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1
Inheritance
3
Pathophys.
7
Phenotypes
4
Pathograph
1
Genes
10
References
1
Deep Research
👪

Inheritance

1
Autosomal dominant inheritance HP:0000006
KdVS is caused by heterozygous loss of KANSL1 function, usually arising de novo through either a recurrent 17q21.31 deletion or a loss-of-function KANSL1 sequence variant.
Autosomal dominant inheritance Expressivity: VARIABLE
Show evidence (1 reference)
PMID:41457108 SUPPORT Human Clinical
"(KdVS), an autosomal dominant NDD caused by KANSL1 haploinsufficiency"
Supports autosomal dominant inheritance mediated by KANSL1 haploinsufficiency.

Pathophysiology

3
KANSL1 haploinsufficiency
Heterozygous loss of KANSL1 is the core molecular lesion in KdVS. KANSL1 is a chromatin-associated regulator within the NSL complex, linking reduced dosage to altered chromatin organization and transcriptional control during brain development.
neuron link
KANSL1 link
chromatin organization link regulation of gene expression link ↓ DECREASED
brain link
Show evidence (2 references)
PMID:22544367 SUPPORT Human Clinical
"These findings indicate that 17q21.31 deletion syndrome is a monogenic disorder caused by haploinsufficiency of KANSL1."
Establishes KANSL1 haploinsufficiency as the disease-defining mechanism.
PMID:22544363 SUPPORT Human Clinical
"The KANSL1 protein is an evolutionarily conserved regulator of the chromatin modifier KAT8, which influences gene expression through histone H4 lysine 16 (H4K16) acetylation."
Supports the chromatin and transcriptional regulatory role of KANSL1 underlying KdVS biology.
Autophagosome accumulation in KANSL1-deficient neurons
In KANSL1-deficient human neurons, reduced SOD1 is associated with increased oxidative stress and subsequent autophagosome accumulation, including at excitatory synapses.
neuron link
KANSL1 link
autophagy link ↑ INCREASED
brain link
Show evidence (1 reference)
PMID:34286667 SUPPORT In Vitro
"we identified SOD1 (superoxide dismutase 1), an antioxidant enzyme, to be significantly decreased, leading to a subsequent increase in oxidative stress and autophagosome accumulation."
Supports oxidative-stress-associated autophagy imbalance in KANSL1-deficient neurons.
Synaptic dysfunction in KANSL1-deficient neurons
Autophagosome accumulation at excitatory synapses in KANSL1-deficient neurons is associated with reduced synaptic density, decreased AMPA receptor-mediated transmission, and impaired neuronal network activity.
neuron link
KANSL1 link
chemical synaptic transmission link ↓ DECREASED
brain link
Show evidence (1 reference)
PMID:34286667 SUPPORT In Vitro
"In KANSL1-deficient neurons, autophagosome accumulation at excitatory synapses resulted in reduced synaptic density, reduced GRIA/AMPA receptor-mediated transmission and impaired neuronal network activity."
Directly links autophagosome accumulation to synaptic and network dysfunction in a human neuronal model.

Pathograph

Use the checkboxes to hide or show graph categories. Hover nodes for evidence and cross-linked metadata.
Pathograph: causal mechanism network for Koolen-de Vries syndrome Interactive directed graph showing how pathophysiology mechanisms, phenotypes, genetic factors and variants, experimental models, environmental triggers, and treatments relate through causal and linked edges.

Phenotypes

7
Cardiovascular 1
Congenital heart defects FREQUENT Abnormal heart morphology (HP:0001627)
Show evidence (1 reference)
PMID:26306646 SUPPORT Human Clinical
"Other frequently reported features include social and friendly behaviour, epilepsy, musculoskeletal anomalies, congenital heart defects, urogenital malformations, and ectodermal anomalies."
Large cohort summary lists congenital heart defects among the recurrent multisystem manifestations.
Musculoskeletal 1
Hypotonia VERY_FREQUENT Hypotonia (HP:0001252)
Show evidence (1 reference)
PMID:18628315 SUPPORT Human Clinical
"Extensive clinical examination reveals that developmental delay, hypotonia, facial dysmorphisms including a long face, a tubular or pear-shaped nose and a bulbous nasal tip, and a friendly/amiable behaviour are the most characteristic features."
Founding syndrome series identifies hypotonia as one of the most characteristic findings.
Nervous System 4
Global developmental delay VERY_FREQUENT Global developmental delay (HP:0001263)
Show evidence (1 reference)
PMID:26306646 SUPPORT Human Clinical
"The Koolen-de Vries syndrome (KdVS; OMIM #610443), also known as the 17q21.31 microdeletion syndrome, is a clinically heterogeneous disorder characterised by (neonatal) hypotonia, developmental delay, moderate intellectual disability, and characteristic facial dysmorphism."
Large cohort summary identifies developmental delay as a defining syndrome feature.
Intellectual disability VERY_FREQUENT Intellectual disability (HP:0001249)
Show evidence (1 reference)
PMID:26306646 SUPPORT Human Clinical
"The Koolen-de Vries syndrome (KdVS; OMIM #610443), also known as the 17q21.31 microdeletion syndrome, is a clinically heterogeneous disorder characterised by (neonatal) hypotonia, developmental delay, moderate intellectual disability, and characteristic facial dysmorphism."
Large cohort summary identifies moderate intellectual disability as a core syndrome manifestation.
Seizures FREQUENT Seizure (HP:0001250)
Show evidence (1 reference)
PMID:28440867 SUPPORT Human Clinical
"The typical epilepsy phenotype of KdVS involves childhood-onset focal seizures that are prolonged and have prominent autonomic features."
Defines the characteristic seizure phenotype in a dedicated KdVS epilepsy cohort.
Abnormal corpus callosum morphology Abnormal corpus callosum morphology (HP:0001273)
Show evidence (1 reference)
PMID:28440867 SUPPORT Human Clinical
"Corpus callosum dysgenesis, abnormal hippocampi, and dilated ventricles were the most common"
Neuroimaging review in the KdVS epilepsy cohort identifies corpus callosum dysgenesis as a recurrent structural brain anomaly.
Other 1
Expressive language delay VERY_FREQUENT Expressive language delay (HP:0002474)
Show evidence (1 reference)
PMID:26306646 SUPPORT Human Clinical
"Expressive language development is particularly impaired compared with receptive language or motor skills."
Directly supports the characteristic disproportionate expressive-language deficit in KdVS.
🧬

