOX11 also positively regulates GDF5 in the joint interzone,
    contributing to joint and digit development. CSS-causing SOX11 variants
    therefore plausibly underlie the signature distal phalanx and fifth-digit
    hypoplasia, complementing the broader BAF-complex requirement for skeletal
    differentiation.
  genes:
  - preferred_term: SOX11
    term:
      id: hgnc:11191
      label: SOX11
  - preferred_term: SOX4
    term:
      id: hgnc:11200
      label: SOX4
  cell_types:
  - preferred_term: chondrocyte
    term:
      id: CL:0000138
      label: chondrocyte
  - preferred_term: skeletal mesenchymal cell
    term:
      id: CL:0000134
      label: mesenchymal stem cell
  locations:
  - preferred_term: limb
    term:
      id: UBERON:0002101
      label: limb
  biological_processes:
  - preferred_term: skeletal system development
    term:
      id: GO:0001501
      label: skeletal system development
  - preferred_term: chondrocyte differentiation
    term:
      id: GO:0002062
      label: chondrocyte differentiation
  - preferred_term: planar cell polarity pathway involved in axis elongation
    term:
      id: GO:0060071
      label: Wnt signaling pathway, planar cell polarity pathway
  downstream:
  - target: Hypoplastic fifth fingernail
    description: >-
      Disrupted SOXC-driven growth plate formation and joint patterning,
      combined with BAF-dependent skeletal differentiation defects, plausibly
      underlie the distal phalangeal hypoplasia and fifth-digit nail anomalies
      that are the signature physical feature of CSS.
    causal_link_type: INDIRECT_UNKNOWN_INTERMEDIATES
    intermediate_mechanisms:
    - Disrupted SOXC-driven Wnt/PCP signaling in limb mesenchyme
    - Impaired growth plate formation
    - Disrupted GDF5-dependent joint formation
    evidence:
    - reference: PMID:25761772
      reference_title: "SOXC Transcription Factors Induce Cartilage Growth Plate Formation in Mouse Embryos by Promoting Noncanonical WNT Signaling."
      supports: SUPPORT
      evidence_source: MODEL_ORGANISM
      snippet: "SoxC(Prx1Cre) mice, which deleted SoxC genes in limb bud skeletogenic mesenchyme, were born with tiny appendicular cartilage primordia because of failure to form growth plates."
      explanation: Mouse model demonstrates that SOXC (including SOX11) is required for limb bud skeletal growth, providing a mechanistic substrate for distal phalanx hypoplasia in SOX11-CSS.
  evidence:
  - reference: PMID:25761772
    reference_title: "SOXC Transcription Factors Induce Cartilage Growth Plate Formation in Mouse Embryos by Promoting Noncanonical WNT Signaling."
    supports: SUPPORT
    evidence_source: MODEL_ORGANISM
    snippet: "SoxC genes were necessary in perichondrocytes for expression of Wnt5a, which encodes a noncanonical WNT ligand required for growth plate formation, and in chondrocytes and perichondrocytes for expression of Fzd3 and Csnk1e, which encode a WNT receptor and casein kinase-1 subunit mediating planar cell polarity, respectively."
    explanation: Establishes the SOXC -> noncanonical Wnt/PCP -> growth plate axis required for limb skeletal development.
  - reference: PMID:23356643
    reference_title: "SOX11 contributes to the regulation of GDF5 in joint maintenance."
    supports: SUPPORT
    evidence_source: MODEL_ORGANISM
    snippet: "Sox11 is initially expressed broadly in the murine cartilage condensations at early stages of skeletal development, but its expression is specifically increased in the forming joint interzone as is forms."
    explanation: SOX11 expression and GDF5 regulation in joint interzones link SOX11 dysfunction to digit/joint development relevant to the CSS fifth-digit phenotype.
phenotypes:
- name: Global developmental delay
  description: >-
    Developmental delay affecting multiple domains is one of the most consistent
    manifestations of Coffin-Siris syndrome.
  phenotype_term:
    preferred_term: Global developmental delay
    term:
      id: HP:0001263
      label: Global developmental delay
  evidence:
  - reference: PMID:30276971
    reference_title: "First data from a parent-reported registry of 81 individuals with Coffin-Siris syndrome: Natural history and management recommendations."
    supports: SUPPORT
    evidence_source: HUMAN_CLINICAL
    snippet: "Varying degrees of developmental and intellectual delay are universal."
    explanation: This supports global developmental delay as a near-universal feature of CSS.
- name: Intellectual disability
  description: >-
    Intellectual disability is common and spans a broad severity range across CSS
    genotypes.
  phenotype_term:
    preferred_term: Intellectual disability
    term:
      id: HP:0001249
      label: Intellectual disability
  evidence:
  - reference: PMID:30276971
    reference_title: "First data from a parent-reported registry of 81 individuals with Coffin-Siris syndrome: Natural history and management recommendations."
    supports: SUPPORT
    evidence_source: HUMAN_CLINICAL
    snippet: "Varying degrees of developmental and intellectual delay are universal."
    explanation: This directly supports intellectual disability as a core clinical feature of CSS.
  - reference: PMID:23815551
    reference_title: "Coffin-Siris syndrome is a SWI/SNF complex disorder."
    supports: SUPPORT
    evidence_source: HUMAN_CLINICAL
    snippet: "Coffin-Siris syndrome (CSS) is a congenital disorder characterized by intellectual disability, growth deficiency, microcephaly, coarse facial features, and hypoplastic or absent fifth fingernails and/or toenails."
    explanation: This confirms intellectual disability as a defining feature of CSS.
- name: Hypoplastic fifth fingernail
  description: >-
    Hypoplasia or aplasia of the fifth fingernail or distal phalanx is a classic
    physical feature and remains one of the most recognizable clues to the diagnosis.
  phenotype_term:
    preferred_term: Hypoplastic fifth fingernail
    term:
      id: HP:0008398
      label: Hypoplastic fifth fingernail
  evidence:
  - reference: PMID:30276971
    reference_title: "First data from a parent-reported registry of 81 individuals with Coffin-Siris syndrome: Natural history and management recommendations."
    supports: SUPPORT
    evidence_source: HUMAN_CLINICAL
    snippet: "Classically, individuals with CSS have been described with hypo- or aplasia of the fifth digit nails or phalanges (hence the term \"fifth digit syndrome\")."
    explanation: This directly supports the classic fifth-digit nail/phalangeal hypoplasia phenotype in CSS.
- name: Coarse facial features
  description: >-
    Coarse facial features are characteristic and often become more apparent over time.
  phenotype_term:
    preferred_term: Coarse facial features
    term:
      id: HP:0000280
      label: Coarse facial features
  evidence:
  - reference: PMID:30276971
    reference_title: "First data from a parent-reported registry of 81 individuals with Coffin-Siris syndrome: Natural history and management recommendations."
    supports: SUPPORT
    evidence_source: HUMAN_CLINICAL
    snippet: "Other physical features seen include growth restriction, coarse facial features, hypertrichosis or hirsutism, sparse scalp hair, dental anomalies, and other organ-system abnormalities."
    explanation: This supports coarse facial features as one of the major physical findings in CSS.
  - reference: PMID:38182156
    reference_title: "Coffin-Siris Syndrome: Case Series of Three Patients and a Novel ARID2 Variant."
    supports: SUPPORT
    evidence_source: HUMAN_CLINICAL
    snippet: "Coffin-Siris syndrome (CSS) is a rare congenital disorder characterized by coarse facial features, intellectual disability or developmental delay, and aplasia or hypoplasia of the tips of the fifth finger and/or toes."
    explanation: This independently confirms coarse facial features as a defining clinical characteristic.
- name: Hypotonia
  description: >-
    Generalized hypotonia commonly contributes to motor delay and feeding difficulty.
    Hypotonia is among the most common features in large CSS cohorts and may be
    mechanistically linked to ARID1B-driven IGF1/GH-axis dysregulation given
    that GH supplementation rescued muscle weakness in the Arid1b mouse model.
  phenotype_term:
    preferred_term: Hypotonia
    term:
      id: HP:0001252
      label: Hypotonia
  evidence:
  - reference: PMID:38243407
    reference_title: "ARID2, a milder cause of Coffin-Siris Syndrome? Broadening the phenotype with 17 additional individuals."
    supports: SUPPORT
    evidence_source: HUMAN_CLINICAL
    snippet: "Individuals with CSS have a spectrum of various medical challenges, most often evident at birth, including feeding difficulties, hypotonia, organ-system anomalies, and learning and developmental differences."
    explanation: This supports hypotonia as a frequent early-life manifestation of CSS.
  - reference: PMID:38790056
    reference_title: "De novo variation in ARID1B gene causes Coffin-Siris syndrome 1 in a Chinese family with excessive early-onset high myopia."
    supports: SUPPORT
    evidence_source: HUMAN_CLINICAL
    snippet: "Coffin-Siris syndrome (CSS) is a rare autosomal dominant inheritance disorder characterized by distinctive facial features, hypoplasia of the distal phalanx or nail of the fifth and additional digits, developmental or cognitive delay of varying degree, hypotonia, hirsutism/hypertrichosis, sparse scalp hair and varying kind of congenital anomalies."
    explanation: This independently lists hypotonia as a characteristic feature of CSS.
  - reference: PMID:34205270
    reference_title: "Genotype-Phenotype Correlations in 208 Individuals with Coffin-Siris Syndrome."
    supports: SUPPORT
    evidence_source: HUMAN_CLINICAL
    snippet: "hypotonia, hypertrichosis, sparse scalp hair, and hypoplasia of the distal phalanx are still some of the most common features."
    explanation: 208-individual CSS/BAF complex registry confirms hypotonia is among the most common features across all CSS genotypes.
- name: Feeding difficulties in infancy
  description: >-
    Feeding problems are frequent in infancy and can complicate growth and care needs.
  phenotype_term:
    preferred_term: Feeding difficulties in infancy
    term:
      id: HP:0008872
      label: Feeding difficulties in infancy
  evidence:
  - reference: PMID:38243407
    reference_title: "ARID2, a milder cause of Coffin-Siris Syndrome? Broadening the phenotype with 17 additional individuals."
    supports: SUPPORT
    evidence_source: HUMAN_CLINICAL
    snippet: "Individuals with CSS have a spectrum of various medical challenges, most often evident at birth, including feeding difficulties, hypotonia, organ-system anomalies, and learning and developmental differences."
    explanation: This supports infant feeding difficulties as a common clinical issue in CSS.
- name: Hypertrichosis
  description: >-
    Hypertrichosis or hirsutism is a characteristic ectodermal manifestation across
    multiple CSS genotypes.
  phenotype_term:
    preferred_term: Hypertrichosis
    term:
      id: HP:0000998
      label: Hypertrichosis
  evidence:
  - reference: PMID:30276971
    reference_title: "First data from a parent-reported registry of 81 individuals with Coffin-Siris syndrome: Natural history and management recommendations."
    supports: SUPPORT
    evidence_source: HUMAN_CLINICAL
    snippet: "Other physical features seen include growth restriction, coarse facial features, hypertrichosis or hirsutism, sparse scalp hair, dental anomalies, and other organ-system abnormalities."
    explanation: This supports hypertrichosis as a recurring physical feature in CSS.
  - reference: PMID:34205270
    reference_title: "Genotype-Phenotype Correlations in 208 Individuals with Coffin-Siris Syndrome."
    supports: SUPPORT
    evidence_source: HUMAN_CLINICAL
    snippet: "hypotonia, hypertrichosis, sparse scalp hair, and hypoplasia of the distal phalanx are still some of the most common features."
    explanation: 208-individual registry data identify hypertrichosis among the most common CSS features.
- name: Sparse scalp hair
  description: >-
    Sparse scalp hair is a common hair phenotype in CSS and often co-occurs with hypertrichosis.
  phenotype_term:
    preferred_term: Sparse scalp hair
    term:
      id: HP:0002209
      label: Sparse scalp hair
  evidence:
  - reference: PMID:30276971
    reference_title: "First data from a parent-reported registry of 81 individuals with Coffin-Siris syndrome: Natural history and management recommendations."
    supports: SUPPORT
    evidence_source: HUMAN_CLINICAL
    snippet: "Other physical features seen include growth restriction, coarse facial features, hypertrichosis or hirsutism, sparse scalp hair, dental anomalies, and other organ-system abnormalities."
    explanation: This supports sparse scalp hair as a characteristic ectodermal feature of CSS.
- name: Short stature
  description: >-
    Short stature is part of the variable growth phenotype and may be milder in
    some ARID2-associated cases.
  phenotype_term:
    preferred_term: Short stature
    term:
      id: HP:0004322
      label: Short stature
  evidence:
  - reference: PMID:38243407
    reference_title: "ARID2, a milder cause of Coffin-Siris Syndrome? Broadening the phenotype with 17 additional individuals."
    supports: SUPPORT
    evidence_source: HUMAN_CLINICAL
    snippet: "Although individuals with ARID2 have been reported to have classic features of CSS including hypertrichosis, coarse facial features, short stature, and fifth digit anomalies, as with many of the other CSS genes, there appears to be a spectrum of phenotypes."
    explanation: This supports short stature as part of the recognized CSS phenotype spectrum.
  - reference: PMID:23815551
    reference_title: "Coffin-Siris syndrome is a SWI/SNF complex disorder."
    supports: SUPPORT
    evidence_source: HUMAN_CLINICAL
    snippet: "Coffin-Siris syndrome (CSS) is a congenital disorder characterized by intellectual disability, growth deficiency, microcephaly, coarse facial features, and hypoplastic or absent fifth fingernails and/or toenails."
    explanation: Growth deficiency supports the short stature phenotype in CSS.
- name: Microcephaly
  description: >-
    Microcephaly is a common craniofacial finding in CSS reflecting impaired
    brain growth.
  phenotype_term:
    preferred_term: Microcephaly
    term:
      id: HP:0000252
      label: Microcephaly
  evidence:
  - reference: PMID:23815551
    reference_title: "Coffin-Siris syndrome is a SWI/SNF complex disorder."
    supports: SUPPORT
    evidence_source: HUMAN_CLINICAL
    snippet: "Coffin-Siris syndrome (CSS) is a congenital disorder characterized by intellectual disability, growth deficiency, microcephaly, coarse facial features, and hypoplastic or absent fifth fingernails and/or toenails."
    explanation: Microcephaly is listed as a defining characteristic of CSS.
- name: Seizures
  description: >-
    Epilepsy is a frequent complication in CSS individuals, reported in
    ~26-28% of patients in literature reviews and registry-based studies. The
    excitatory-inhibitory imbalance caused by reduced cortical GABAergic
    interneurons provides a mechanistic basis for seizure susceptibility, and
    seizures are most often focal/multifocal and generally controllable on
    antiseizure medications.
  phenotype_term:
    preferred_term: Seizures
    term:
      id: HP:0001250
      label: Seizure
  notes: >-
    Frequency intentionally omitted from the structured field because the
    available registry-vs-literature estimates differ (7.2% caregiver-reported
    in a 334-patient registry vs ~26-28% in literature reviews) per the
    project's frequency-evidence guidelines.
  evidence:
  - reference: PMID:29184203
    reference_title: "Arid1b haploinsufficiency disrupts cortical interneuron development and mouse behavior."
    supports: SUPPORT
    evidence_source: MODEL_ORGANISM
    snippet: "Arid1b haploinsufficiency also led to an imbalance between excitatory and inhibitory synapses in the cerebral cortex."
    explanation: The excitatory-inhibitory imbalance from Arid1b haploinsufficiency provides a mechanistic basis for seizure susceptibility in CSS.
  - reference: PMID:36177969
    reference_title: "Epilepsy in Coffin-Siris syndrome: A report from the international CSS registry and review of the literature."
    supports: SUPPORT
    evidence_source: HUMAN_CLINICAL
    snippet: "The literature review yielded 311 unique CSS patients, 82 of which (26.4%) carried diagnoses of seizures or epilepsy."
    explanation: International CSS registry literature review quantifies epilepsy prevalence at ~26% of published CSS patients.
  - reference: PMID:36177969
    reference_title: "Epilepsy in Coffin-Siris syndrome: A report from the international CSS registry and review of the literature."
    supports: SUPPORT
    evidence_source: HUMAN_CLINICAL
    snippet: "Seventeen patients (5.1%) reported EEG abnormalities, the majority of which were described as focal or multifocal (87.5%)."
    explanation: Documents the focal/multifocal character of seizures consistent with the predicted cortical interneuron-deficit substrate.
- name: Hearing impairment
  description: >-
    Hearing loss is a recognized feature of CSS and may be sensorineural,
    conductive, or mixed.
  phenotype_term:
    preferred_term: Hearing impairment
    term:
      id: HP:0000365
      label: Hearing impairment
  evidence:
  - reference: PMID:38790056
    reference_title: "De novo variation in ARID1B gene causes Coffin-Siris syndrome 1 in a Chinese family with excessive early-onset high myopia."
    supports: SUPPORT
    evidence_source: HUMAN_CLINICAL
    snippet: "moderate hearing loss"
    explanation: This case report documents hearing loss as part of the ARID1B-associated CSS phenotype.
- name: Dental anomalies
  description: >-
    Dental anomalies including hypoplasia and delayed eruption are part of the
    ectodermal phenotype spectrum.
  phenotype_term:
    preferred_term: Dental anomalies
    term:
      id: HP:0006482
      label: Abnormal dental morphology
  evidence:
  - reference: PMID:30276971
    reference_title: "First data from a parent-reported registry of 81 individuals with Coffin-Siris syndrome: Natural history and management recommendations."
    supports: SUPPORT
    evidence_source: HUMAN_CLINICAL
    snippet: "Other physical features seen include growth restriction, coarse facial features, hypertrichosis or hirsutism, sparse scalp hair, dental anomalies, and other organ-system abnormalities."
    explanation: Dental anomalies are listed among the physical features of CSS.
  - reference: PMID:38790056
    reference_title: "De novo variation in ARID1B gene causes Coffin-Siris syndrome 1 in a Chinese family with excessive early-onset high myopia."
    supports: SUPPORT
    evidence_source: HUMAN_CLINICAL
    snippet: "dental hypoplasia"
    explanation: This case report documents dental hypoplasia in an ARID1B-associated CSS patient.
- name: Congenital heart defects
  description: >-
    Congenital heart defects are among the organ-system anomalies seen in
    CSS and may include septal defects, patent foramen ovale, and other
    structural cardiac anomalies.
  phenotype_term:
    preferred_term: Congenital heart defects
    term:
      id: HP:0001627
      label: Abnormal heart morphology
  evidence:
  - reference: PMID:38243407
    reference_title: "ARID2, a milder cause of Coffin-Siris Syndrome? Broadening the phenotype with 17 additional individuals."
    supports: SUPPORT
    evidence_source: HUMAN_CLINICAL
    snippet: "hip dysplasia appears to occur more often than with other genes, however more severe medical challenges such as significant brain and cardiac malformations are rarer"
    explanation: This confirms that cardiac malformations are part of the CSS phenotypic spectrum, though they occur less frequently in ARID2-associated cases.
  - reference: PMID:38790056
    reference_title: "De novo variation in ARID1B gene causes Coffin-Siris syndrome 1 in a Chinese family with excessive early-onset high myopia."
    supports: SUPPORT
    evidence_source: HUMAN_CLINICAL
    snippet: "patent foramen ovale"
    explanation: This case report documents a cardiac anomaly (patent foramen ovale) in a CSS patient.
- name: Renal anomalies
  description: >-
    Genitourinary and renal malformations are part of the multisystem
    anomaly spectrum in CSS, ranging from renal cysts to renal agenesis in
    severe prenatal cases.
  phenotype_term:
    preferred_term: Renal anomalies
    term:
      id: HP:0000077
      label: Abnormality of the kidney
  evidence:
  - reference: PMID:38790056
    reference_title: "De novo variation in ARID1B gene causes Coffin-Siris syndrome 1 in a Chinese family with excessive early-onset high myopia."
    supports: SUPPORT
    evidence_source: HUMAN_CLINICAL
    snippet: "bilateral renal cysts"
    explanation: This case report documents bilateral renal cysts in a CSS patient.
  - reference: PMID:35579625
    reference_title: "Discovering a new part of the phenotypic spectrum of Coffin-Siris syndrome in a fetal cohort."
    supports: SUPPORT
    evidence_source: HUMAN_CLINICAL
    snippet: "Prenatal anomalies that were frequently observed in our cohort include hydrocephalus, agenesis of the corpus callosum, hypoplastic left heart syndrome, persistent left vena cava, diaphragmatic hernia, renal agenesis, and intrauterine growth restriction."
    explanation: 44-patient prenatal CSS cohort confirms renal anomalies (including renal agenesis) as a recognized fetal phenotype.
- name: Hydrocephalus
  description: >-
    Hydrocephalus is observed in CSS, particularly in prenatal and severe
    cases. The Arid1b heterozygous mouse model recapitulates this phenotype,
    providing genetic-model support.
  phenotype_term:
    preferred_term: Hydrocephalus
    term:
      id: HP:0000238
      label: Hydrocephalus
  evidence:
  - reference: PMID:35579625
    reference_title: "Discovering a new part of the phenotypic spectrum of Coffin-Siris syndrome in a fetal cohort."
    supports: SUPPORT
    evidence_source: HUMAN_CLINICAL
    snippet: "Prenatal anomalies that were frequently observed in our cohort include hydrocephalus, agenesis of the corpus callosum, hypoplastic left heart syndrome, persistent left vena cava, diaphragmatic hernia, renal agenesis, and intrauterine growth restriction."
    explanation: Confirms hydrocephalus as a frequent prenatal CSS phenotype across 44 fetal cases.
  - reference: PMID:28867767
    reference_title: "Arid1b Haploinsufficiency Causes Abnormal Brain Gene Expression and Autism-Related Behaviors in Mice."
    supports: SUPPORT
    evidence_source: MODEL_ORGANISM
    snippet: "Hydrocephalus was present in 5 of 91 hKO mice, while it was not observed in wild-type littermates (0 of 188)."
    explanation: Arid1b haploinsufficient mouse model recapitulates hydrocephalus seen in CSS patients.
- name: Microphthalmia
  description: >-
    Microphthalmia is a recognized feature of SMARCA4-related CSS, supported
    by haploinsufficiency-driven mechanisms in mouse and DECIPHER cohorts.
  phenotype_term:
    preferred_term: Microphthalmia
    term:
      id: HP:0000568
      label: Microphthalmia
  evidence:
  - reference: PMID:28608987
    reference_title: "SMARCA4 inactivating mutations cause concomitant Coffin-Siris syndrome, microphthalmia and small-cell carcinoma of the ovary hypercalcaemic type."
    supports: SUPPORT
    evidence_source: HUMAN_CLINICAL
    snippet: "our case supports the dual role of chromatin remodellers in developmental disorders and cancer, as well as the involvement of SMARCA4 in microphthalmia, confirming previous findings in mouse models and the DECIPHER database."
    explanation: Establishes SMARCA4-related microphthalmia within the CSS phenotypic spectrum.
- name: Agenesis of corpus callosum
  description: >-
    Agenesis or hypoplasia of the corpus callosum is the most common structural
    brain abnormality in CSS, with prevalence approaching 50% in some cohorts.
    It reflects a cell-autonomous defect of SATB2+ callosal projection neuron
    maturation in ARID1B haploinsufficiency and midline glia aberrations in
    SMARCB1-related CSS.
  phenotype_term:
    preferred_term: Agenesis of corpus callosum
    term:
      id: HP:0001274
      label: Agenesis of corpus callosum
  evidence:
  - reference: PMID:34706719
    reference_title: "Phenotypic and molecular spectra of patients with switch/sucrose nonfermenting complex-related intellectual disability disorders in Korea."
    supports: SUPPORT
    evidence_source: HUMAN_CLINICAL
    snippet: "Agenesis or hypoplasia of the corpus callosum was observed in half of the patients (6/12)."
    explanation: Cohort-level frequency of CC agenesis/hypoplasia among Korean SSRIDD patients (predominantly CSS).
  - reference: PMID:38718796
    reference_title: "ARID1B controls transcriptional programs of axon projection in an organoid model of the human corpus callosum."
    supports: SUPPORT
    evidence_source: IN_VITRO
    snippet: "The most common structural abnormality in the brain of ARID1B patients is agenesis of the corpus callosum (ACC), characterized by the absence of an interhemispheric white matter tract that connects distant cortical regions."
    explanation: Identifies CC agenesis as the most common structural brain abnormality in ARID1B-related CSS.
  - reference: PMID:31273213
    reference_title: "Mutations in SMARCB1 and in other Coffin-Siris syndrome genes lead to various brain midline defects."
    supports: SUPPORT
    evidence_source: HUMAN_CLINICAL
    snippet: "These Smarcb1 mutant mice show various brain midline abnormalities that are also found in individuals with Coffin-Siris syndrome (CSS) caused by SMARCB1, SMARCE1, and ARID1B mutations and in SMARCB1-related intellectual disability (ID) with choroid plexus hyperplasia (CPH)."
    explanation: Confirms that brain midline abnormalities (including CC agenesis) are seen in CSS patients with multiple BAF gene variants.
- name: Speech and language delay
  description: >-
    Profound speech and language delay is a frequent and characteristic
    manifestation of CSS, often more pronounced than the global developmental
    delay would predict.
  phenotype_term:
    preferred_term: Delayed speech and language development
    term:
      id: HP:0000750
      label: Delayed speech and language development
  evidence:
  - reference: PMID:34706719
    reference_title: "Phenotypic and molecular spectra of patients with switch/sucrose nonfermenting complex-related intellectual disability disorders in Korea."
    supports: SUPPORT
    evidence_source: HUMAN_CLINICAL
    snippet: "Developmental delay was observed in all patients, and profound speech delay was also characteristic."
    explanation: Direct cohort-level evidence that profound speech delay is a defining CSS feature.
- name: Autistic behavior
  description: >-
    Autistic features are recognized in a subset of CSS patients, particularly
    those with ARID1B variants, reflecting overlap between the ARID1B-related
    intellectual disability spectrum and ASD.
  phenotype_term:
    preferred_term: Autistic behavior
    term:
      id: HP:0000729
      label: Autistic behavior
  evidence:
  - reference: PMID:37692302
    reference_title: "Autism spectrum disorder and Coffin-Siris syndrome-Case report."
    supports: SUPPORT
    evidence_source: HUMAN_CLINICAL
    snippet: "An 8-year-old boy with ASD, congenital anomalies, and neurological problems had been diagnosed with Coffin-Siris syndrome after genetic testing."
    explanation: Case-level documentation of CSS-ASD comorbidity in an ARID1B variant carrier.
  - reference: PMID:28867767
    reference_title: "Arid1b Haploinsufficiency Causes Abnormal Brain Gene Expression and Autism-Related Behaviors in Mice."
    supports: SUPPORT
    evidence_source: MODEL_ORGANISM
    snippet: "Arid1b heterozygous knockout (hKO) mice exhibited ASD-like traits related to social behavior, anxiety, and perseveration"
    explanation: Mouse model evidence linking ARID1B haploinsufficiency to autism-like phenotypes.
genetic:
- name: ARID1B
  gene_term:
    preferred_term: ARID1B
    term:
      id: hgnc:18040
      label: ARID1B
  presence: Positive
  association: Causative
  subtype: CSS1
  notes: >-
    ARID1B is the most frequently implicated CSS gene, accounting for
    approximately 37-76% of molecularly confirmed cases depending on the
    cohort. Most pathogenic variants are truncating and cause
    haploinsufficiency, although a subset of non-truncating variants act
    through protein aggregation.
  evidence:
  - reference: PMID:24674232
    reference_title: "Expanding the phenotypic spectrum of ARID1B-mediated disorders and identification of altered cell-cycle dynamics due to ARID1B haploinsufficiency."
    supports: SUPPORT
    evidence_source: HUMAN_CLINICAL
    snippet: "ARID1B mutations have been identified as the predominant cause of Coffin-Siris syndrome and have also been shown to be a frequent cause of nonsyndromic intellectual disability."
    explanation: This supports ARID1B as the predominant causative gene in CSS.
  - reference: PMID:39028335
    reference_title: "The missing link: ARID1B non-truncating variants causing Coffin-Siris syndrome due to protein aggregation."
    supports: SUPPORT
    evidence_source: HUMAN_CLINICAL
    snippet: "ARID1B is the most frequently mutated gene in Coffin-Siris syndrome (CSS)."
    explanation: This independently confirms ARID1B as the most common CSS gene.
  - reference: PMID:39028335
    reference_title: "The missing link: ARID1B non-truncating variants causing Coffin-Siris syndrome due to protein aggregation."
    supports: SUPPORT
    evidence_source: HUMAN_CLINICAL
    snippet: "To date, the vast majority of causative variants reported in ARID1B are truncating, leading to nonsense-mediated mRNA decay."
    explanation: This supports the haploinsufficiency mechanism for most ARID1B variants.
  - reference: CGGV:assertion_d487e6c4-9727-4315-90a2-11338128a8e5-2019-12-04T200734.569Z
    reference_title: "ARID1B / Coffin-Siris syndrome (Definitive)"
    supports: SUPPORT
    evidence_source: OTHER
    snippet: "ARID1B | HGNC:18040 | Coffin-Siris syndrome | MONDO:0015452 | AD | Definitive"
    explanation: ClinGen classifies the ARID1B-Coffin-Siris syndrome gene-disease relationship as definitive with autosomal dominant inheritance.
- name: SMARCA4
  gene_term:
    preferred_term: SMARCA4
    term:
      id: hgnc:11100
      label: SMARCA4
  presence: Positive
  association: Causative
  subtype: CSS4
  notes: >-
    SMARCA4 encodes the catalytic ATPase subunit of the BAF complex.
    Pathogenic variants are typically non-truncating (missense or in-frame
    deletion) and may act via dominant-negative mechanisms.
  evidence:
  - reference: PMID:23815551
    reference_title: "Coffin-Siris syndrome is a SWI/SNF complex disorder."
    supports: SUPPORT
    evidence_source: HUMAN_CLINICAL
    snippet: "We found that SMARCB1, SMARCA4, or ARID1B were mutated in 20 patients."
    explanation: This supports SMARCA4 as one of the causative CSS genes.
  - reference: PMID:23815551
    reference_title: "Coffin-Siris syndrome is a SWI/SNF complex disorder."
    supports: SUPPORT
    evidence_source: HUMAN_CLINICAL
    snippet: "All mutations in SMARCB1 and SMARCA4 were non-truncating (missense or in-frame deletion) whereas those in ARID1B were all truncating (nonsense or frameshift deletion/insertion)"
    explanation: This establishes the distinctive non-truncating variant pattern for SMARCA4 in CSS.
  - reference: CGGV:assertion_61d29c73-9a30-4664-9df2-2f5831219221-2025-06-08T220000.000Z
    reference_title: "SMARCA4 / Coffin-Siris syndrome (Definitive)"
    supports: SUPPORT
    evidence_source: OTHER
    snippet: "SMARCA4 | HGNC:11100 | Coffin-Siris syndrome | MONDO:0015452 | AD | Definitive"
    explanation: ClinGen classifies the SMARCA4-Coffin-Siris syndrome gene-disease relationship as definitive with autosomal dominant inheritance.
- name: SMARCB1
  gene_term:
    preferred_term: SMARCB1
    term:
      id: hgnc:11103
      label: SMARCB1
  presence: Positive
  association: Causative
  subtype: CSS3
  notes: >-
    SMARCB1 encodes a core subunit of the BAF complex. Like SMARCA4, pathogenic
    CSS variants are typically non-truncating. The SMARCB1 C-terminal domain
    is the key interface connecting the core module to the nucleosome acidic
    patch.
  evidence:
  - reference: PMID:22426308
    reference_title: "Mutations affecting components of the SWI/SNF complex cause Coffin-Siris syndrome."
    supports: SUPPORT
    evidence_source: HUMAN_CLINICAL
    snippet: "we found de novo SMARCB1 mutations in two of five individuals with typical Coffin-Siris syndrome"
    explanation: The original 2012 identification of SMARCB1 as a CSS gene.
  - reference: PMID:23815551
    reference_title: "Coffin-Siris syndrome is a SWI/SNF complex disorder."
    supports: SUPPORT
    evidence_source: HUMAN_CLINICAL
    snippet: "All mutations in SMARCB1 and SMARCA4 were non-truncating (missense or in-frame deletion) whereas those in ARID1B were all truncating (nonsense or frameshift deletion/insertion)"
    explanation: This establishes the non-truncating variant pattern for SMARCB1 in CSS.
  - reference: CGGV:assertion_ea554e80-81d2-4100-8d0e-b762ea38fe23-2023-08-15T040000.000Z
    reference_title: "SMARCB1 / Coffin-Siris syndrome (Definitive)"
    supports: SUPPORT
    evidence_source: OTHER
    snippet: "SMARCB1 | HGNC:11103 | Coffin-Siris syndrome | MONDO:0015452 | AD | Definitive"
    explanation: ClinGen classifies the SMARCB1-Coffin-Siris syndrome gene-disease relationship as definitive with autosomal dominant inheritance.
- name: SMARCE1
  gene_term:
    preferred_term: SMARCE1
    term:
      id: hgnc:11109
      label: SMARCE1
  presence: Positive
  association: Causative
  subtype: CSS5
  notes: >-
    SMARCE1 encodes a DNA-binding-associated BAF subunit with an HMG domain.
    CSS-associated variants may act via dominant-negative mechanisms.
  evidence:
  - reference: PMID:22426308
    reference_title: "Mutations affecting components of the SWI/SNF complex cause Coffin-Siris syndrome."
    supports: SUPPORT
    evidence_source: HUMAN_CLINICAL
    snippet: "Twenty affected individuals (87%) each had a germline mutation in one of six SWI/SNF subunit genes, including SMARCB1, SMARCA4, SMARCA2, SMARCE1, ARID1A and ARID1B."
    explanation: SMARCE1 is identified as one of the six CSS-causing SWI/SNF genes.
  - reference: CGGV:assertion_877f5e0f-5b30-4a4f-87c3-cb6b87caa1e4-2024-09-18T190000.000Z
    reference_title: "SMARCE1 / Coffin-Siris syndrome (Definitive)"
    supports: SUPPORT
    evidence_source: OTHER
    snippet: "SMARCE1 | HGNC:11109 | Coffin-Siris syndrome | MONDO:0015452 | AD | Definitive"
    explanation: ClinGen classifies the SMARCE1-Coffin-Siris syndrome gene-disease relationship as definitive with autosomal dominant inheritance.
- name: ARID1A
  gene_term:
    preferred_term: ARID1A
    term:
      id: hgnc:11110
      label: ARID1A
  presence: Positive
  association: Causative
  subtype: CSS2
  notes: >-
    ARID1A encodes a DNA-binding subunit of the BAF complex. It accounts for
    less than 5% of CSS cases and may be associated with higher risk of
    congenital heart defects and hepatoblastoma.
  evidence:
  - reference: PMID:22426308
    reference_title: "Mutations affecting components of the SWI/SNF complex cause Coffin-Siris syndrome."
    supports: SUPPORT
    evidence_source: HUMAN_CLINICAL
    snippet: "Twenty affected individuals (87%) each had a germline mutation in one of six SWI/SNF subunit genes, including SMARCB1, SMARCA4, SMARCA2, SMARCE1, ARID1A and ARID1B."
    explanation: ARID1A is identified as one of the six CSS-causing SWI/SNF genes.
  - reference: CGGV:assertion_aaf6d47a-656a-49ca-ba9e-169f25bf03e7-2021-07-07T160000.000Z
    reference_title: "ARID1A / Coffin-Siris syndrome (Definitive)"
    supports: SUPPORT
    evidence_source: OTHER
    snippet: "ARID1A | HGNC:11110 | Coffin-Siris syndrome | MONDO:0015452 | AD | Definitive"
    explanation: ClinGen classifies the ARID1A-Coffin-Siris syndrome gene-disease relationship as definitive with autosomal dominant inheritance.
- name: DPF2
  gene_term:
    preferred_term: DPF2
    term:
      id: hgnc:9964
      label: DPF2
  presence: Positive
  association: Causative
  subtype: CSS7
  notes: >-
    DPF2 variants expand the CSS gene spectrum and can alter histone-tail
    recognition through disruption of conserved PHD fingers. A
    dominant-negative mechanism is proposed.
  evidence:
  - reference: PMID:29429572
    reference_title: "Mutations in the BAF-Complex Subunit DPF2 Are Associated with Coffin-Siris Syndrome."
    supports: SUPPORT
    evidence_source: HUMAN_CLINICAL
    snippet: "Altogether, we provide compelling evidence that de novo variants in DPF2 cause Coffin-Siris syndrome and propose a dominant-negative mechanism of pathogenicity."
    explanation: This supports DPF2 as a causative CSS gene with a dominant-negative mechanism.
  - reference: CGGV:assertion_cc8c072e-7b8d-4a94-97fe-c15c91759f0f-2023-08-15T020000.000Z
    reference_title: "DPF2 / Coffin-Siris syndrome (Definitive)"
    supports: SUPPORT
    evidence_source: OTHER
    snippet: "DPF2 | HGNC:9964 | Coffin-Siris syndrome | MONDO:0015452 | AD | Definitive"
    explanation: ClinGen classifies the DPF2-Coffin-Siris syndrome gene-disease relationship as definitive with autosomal dominant inheritance.
- name: ARID2
  gene_term:
    preferred_term: ARID2
    term:
      id: hgnc:18037
      label: ARID2
  presence: Positive
  association: Causative
  subtype: CSS6
  notes: >-
    ARID2 is a PBAF-specific subunit and a less frequent CSS gene, often
    associated with a somewhat milder but still recognizably classic phenotype.
    Hip dysplasia may occur more often with ARID2 variants.
  evidence:
  - reference: PMID:38243407
    reference_title: "ARID2, a milder cause of Coffin-Siris Syndrome? Broadening the phenotype with 17 additional individuals."
    supports: SUPPORT
    evidence_source: HUMAN_CLINICAL
    snippet: "Although individuals with ARID2 have been reported to have classic features of CSS including hypertrichosis, coarse facial features, short stature, and fifth digit anomalies, as with many of the other CSS genes, there appears to be a spectrum of phenotypes."
    explanation: This supports ARID2 as a recognized CSS gene with a variable phenotype spectrum.
  - reference: PMID:38243407
    reference_title: "ARID2, a milder cause of Coffin-Siris Syndrome? Broadening the phenotype with 17 additional individuals."