Genetic Associations

1
KANSL1 (Causative)
Show evidence (2 references)
PMID:26306646 SUPPORT Human Clinical
"Comparison of the phenotype of both the microdeletion and SNV patients does not show differences of clinical importance, stressing that haploinsufficiency of KANSL1 is sufficient to cause the full KdVS phenotype."
Supports KANSL1 haploinsufficiency as sufficient across the major molecular classes of KdVS.
"KANSL1 | HGNC:24565 | Koolen-de Vries syndrome | MONDO:0012496 | AD | Definitive"
ClinGen classifies the KANSL1-Koolen-de Vries syndrome gene-disease relationship as definitive with autosomal dominant inheritance.
🔬

Biochemical Markers

1
Blood DNA methylation episignature (Positive)
Context: Diagnostic biomarker for molecular confirmation and missense/VUS classification
Show evidence (1 reference)
PMID:38282074 SUPPORT Human Clinical
"In this study, we identified a robust DNAm signature of 456 significant CpG sites in 8 individuals with KdVS, a pattern independently validated in an additional 7 individuals with KdVS."
Supports a reproducible blood DNA methylation signature as a diagnostic biomarker in KdVS.
{ }

Source YAML

click to show
name: Koolen-de Vries syndrome
creation_date: '2026-04-09T17:11:02Z'
updated_date: '2026-05-09T20:37:58Z'
category: Mendelian
description: >
  Koolen-de Vries syndrome is a multisystem neurodevelopmental disorder caused
  by KANSL1 haploinsufficiency, either through a recurrent 17q21.31
  microdeletion encompassing KANSL1 or a heterozygous pathogenic KANSL1
  variant. Core manifestations include hypotonia, global developmental delay,
  moderate intellectual disability, marked expressive language impairment, and a
  characteristic craniofacial and behavioral phenotype with additional
  structural brain, cardiac, urogenital, and musculoskeletal anomalies in a
  subset of affected individuals.
disease_term:
  preferred_term: Koolen-de Vries syndrome
  term:
    id: MONDO:0012496
    label: Koolen-de Vries syndrome
parents:
- Neurodevelopmental disorder
- Chromatin disorder
synonyms:
- KdVS
- 17q21.31 microdeletion syndrome
- KANSL1 haploinsufficiency syndrome
inheritance:
- name: Autosomal dominant inheritance
  inheritance_term:
    preferred_term: Autosomal dominant inheritance
    term:
      id: HP:0000006
      label: Autosomal dominant inheritance
  expressivity: VARIABLE
  description: >
    KdVS is caused by heterozygous loss of KANSL1 function, usually arising de
    novo through either a recurrent 17q21.31 deletion or a loss-of-function
    KANSL1 sequence variant.
  evidence:
  - reference: PMID:41457108
    reference_title: "Improving variant interpretation and diagnosis in Koolen-de Vries syndrome through a curated genotype-phenotype repository."
    supports: SUPPORT
    evidence_source: HUMAN_CLINICAL
    snippet: "(KdVS), an autosomal dominant NDD caused by KANSL1 haploinsufficiency"
    explanation: Supports autosomal dominant inheritance mediated by KANSL1 haploinsufficiency.
prevalence:
- population: Historically estimated general population prevalence
  percentage: ~1 in 16,000
  notes: >
    This estimate comes from early microdeletion ascertainment studies and is
    likely conservative because the syndrome was considered substantially
    underdiagnosed. True prevalence of all KANSL1-related molecular classes
    remains uncertain.
  evidence:
  - reference: PMID:18628315
    reference_title: "Clinical and molecular delineation of the 17q21.31 microdeletion syndrome."
    supports: SUPPORT
    evidence_source: HUMAN_CLINICAL
    snippet: "We estimate the prevalence of the syndrome to be 1 in 16,000 and show that it is highly underdiagnosed."
    explanation: Provides the widely cited historical prevalence estimate and explicitly notes underdiagnosis.
pathophysiology:
- name: KANSL1 haploinsufficiency
  description: >
    Heterozygous loss of KANSL1 is the core molecular lesion in KdVS. KANSL1 is
    a chromatin-associated regulator within the NSL complex, linking reduced
    dosage to altered chromatin organization and transcriptional control during
    brain development.
  genes:
  - preferred_term: KANSL1
    term:
      id: hgnc:24565
      label: KANSL1
  cell_types:
  - preferred_term: neuron
    term:
      id: CL:0000540
      label: neuron
  biological_processes:
  - preferred_term: chromatin organization
    term:
      id: GO:0006325
      label: chromatin organization
  - preferred_term: regulation of gene expression
    term:
      id: GO:0010468
      label: regulation of gene expression
    modifier: DECREASED
  locations:
  - preferred_term: brain
    term:
      id: UBERON:0000955
      label: brain
  downstream:
  - target: Autophagosome accumulation in KANSL1-deficient neurons
    description: Reduced KANSL1 dosage perturbs neuronal homeostatic programs that culminate in autophagosome accumulation.
  evidence:
  - reference: PMID:22544367
    reference_title: "Mutations in KANSL1 cause the 17q21.31 microdeletion syndrome phenotype."
    supports: SUPPORT
    evidence_source: HUMAN_CLINICAL
    snippet: "These findings indicate that 17q21.31 deletion syndrome is a monogenic disorder caused by haploinsufficiency of KANSL1."
    explanation: Establishes KANSL1 haploinsufficiency as the disease-defining mechanism.
  - reference: PMID:22544363
    reference_title: "Mutations in the chromatin modifier gene KANSL1 cause the 17q21.31 microdeletion syndrome."
    supports: SUPPORT
    evidence_source: HUMAN_CLINICAL
    snippet: "The KANSL1 protein is an evolutionarily conserved regulator of the chromatin modifier KAT8, which influences gene expression through histone H4 lysine 16 (H4K16) acetylation."
    explanation: Supports the chromatin and transcriptional regulatory role of KANSL1 underlying KdVS biology.
- name: Autophagosome accumulation in KANSL1-deficient neurons
  description: >
    In KANSL1-deficient human neurons, reduced SOD1 is associated with increased
    oxidative stress and subsequent autophagosome accumulation, including at
    excitatory synapses.
  genes:
  - preferred_term: KANSL1
    term:
      id: hgnc:24565
      label: KANSL1
  cell_types:
  - preferred_term: neuron
    term:
      id: CL:0000540
      label: neuron
  biological_processes:
  - preferred_term: autophagy
    term:
      id: GO:0006914
      label: autophagy
    modifier: INCREASED
  locations:
  - preferred_term: brain
    term:
      id: UBERON:0000955
      label: brain
  downstream:
  - target: Synaptic dysfunction in KANSL1-deficient neurons
    description: Autophagosome accumulation at excitatory synapses precedes impaired synaptic transmission and neuronal network activity.
  evidence:
  - reference: PMID:34286667
    reference_title: "Imbalanced autophagy causes synaptic deficits in a human model for neurodevelopmental disorders."
    supports: SUPPORT
    evidence_source: IN_VITRO
    snippet: "we identified SOD1 (superoxide dismutase 1), an antioxidant enzyme, to be significantly decreased, leading to a subsequent increase in oxidative stress and autophagosome accumulation."
    explanation: Supports oxidative-stress-associated autophagy imbalance in KANSL1-deficient neurons.
- name: Synaptic dysfunction in KANSL1-deficient neurons
  description: >
    Autophagosome accumulation at excitatory synapses in KANSL1-deficient
    neurons is associated with reduced synaptic density, decreased AMPA
    receptor-mediated transmission, and impaired neuronal network activity.
  genes:
  - preferred_term: KANSL1
    term:
      id: hgnc:24565
      label: KANSL1
  cell_types:
  - preferred_term: neuron
    term:
      id: CL:0000540
      label: neuron
  biological_processes:
  - preferred_term: chemical synaptic transmission
    term:
      id: GO:0007268
      label: chemical synaptic transmission
    modifier: DECREASED
  locations:
  - preferred_term: brain
    term:
      id: UBERON:0000955
      label: brain
  evidence:
  - reference: PMID:34286667
    reference_title: "Imbalanced autophagy causes synaptic deficits in a human model for neurodevelopmental disorders."
    supports: SUPPORT
    evidence_source: IN_VITRO
    snippet: "In KANSL1-deficient neurons, autophagosome accumulation at excitatory synapses resulted in reduced synaptic density, reduced GRIA/AMPA receptor-mediated transmission and impaired neuronal network activity."
    explanation: Directly links autophagosome accumulation to synaptic and network dysfunction in a human neuronal model.
phenotypes:
- category: Cognitive
  name: Global developmental delay
  frequency: VERY_FREQUENT
  diagnostic: true
  description: >
    Global developmental delay is a core and usually early-recognized feature of
    KdVS.
  phenotype_term:
    preferred_term: Global developmental delay
    term:
      id: HP:0001263
      label: Global developmental delay
  evidence:
  - reference: PMID:26306646
    reference_title: "The Koolen-de Vries syndrome: a phenotypic comparison of patients with a 17q21.31 microdeletion versus a KANSL1 sequence variant."
    supports: SUPPORT
    evidence_source: HUMAN_CLINICAL
    snippet: "The Koolen-de Vries syndrome (KdVS; OMIM #610443), also known as the 17q21.31 microdeletion syndrome, is a clinically heterogeneous disorder characterised by (neonatal) hypotonia, developmental delay, moderate intellectual disability, and characteristic facial dysmorphism."
    explanation: Large cohort summary identifies developmental delay as a defining syndrome feature.
- category: Cognitive
  name: Intellectual disability
  frequency: VERY_FREQUENT
  diagnostic: true
  description: >
    Intellectual disability is typically moderate but varies across affected
    individuals.
  phenotype_term:
    preferred_term: Intellectual disability
    term:
      id: HP:0001249
      label: Intellectual disability
  evidence:
  - reference: PMID:26306646
    reference_title: "The Koolen-de Vries syndrome: a phenotypic comparison of patients with a 17q21.31 microdeletion versus a KANSL1 sequence variant."
    supports: SUPPORT
    evidence_source: HUMAN_CLINICAL
    snippet: "The Koolen-de Vries syndrome (KdVS; OMIM #610443), also known as the 17q21.31 microdeletion syndrome, is a clinically heterogeneous disorder characterised by (neonatal) hypotonia, developmental delay, moderate intellectual disability, and characteristic facial dysmorphism."
    explanation: Large cohort summary identifies moderate intellectual disability as a core syndrome manifestation.
- category: Neurologic
  name: Hypotonia
  frequency: VERY_FREQUENT
  diagnostic: true
  description: >
    Hypotonia is usually evident from infancy and is among the most recognizable
    early clinical findings.
  phenotype_term:
    preferred_term: Hypotonia
    term:
      id: HP:0001252
      label: Hypotonia
  evidence:
  - reference: PMID:18628315
    reference_title: "Clinical and molecular delineation of the 17q21.31 microdeletion syndrome."
    supports: SUPPORT
    evidence_source: HUMAN_CLINICAL
    snippet: "Extensive clinical examination reveals that developmental delay, hypotonia, facial dysmorphisms including a long face, a tubular or pear-shaped nose and a bulbous nasal tip, and a friendly/amiable behaviour are the most characteristic features."
    explanation: Founding syndrome series identifies hypotonia as one of the most characteristic findings.
- category: Communication
  name: Expressive language delay
  frequency: VERY_FREQUENT
  description: >
    Expressive language is disproportionately impaired relative to receptive
    language and motor development.
  phenotype_term:
    preferred_term: Expressive language delay
    term:
      id: HP:0002474
      label: Expressive language delay
  evidence:
  - reference: PMID:26306646
    reference_title: "The Koolen-de Vries syndrome: a phenotypic comparison of patients with a 17q21.31 microdeletion versus a KANSL1 sequence variant."
    supports: SUPPORT
    evidence_source: HUMAN_CLINICAL
    snippet: "Expressive language development is particularly impaired compared with receptive language or motor skills."
    explanation: Directly supports the characteristic disproportionate expressive-language deficit in KdVS.
- category: Neurologic
  name: Seizures
  frequency: FREQUENT
  description: >
    Epilepsy commonly begins in childhood and often features prolonged focal
    seizures with autonomic features.
  phenotype_term:
    preferred_term: Seizure
    term:
      id: HP:0001250
      label: Seizure
  evidence:
  - reference: PMID:28440867
    reference_title: "The epileptology of Koolen-de Vries syndrome: Electro-clinico-radiologic findings in 31 patients."