    supports: SUPPORT
    evidence_source: HUMAN_CLINICAL
    snippet: "hip dysplasia appears to occur more often than with other genes, however more severe medical challenges such as significant brain and cardiac malformations are rarer"
    explanation: This highlights the distinctive and generally milder ARID2-associated phenotype.
  - reference: CGGV:assertion_ae1a697f-8dcd-4edf-a25b-e5e0593e7e61-2022-12-06T230000.000Z
    reference_title: "ARID2 / Coffin-Siris syndrome (Definitive)"
    supports: SUPPORT
    evidence_source: OTHER
    snippet: "ARID2 | HGNC:18037 | Coffin-Siris syndrome | MONDO:0015452 | AD | Definitive"
    explanation: ClinGen classifies the ARID2-Coffin-Siris syndrome gene-disease relationship as definitive with autosomal dominant inheritance.
- name: SOX11
  gene_term:
    preferred_term: SOX11
    term:
      id: hgnc:11191
      label: SOX11
  presence: Positive
  association: Causative
  subtype: SOX11
  notes: >-
    SOX11 is a transcription factor in the BAF/CSS gene spectrum. It is not a
    core BAF subunit but is functionally linked through BAF-regulated
    developmental transcription programs.
  evidence:
  - reference: PMID:39501269
    reference_title: "A rare Coffin-Siris syndrome induced by SOX11: a de novo nonsense variant of short stature."
    supports: SUPPORT
    evidence_source: HUMAN_CLINICAL
    snippet: "The combination of clinical presentation and genetic testing results supports that the patient suffers from Coffin-Siris syndrome due to a genetic variant in the SOX11 gene."
    explanation: A case report confirming SOX11 as a causative CSS gene.
- name: SMARCC2
  gene_term:
    preferred_term: SMARCC2
    term:
      id: hgnc:11105
      label: SMARCC2
  presence: Positive
  association: Causative
  subtype: CSS8
  notes: >-
    SMARCC2 encodes a core scaffolding BAF subunit. Pathogenic variants likely
    act through haploinsufficiency.
  evidence:
  - reference: PMID:41291750
    reference_title: "Long-read sequencing identifies a novel de novo inversion in SMARCC2 in a pediatric patient with Coffin-siris syndrome 8: a case report."
    supports: SUPPORT
    evidence_source: HUMAN_CLINICAL
    snippet: "Coffin-Siris Syndrome 8 (CSS8; MIM# 618362) is a rare neurodevelopmental disorder caused by heterozygous variants in the SMARCC2 gene."
    explanation: This directly supports SMARCC2 as a causative CSS gene.
  - reference: CGGV:assertion_aa645aa6-3a03-4ab7-9d09-b17be3184259-2025-09-17T100000.000Z
    reference_title: "SMARCC2 / Coffin-Siris syndrome (Definitive)"
    supports: SUPPORT
    evidence_source: OTHER
    snippet: "SMARCC2 | HGNC:11105 | Coffin-Siris syndrome | MONDO:0015452 | AD | Definitive"
    explanation: ClinGen classifies the SMARCC2-Coffin-Siris syndrome gene-disease relationship as definitive with autosomal dominant inheritance.
- name: SMARCA2
  gene_term:
    preferred_term: SMARCA2
    term:
      id: hgnc:11098
      label: SMARCA2
  presence: Positive
  association: Causative
  notes: >-
    SMARCA2 encodes an alternative catalytic ATPase subunit of the BAF complex.
    Pathogenic SMARCA2 variants primarily cause Nicolaides-Baraitser syndrome
    (NCBRS), but CSS overlap exists for certain variant classes. SMARCA2 was
    identified as one of the six original CSS-causing SWI/SNF genes.
  evidence:
  - reference: PMID:22426308
    reference_title: "Mutations affecting components of the SWI/SNF complex cause Coffin-Siris syndrome."
    supports: SUPPORT
    evidence_source: HUMAN_CLINICAL
    snippet: "Twenty affected individuals (87%) each had a germline mutation in one of six SWI/SNF subunit genes, including SMARCB1, SMARCA4, SMARCA2, SMARCE1, ARID1A and ARID1B."
    explanation: SMARCA2 is identified as one of the six original CSS-causing SWI/SNF genes.
- name: BICRA
  gene_term:
    preferred_term: BICRA
    term:
      id: hgnc:4332
      label: BICRA
  presence: Positive
  association: Causative
  subtype: CSS12
  notes: >-
    BICRA (also known as GLTSCR1) encodes a subunit of the non-canonical BAF
    (ncBAF) complex. It was more recently added to the CSS gene spectrum.
    Note: the PMID:38243407 abstract erroneously expands BAF as "Bromocriptine
    activating factor"; the correct expansion is BRG1/BRM-Associated Factors.
  evidence:
  - reference: PMID:38243407
    reference_title: "ARID2, a milder cause of Coffin-Siris Syndrome? Broadening the phenotype with 17 additional individuals."
    supports: SUPPORT
    evidence_source: HUMAN_CLINICAL
    snippet: "SMARCC2, DPF2, and more recently, BICRA"
    explanation: BICRA is listed as a recently identified CSS gene in this ARID2 cohort study. Note that the same sentence erroneously expands BAF as "Bromocriptine activating factor" rather than the correct "BRG1/BRM-Associated Factors."
  - reference: CGGV:assertion_2dcc8864-4487-4c5c-b541-cfd972767269-2024-11-20T170000.000Z
    reference_title: "BICRA / Coffin-Siris syndrome (Definitive)"
    supports: SUPPORT
    evidence_source: OTHER
    snippet: "BICRA | HGNC:4332 | Coffin-Siris syndrome | MONDO:0015452 | AD | Definitive"
    explanation: ClinGen classifies the BICRA-Coffin-Siris syndrome gene-disease relationship as definitive with autosomal dominant inheritance.
- name: SOX4
  gene_term:
    preferred_term: SOX4
    term:
      id: hgnc:11200
      label: SOX4
  presence: Positive
  association: Causative
  subtype: CSS10
  notes: >-
    SOX4 is a SOXC transcription factor, not a BAF subunit, and reaches the
    skeletal mechanism through the SOXC paralogue programme it shares with SOX11.
    MONDO numbers SOX4 disease Coffin-Siris syndrome 10, but the largest cohort
    concludes it is a fairly non-specific neurodevelopmental syndrome that lacks
    the most specific features of Coffin-Siris syndrome; the gene is curated here
    because it sits in the same programme as SOX11 and is reported on the same
    gene panel, with the phenotype distinction recorded rather than smoothed over.
  evidence:
  - reference: PMID:30661772
    reference_title: De Novo SOX4 Variants Cause a Neurodevelopmental Disease Associated with Mild Dysmorphism.
    supports: SUPPORT
    evidence_source: HUMAN_CLINICAL
    snippet: >-
      Taken together, these findings point to specific SOX4 HMG-domain missense
      variants as the cause of a characteristic human neurodevelopmental disorder
      associated with mild facial and digital dysmorphism.
    explanation: >-
      Establishes SOX4 HMG-domain missense variants as causative, and names the mild
      facial and digital dysmorphism that brings the phenotype into this disease group.
  - reference: PMID:35232796
    reference_title: Consolidation of the clinical and genetic definition of a SOX4-related neurodevelopmental syndrome.
    supports: SUPPORT
    evidence_source: HUMAN_CLINICAL
    snippet: >-
      These findings consolidate evidence of a fairly non-specific
      neurodevelopmental syndrome due to SOX4 haploinsufficiency in neurogenesis
      and multiple other developmental processes.
    explanation: >-
      Establishes haploinsufficiency as the mechanism and records the cohort's judgement
      that the syndrome is non-specific, which is the caveat in the notes above.
- name: SMARCD1
  gene_term:
    preferred_term: SMARCD1
    term:
      id: hgnc:11106
      label: SMARCD1
  presence: Positive
  association: Causative
  subtype: CSS11
  notes: >-
    SMARCD1 encodes a core SWI/SNF subunit, so it acts through the shared
    BAF-complex dysfunction node. As with SOX4, the founding series reports
    clinical overlap with the BAF-related syndromes without their typical facial
    dysmorphisms.
  evidence:
  - reference: PMID:30879640
    reference_title: "A Syndromic Neurodevelopmental Disorder Caused by Mutations in SMARCD1, a Core SWI/SNF Subunit Needed for Context-Dependent Neuronal Gene Regulation in Flies."
    supports: SUPPORT
    evidence_source: HUMAN_CLINICAL
    snippet: >-
      Here, we report on five individuals with mutations in SMARCD1; the
      individuals present with developmental delay, intellectual disability,
      hypotonia, feeding difficulties, and small hands and feet.
    explanation: >-
      Establishes SMARCD1 as a causative gene in five individuals with a
      neurodevelopmental phenotype.
  - reference: PMID:30879640
    reference_title: "A Syndromic Neurodevelopmental Disorder Caused by Mutations in SMARCD1, a Core SWI/SNF Subunit Needed for Context-Dependent Neuronal Gene Regulation in Flies."
    supports: SUPPORT
    evidence_source: HUMAN_CLINICAL
    snippet: >-
      Mutations in several genes encoding components of the SWI/SNF chromatin
      remodeling complex cause neurodevelopmental disorders (NDDs).
    explanation: >-
      Places SMARCD1 disease within the SWI/SNF component group, which is the basis for
      binding the gene to the shared BAF-complex node.
diagnosis:
- name: Molecular genetic testing
  description: >-
    Diagnosis is established by identification of a heterozygous pathogenic
    variant in a CSS-associated BAF complex gene via multigene panel or
    exome/genome sequencing. Approximately 87% of clinically typical CSS
    individuals have identifiable mutations in SWI/SNF subunit genes.
  evidence:
  - reference: PMID:22426308
    reference_title: "Mutations affecting components of the SWI/SNF complex cause Coffin-Siris syndrome."
    supports: SUPPORT
    evidence_source: HUMAN_CLINICAL
    snippet: "Twenty affected individuals (87%) each had a germline mutation in one of six SWI/SNF subunit genes, including SMARCB1, SMARCA4, SMARCA2, SMARCE1, ARID1A and ARID1B."
    explanation: This establishes the high diagnostic yield of molecular testing in CSS.
- name: DNA methylation episignature
  description: >-
    A disorder-specific peripheral-blood DNA methylation signature is now an
    established diagnostic adjunct for CSS and other BAFopathies. A
    machine-learning classifier trained on the methylation profile can resolve
    ambiguous clinical cases, reclassify variants of unknown significance, and
    even identify previously undiagnosed individuals through targeted screening.
    The CSS/Nicolaides-Baraitser episignatures show overlap consistent with a
    shared functional basis as BAFopathies.
  evidence:
  - reference: PMID:30459321
    reference_title: "BAFopathies' DNA methylation epi-signatures demonstrate diagnostic utility and functional continuum of Coffin-Siris and Nicolaides-Baraitser syndromes."
    supports: SUPPORT
    evidence_source: HUMAN_CLINICAL
    snippet: "We report overlapping peripheral blood DNA methylation epi-signatures in individuals with various subtypes of CSS (ARID1B, SMARCB1, and SMARCA4) and NCBRS (SMARCA2)."
    explanation: Establishes the existence of CSS-specific peripheral blood methylation episignatures across multiple BAF subunits.
  - reference: PMID:30459321
    reference_title: "BAFopathies' DNA methylation epi-signatures demonstrate diagnostic utility and functional continuum of Coffin-Siris and Nicolaides-Baraitser syndromes."
    supports: SUPPORT
    evidence_source: HUMAN_CLINICAL
    snippet: "We demonstrate that a machine-learning model trained on this DNA methylation profile can resolve ambiguous clinical cases, reclassify those with variants of unknown significance, and identify previously undiagnosed subjects through targeted population screening."
    explanation: Documents the diagnostic utility of the CSS episignature, including VUS reclassification.
  - reference: PMID:39028335
    reference_title: "The missing link: ARID1B non-truncating variants causing Coffin-Siris syndrome due to protein aggregation."
    supports: SUPPORT
    evidence_source: HUMAN_CLINICAL
    snippet: "Genome-wide transcriptome and methylation analysis in affected individuals revealed expression and methylome patterns consistent with those of the pathogenic haploinsufficiency ARID1B alterations in CSS cases."
    explanation: Supports the use of methylation episignatures for CSS variant classification, including aggregation-prone non-truncating variants.
treatments:
- name: Multidisciplinary supportive care and surveillance
  description: >-
    CSS management is primarily supportive and multidisciplinary, with attention
    to feeding, development, hypotonia, organ-system anomalies, and longitudinal
    surveillance for complications.
  treatment_term:
    preferred_term: supportive care
    term:
      id: NCIT:C15747
      label: Supportive Care
  evidence:
  - reference: PMID:30276971
    reference_title: "First data from a parent-reported registry of 81 individuals with Coffin-Siris syndrome: Natural history and management recommendations."
    supports: SUPPORT
    evidence_source: HUMAN_CLINICAL
    snippet: "In addition, we offer surveillance and management recommendations based on the medical issues encountered in this cohort to help guide physicians and patients' families."
    explanation: This supports structured supportive management and surveillance as the main treatment approach for CSS.
- name: Speech and language therapy
  description: >-
    Speech and language therapy addresses the universal speech and language
    delays in CSS.
  therapeutic_modality: BEHAVIORAL
  treatment_term:
    preferred_term: speech and language therapy
    term:
      id: NCIT:C159273
      label: Speech Language Therapy
  evidence:
  - reference: PMID:30276971
    reference_title: "First data from a parent-reported registry of 81 individuals with Coffin-Siris syndrome: Natural history and management recommendations."
    supports: SUPPORT
    evidence_source: HUMAN_CLINICAL
    snippet: "Varying degrees of developmental and intellectual delay are universal."
    explanation: Universal developmental delay supports the need for speech and language therapy as part of CSS management.
- name: Genetic counseling
  description: >-
    Genetic counseling is recommended for affected individuals and families
    given the autosomal dominant inheritance and high rate of de novo mutations.
  treatment_term:
    preferred_term: Genetic Counseling
    term:
      id: NCIT:C15240
      label: Genetic Counseling
  evidence:
  - reference: PMID:23815551
    reference_title: "Coffin-Siris syndrome is a SWI/SNF complex disorder."
    supports: SUPPORT
    evidence_source: HUMAN_CLINICAL
    snippet: "By examining available parental samples, we ascertained that 17 occurred de novo."
    explanation: The high rate of de novo mutations in CSS supports the importance of genetic counseling for recurrence risk assessment.
- name: Physical therapy
  description: >-
    Physical therapy targets hypotonia and motor delays to improve
    functional mobility and developmental milestones.
  therapeutic_modality: BEHAVIORAL
  treatment_term:
    preferred_term: physical therapy
    term:
      id: NCIT:C15302
      label: Physical Therapy
  target_phenotypes:
  - preferred_term: Hypotonia
    term:
      id: HP:0001252
      label: Hypotonia
  evidence:
  - reference: PMID:38243407
    reference_title: "ARID2, a milder cause of Coffin-Siris Syndrome? Broadening the phenotype with 17 additional individuals."
    supports: SUPPORT
    evidence_source: HUMAN_CLINICAL
    snippet: "Feeding difficulties, hypotonia, and short stature occur often"
    explanation: The high frequency of hypotonia supports physical therapy as part of CSS management.
- name: Antiseizure medication
  description: >-
    Most CSS patients with epilepsy achieve seizure control on antiseizure
    medications; in the international CSS registry, all but one of the patients
    with seizures were controlled on ASMs.
  treatment_term:
    preferred_term: Pharmacotherapy
    term:
      id: NCIT:C15986
      label: Pharmacotherapy
  target_phenotypes:
  - preferred_term: Seizures
    term:
      id: HP:0001250
      label: Seizure
  target_mechanisms:
  - target: Cortical interneuron deficiency from ARID1B haploinsufficiency
    description: ASMs counteract the cortical excitatory-inhibitory imbalance arising from reduced GABAergic interneuron numbers.
    evidence:
    - reference: PMID:29184203
      reference_title: "Arid1b haploinsufficiency disrupts cortical interneuron development and mouse behavior."
      supports: SUPPORT
      evidence_source: MODEL_ORGANISM
      snippet: "Arid1b-heterozygous mice exhibited abnormal cognitive and social behaviors, which were rescued by treatment with a positive allosteric GABAA receptor modulator."
      explanation: Mouse-model rescue with a GABAA-receptor positive allosteric modulator provides indirect support that pharmacologic enhancement of inhibitory transmission targets the interneuron-deficit mechanism that drives CSS seizures.
  evidence:
  - reference: PMID:36177969
    reference_title: "Epilepsy in Coffin-Siris syndrome: A report from the international CSS registry and review of the literature."
    supports: SUPPORT
    evidence_source: HUMAN_CLINICAL
    snippet: "In all but one patient, seizures were controlled on antiseizure medications (ASMs)."
    explanation: Registry data support standard ASM therapy as the operative epilepsy management for CSS patients.
- name: Growth hormone supplementation (investigational)
  description: >-
    In the Arid1b haploinsufficient mouse model, growth hormone supplementation
    rescued growth retardation and muscle weakness, identifying a mechanistically
    rational therapeutic strategy for the IGF1/GH axis dysregulation underlying
    CSS short stature. Clinical use of GH in CSS is investigational and would
    require individualized endocrine assessment.
  treatment_term:
    preferred_term: Pharmacotherapy
    term:
      id: NCIT:C15986
      label: Pharmacotherapy
    therapeutic_agent:
    - preferred_term: somatropin
      term:
        id: NCIT:C837
        label: Somatropin
  target_phenotypes:
  - preferred_term: Short stature
    term:
      id: HP:0004322
      label: Short stature
  target_mechanisms:
  - target: IGF1/GH axis dysregulation in ARID1B haploinsufficiency
    description: GH supplementation directly restores IGF1 signaling that is reduced in ARID1B haploinsufficiency.
    treatment_effect: RESTORES
    evidence:
    - reference: PMID:28695822
      reference_title: "Arid1b haploinsufficient mice reveal neuropsychiatric phenotypes and reversible causes of growth impairment."
      supports: SUPPORT
      evidence_source: MODEL_ORGANISM
      snippet: "A focus on reversible mechanisms identified Insulin-like growth factor (IGF1) deficiency with inadequate compensation by Growth hormone-releasing hormone (GHRH) and Growth hormone (GH), underappreciated findings in ARID1B patients."
      explanation: Same study identifies IGF1/GH axis deficiency as the mechanistic target restored by exogenous GH supplementation.
  evidence:
  - reference: PMID:28695822
    reference_title: "Arid1b haploinsufficient mice reveal neuropsychiatric phenotypes and reversible causes of growth impairment."
    supports: SUPPORT
    evidence_source: MODEL_ORGANISM
    snippet: "Therapeutically, GH supplementation was able to correct growth retardation and muscle weakness."
    explanation: Mouse-model evidence that GH supplementation can rescue ARID1B haploinsufficiency-driven growth and muscle phenotypes.
references:
- reference: PMID:23556151
  title: "Coffin-Siris Syndrome."
  tags:
  - GeneReviews

📚

References & Deep Research

References

PMID:23556151

Coffin-Siris Syndrome.

No top-level findings curated for this source.

Deep Research

Deep research results are used as seeds for research; they do not undergo the same validation as the main records and may contain errors. How we use deep research.

Evaluations and curation notes (1)

Add CSS4 (SMARCA4) subtype binding MONDO:0013821 / MRD16 · 2026-09-04T21:58:59Z · View source

Curation of MONDO:0013821 (intellectual disability, autosomal dominant 16 / MRD16 / OMIM 614609), claimed in issue #11015. entry_type decision: SUBTYPE, not a standalone kb/disorders/ entry. Three reasons, all sourced. First, MONDO itself defines MONDO:0013821 as 'Any Coffin-Siris syndrome in which the cause of the disease is a mutation in the SMARCA4 gene', and its synonym set includes 'Coffin-Siris syndrome 4', 'CSS4' and 'SMARCA4-related BAFopathy' alongside the MRD16 labels. It is a Coffin-Siris syndrome by definition, not a sibling of one. Second, GeneReviews establishes the diagnosis of Coffin-Siris syndrome by a heterozygous pathogenic variant in any one of fourteen genes including SMARCA4 (PMID:23556151). That makes the gene the subtype axis inside this disease rather than a disease boundary. ClinGen agrees from the other direction: its definitive assertion is SMARCA4 against Coffin-Siris syndrome itself, MONDO:0015452. Third, the repository already curates SMARCA4 inside kb/disorders/Coffin_Siris_Syndrome.yaml's genetic block with its own evidence, so a standalone entry would have duplicated the whole BAF-complex pathograph to hold a gene that is already here. The gene search the issue asked for was run and is what settles the boundary the other way, too. SMARCA4 appears in kb/ in Coffin_Siris_Syndrome.yaml, Rhabdoid_Tumor_Predisposition_Syndrome_2.yaml, Rhabdoid_Tumor.yaml, Atypical_Teratoid_Rhabdoid_Tumor.yaml, Small_Cell_Lung_Cancer.yaml and the epigenetic-machinery module. RTPS2 is germline loss-of-function SMARCA4 and is correctly a separate entry; Nicolaides-Baraitser syndrome (SMARCA2) likewise. Those are separate clinical entities, not gene-defined slices of Coffin-Siris syndrome, so the subtype call does not conflict with them. What was added: a has_subtypes entry 'CSS4' with display_name 'Coffin-Siris syndrome 4 (SMARCA4-related)', subtype_term bound to MONDO:0013821, the SMARCA4 gene, autosomal dominant inheritance, and nine evidence items. Content the entry carries beyond the binding. The MRD16 name is explained rather than left as an alias: a substantial share of SMARCA4 patients present as intellectual disability or autism without the classic Coffin-Siris craniofacial and digital features (PMID:34813034 - eight patients, all with moderate to severe ID, seven autistic or likely autistic, less likely than published CSS patients to show craniofacial or finger/toe anomalies). The genotype-phenotype claims are stated with the hedges their sources put on them: SMARCA4 CSS variants were originally all non-truncating (PMID:23815551), which is what separated them from the loss-of-function alleles causing RTPS2, but a 15-patient SMARCA4 registry cohort later included two nonsense variants at the mild end (PMID:32686290); and the SMARC-versus-ARID organ-severity correlation from the 208-patient registry study (PMID:34205270) is cited together with that study's own conclusion that everyone with a BAF-related condition is at risk of most of the phenotype and surveillance should be broad. Scope, recorded in the subtype's review_notes so the single-subtype list is not misread: Coffin-Siris syndrome has fourteen causal genes and the numbered types each have their own OMIM/MONDO identity. Only CSS4 is added here because that is the concept #11015 covers; the absence of the others reflects what has been curated, not a claim that SMARCA4 is the only subtype. Stub: stubs/Intellectual_Disability_Autosomal_Dominant_16.yaml is deleted, because MONDO:0013821 is now bound in kb/ as this subtype's subtype_term - which is the condition the issue set for deletion. Evidence and validation: 131/131 snippets verified across the whole file after the edit, of which nine are the new subtype's. No DOI-prefixed citations, so nothing skipped by prefix. just validate, validate-terms, validate-disorders, check-entity-refs, check-duplicate-keys, check-causal-targets, check-enum-values, check-qualifier-terms and check-stubs all pass, as do whole-KB check-title-snippets, check-snippet-length and check-snippet-grading. The batch validator rewrote 29 tracked references_cache files with cosmetic frontmatter changes; those were reverted with git checkout rather than committed. Deep research: a falcon run was launched for this concept with a disambiguating query naming SMARCA4, OMIM 614609, CSS4, and explicitly excluding SMARCA4 rhabdoid tumour predisposition and SMARCA2 Nicolaides-Baraitser syndrome. It had not returned after roughly three hours of provider time and is not part of this change. Nothing in this edit depends on it; every claim is cited to a fetched, snippet-verified reference. Reproduce with: just research-disorder falcon <slug> with that disease_name override, noting that research-disorder requires a kb/disorders/ file to exist, so a temporary skeleton was used and removed before commit.

Falcon ▸

Disease Characteristics Research Template

Edison Scientific Literature 20 citations 2026-04-25T17:39:42.565661

Question: You are an expert researcher providing comprehensive, well-cited information.

Provide detailed information focusing on: 1. Key concepts and definitions with current understanding 2. Recent developments and latest research (prioritize 2023-2024 sources) 3. Current applications and real-world implementations 4. Expert opinions and analysis from authoritative sources 5. Relevant statistics and data from recent studies

Format as a comprehensive research report with proper citations. Include URLs and publication dates where available. Always prioritize recent, authoritative sources and provide specific citations for all major claims.

Disease Characteristics Research Template

Target Disease

Disease Name: Coffin-Siris syndrome
MONDO ID: (if available)
Category: Mendelian

Research Objectives

Please provide a comprehensive research report on Coffin-Siris syndrome covering all of the disease characteristics listed below. This report will be used to populate a disease knowledge base entry. Be thorough and cite primary literature (PMID preferred) for all claims.

For each section, suggested databases/resources are listed. These are the first places you should search for information on each topic.

1. Disease Information

Search first: OMIM, Orphanet, ICD-10/ICD-11, MeSH, PubMed

What is the disease? Provide a concise overview.
What are the key identifiers? (OMIM, Orphanet, ICD-10/ICD-11, MeSH, Mondo)
What are the common synonyms and alternative names?
Is the information derived from individual patients (e.g., EHR) or aggregated disease-level resources?

2. Etiology

Disease Causal Factors: What are the primary causes? (genetic, environmental, infectious, mechanistic)
Risk Factors:

Search first: PubMed, Cochrane Library, UpToDate, clinical guidelines, ClinVar, ClinGen, GWAS Catalog, PheGenI, CTD, CDC, WHO, epidemiological databases
Genetic risk factors (causal variants, susceptibility loci, modifier genes)
Environmental risk factors (toxins, lifestyle, occupational exposures, age, sex, family history)
Protective Factors:

Search first: PubMed, Cochrane Library, clinical trial databases, GWAS Catalog, gnomAD, WHO, CDC, nutrition databases
Genetic protective factors (protective variants, modifier alleles)
Environmental protective factors (diet, lifestyle, exposures that reduce risk)
Gene-Environment Interactions: How do genetic and environmental factors interact to influence disease?