    supports: SUPPORT
    evidence_source: HUMAN_CLINICAL
    snippet: "The typical epilepsy phenotype of KdVS involves childhood-onset focal seizures that are prolonged and have prominent autonomic features."
    explanation: Defines the characteristic seizure phenotype in a dedicated KdVS epilepsy cohort.
- category: Cardiovascular
  name: Congenital heart defects
  frequency: FREQUENT
  description: >
    Structural heart defects are part of the recurrent multisystem anomaly
    spectrum in KdVS.
  phenotype_term:
    preferred_term: Congenital heart defect
    term:
      id: HP:0001627
      label: Abnormal heart morphology
  evidence:
  - reference: PMID:26306646
    reference_title: "The Koolen-de Vries syndrome: a phenotypic comparison of patients with a 17q21.31 microdeletion versus a KANSL1 sequence variant."
    supports: SUPPORT
    evidence_source: HUMAN_CLINICAL
    snippet: "Other frequently reported features include social and friendly behaviour, epilepsy, musculoskeletal anomalies, congenital heart defects, urogenital malformations, and ectodermal anomalies."
    explanation: Large cohort summary lists congenital heart defects among the recurrent multisystem manifestations.
- category: Structural
  name: Abnormal corpus callosum morphology
  description: >
    Structural brain anomalies, including corpus callosum dysgenesis, are
    common on neuroimaging in the epilepsy-enriched KdVS cohort.
  phenotype_term:
    preferred_term: Abnormal corpus callosum morphology
    term:
      id: HP:0001273
      label: Abnormal corpus callosum morphology
  evidence:
  - reference: PMID:28440867
    reference_title: "The epileptology of Koolen-de Vries syndrome: Electro-clinico-radiologic findings in 31 patients."
    supports: SUPPORT
    evidence_source: HUMAN_CLINICAL
    snippet: "Corpus callosum dysgenesis, abnormal hippocampi, and dilated ventricles were the most common"
    explanation: Neuroimaging review in the KdVS epilepsy cohort identifies corpus callosum dysgenesis as a recurrent structural brain anomaly.
genetic:
- name: KANSL1
  gene_term:
    preferred_term: KANSL1
    term:
      id: hgnc:24565
      label: KANSL1
  association: Causative
  notes: >
    Heterozygous loss of KANSL1 function, whether from a recurrent 17q21.31
    deletion or a pathogenic sequence variant, is sufficient to cause the full
    KdVS phenotype. Clinically important phenotypic differences between
    microdeletion and sequence-variant cases have not been established.
  evidence:
  - reference: PMID:26306646
    reference_title: "The Koolen-de Vries syndrome: a phenotypic comparison of patients with a 17q21.31 microdeletion versus a KANSL1 sequence variant."
    supports: SUPPORT
    evidence_source: HUMAN_CLINICAL
    snippet: "Comparison of the phenotype of both the microdeletion and SNV patients does not show differences of clinical importance, stressing that haploinsufficiency of KANSL1 is sufficient to cause the full KdVS phenotype."
    explanation: Supports KANSL1 haploinsufficiency as sufficient across the major molecular classes of KdVS.
  - reference: CGGV:assertion_e89a0e87-314a-49b1-bb50-6b26aeaa1037-2022-02-18T120936.714Z
    reference_title: "KANSL1 / Koolen-de Vries syndrome (Definitive)"
    supports: SUPPORT
    evidence_source: OTHER
    snippet: "KANSL1 | HGNC:24565 | Koolen-de Vries syndrome | MONDO:0012496 | AD | Definitive"
    explanation: ClinGen classifies the KANSL1-Koolen-de Vries syndrome gene-disease relationship as definitive with autosomal dominant inheritance.
biochemical:
- name: Blood DNA methylation episignature
  presence: Positive
  context: Diagnostic biomarker for molecular confirmation and missense/VUS classification
  notes: >
    Whole-blood DNA methylation profiling identifies a reproducible KdVS
    episignature that can support diagnosis and variant interpretation in the
    structurally complex KANSL1 region.
  evidence:
  - reference: PMID:38282074
    reference_title: "A new blood DNA methylation signature for Koolen-de Vries syndrome: Classification of missense KANSL1 variants and comparison to fibroblast cells."
    supports: SUPPORT
    evidence_source: HUMAN_CLINICAL
    snippet: "In this study, we identified a robust DNAm signature of 456 significant CpG sites in 8 individuals with KdVS, a pattern independently validated in an additional 7 individuals with KdVS."
    explanation: Supports a reproducible blood DNA methylation signature as a diagnostic biomarker in KdVS.
treatments: []
references:
- reference: DOI:10.1002/ajmg.a.62008
  title: 'Koolen‐de Vries syndrome: First report of two unrelated Indian patients'
  found_in:
  - Koolen_de_Vries_syndrome-deep-research-falcon.md
  findings:
  - statement: Koolen‐de Vries syndrome is a recurrent microdeletion syndrome caused due to deletion of around 400–600 kb region at 17q21.31.
    supporting_text: Koolen‐de Vries syndrome is a recurrent microdeletion syndrome caused due to deletion of around 400–600 kb region at 17q21.31.
    evidence:
    - reference: DOI:10.1002/ajmg.a.62008
      reference_title: 'Koolen‐de Vries syndrome: First report of two unrelated Indian patients'
      supports: SUPPORT
      evidence_source: HUMAN_CLINICAL
      snippet: Koolen‐de Vries syndrome is a recurrent microdeletion syndrome caused due to deletion of around 400–600 kb region at 17q21.31.
      explanation: Deep research cited this publication as relevant literature for Koolen de Vries syndrome.
- reference: DOI:10.1002/ajmg.a.62536
  title: 'Koolen‐de Vries syndrome in a 63‐year‐old woman: Report of the oldest patient and a review of the adult phenotype'
  found_in:
  - Koolen_de_Vries_syndrome-deep-research-falcon.md
  findings:
  - statement: Koolen‐de Vries syndrome (KdVS) is a rare genetic disorder caused by a de novo microdeletion in chromosomal region 17q21.31 encompassing KANSL1 or by a de novo intragenic pathogenic variant of KANSL1.
    supporting_text: Koolen‐de Vries syndrome (KdVS) is a rare genetic disorder caused by a de novo microdeletion in chromosomal region 17q21.31 encompassing KANSL1 or by a de novo intragenic pathogenic variant of KANSL1.
    evidence:
    - reference: DOI:10.1002/ajmg.a.62536