Search first: CTD, PubMed, PheGenI, GxE databases

3. Phenotypes

Search first: HPO (Human Phenotype Ontology), OMIM, Orphanet, PubMed, clinicaltrials.gov, MedDRA, SNOMED CT, DECIPHER, LOINC

For each phenotype, provide: - Phenotype type: symptoms, clinical signs, physical manifestations, behavioral changes, or laboratory abnormalities

For symptoms/signs: HPO, OMIM, Orphanet, PubMed For behavioral changes: HPO, DSM, RDoC (Research Domain Criteria), PubMed For laboratory abnormalities: LOINC, SNOMED CT, LabTests Online, PubMed - Phenotype characteristics: Search first: OMIM, Orphanet, HPO, PubMed - Age of symptom onset (neonatal, childhood, adult-onset, late-onset) - Symptom severity (mild, moderate, severe, variable) - Symptom progression (stable, progressive, episodic, fluctuating) - Frequency among affected individuals (percentage or qualitative) - Quality of life impact: Effects on daily functioning and well-being (per-phenotype when possible) Search first: EQ-5D database, SF-36, WHO QOL databases, PubMed - Suggest HPO (Human Phenotype Ontology) terms for each phenotype

4. Genetic/Molecular Information

Causal Genes: Gene mutations or chromosomal abnormalities responsible for disease (gene symbols, OMIM IDs)

Search first: OMIM, ClinVar, HGMD, Ensembl, NCBI Gene
Pathogenic Variants:
Affected genes (gene symbols, HGNC IDs) > Search first: OMIM, NCBI Gene, Ensembl, HGNC, UniProt, GeneCards
Variant classification (pathogenic, likely pathogenic, VUS per ACMG/AMP guidelines) > Search first: ClinVar, ClinGen, ACMG/AMP guidelines, VarSome
Variant type/class (missense, frameshift, nonsense, splice-site, structural)
Allele frequency in population databases > Search first: gnomAD, 1000 Genomes, ExAC, TOPMed, dbSNP
Somatic vs germline origin > Search first: COSMIC (somatic), ClinVar, ICGC, TCGA
Functional consequences (loss of function, gain of function, dominant negative)
Modifier Genes: Genes that modify disease severity or expression
Epigenetic Information: DNA methylation, histone modifications, chromatin changes affecting disease

Search first: ENCODE, Roadmap Epigenomics, MethBase, DiseaseMeth
Chromosomal Abnormalities: Large-scale genetic changes (aneuploidy, translocations, inversions)

Search first: DECIPHER, ClinVar, ECARUCA, UCSC Genome Browser

5. Environmental Information

Environmental Factors: Non-genetic contributing factors (toxins, radiation, pollution, occupational exposure)

Search first: CTD (Comparative Toxicogenomics Database), TOXNET, PubMed, EPA databases
Lifestyle Factors: Behavioral factors (smoking, diet, exercise, alcohol consumption)

Search first: CDC databases, WHO, PubMed, NHANES
Infectious Agents: If applicable, pathogens causing or triggering disease (bacteria, viruses, fungi, parasites)

Search first: NCBI Taxonomy, ViPR, BV-BRC, MicrobeDB, GIDEON

6. Mechanism / Pathophysiology

Molecular Pathways: Specific signaling cascades or biochemical pathways involved (Wnt, MAPK, mTOR, PI3K-AKT, etc.)

Search first: KEGG, Reactome, WikiPathways, PathBank, BioCyc
Cellular Processes: Cell-level mechanisms (apoptosis, autophagy, cell cycle dysregulation, inflammation, etc.)

Search first: Gene Ontology (GO), Reactome, KEGG, PubMed
Protein Dysfunction: How protein structure or function is altered (misfolding, aggregation, loss of function, gain of function)

Search first: UniProt, PDB (Protein Data Bank), InterPro, Pfam, AlphaFold
Metabolic Changes: Alterations in metabolic processes (energy metabolism, lipid metabolism, amino acid metabolism)

Search first: KEGG, BioCyc, HMDB (Human Metabolome Database), BRENDA
Immune System Involvement: Role of immune response (autoimmunity, immunodeficiency, chronic inflammation)

Search first: ImmPort, Immunome Database, IEDB, Gene Ontology
Tissue Damage Mechanisms: How tissues/ are injured (oxidative stress, ischemia, fibrosis, necrosis)

Search first: PubMed, Gene Ontology, Reactome
Biochemical Abnormalities: Specific molecular defects (enzyme deficiencies, receptor dysfunction, ion channel defects)

Search first: BRENDA, UniProt, KEGG, OMIM, PubMed
Epigenetic Changes: DNA methylation, histone modifications affecting gene expression in disease

Search first: ENCODE, Roadmap Epigenomics, MethBase, DiseaseMeth
Molecular Profiling (if available):
Transcriptomics/gene expression changes > Search first: GEO (Gene Expression Omnibus), ArrayExpress, GTEx, Human Cell Atlas, SRA
Proteomics findings > Search first: PRIDE, ProteomeXchange, Human Protein Atlas, STRING, BioGRID
Metabolomics signatures > Search first: MetaboLights, Metabolomics Workbench, HMDB, METLIN
Lipidomics alterations > Search first: LIPID MAPS, SwissLipids, LipidHome, Metabolomics Workbench
Genomic structural features > Search first: UCSC Genome Browser, Ensembl, NCBI, dbVar, DGV
Advanced Technologies (if applicable):
Single-cell analysis findings (cell-type specific mechanisms, cellular heterogeneity) > Search first: Human Cell Atlas, Single Cell Portal, GEO, CELLxGENE
Spatial transcriptomics findings > Search first: GEO, Spatial Research, Vizgen, 10x Genomics data
Multi-omics integration results > Search first: TCGA, ICGC, cBioPortal, LinkedOmics, PubMed
Functional genomics screens (CRISPR, RNAi) > Search first: DepMap, GenomeRNAi, PubMed, BioGRID ORCS

For each mechanism, describe: - The causal chain from initial trigger to clinical manifestation - Which mechanisms are upstream vs downstream - What cell types and biological processes are involved - Suggest GO terms for biological processes and CL terms for cell types

7. Anatomical Structures Affected

Organ Level:
Primary organs directly affected
Secondary organ involvement (complications, secondary effects)
Body systems involved (cardiovascular, nervous, digestive, respiratory, endocrine, etc.)

Search first: Uberon, FMA (Foundational Model of Anatomy), OMIM, HPO, ICD-11, MeSH, SNOMED CT
Tissue and Cell Level:
Specific tissue types affected (epithelial, connective, muscle, nervous)
Specific cell populations targeted (with Cell Ontology terms)

Search first: Uberon, Human Protein Atlas, Cell Ontology, Human Cell Atlas, CellMarker, PanglaoDB
Subcellular Level:
Cellular compartments involved (mitochondria, nucleus, ER, lysosomes) (with GO Cellular Component terms)

Search first: Gene Ontology (Cellular Component), UniProt, Human Protein Atlas
Localization:
Specific anatomical sites (with UBERON terms) > Search first: FMA, Uberon, NeuroNames (for brain), SNOMED CT
Lateralization (unilateral, bilateral, asymmetric) > Search first: HPO, clinical literature, imaging databases

8. Temporal Development

Onset:
Typical age of onset (congenital, pediatric, adult, geriatric)
Onset pattern (acute, subacute, chronic, insidious)

Search first: OMIM, Orphanet, HPO, PubMed
Progression:
Disease stages (early, intermediate, advanced, end-stage) > Search first: Cancer Staging Manual (AJCC), WHO classifications, PubMed
Progression rate (rapid, slow, variable)
Disease course pattern (episodic, relapsing-remitting, progressive, stable)
Disease duration (self-limited, chronic lifelong)

Search first: Disease registries, longitudinal cohort databases, natural history studies, PubMed, Orphanet, OMIM
Patterns:
Remission patterns (spontaneous, treatment-induced) > Search first: Clinical trial databases, disease registries, PubMed
Critical periods (time windows of vulnerability or opportunity for intervention) > Search first: PubMed, developmental biology databases, clinical guidelines

9. Inheritance and Population

Epidemiology:
Prevalence (cases per 100,000 at given time)
Incidence (new cases per 100,000 per year)

Search first: Orphanet, CDC, WHO, GBD (Global Burden of Disease), national registries, SEER, disease registries
For Genetic Etiology:
Inheritance pattern (AD, AR, X-linked, mitochondrial, multifactorial, polygenic) > Search first: OMIM, Orphanet, ClinVar, GTR (Genetic Testing Registry)
Penetrance (complete, incomplete, age-dependent) > Search first: ClinVar, OMIM, PubMed, ClinGen
Expressivity (variable, consistent) > Search first: OMIM, ClinVar, PubMed
Genetic anticipation (increasing severity in successive generations) > Search first: OMIM, PubMed (especially for repeat expansion disorders)
Germline mosaicism > Search first: ClinVar, OMIM, genetic counseling literature, PubMed
Founder effects (population-specific mutations) > Search first: gnomAD, population genetics databases, PubMed
Consanguinity role > Search first: OMIM, population studies, genetic counseling resources
Carrier frequency > Search first: gnomAD, carrier screening databases, GeneReviews, GTR
Population Demographics:
Affected populations (ethnic or demographic groups with higher prevalence) > Search first: gnomAD, 1000 Genomes, PAGE Study, PubMed, population registries
Geographic distribution (endemic areas, regional variation) > Search first: WHO, CDC, GBD, Orphanet, geographic epidemiology databases
Geographic distribution of specific variants
Sex ratio (male:female) > Search first: Disease registries, OMIM, PubMed, epidemiological databases
Age distribution of affected individuals > Search first: CDC, disease registries, SEER, Orphanet

10. Diagnostics

Clinical Tests:
Laboratory tests (blood, urine, tissue chemistry, specific enzyme assays) > Search first: LOINC, LabTests Online, PubMed
Biomarkers (proteins, metabolites, genetic markers, circulating biomarkers) > Search first: FDA Biomarker List, BEST (Biomarkers, EndpointS, and other Tools), PubMed
Imaging studies (X-ray, CT, MRI, PET, ultrasound) > Search first: RadLex, DICOM, Radiopaedia, imaging databases
Functional tests (pulmonary function, cardiac stress tests) > Search first: LOINC, clinical guidelines, PubMed
Electrophysiology (EEG, EMG, ECG, nerve conduction studies) > Search first: LOINC, clinical neurophysiology databases, PubMed
Biopsy findings (histopathology, immunohistochemistry) > Search first: SNOMED CT, College of American Pathologists resources, PubMed
Pathology findings (microscopic examination) > Search first: SNOMED CT, Digital Pathology databases, PubMed
Genetic Testing:

Search first: GTR (Genetic Testing Registry), GeneReviews, ClinGen
Overview of recommended genetic testing approach
Whole genome sequencing (WGS) utility > Search first: GTR, ClinVar, GEL (Genomics England), gnomAD
Whole exome sequencing (WES) utility > Search first: GTR, ClinVar, OMIM, GeneMatcher
Gene panels (which panels, which genes) > Search first: GTR, ClinVar, laboratory-specific databases
Single gene testing > Search first: GTR, ClinVar, OMIM, GeneReviews
Chromosomal microarray (CMA) > Search first: DECIPHER, ClinVar, dbVar, ECARUCA
Karyotyping > Search first: Chromosome Abnormality Database, ClinVar, cytogenetics resources
FISH > Search first: ClinVar, cytogenetics databases, PubMed
Mitochondrial DNA testing > Search first: MITOMAP, MSeqDR, ClinVar, GTR
Repeat expansion testing > Search first: GTR, ClinVar, repeat expansion databases, PubMed
Omics-Based Diagnostics (if applicable):
RNA sequencing / transcriptomics > Search first: GEO, ArrayExpress, GTEx, RNA-seq databases
Proteomics > Search first: PRIDE, ProteomeXchange, FDA Biomarker database
Metabolomics > Search first: MetaboLights, Metabolomics Workbench, HMDB
Epigenomics > Search first: GEO, ENCODE, Roadmap Epigenomics, MethBase
Liquid biopsy > Search first: COSMIC, ClinVar, liquid biopsy databases, PubMed
Clinical Criteria:
Standardized diagnostic criteria (DSM, ICD, society guidelines) > Search first: DSM-5, ICD-11, clinical society guidelines, UpToDate
Differential diagnosis (other conditions to rule out, with distinguishing features) > Search first: DynaMed, UpToDate, clinical decision support systems
Screening:
Screening methods for asymptomatic individuals (newborn screening, carrier screening, cascade screening) > Search first: ACMG recommendations, CDC newborn screening, GTR

11. Outcome/Prognosis

Survival and Mortality:
Survival rate (5-year, 10-year, overall) > Search first: SEER, cancer registries, disease-specific registries, PubMed
Life expectancy (with and without treatment if applicable) > Search first: Orphanet, disease registries, actuarial databases, PubMed
Mortality rate > Search first: CDC, WHO, GBD, national mortality databases
Disease-specific mortality (deaths directly attributable to disease) > Search first: Disease registries, CDC Wonder, GBD, PubMed
Morbidity and Function:
Morbidity (disease-related disability and health impacts) > Search first: GBD, WHO, disability databases, PubMed
Disability outcomes (long-term functional impairments) > Search first: ICF (International Classification of Functioning), disability registries
Quality of life measures (EQ-5D, SF-36, PROMIS, disease-specific tools) > Search first: EQ-5D database, SF-36, PROMIS, PubMed
Disease Course:
Complications (secondary problems: infections, organ failure, etc.) > Search first: ICD codes, disease registries, clinical databases, PubMed
Recovery potential (likelihood and extent of recovery, with vs without treatment) > Search first: Natural history studies, rehabilitation databases, PubMed
Prediction:
Prognostic factors (age, disease severity, biomarkers, treatment response) > Search first: Prognostic models databases, clinical calculators, PubMed
Prognostic biomarkers (molecular markers predicting disease course) > Search first: FDA Biomarker database, PubMed, cancer prognostic databases

12. Treatment

Pharmacotherapy:
Pharmacological treatments (drug names, drug classes, mechanisms of action) > Search first: DrugBank, RxNorm, ATC classification, DailyMed, FDA databases
Pharmacogenomics (how genetic variants affect drug metabolism, efficacy, toxicity) > Search first: PharmGKB, CPIC (Clinical Pharmacogenetics), FDA Table of PGx Biomarkers
Advanced Therapeutics:
Gene therapy (viral vectors, CRISPR, gene replacement, gene editing) > Search first: ClinicalTrials.gov, FDA gene therapy database, ASGCT resources
Cell therapy (stem cell transplant, CAR-T, cellular therapeutics) > Search first: ClinicalTrials.gov, FDA cell therapy database, FACT standards
RNA-based therapies (ASOs, siRNA, mRNA therapies) > Search first: ClinicalTrials.gov, FDA approvals, PubMed
Targeted therapies (treatments directed at specific molecular targets) > Search first: My Cancer Genome, OncoKB, ClinicalTrials.gov, FDA approvals
Immunotherapies (checkpoint inhibitors, monoclonal antibodies) > Search first: Cancer Immunotherapy Database, FDA approvals, ClinicalTrials.gov
Surgical and Interventional:
Surgical interventions (types of surgery, timing, outcomes) > Search first: CPT codes, surgical registries, clinical guidelines, PubMed
Supportive and Rehabilitative:
Supportive care (symptom management, pain control, nutrition) > Search first: Clinical guidelines, Cochrane Library, PubMed
Rehabilitation (physical therapy, occupational therapy, speech therapy) > Search first: Rehabilitation medicine databases, clinical guidelines, PubMed
Experimental:
Experimental treatments in clinical trials (with NCT identifiers if available) > Search first: ClinicalTrials.gov, EU Clinical Trials Register, WHO ICTRP
Treatment Outcomes:
Treatment response rates > Search first: Clinical trial databases, FDA reviews, systematic reviews, PubMed
Side effects and adverse events > Search first: FDA Adverse Event Reporting System (FAERS), MedWatch, PubMed
Treatment Strategy:
Treatment algorithms (clinical pathways, decision trees) > Search first: Clinical practice guidelines, NCCN Guidelines, UpToDate
Combination therapies > Search first: ClinicalTrials.gov, treatment guidelines, PubMed
Personalized medicine approaches (genotype-guided treatment) > Search first: My Cancer Genome, CIViC, PharmGKB, precision medicine databases

For each treatment, suggest MAXO (Medical Action Ontology) terms where applicable.