      reference_title: 'Koolen‐de Vries syndrome in a 63‐year‐old woman: Report of the oldest patient and a review of the adult phenotype'
      supports: SUPPORT
      evidence_source: HUMAN_CLINICAL
      snippet: Koolen‐de Vries syndrome (KdVS) is a rare genetic disorder caused by a de novo microdeletion in chromosomal region 17q21.31 encompassing KANSL1 or by a de novo intragenic pathogenic variant of KANSL1.
      explanation: Deep research cited this publication as relevant literature for Koolen de Vries syndrome.
- reference: DOI:10.1016/j.gimo.2023.100817
  title: GenIDA, a participatory patient registry for genetic forms of intellectual disability provides detailed caregiver-reported information on 237 individuals with Koolen-de Vries syndrome
  found_in:
  - Koolen_de_Vries_syndrome-deep-research-falcon.md
  findings:
  - statement: GenIDA, a participatory patient registry for genetic forms of intellectual disability provides detailed caregiver-reported information on 237 individuals with Koolen-de Vries syndrome
    supporting_text: GenIDA, a participatory patient registry for genetic forms of intellectual disability provides detailed caregiver-reported information on 237 individuals with Koolen-de Vries syndrome
- reference: DOI:10.1038/s41431-022-01230-7
  title: 'Expanding the speech and language phenotype in Koolen-de Vries syndrome: late onset and periodic stuttering a novel feature'
  found_in:
  - Koolen_de_Vries_syndrome-deep-research-falcon.md
  findings:
  - statement: 'Expanding the speech and language phenotype in Koolen-de Vries syndrome: late onset and periodic stuttering a novel feature'
    supporting_text: 'Expanding the speech and language phenotype in Koolen-de Vries syndrome: late onset and periodic stuttering a novel feature'
- reference: DOI:10.1038/s41431-024-01538-6
  title: 'A new blood DNA methylation signature for Koolen-de Vries syndrome: Classification of missense KANSL1 variants and comparison to fibroblast cells'
  found_in:
  - Koolen_de_Vries_syndrome-deep-research-falcon.md
  findings:
  - statement: 'A new blood DNA methylation signature for Koolen-de Vries syndrome: Classification of missense KANSL1 variants and comparison to fibroblast cells'
    supporting_text: 'A new blood DNA methylation signature for Koolen-de Vries syndrome: Classification of missense KANSL1 variants and comparison to fibroblast cells'
- reference: DOI:10.1038/s41467-022-28613-0
  title: Kansl1 haploinsufficiency impairs autophagosome-lysosome fusion and links autophagic dysfunction with Koolen-de Vries syndrome in mice
  found_in:
  - Koolen_de_Vries_syndrome-deep-research-falcon.md
  findings:
  - statement: Koolen-de Vries syndrome (KdVS) is a rare disorder caused by haploinsufficiency of KAT8 regulatory NSL complex subunit 1 (KANSL1), which is characterized by intellectual disability, heart failure, hypotonia, and congenital malformations.
    supporting_text: Koolen-de Vries syndrome (KdVS) is a rare disorder caused by haploinsufficiency of KAT8 regulatory NSL complex subunit 1 (KANSL1), which is characterized by intellectual disability, heart failure, hypotonia, and congenital malformations.
    evidence:
    - reference: DOI:10.1038/s41467-022-28613-0
      reference_title: Kansl1 haploinsufficiency impairs autophagosome-lysosome fusion and links autophagic dysfunction with Koolen-de Vries syndrome in mice
      supports: SUPPORT
      evidence_source: MODEL_ORGANISM
      snippet: Koolen-de Vries syndrome (KdVS) is a rare disorder caused by haploinsufficiency of KAT8 regulatory NSL complex subunit 1 (KANSL1), which is characterized by intellectual disability, heart failure, hypotonia, and congenital malformations.
      explanation: Deep research cited this publication as relevant literature for Koolen de Vries syndrome.
- reference: DOI:10.1080/13816810.2020.1868012
  title: Ocular manifestations and surgical interventions in pediatric patients with Koolen-de-Vries syndrome
  found_in:
  - Koolen_de_Vries_syndrome-deep-research-falcon.md
  findings:
  - statement: Ocular manifestations and surgical interventions in pediatric patients with Koolen-de-Vries syndrome
    supporting_text: Ocular manifestations and surgical interventions in pediatric patients with Koolen-de-Vries syndrome
- reference: DOI:10.1080/15548627.2021.1936777
  title: Imbalanced autophagy causes synaptic deficits in a human model for neurodevelopmental disorders
  found_in:
  - Koolen_de_Vries_syndrome-deep-research-falcon.md
  findings:
  - statement: Imbalanced autophagy causes synaptic deficits in a human model for neurodevelopmental disorders
    supporting_text: Imbalanced autophagy causes synaptic deficits in a human model for neurodevelopmental disorders
- reference: DOI:10.1177/26330040241265414
  title: 'Koolen-de Vries Syndrome: a journey from diagnosis to treatments'
  found_in:
  - Koolen_de_Vries_syndrome-deep-research-falcon.md
  findings:
  - statement: The Koolen-de Vries Syndrome Foundation was founded in 2013 with the mission to educate, increase awareness, promote research and develop treatments for individuals living with Koolen-de Vries Syndrome (KdVS) and their families.
    supporting_text: The Koolen-de Vries Syndrome Foundation was founded in 2013 with the mission to educate, increase awareness, promote research and develop treatments for individuals living with Koolen-de Vries Syndrome (KdVS) and their families.
    evidence:
    - reference: DOI:10.1177/26330040241265414
      reference_title: 'Koolen-de Vries Syndrome: a journey from diagnosis to treatments'
      supports: SUPPORT
      evidence_source: HUMAN_CLINICAL
      snippet: The Koolen-de Vries Syndrome Foundation was founded in 2013 with the mission to educate, increase awareness, promote research and develop treatments for individuals living with Koolen-de Vries Syndrome (KdVS) and their families.
      explanation: Deep research cited this publication as relevant literature for Koolen de Vries syndrome.
- reference: DOI:10.7759/cureus.79194
  title: 'Neuroimaging of Koolen-De Vries Syndrome: A Rare Genetic Disorder'
  found_in:
  - Koolen_de_Vries_syndrome-deep-research-falcon.md
  findings:
  - statement: 'Neuroimaging of Koolen-De Vries Syndrome: A Rare Genetic Disorder'
    supporting_text: 'Neuroimaging of Koolen-De Vries Syndrome: A Rare Genetic Disorder'
📚