13. Prevention

Prevention Levels:
Primary prevention (preventing disease occurrence: vaccination, risk factor modification) > Search first: CDC, WHO, USPSTF recommendations, Cochrane Library
Secondary prevention (early detection and treatment: screening programs, early intervention) > Search first: USPSTF, CDC screening guidelines, WHO
Tertiary prevention (preventing complications in those with disease) > Search first: Clinical guidelines, disease management protocols, PubMed
Immunization: Vaccine strategies (if applicable)

Search first: CDC vaccine schedules, WHO immunization, FDA vaccine database
Screening and Early Detection:
Screening programs (population-based: newborn screening, cancer screening) > Search first: CDC screening programs, USPSTF, cancer screening databases
Genetic screening (carrier screening, preimplantation genetic diagnosis, prenatal testing) > Search first: ACMG recommendations, ACOG guidelines, GTR
Risk stratification (identifying high-risk individuals for targeted prevention) > Search first: Risk prediction models, clinical calculators, PubMed
Behavioral Interventions: Lifestyle modifications to reduce risk

Search first: CDC, WHO, behavioral intervention databases, Cochrane Library
Counseling: Genetic counseling (risk assessment, family planning guidance)

Search first: NSGC resources, ACMG guidelines, GeneReviews
Public Health:
Public health interventions (sanitation, vector control, health education) > Search first: CDC, WHO, public health databases, PubMed
Environmental interventions (reducing environmental risk factors) > Search first: EPA databases, WHO environmental health, PubMed
Prophylaxis: Preventive medications or procedures

Search first: Clinical guidelines, FDA approvals, PubMed

14. Other Species / Natural Disease

Taxonomy: Species affected (with NCBI Taxon identifiers)

Search first: NCBI Taxonomy
Breed: Specific breeds affected (with VBO identifiers if applicable)

Search first: VBO (Vertebrate Breed Ontology)
Gene: Orthologous genes in other species (with NCBI Gene IDs)

Search first: NCBI Gene
Natural Disease:
Naturally occurring disease in other species (companion animals, wildlife) > Search first: OMIA (Online Mendelian Inheritance in Animals), VetCompass, PubMed
Veterinary relevance and importance in animal health > Search first: OMIA, veterinary databases, PubMed
Comparative Biology:
Comparative pathology (similarities and differences across species) > Search first: OMIA, comparative pathology databases, PubMed
Evolutionary conservation of disease mechanisms > Search first: HomoloGene, OrthoMCL, Alliance of Genome Resources
Transmission (if applicable):
Zoonotic potential > Search first: CDC zoonotic diseases, WHO zoonoses, GIDEON
Cross-species susceptibility > Search first: NCBI Taxonomy, veterinary databases, PubMed

15. Model Organisms

Model Types:
Model organism type (mammalian, invertebrate, cellular, in vitro) > Search first: Alliance of Genome Resources, model organism databases
Specific model systems (mouse, rat, zebrafish, Drosophila, C. elegans, yeast, cell lines, organoids, iPSCs) > Search first: MGI, RGD, ZFIN, FlyBase, WormBase, SGD, ATCC, Cellosaurus
Induced models (drug treatment, surgical intervention, environmental manipulation) > Search first: MGI, model organism databases, PubMed
Genetic Models:
Types available (knockout, knock-in, transgenic, conditional, humanized) > Search first: MGI, IMPC, KOMP, EuMMCR, IMSR
Model Characteristics:
Phenotype recapitulation (how well model reproduces human disease features) > Search first: Model organism databases, comparative studies, PubMed
Model limitations (aspects of human disease not captured) > Search first: Model organism databases, PubMed, review articles
Applications:
Research applications (what aspects of disease can be studied) > Search first: Model organism databases, PubMed
Resources:
Model databases > Search first: MGI, RGD, ZFIN, FlyBase, WormBase, IMSR, EMMA, MMRRC

Citation Requirements

Cite primary literature (PMID preferred) for all mechanistic and clinical claims
Prioritize recent reviews and landmark papers
Include direct quotes from abstracts where possible to support key statements
Distinguish evidence source types: human clinical, model organism, in vitro, computational

Output Format

Structure your response as a comprehensive narrative organized by the sections above. For each section, provide: - Factual content with specific details (numbers, percentages, gene names, variant nomenclature) - Ontology term suggestions (HPO, GO, CL, UBERON, CHEBI, MAXO, MONDO) where applicable - Evidence citations with PMIDs - Direct quotes from abstracts to support key claims - Clear indication when information is not available or not applicable for this disease

This report will be used to populate a disease knowledge base entry with: - Pathophysiology descriptions with causal chains - Gene/protein annotations (HGNC, GO terms) - Phenotype associations (HP terms) with frequencies - Cell type involvement (CL terms) - Anatomical locations (UBERON terms) - Chemical entities (CHEBI terms) - Treatment annotations (MAXO terms) - Evidence items with PMIDs and exact abstract quotes - Epidemiology, prognosis, diagnostic, and prevention information - Animal model descriptions with phenotype recapitulation details

Coffin–Siris syndrome (CSS): Disease characteristics research report (Mendelian)

Executive summary

Coffin–Siris syndrome (CSS) is a rare multisystem neurodevelopmental disorder most classically defined by the triad of intellectual disability/developmental delay, coarse/dysmorphic facial features, and hypoplasia/aplasia of the fifth digit distal phalanx or nail. It is primarily caused by pathogenic germline variants affecting the SWI/SNF (BAF) chromatin remodeling complex (and closely related factors), with ARID1B as the most common gene. Recent work emphasizes (i) broad clinical heterogeneity across BAF-pathway genes, (ii) the growing role of genome-wide DNA methylation “episignatures” as functional biomarkers to resolve ambiguous cases, and (iii) expanding prenatal and adult phenotypes reported in 2023–2024 publications. (sekiguchi2019geneticabnormalitiesin pages 1-2, lee2021phenotypicandmolecular pages 1-2, milutinovic2023autismspectrumdisorder pages 1-2, arefeshghi2018bafopathies’dnamethylation pages 1-2, keskinen2024prenatalcoffinsirissyndrome pages 5-6)

A structured quantitative summary of key cohort and registry statistics from the evidence gathered is provided in the table artifact below.

Evidence type	Source (first author year, journal)	Publication date (month/year)	URL/DOI	Key quantitative statistics	Key quoted phrase from abstract
Cohort	Sekiguchi 2019, Journal of Human Genetics	09/2019	https://doi.org/10.1038/s10038-019-0667-4	78 pathogenic variations in 78 patients; gene counts: ARID1B 48, SMARCB1 8, SMARCA4 7, ARID1A 6, SOX11 4, SMARCE1 1, PHF6 1; plus CNVs including SMARCA2 and partial SMARCB1 deletion (sekiguchi2019geneticabnormalitiesin pages 1-2)	“confirmed 78 pathogenic variations in 78 patients” (sekiguchi2019geneticabnormalitiesin pages 1-2)
Cohort/registry	Vasko 2021, Genes	06/2021	https://doi.org/10.3390/genes12060937	208 individuals in CSS/BAF complex registry; ARID1B n=130, SMARCA4 n=32 specifically noted; common features included hypotonia, hypertrichosis, sparse scalp hair, distal phalanx hypoplasia (ciliberto2023epilepsyincoffin–siris pages 7-7)	“Genotype-Phenotype Correlations in 208 Individuals with Coffin-Siris Syndrome” (ciliberto2023epilepsyincoffin–siris pages 7-7)
Cohort	Lee 2021, BMC Medical Genomics	10/2021	https://doi.org/10.1186/s12920-021-01104-9	In 564 neurodevelopmental cases, 12/564 (2.1%) had SSRIDDs; 10 CSS; ARID1B 8/12; frequent phenotypes: thick eyebrows 10/12, hypertrichosis 8/12, coarse face 8/12, thick lips 8/12, long eyelashes 8/12, corpus callosum agenesis/hypoplasia 6/12 (lee2021phenotypicandmolecular pages 1-2)	“ARID1B, found in eight patients, was the most frequently altered gene.” (lee2021phenotypicandmolecular pages 1-2)
DNA methylation cohort	Aref-Eshghi 2018, Nature Communications	11/2018	https://doi.org/10.1038/s41467-018-07193-y	CSS methylation probe sets: 146 CpGs (CSS1/ARID1B), 135 CpGs (CSS3/SMARCB1), 356 CpGs (NCBRS/SMARCA2); no CpGs met cutoffs for CSS4 in n=2; model used 0.5 probability cutoff and 10-fold cross-validation (arefeshghi2018bafopathies’dnamethylation pages 1-2, arefeshghi2018bafopathies’dnamethylation pages 14-15)	“Specificity of this epi-signature was confirmed across a wide range of neurodevelopmental conditions” (arefeshghi2018bafopathies’dnamethylation pages 1-2)
Case report/literature review	Milutinovic 2023, Frontiers in Psychiatry	08/2023	https://doi.org/10.3389/fpsyt.2023.1199710	ARID1B abnormalities reported in 68–83% of CSS cases; index patient had heterozygous de novo ARID1B c.1638_1647del (milutinovic2023autismspectrumdisorder pages 1-2)	“being found in 68–83% of cases” (milutinovic2023autismspectrumdisorder pages 1-2)
Case report	Huang 2024, BMC Medical Genomics	05/2024	https://doi.org/10.1186/s12920-024-01904-9	Estimated incidence 1:10,000–1:100,000; ARID1B 51–75% of cases; de novo heterozygous frameshift c.3981dup (p.Glu1328ArgfsTer5); ARID1B mRNA approximately 30% lower in proband (huang2024denovovariation pages 1-2)	“a rare autosomal dominant inheritance disorder” (huang2024denovovariation pages 1-2)
Registry/review	Ciliberto 2023, American Journal of Medical Genetics Part A	09/2023	https://doi.org/10.1002/ajmg.a.62979	Prior ARID1B series: epilepsy in 28.2% of 143 patients; neuroimaging abnormalities in about half of patients: 20/41 and 20/47 in cited series; registry gene distribution: ARID1B 60%, SMARCA4 14%, SMARCB1 7%, ARID1A 6%, ARID2 5%, SOX11 3%, SMARCE1 2%, DPF2 1%, SMARCC2/PHF6/ACTL6A <1% (ciliberto2023epilepsyincoffin–siris pages 1-2, ciliberto2023epilepsyincoffin–siris pages 6-6)	“up to 28% of patients have previously been reported to have seizures” (ciliberto2023epilepsyincoffin–siris pages 1-1)
Registry subgroup	Ciliberto 2023, American Journal of Medical Genetics Part A	09/2023	https://doi.org/10.1002/ajmg.a.62979	In registry patients with epilepsy, 14 cases reported; Lennox-Gastaut syndrome diagnosed in 1/14 (7%); LGS-consistent findings in 3/14 (21%) (ciliberto2023epilepsyincoffin–siris pages 5-6)	“Epilepsy in these patients tends to be focal or multifocal in origin and usually relatively easy to control” (ciliberto2023epilepsyincoffin–siris pages 5-6)
Prenatal case series	Keskinen 2024, Pediatric and Developmental Pathology	11/2024	https://doi.org/10.1177/10935266231210155	2 prenatal cases; cites broader literature with 208 individuals and 63 patients; emphasizes recurrent severe prenatal CNS/cardiac malformations and increased fetal genetic testing (keskinen2024prenatalcoffinsirissyndrome pages 5-6)	“The CNS malformations and serious cardiac malformations are recurrent malformations in prenatal CSS cases.” (keskinen2024prenatalcoffinsirissyndrome pages 5-6)

Table: This table summarizes the main quantitative genetics, registry, cohort, and diagnostic epigenetics findings for Coffin–Siris syndrome from the gathered evidence. It highlights recurring gene distributions, cohort sizes, phenotype frequencies, and key quoted phrases useful for a knowledge-base entry.

1. Disease information

1.1 What is the disease?

CSS is a congenital/neurodevelopmental syndrome characterized by developmental delay/intellectual disability with recognizable craniofacial and limb/nail anomalies and frequent multisystem involvement. In a large cohort study, CSS is described as “a congenital disorder characterized by coarse facial features, intellectual disability, and hypoplasia of the fifth digit and nails.” (sekiguchi2019geneticabnormalitiesin pages 1-2)

A clinical cohort defining features within SWI/SNF-complex-related intellectual disability disorders (SSRIDDs) describes CSS as “characterized by intellectual disability (ID) and is often accompanied by a coarse face, hypertrichosis, sparse scalp hair, and hypoplasia/aplasia of the distal phalanx or nail of the fifth digit.” (lee2021phenotypicandmolecular pages 1-2)

A 2023 case report reiterates the classic phenotypic core as “aplasia or hypoplasia of the distal phalanx or nail of the fifth and additional digits, developmental or cognitive delay of varying degrees, distinctive facial features, hypotonia, hirsutism/hypertrichosis, and sparse scalp hair.” (milutinovic2023autismspectrumdisorder pages 1-2)

1.2 Key identifiers (from available evidence)

The retrieved evidence explicitly references: - OMIM/MIM: CSS “MIM 135900” (lee2021phenotypicandmolecular pages 1-2, ciliberto2023epilepsyincoffin–siris pages 1-1)

Not available in the retrieved evidence set (requires external disease databases not captured in the current document corpus): Orphanet ID, ICD-10/ICD-11 codes, MeSH ID, and MONDO ID.

1.3 Synonyms / alternative names

From the retrieved evidence, CSS is frequently discussed as part of a broader umbrella: - “SWI/SNF complex-related intellectual disability disorders (SSRIDDs)” (review framing) (lee2021phenotypicandmolecular pages 1-2) - “BAFopathies” (epigenomic/episignature framing across CSS and related disorders) (arefeshghi2018bafopathies’dnamethylation pages 1-2)

1.4 Evidence provenance (individual vs aggregated)

Aggregated resources/cohorts/registries: Large gene-ascertained cohorts and registries (e.g., a large genetic cohort confirming 78 pathogenic variants; registry studies with gene distributions) (sekiguchi2019geneticabnormalitiesin pages 1-2, ciliberto2023epilepsyincoffin–siris pages 6-6)
Individual patient reports: Several 2023–2024 papers are case reports expanding phenotype (e.g., ASD association; early-onset high myopia; SOX11 cases; prenatal cases) (milutinovic2023autismspectrumdisorder pages 1-2, huang2024denovovariation pages 1-2, keskinen2024prenatalcoffinsirissyndrome pages 5-6)

2. Etiology

2.1 Disease causal factors

Primary cause: germline pathogenic variants in genes encoding components of the SWI/SNF (BAF) chromatin-remodeling complex and related transcription factors (e.g., SOX11/SOX4). Cohort work notes CSS is “an autosomal dominant developmental disorder” (sekiguchi2019geneticabnormalitiesin pages 1-2) and emphasizes pathogenic variants in BAF-complex components (sekiguchi2019geneticabnormalitiesin pages 1-2, lee2021phenotypicandmolecular pages 1-2).

A genotype–phenotype review/cohort abstract lists multiple causative genes including ARID1A, ARID1B, ARID2, DPF2, SMARCA4, SMARCB1, SMARCC2, SMARCE1, SOX11, SOX4 (milutinovic2023autismspectrumdisorder pages 1-2), consistent with cohort findings of recurrent pathogenic variants in these genes (sekiguchi2019geneticabnormalitiesin pages 1-2, lee2021phenotypicandmolecular pages 1-2).

2.2 Risk factors

For CSS (a Mendelian disorder), the dominant “risk factor” is carrying a pathogenic variant in a causal gene. Most reported cases are de novo in published case reports (e.g., de novo ARID1B deletion variant and de novo frameshift; prenatal de novo examples) (huang2024denovovariation pages 1-2, milutinovic2023autismspectrumdisorder pages 1-2).

No environmental risk factors, lifestyle risk factors, or infectious triggers are described in the retrieved evidence.

2.3 Protective factors / Gene–environment interactions

No protective factors or gene–environment interactions were identified in the retrieved evidence.

3. Phenotypes

3.1 Core phenotype domains and suggested HPO terms

Below are phenotype domains supported by the retrieved evidence, with example HPO suggestions (for knowledge-base mapping). Frequencies are included only when explicitly available.

Neurodevelopment / behavior

Developmental delay / intellectual disability (near-universal across cohorts) (sekiguchi2019geneticabnormalitiesin pages 1-2, lee2021phenotypicandmolecular pages 1-2)
HPO: HP:0001263 (Global developmental delay), HP:0001249 (Intellectual disability)
Speech delay (often profound) (lee2021phenotypicandmolecular pages 1-2)
HPO: HP:0000750 (Delayed speech and language development)
Autism spectrum disorder / autistic traits reported in ARID1B-related CSS spectrum case report (milutinovic2023autismspectrumdisorder pages 1-2)
HPO: HP:0000729 (Autistic behavior)

Craniofacial / ectodermal

Coarse facial features / dysmorphic facial features (sekiguchi2019geneticabnormalitiesin pages 1-2, lee2021phenotypicandmolecular pages 1-2, huang2024denovovariation pages 1-2)
HPO: HP:0000280 (Coarse facial features)
Hypertrichosis / hirsutism (frequent) (lee2021phenotypicandmolecular pages 1-2, milutinovic2023autismspectrumdisorder pages 1-2)
HPO: HP:0000998 (Hypertrichosis)
Sparse scalp hair (lee2021phenotypicandmolecular pages 1-2, milutinovic2023autismspectrumdisorder pages 1-2, huang2024denovovariation pages 1-2)
HPO: HP:0002200 (Sparse scalp hair)

Limbs / nails

Hypoplasia/aplasia of distal phalanx or nail of fifth digit (signature feature) (sekiguchi2019geneticabnormalitiesin pages 1-2, lee2021phenotypicandmolecular pages 1-2, milutinovic2023autismspectrumdisorder pages 1-2, huang2024denovovariation pages 1-2)
HPO: HP:0001819 (Fifth finger clinodactyly) is not precise; more appropriate: HP:0001817 (Fifth finger brachydactyly) and nail terms such as HP:0001800 (Nail dysplasia) may be used depending on the specific finding.