References & Deep Research

References

10
Koolen‐de Vries syndrome: First report of two unrelated Indian patients
1 finding
Koolen‐de Vries syndrome is a recurrent microdeletion syndrome caused due to deletion of around 400–600 kb region at 17q21.31.
"Koolen‐de Vries syndrome is a recurrent microdeletion syndrome caused due to deletion of around 400–600 kb region at 17q21.31."
Show evidence (1 reference)
DOI:10.1002/ajmg.a.62008 SUPPORT Human Clinical
"Koolen‐de Vries syndrome is a recurrent microdeletion syndrome caused due to deletion of around 400–600 kb region at 17q21.31."
Deep research cited this publication as relevant literature for Koolen de Vries syndrome.
Koolen‐de Vries syndrome in a 63‐year‐old woman: Report of the oldest patient and a review of the adult phenotype
1 finding
Koolen‐de Vries syndrome (KdVS) is a rare genetic disorder caused by a de novo microdeletion in chromosomal region 17q21.31 encompassing KANSL1 or by a de novo intragenic pathogenic variant of KANSL1.
"Koolen‐de Vries syndrome (KdVS) is a rare genetic disorder caused by a de novo microdeletion in chromosomal region 17q21.31 encompassing KANSL1 or by a de novo intragenic pathogenic variant of KANSL1."
Show evidence (1 reference)
DOI:10.1002/ajmg.a.62536 SUPPORT Human Clinical
"Koolen‐de Vries syndrome (KdVS) is a rare genetic disorder caused by a de novo microdeletion in chromosomal region 17q21.31 encompassing KANSL1 or by a de novo intragenic pathogenic variant of KANSL1."
Deep research cited this publication as relevant literature for Koolen de Vries syndrome.
GenIDA, a participatory patient registry for genetic forms of intellectual disability provides detailed caregiver-reported information on 237 individuals with Koolen-de Vries syndrome
1 finding
GenIDA, a participatory patient registry for genetic forms of intellectual disability provides detailed caregiver-reported information on 237 individuals with Koolen-de Vries syndrome
"GenIDA, a participatory patient registry for genetic forms of intellectual disability provides detailed caregiver-reported information on 237 individuals with Koolen-de Vries syndrome"
Expanding the speech and language phenotype in Koolen-de Vries syndrome: late onset and periodic stuttering a novel feature
1 finding
Expanding the speech and language phenotype in Koolen-de Vries syndrome: late onset and periodic stuttering a novel feature
"Expanding the speech and language phenotype in Koolen-de Vries syndrome: late onset and periodic stuttering a novel feature"
A new blood DNA methylation signature for Koolen-de Vries syndrome: Classification of missense KANSL1 variants and comparison to fibroblast cells
1 finding
A new blood DNA methylation signature for Koolen-de Vries syndrome: Classification of missense KANSL1 variants and comparison to fibroblast cells
"A new blood DNA methylation signature for Koolen-de Vries syndrome: Classification of missense KANSL1 variants and comparison to fibroblast cells"
Kansl1 haploinsufficiency impairs autophagosome-lysosome fusion and links autophagic dysfunction with Koolen-de Vries syndrome in mice
1 finding
Koolen-de Vries syndrome (KdVS) is a rare disorder caused by haploinsufficiency of KAT8 regulatory NSL complex subunit 1 (KANSL1), which is characterized by intellectual disability, heart failure, hypotonia, and congenital malformations.
"Koolen-de Vries syndrome (KdVS) is a rare disorder caused by haploinsufficiency of KAT8 regulatory NSL complex subunit 1 (KANSL1), which is characterized by intellectual disability, heart failure, hypotonia, and congenital malformations."
Show evidence (1 reference)
DOI:10.1038/s41467-022-28613-0 SUPPORT Model Organism
"Koolen-de Vries syndrome (KdVS) is a rare disorder caused by haploinsufficiency of KAT8 regulatory NSL complex subunit 1 (KANSL1), which is characterized by intellectual disability, heart failure, hypotonia, and congenital malformations."
Deep research cited this publication as relevant literature for Koolen de Vries syndrome.
Ocular manifestations and surgical interventions in pediatric patients with Koolen-de-Vries syndrome
1 finding
Ocular manifestations and surgical interventions in pediatric patients with Koolen-de-Vries syndrome
"Ocular manifestations and surgical interventions in pediatric patients with Koolen-de-Vries syndrome"
Imbalanced autophagy causes synaptic deficits in a human model for neurodevelopmental disorders
1 finding
Imbalanced autophagy causes synaptic deficits in a human model for neurodevelopmental disorders
"Imbalanced autophagy causes synaptic deficits in a human model for neurodevelopmental disorders"
Koolen-de Vries Syndrome: a journey from diagnosis to treatments
1 finding
The Koolen-de Vries Syndrome Foundation was founded in 2013 with the mission to educate, increase awareness, promote research and develop treatments for individuals living with Koolen-de Vries Syndrome (KdVS) and their families.
"The Koolen-de Vries Syndrome Foundation was founded in 2013 with the mission to educate, increase awareness, promote research and develop treatments for individuals living with Koolen-de Vries Syndrome (KdVS) and their families."
Show evidence (1 reference)
DOI:10.1177/26330040241265414 SUPPORT Human Clinical
"The Koolen-de Vries Syndrome Foundation was founded in 2013 with the mission to educate, increase awareness, promote research and develop treatments for individuals living with Koolen-de Vries Syndrome (KdVS) and their families."
Deep research cited this publication as relevant literature for Koolen de Vries syndrome.
Neuroimaging of Koolen-De Vries Syndrome: A Rare Genetic Disorder
1 finding
Neuroimaging of Koolen-De Vries Syndrome: A Rare Genetic Disorder
"Neuroimaging of Koolen-De Vries Syndrome: A Rare Genetic Disorder"