Neurologic

Hypotonia (lee2021phenotypicandmolecular pages 1-2, milutinovic2023autismspectrumdisorder pages 1-2, huang2024denovovariation pages 1-2)
HPO: HP:0001252 (Muscular hypotonia)
Brain structural abnormalities/neuroimaging findings common in series: ~half in two cited cohorts (20/41; 20/47) (ciliberto2023epilepsyincoffin–siris pages 1-2)
HPO example: HP:0001276 (Brain morphology abnormality)
Corpus callosum agenesis/hypoplasia in 6/12 of a Korean SSRIDD cohort (lee2021phenotypicandmolecular pages 1-2)
HPO: HP:0001274 (Agenesis of corpus callosum)

Seizures / epilepsy

Epilepsy is a recognized complication, with reported prevalence 28.2% in an ARID1B cohort (n=143) (ciliberto2023epilepsyincoffin–siris pages 1-2), and registry analysis suggesting variable/possibly lower reporting depending on ascertainment (ciliberto2023epilepsyincoffin–siris pages 5-6).
HPO: HP:0001250 (Seizures), HP:0002353 (EEG abnormality)

Multiorgan congenital anomalies (examples)

Cardiac anomalies are recurrent, including prenatal severe cardiovascular malformations (keskinen2024prenatalcoffinsirissyndrome pages 5-6) and case-level defects such as patent foramen ovale/ventricular septal defect (huang2024denovovariation pages 1-2).
HPO: HP:0001627 (Abnormality of the cardiovascular system)
Renal anomalies (e.g., renal cysts) (huang2024denovovariation pages 1-2)
HPO: HP:0000077 (Kidney abnormality)

3.2 Phenotype frequencies / statistics (from cohorts in evidence)

Korean WES cohort of SSRIDDs (n=12): thick eyebrows 10/12, hypertrichosis 8/12, coarse face 8/12, thick lips 8/12, long eyelashes 8/12, corpus callosum agenesis/hypoplasia 6/12, developmental delay 12/12 (lee2021phenotypicandmolecular pages 1-2).
Neuroimaging abnormalities: approximately half in two cited CSS cohorts (20/41 and 20/47) (ciliberto2023epilepsyincoffin–siris pages 1-2).
Epilepsy: 28.2% in an ARID1B cohort (n=143) (ciliberto2023epilepsyincoffin–siris pages 1-2); registry-based epilepsy subgroup analysis included 14 epilepsy cases with Lennox–Gastaut syndrome diagnosed in 1/14 (7%) and LGS-consistent findings in 3/14 (21%) (ciliberto2023epilepsyincoffin–siris pages 5-6).

3.3 Quality-of-life impacts

Formal QoL instruments (EQ-5D/SF-36/PROMIS) were not reported in the retrieved evidence set.

4. Genetic / molecular information

4.1 Causal genes (supported by retrieved evidence)

Multiple sources converge on CSS as a BAF/SWI-SNF chromatin remodeling disorder with genetic heterogeneity: - Large cohort lists implicated genes including ARID1A, ARID1B, ARID2, SMARCA4, SMARCB1, SMARCE1, SOX11, PHF6, DPF2 (sekiguchi2019geneticabnormalitiesin pages 1-2). - SSRIDD cohort emphasizes SWI/SNF complex components (ARID1B, SMARCA4, SMARCB1, ARID2, SMARCA2) (lee2021phenotypicandmolecular pages 1-2). - Case report review notes ARID1B plus additional genes (ARID1A/2, DPF2, PHF6, SMARCA2/4, SMARCB1, SMARCC2, SMARCE1, SOX4/11) (milutinovic2023autismspectrumdisorder pages 1-2).

4.2 Gene contribution and registry distributions

ARID1B is often the leading gene. A 2023 case report/literature review states ARID1B abnormalities are found in 68–83% of cases (milutinovic2023autismspectrumdisorder pages 1-2).
A 2024 study reports ARID1B is most commonly implicated in 51–75% of cases (huang2024denovovariation pages 1-2).
International registry gene distribution (as reported in an epilepsy-focused registry analysis): ARID1B 60%, SMARCA4 14%, SMARCB1 7%, ARID1A 6%, ARID2 5%, SOX11 3%, SMARCE1 2%, DPF2 1%, SMARCC2/PHF6/ACTL6A <1% (ciliberto2023epilepsyincoffin–siris pages 6-6).

4.3 Pathogenic variant classes and functional consequences

Across evidence, CSS is generally consistent with haploinsufficiency/loss-of-function for some genes (notably ARID1B), while other SWI/SNF genes often show missense/nontruncating variants in cohorts. - In the Korean cohort: “All pathogenic variants in ARID1B were truncating, whereas variants in SMARCA2, SMARCB1, and SMARCA4 were nontruncating (missense).” (lee2021phenotypicandmolecular pages 1-2) - A 2024 ARID1B report states “almost all ARID1B gene variants are non-functional” and includes nonsense/frameshift/splice-site and deletion mechanisms (huang2024denovovariation pages 1-2). - Large cohort confirmed numerous ARID1B variants (48) and additional variants in SMARCB1, SMARCA4, ARID1A, SOX11, etc., and noted CNVs involving SMARCA2 (sekiguchi2019geneticabnormalitiesin pages 1-2).

Example pathogenic variants (from 2023–2024 case reports): - ARID1B de novo pathogenic deletion c.1638_1647del (milutinovic2023autismspectrumdisorder pages 1-2) - ARID1B de novo frameshift insertion c.3981dup (p.Glu1328ArgfsTer5) with ~30% reduced ARID1B mRNA in proband (huang2024denovovariation pages 1-2)

4.4 Epigenetic information (DNA methylation episignatures)

A major mechanistic and diagnostic advance for CSS/BAFopathies is the identification of disorder-specific peripheral blood DNA methylation profiles: - A Nature Communications study reports “overlapping peripheral blood DNA methylation epi-signatures” for CSS subtypes (ARID1B, SMARCB1, SMARCA4) and Nicolaides–Baraitser syndrome (SMARCA2), supporting a functional continuum. (arefeshghi2018bafopathies’dnamethylation pages 1-2) - The same work demonstrates diagnostic potential: a machine-learning classifier trained on the methylation profile can “resolve ambiguous clinical cases,” “reclassify those with variants of unknown significance,” and identify “previously undiagnosed subjects through targeted population screening.” (arefeshghi2018bafopathies’dnamethylation pages 1-2) - Specificity testing was “confirmed across a wide range of neurodevelopmental conditions including other chromatin remodeling and epigenetic machinery disorders.” (arefeshghi2018bafopathies’dnamethylation pages 1-2)

Episignature feature sizes reported: 146 CpGs for CSS1/ARID1B, 135 CpGs for CSS3/SMARCB1, 356 CpGs for NCBRS/SMARCA2 (arefeshghi2018bafopathies’dnamethylation pages 1-2).

4.5 Modifier genes / chromosomal abnormalities

The retrieved evidence supports a role for copy number variants (CNVs) including ARID1B microdeletions and CNVs involving SMARCA2 in cohorts (sekiguchi2019geneticabnormalitiesin pages 1-2, arefeshghi2018bafopathies’dnamethylation pages 1-2). However, specific modifier genes were not identified in the retrieved evidence.

5. Environmental information

No non-genetic environmental, lifestyle, or infectious causal contributors were identified in the retrieved evidence for CSS.

6. Mechanism / pathophysiology

6.1 Current mechanistic understanding

CSS is a disorder of chromatin remodeling and transcriptional regulation through disruption of the SWI/SNF (BAF) complex: - CSS is repeatedly described as caused by mutations affecting BAF chromatin remodeling complex components (sekiguchi2019geneticabnormalitiesin pages 1-2, lee2021phenotypicandmolecular pages 1-2, arefeshghi2018bafopathies’dnamethylation pages 1-2). - The presence of blood DNA methylation episignatures in CSS/BAFopathies supports that perturbation of chromatin remodeling can lead to systemic, measurable epigenomic consequences that correlate with genotype and can aid diagnosis (arefeshghi2018bafopathies’dnamethylation pages 1-2).

6.2 Causal chain (high-level)

1) Germline pathogenic variant in a BAF/SWI-SNF gene →
2) altered chromatin remodeling / DNA accessibility →
3) dysregulated developmental gene expression programs (neurodevelopment, craniofacial, limb/nail, organogenesis) →
4) multisystem congenital anomalies and neurodevelopmental phenotype (developmental delay/ID, hypotonia, fifth digit/nail hypoplasia, dysmorphisms, brain/cardiac anomalies). (sekiguchi2019geneticabnormalitiesin pages 1-2, lee2021phenotypicandmolecular pages 1-2, arefeshghi2018bafopathies’dnamethylation pages 1-2)

6.3 Suggested ontology terms

Because the retrieved evidence does not provide pathway-specific GO enrichments, suggestions are conservative and align with SWI/SNF/BAF biology: - GO Biological Process: chromatin remodeling, regulation of transcription, nervous system development (supported conceptually by SWI/SNF roles; disease–mechanism link supported by CSS being BAF-related) (lee2021phenotypicandmolecular pages 1-2, arefeshghi2018bafopathies’dnamethylation pages 1-2) - GO Cellular Component: SWI/SNF complex / BAF complex (lee2021phenotypicandmolecular pages 1-2, arefeshghi2018bafopathies’dnamethylation pages 1-2)

Cell Ontology (CL) terms were not directly supported by evidence in the retrieved corpus.

7. Anatomical structures affected

Evidence supports involvement of multiple systems: - Central nervous system (UBERON:0001017): brain structural abnormalities and corpus callosum involvement; prenatal CNS malformations recurrent (keskinen2024prenatalcoffinsirissyndrome pages 5-6, ciliberto2023epilepsyincoffin–siris pages 1-2, lee2021phenotypicandmolecular pages 1-2) - Cardiovascular system (UBERON:0004535): congenital heart defects, including severe prenatal cardiovascular malformations (keskinen2024prenatalcoffinsirissyndrome pages 5-6, huang2024denovovariation pages 1-2) - Integument/hair and nails: sparse scalp hair, hypertrichosis, nail dysplasia (lee2021phenotypicandmolecular pages 1-2, milutinovic2023autismspectrumdisorder pages 1-2) - Limbs/digits: fifth digit distal phalanx/nail hypoplasia/aplasia (sekiguchi2019geneticabnormalitiesin pages 1-2, lee2021phenotypicandmolecular pages 1-2)

Subcellular localization: disease mechanism centers on nuclear chromatin regulation (supported by chromatin-remodeling complex etiology) (lee2021phenotypicandmolecular pages 1-2, arefeshghi2018bafopathies’dnamethylation pages 1-2).

8. Temporal development

8.1 Onset

Typically congenital/early childhood, consistent with congenital anomalies and neurodevelopmental delay described across cohorts (sekiguchi2019geneticabnormalitiesin pages 1-2, lee2021phenotypicandmolecular pages 1-2).
Prenatal presentations are increasingly recognized, with recurrent prenatal CNS and cardiac malformations noted and molecular diagnosis in pregnancy becoming more common (keskinen2024prenatalcoffinsirissyndrome pages 5-6).

8.2 Progression/course

Longitudinal/natural history staging is not provided in the retrieved evidence.
Epilepsy phenotype in registry cases is described as often “relatively easy to control,” suggesting some aspects may be medically manageable, but systematic long-term outcome data are limited in the retrieved excerpts (ciliberto2023epilepsyincoffin–siris pages 5-6).

9. Inheritance and population

9.1 Inheritance

Multiple sources describe CSS as autosomal dominant, with many cases arising de novo: - Cohort: CSS is “an autosomal dominant developmental disorder” (sekiguchi2019geneticabnormalitiesin pages 1-2). - 2024 ARID1B-focused report: CSS is “a rare autosomal dominant inheritance disorder” (huang2024denovovariation pages 1-2). - Case reports document de novo heterozygous pathogenic variants (huang2024denovovariation pages 1-2, milutinovic2023autismspectrumdisorder pages 1-2).

9.2 Epidemiology

The retrieved evidence provides limited population-level epidemiology: - A 2024 ARID1B/CSS report gives an incidence estimate of 1:10,000–1:100,000 (huang2024denovovariation pages 1-2).

No prevalence per 100,000 and no geographic/ethnic prevalence differences were available in the evidence set.

9.3 Penetrance/expressivity

While systematic penetrance estimates are not provided in the retrieved evidence, multiple studies emphasize broad phenotypic variability and overlap across SWI/SNF disorders, implying variable expressivity (lee2021phenotypicandmolecular pages 1-2, keskinen2024prenatalcoffinsirissyndrome pages 5-6).

10. Diagnostics

10.1 Genetic testing (real-world implementation)

Current standard diagnostic approach is genomic sequencing (often WES) with confirmatory testing, supported by multiple contemporary case reports and cohorts: - A Korean SSRIDD study used whole-exome sequencing of 564 NDD patients to identify 12 SSRIDD cases (including CSS) (lee2021phenotypicandmolecular pages 1-2). - 2024 ARID1B case report used whole-exome sequencing with Sanger confirmation and functional follow-up (RT-qPCR) (huang2024denovovariation pages 1-2). - 2023 ASD+CSS case report emphasizes genetic testing for diagnosis confirmation and provides a de novo ARID1B pathogenic variant (milutinovic2023autismspectrumdisorder pages 1-2).

CNV detection / microdeletions: Large cohort work included CNVs (e.g., SMARCA2 CNVs) (sekiguchi2019geneticabnormalitiesin pages 1-2), and BAFopathy methylation work notes 6q25 microdeletion syndrome with ARID1B deletions shares a CSS/NCBRS methylation profile (arefeshghi2018bafopathies’dnamethylation pages 1-2), supporting inclusion of CNV assessment in diagnostic workups.

10.2 DNA methylation episignatures (advanced diagnostics)

Genome-wide DNA methylation episignatures provide an additional diagnostic layer for CSS/BAFopathies: - The 2018 Nature Communications paper demonstrates that disease-associated episignatures can “resolve ambiguous clinical cases” and “reclassify those with variants of unknown significance.” (arefeshghi2018bafopathies’dnamethylation pages 1-2)

In practice, this supports incorporation of episignature testing when sequencing yields VUS or when phenotype-genotype fit is uncertain, although the retrieved evidence does not include a CSS-specific 2023–2024 clinical guideline excerpt.

10.3 Differential diagnosis

The retrieved evidence indicates notable phenotypic overlap among chromatinopathies and recommends broad surveillance. A 2024 prenatal CSS paper and overlap study emphasize overlap with other epigenetic machinery disorders and that craniofacial/skeletal features may be less detectable prenatally (keskinen2024prenatalcoffinsirissyndrome pages 5-6). (Differential diagnosis lists are not explicitly enumerated in the provided excerpts.)

11. Outcome / prognosis

11.1 Neurologic outcomes (epilepsy)

Epilepsy prevalence varies by cohort; one ARID1B cohort reported 28.2% epilepsy (ciliberto2023epilepsyincoffin–siris pages 1-2), while registry-based analyses suggest ascertainment/reporting effects and describe epilepsy as often focal/multifocal and “usually relatively easy to control” (ciliberto2023epilepsyincoffin–siris pages 5-6).

11.2 Prenatal outcomes

Prenatal CSS can present with serious CNS and cardiovascular malformations and may be associated with severe outcomes including intrauterine death in some reported cases (keskinen2024prenatalcoffinsirissyndrome pages 5-6).

No survival curves, life expectancy estimates, or systematic mortality data were available in the retrieved evidence.

12. Treatment

12.1 Disease-modifying therapy

No disease-modifying pharmacologic therapy for CSS was identified in the retrieved evidence.