Deep Research

1
Falcon
1. Disease Information
Edison Scientific Literature 38 citations 2026-05-09T10:07:48.243912

1. Disease Information

1.1 Concise overview (current understanding)

Koolen–de Vries syndrome is a rare, multisystem neurodevelopmental disorder caused by either a recurrent 17q21.31 microdeletion that includes KANSL1 or by a heterozygous intragenic pathogenic variant in KANSL1. Core features across cohorts include developmental delay, hypotonia, intellectual disability (often moderate), speech/language disorder, and frequent multisystem comorbidities (cardiac, renal/urogenital, musculoskeletal, sensory, sleep, and behavioral features). (colin2023genidaaparticipatory pages 2-3, houser2025neuroimagingofkoolende pages 2-8)

1.2 Key identifiers

  • OMIM: 610443 (colin2023genidaaparticipatory pages 2-3)
  • Orphanet / ICD-10/ICD-11 / MeSH / MONDO: Not retrievable from the provided full-text evidence in this run (see “Evidence gaps”).

1.3 Synonyms and alternative names

Commonly used synonyms in the clinical literature include: - 17q21.31 microdeletion syndrome (farne2022koolen‐devriessyndrome pages 10-12) - KANSL1-related intellectual disability syndrome (farne2022koolen‐devriessyndrome pages 10-12)

1.4 Evidence source types

The report integrates: - Aggregated disease-level resources via cohorts/registries: e.g., GenIDA caregiver-reported cohort (n=237) (colin2023genidaaparticipatory pages 3-4) - Clinician-assessed cohort study: large speech/language and medical phenotype cohort (n=81) (john2023expandingthespeech pages 2-2) - Primary mechanistic studies: mouse model and human iPSC-derived neuronal models (li2022kansl1haploinsufficiencyimpairs pages 1-2, linda2022imbalancedautophagycauses pages 1-3)


2. Etiology

2.1 Disease causal factors

KdVS is a genetic disorder caused by KANSL1 haploinsufficiency, either from: - a 17q21.31 deletion including KANSL1, or - a heterozygous pathogenic variant in KANSL1 (houser2025neuroimagingofkoolende pages 2-8, colin2023genidaaparticipatory pages 2-3)

2.2 Risk factors

  • Primary genetic risk factor: de novo heterozygous 17q21.31 deletion or de novo heterozygous pathogenic KANSL1 variant (autosomal dominant) (houser2025neuroimagingofkoolende pages 2-8, saxena2021koolen‐devriessyndrome pages 2-4)
  • Environmental risk factors / protective factors / gene–environment interactions: No KdVS-specific evidence identified in the retrieved texts.

2.3 Inheritance

KdVS is described as autosomal dominant, typically arising de novo (houser2025neuroimagingofkoolende pages 2-8, saxena2021koolen‐devriessyndrome pages 2-4).