12.2 Supportive and symptomatic management (current practice)

Direct, detailed multidisciplinary management guidelines were not present in the retrieved excerpt set; however, the syndrome’s multisystem nature and reported complications imply typical real-world management includes: - developmental therapies (speech/OT/PT), - management of seizures when present, - screening and treatment for congenital anomalies (cardiac, CNS, etc.), - hearing/vision evaluation.

Epilepsy treatment: registry-based review notes that responsiveness data are limited overall but that epilepsy “tends to be focal or multifocal… and usually relatively easy to control” in their series (ciliberto2023epilepsyincoffin–siris pages 5-6).

12.3 MAXO term suggestions (non-exhaustive; not directly enumerated in evidence)

Because explicit action ontology mapping was not provided in the evidence, suggestions are generic: - MAXO:0001175 (Genetic testing) (for WES/CNV analysis; concept supported) (lee2021phenotypicandmolecular pages 1-2, huang2024denovovariation pages 1-2) - MAXO:0000127 (Seizure management) (supported by epilepsy discussion) (ciliberto2023epilepsyincoffin–siris pages 5-6) - MAXO:0000013 (Physical therapy), MAXO:0000014 (Occupational therapy), MAXO:0000015 (Speech therapy) (consistent with developmental delay; not explicitly mentioned in excerpts)

12.4 Clinical trials

A clinical-trials search did not retrieve CSS-specific interventional trials in the current evidence set; trials returned were largely oncology or broad genetic/autism registries rather than CSS-targeted therapeutic studies.

13. Prevention

Primary prevention is not applicable for most de novo Mendelian CSS cases. Secondary/tertiary prevention in practice involves: - early genetic diagnosis and anticipatory screening for associated anomalies, - prenatal diagnosis when a causal variant is detected (noting increasing fetal genetic testing) (keskinen2024prenatalcoffinsirissyndrome pages 5-6).

No vaccine, chemoprophylaxis, or modifiable environmental prevention strategies were identified.

14. Other species / natural disease

No naturally occurring CSS analogs in non-human species were identified in the retrieved evidence.

15. Model organisms

The retrieved evidence set did not contain specific model-organism studies of CSS genes; therefore, no model details can be cited from this corpus.

Recent developments and latest research (prioritizing 2023–2024)

2023–2024 phenotype expansion and implementation themes

Expanded phenotypes and variable presentations: 2023–2024 case reports highlight diagnostic challenges and expansion into ophthalmologic (early-onset high myopia) and neuropsychiatric (ASD traits) presentations, reinforcing that CSS can initially be recognized outside genetics clinics and requires interdisciplinary assessment plus molecular testing. (milutinovic2023autismspectrumdisorder pages 1-2, huang2024denovovariation pages 1-2)
Registry-based quantification of complications: 2023 registry-based epilepsy work provides gene distribution statistics and characterizes epilepsy subtypes (including a small proportion with Lennox–Gastaut syndrome diagnosis/phenotype), while emphasizing limitations of caregiver-reported registries. (ciliberto2023epilepsyincoffin–siris pages 5-6, ciliberto2023epilepsyincoffin–siris pages 6-6)
Prenatal recognition: 2024 prenatal reports and reviews emphasize recurrent severe prenatal CNS/cardiac malformations and recommend detailed molecular, radiologic, and pathologic examinations, reflecting increasing fetal genetic testing uptake. (keskinen2024prenatalcoffinsirissyndrome pages 5-6)

Limitations of this report (evidence coverage)

Identifiers (MONDO/Orphanet/ICD/MeSH) could not be extracted from the current retrieved literature corpus.
Model organism and molecular pathway details (e.g., specific downstream signaling pathways) were not captured in the available excerpts.
Formal management guidelines, QoL measures, and long-term survival statistics were not present in the retrieved evidence snippets.

Source URLs (as retrieved) and publication dates

Key sources used in the evidence: - Sekiguchi et al., Journal of Human Genetics (Sep 2019). DOI/URL: https://doi.org/10.1038/s10038-019-0667-4 (sekiguchi2019geneticabnormalitiesin pages 1-2) - Aref-Eshghi et al., Nature Communications (Nov 2018). DOI/URL: https://doi.org/10.1038/s41467-018-07193-y (arefeshghi2018bafopathies’dnamethylation pages 1-2) - Lee et al., BMC Medical Genomics (Oct 2021). DOI/URL: https://doi.org/10.1186/s12920-021-01104-9 (lee2021phenotypicandmolecular pages 1-2) - Ciliberto et al., American Journal of Medical Genetics Part A (Sep 2023). DOI/URL: https://doi.org/10.1002/ajmg.a.62979 (ciliberto2023epilepsyincoffin–siris pages 1-2) - Milutinovic et al., Frontiers in Psychiatry (Aug 2023). DOI/URL: https://doi.org/10.3389/fpsyt.2023.1199710 (milutinovic2023autismspectrumdisorder pages 1-2) - Huang et al., BMC Medical Genomics (May 2024). DOI/URL: https://doi.org/10.1186/s12920-024-01904-9 (huang2024denovovariation pages 1-2) - Keskinen et al., Pediatric and Developmental Pathology (Nov 2024). DOI/URL: https://doi.org/10.1177/10935266231210155 (keskinen2024prenatalcoffinsirissyndrome pages 5-6)

References

(sekiguchi2019geneticabnormalitiesin pages 1-2): Futoshi Sekiguchi, Yoshinori Tsurusaki, Nobuhiko Okamoto, Keng Wee Teik, Seiji Mizuno, Hiroshi Suzumura, Bertrand Isidor, Winnie Peitee Ong, Muzhirah Haniffa, Susan M. White, Mari Matsuo, Kayoko Saito, Shubha Phadke, Tomoki Kosho, Patrick Yap, Manisha Goyal, Lorne A. Clarke, Rani Sachdev, George McGillivray, Richard J. Leventer, Chirag Patel, Takanori Yamagata, Hitoshi Osaka, Yoshiya Hisaeda, Hirofumi Ohashi, Kenji Shimizu, Keisuke Nagasaki, Junpei Hamada, Sumito Dateki, Takashi Sato, Yasutsugu Chinen, Tomonari Awaya, Takeo Kato, Kougoro Iwanaga, Masahiko Kawai, Takashi Matsuoka, Yoshikazu Shimoji, Tiong Yang Tan, Seema Kapoor, Nerine Gregersen, Massimiliano Rossi, Mathieu Marie-Laure, Lesley McGregor, Kimihiko Oishi, Lakshmi Mehta, Greta Gillies, Paul J. Lockhart, Kate Pope, Anju Shukla, Katta Mohan Girisha, Ghada M. H. Abdel-Salam, David Mowat, David Coman, Ok Hwa Kim, Marie-Pierre Cordier, Kate Gibson, Jeff Milunsky, Jan Liebelt, Helen Cox, Salima El Chehadeh, Annick Toutain, Ken Saida, Hiromi Aoi, Gaku Minase, Naomi Tsuchida, Kazuhiro Iwama, Yuri Uchiyama, Toshifumi Suzuki, Kohei Hamanaka, Yoshiteru Azuma, Atsushi Fujita, Eri Imagawa, Eriko Koshimizu, Atsushi Takata, Satomi Mitsuhashi, Satoko Miyatake, Takeshi Mizuguchi, Noriko Miyake, and Naomichi Matsumoto. Genetic abnormalities in a large cohort of coffin–siris syndrome patients. Journal of Human Genetics, 64:1173-1186, Sep 2019. URL: https://doi.org/10.1038/s10038-019-0667-4, doi:10.1038/s10038-019-0667-4. This article has 86 citations and is from a peer-reviewed journal.
(lee2021phenotypicandmolecular pages 1-2): Yena Lee, Yunha Choi, Go Hun Seo, Gu-Hwan Kim, Changwon Keum, Yoo-Mi Kim, Hyo-Sang Do, Jeongmin Choi, In Hee Choi, Han-Wook Yoo, and Beom Hee Lee. Phenotypic and molecular spectra of patients with switch/sucrose nonfermenting complex-related intellectual disability disorders in korea. BMC Medical Genomics, Oct 2021. URL: https://doi.org/10.1186/s12920-021-01104-9, doi:10.1186/s12920-021-01104-9. This article has 6 citations and is from a peer-reviewed journal.
(milutinovic2023autismspectrumdisorder pages 1-2): Luka Milutinovic, Roberto Grujicic, Vanja Mandic Maravic, Ivana Joksic, Natasa Ljubomirovic, and Milica Pejovic Milovancevic. Autism spectrum disorder and coffin–siris syndrome—case report. Frontiers in Psychiatry, Aug 2023. URL: https://doi.org/10.3389/fpsyt.2023.1199710, doi:10.3389/fpsyt.2023.1199710. This article has 5 citations.
(arefeshghi2018bafopathies’dnamethylation pages 1-2): Erfan Aref-Eshghi, Eric G. Bend, Rebecca L. Hood, Laila C. Schenkel, Deanna Alexis Carere, Rana Chakrabarti, Sandesh C. S. Nagamani, Sau Wai Cheung, Philippe M. Campeau, Chitra Prasad, Victoria Mok Siu, Lauren Brady, Mark A. Tarnopolsky, David J. Callen, A. Micheil Innes, Susan M. White, Wendy S. Meschino, Andrew Y. Shuen, Guillaume Paré, Dennis E. Bulman, Peter J. Ainsworth, Hanxin Lin, David I. Rodenhiser, Raoul C. Hennekam, Kym M. Boycott, Charles E. Schwartz, and Bekim Sadikovic. Bafopathies’ dna methylation epi-signatures demonstrate diagnostic utility and functional continuum of coffin–siris and nicolaides–baraitser syndromes. Nature Communications, Nov 2018. URL: https://doi.org/10.1038/s41467-018-07193-y, doi:10.1038/s41467-018-07193-y. This article has 156 citations and is from a highest quality peer-reviewed journal.
(keskinen2024prenatalcoffinsirissyndrome pages 5-6): Sini Keskinen, Teija Paakkola, Mirjami Mattila, Marja Hietala, Hannele Koillinen, Jukka Laine, and Maria K. Haanpää. Prenatal coffin-siris syndrome: expanding the phenotypic and genotypic spectrum of the disease. Pediatric and Developmental Pathology, 27:181-186, Nov 2024. URL: https://doi.org/10.1177/10935266231210155, doi:10.1177/10935266231210155. This article has 10 citations and is from a peer-reviewed journal.
(ciliberto2023epilepsyincoffin–siris pages 7-7): Michael Ciliberto, Karen Skjei, Ashley Vasko, and Samantha Schrier Vergano. Epilepsy in coffin–siris syndrome: a report from the international css registry and review of the literature. American Journal of Medical Genetics Part A, 191:22-28, Sep 2023. URL: https://doi.org/10.1002/ajmg.a.62979, doi:10.1002/ajmg.a.62979. This article has 13 citations.
(arefeshghi2018bafopathies’dnamethylation pages 14-15): Erfan Aref-Eshghi, Eric G. Bend, Rebecca L. Hood, Laila C. Schenkel, Deanna Alexis Carere, Rana Chakrabarti, Sandesh C. S. Nagamani, Sau Wai Cheung, Philippe M. Campeau, Chitra Prasad, Victoria Mok Siu, Lauren Brady, Mark A. Tarnopolsky, David J. Callen, A. Micheil Innes, Susan M. White, Wendy S. Meschino, Andrew Y. Shuen, Guillaume Paré, Dennis E. Bulman, Peter J. Ainsworth, Hanxin Lin, David I. Rodenhiser, Raoul C. Hennekam, Kym M. Boycott, Charles E. Schwartz, and Bekim Sadikovic. Bafopathies’ dna methylation epi-signatures demonstrate diagnostic utility and functional continuum of coffin–siris and nicolaides–baraitser syndromes. Nature Communications, Nov 2018. URL: https://doi.org/10.1038/s41467-018-07193-y, doi:10.1038/s41467-018-07193-y. This article has 156 citations and is from a highest quality peer-reviewed journal.
(huang2024denovovariation pages 1-2): Xiaoyu Huang, Huiping Li, Shangying Yang, Meijiao Ma, Yuanyuan Lian, Xueli Wu, Xiaolong Qi, Xuhui Wang, Weining Rong, and Xunlun Sheng. De novo variation in arid1b gene causes coffin-siris syndrome 1 in a chinese family with excessive early-onset high myopia. BMC Medical Genomics, May 2024. URL: https://doi.org/10.1186/s12920-024-01904-9, doi:10.1186/s12920-024-01904-9. This article has 4 citations and is from a peer-reviewed journal.
(ciliberto2023epilepsyincoffin–siris pages 1-2): Michael Ciliberto, Karen Skjei, Ashley Vasko, and Samantha Schrier Vergano. Epilepsy in coffin–siris syndrome: a report from the international css registry and review of the literature. American Journal of Medical Genetics Part A, 191:22-28, Sep 2023. URL: https://doi.org/10.1002/ajmg.a.62979, doi:10.1002/ajmg.a.62979. This article has 13 citations.
(ciliberto2023epilepsyincoffin–siris pages 6-6): Michael Ciliberto, Karen Skjei, Ashley Vasko, and Samantha Schrier Vergano. Epilepsy in coffin–siris syndrome: a report from the international css registry and review of the literature. American Journal of Medical Genetics Part A, 191:22-28, Sep 2023. URL: https://doi.org/10.1002/ajmg.a.62979, doi:10.1002/ajmg.a.62979. This article has 13 citations.
(ciliberto2023epilepsyincoffin–siris pages 1-1): Michael Ciliberto, Karen Skjei, Ashley Vasko, and Samantha Schrier Vergano. Epilepsy in coffin–siris syndrome: a report from the international css registry and review of the literature. American Journal of Medical Genetics Part A, 191:22-28, Sep 2023. URL: https://doi.org/10.1002/ajmg.a.62979, doi:10.1002/ajmg.a.62979. This article has 13 citations.
(ciliberto2023epilepsyincoffin–siris pages 5-6): Michael Ciliberto, Karen Skjei, Ashley Vasko, and Samantha Schrier Vergano. Epilepsy in coffin–siris syndrome: a report from the international css registry and review of the literature. American Journal of Medical Genetics Part A, 191:22-28, Sep 2023. URL: https://doi.org/10.1002/ajmg.a.62979, doi:10.1002/ajmg.a.62979. This article has 13 citations.

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Classifications

Inheritance

Subtypes

Pathophysiology

Pathograph

Phenotypes

Genetic Associations

Medical Actions

Diagnosis

Prevalence

Source YAML

References & Deep Research

References

Deep Research

Disease Characteristics Research Template

Target Disease

Research Objectives

1. Disease Information

2. Etiology

3. Phenotypes

4. Genetic/Molecular Information

5. Environmental Information

6. Mechanism / Pathophysiology

7. Anatomical Structures Affected

8. Temporal Development

9. Inheritance and Population

10. Diagnostics

11. Outcome/Prognosis

12. Treatment

13. Prevention

14. Other Species / Natural Disease

15. Model Organisms

Citation Requirements

Output Format

Coffin–Siris syndrome (CSS): Disease characteristics research report (Mendelian)

Executive summary

1. Disease information

1.1 What is the disease?

1.2 Key identifiers (from available evidence)

1.3 Synonyms / alternative names

1.4 Evidence provenance (individual vs aggregated)

2. Etiology

2.1 Disease causal factors

2.2 Risk factors

2.3 Protective factors / Gene–environment interactions

3. Phenotypes

3.1 Core phenotype domains and suggested HPO terms

Neurodevelopment / behavior

Craniofacial / ectodermal

Limbs / nails

Neurologic

Seizures / epilepsy

Multiorgan congenital anomalies (examples)

3.2 Phenotype frequencies / statistics (from cohorts in evidence)

3.3 Quality-of-life impacts

4. Genetic / molecular information

4.1 Causal genes (supported by retrieved evidence)

4.2 Gene contribution and registry distributions

4.3 Pathogenic variant classes and functional consequences

4.4 Epigenetic information (DNA methylation episignatures)

4.5 Modifier genes / chromosomal abnormalities

5. Environmental information

6. Mechanism / pathophysiology

6.1 Current mechanistic understanding

6.2 Causal chain (high-level)

6.3 Suggested ontology terms

7. Anatomical structures affected

8. Temporal development

8.1 Onset

8.2 Progression/course

9. Inheritance and population

9.1 Inheritance

9.2 Epidemiology

9.3 Penetrance/expressivity

10. Diagnostics

10.1 Genetic testing (real-world implementation)

10.2 DNA methylation episignatures (advanced diagnostics)

10.3 Differential diagnosis