3. Phenotypes (with frequencies, onset, and suggested HPO terms)

3.1 Summary of highest-yield phenotypes (recent large cohorts)

Two major recent data sources provide quantitative phenotype frequencies: - GenIDA caregiver registry (n=237; mean age 14.0 years; 116 males/121 females) (colin2023genidaaparticipatory pages 3-4) - St John et al. 2023 clinical cohort (n=81; mean age 9y10mo; age range 1.5–40.2y) (john2023expandingthespeech pages 2-2)

Neurodevelopmental

  • Developmental delay: 96.3% (78/81) (john2023expandingthespeech pages 2-2)
  • Suggested HPO: Global developmental delay (HP:0001263)
  • Intellectual disability (ID): 89.2% (GenIDA); severity distribution: mild 16.9%, moderate 60.2%, severe 2.4%, profound 20.5% (colin2023genidaaparticipatory pages 3-4)
  • Suggested HPO: Intellectual disability (HP:0001249)
  • Hypotonia: 61.5% (colin2023genidaaparticipatory pages 3-4)
  • Suggested HPO: Hypotonia (HP:0001252)

Speech/language and communication

  • Speech/language delay: 73.6% in children >2y; first words mean 2.2 years (colin2023genidaaparticipatory pages 3-4)
  • Suggested HPO: Speech delay (HP:0000750), Delayed speech and language development (HP:0000750 / HP:0000750-related)
  • Motor speech disorders (verbal subgroup): apraxia features 63.9% (39/61); dysarthria 45.9% (28/61) (john2023expandingthespeech pages 1-2)
  • Suggested HPO: Childhood apraxia of speech (HP:0002465), Dysarthria (HP:0001260)
  • Stuttering: 76.6% of verbal participants (36/47), described as late-onset and fluctuating (john2023expandingthespeech pages 1-2)
  • Suggested HPO: Stuttering (HP:0000755)
  • AAC use (implementation): Minimally verbal communicators used AAC successfully; early AAC recommended (john2023expandingthespeech pages 1-2)

Epilepsy and seizures

  • Epilepsy prevalence: 47.3% (97/204) in GenIDA (colin2023genidaaparticipatory pages 6-7) vs 35.8% (29/81) in St John et al. cohort (john2023expandingthespeech pages 2-2)
  • Suggested HPO: Seizure (HP:0001250), Epilepsy (HP:0001250)
  • Age at first seizure: mean 3.4 years; median 2.0 years (colin2023genidaaparticipatory pages 7-9)
  • Seizure-type distribution among epilepsy cases: tonic-clonic 38.1%, absence 28.9%, complex partial 22.7%, nocturnal 21.6%, febrile convulsions 19.6%, infantile spasms 14.4%, atonic 9.3% (colin2023genidaaparticipatory pages 6-7)

Motor development / musculoskeletal

  • Motor milestone delays (GenIDA median): sit 10.7 mo; stand 17.5 mo; walk 23.4 mo (colin2023genidaaparticipatory pages 3-4)
  • Suggested HPO: Delayed gross motor development (HP:0002194)
  • Musculoskeletal anomalies: 75.5% overall; joint laxity 50.0%; scoliosis 25.5%; hip dysplasia/dislocation 18.0%; pes planus 22.0% (colin2023genidaaparticipatory pages 7-9, colin2023genidaaparticipatory pages 3-4)
  • Suggested HPO: Joint hypermobility (HP:0001382), Scoliosis (HP:0002650), Developmental dysplasia of the hip (HP:0001374), Pes planus (HP:0001763)

Congenital anomalies and organ involvement

  • Cardiac defects: ASD 18.9%; VSD 10.9% (GenIDA) (colin2023genidaaparticipatory pages 3-4)
  • Suggested HPO: Atrial septal defect (HP:0001631), Ventricular septal defect (HP:0001629)
  • Renal/urogenital issues: ~38.3%; male cryptorchidism 22.6% (GenIDA) and 45.7% among males in St John cohort (colin2023genidaaparticipatory pages 3-4, john2023expandingthespeech pages 2-2)
  • Suggested HPO: Cryptorchidism (HP:0000028)

Sleep, dental, sensory, behavior

  • Sleep disorders: 42.6% (GenIDA) and 40.7% (St John cohort) (colin2023genidaaparticipatory pages 3-4, john2023expandingthespeech pages 2-2)
  • Suggested HPO: Sleep disturbance (HP:0002360)
  • Dental problems: 65.1% (GenIDA); 50% (36/72) in St John cohort (colin2023genidaaparticipatory pages 3-4, john2023expandingthespeech pages 2-2)
  • Suggested HPO: Abnormality of dentition (HP:0006482)
  • Vision/hearing: hypermetropia 38.8%, strabismus 34.7%, hearing problems 40.8% (colin2023genidaaparticipatory pages 6-7)
  • Suggested HPO: Hyperopia (HP:0000540), Strabismus (HP:0000486), Hearing impairment (HP:0000365)
  • Behavior: behavioral problems 54.8%; repetitive behaviors 35.2%; attention deficit 32.7%; anxiety 31.2%; hyperactivity 27.6%; sociability high with familiar adults 98.1% and children 88.6% (colin2023genidaaparticipatory pages 6-7)
  • Suggested HPO: Stereotypy (HP:0000733), Attention deficit hyperactivity disorder (HP:0007018), Anxiety (HP:0000739)

3.2 Quality of life and adaptive function

The 2023 speech/language cohort reported relative strengths in social competence and behavioral/emotional control, but communication difficulties impacted daily living skills (john2023expandingthespeech pages 1-2).


4. Genetic/Molecular Information

4.1 Causal gene(s)

  • KANSL1 (haploinsufficiency) is central to KdVS pathogenesis; causal by deletion or intragenic variant (colin2023genidaaparticipatory pages 2-3, houser2025neuroimagingofkoolende pages 2-8).

4.2 Variant spectrum (examples and classes)

  • Recurrent CNV: typical 500–650 kb 17q21.31 deletion (houser2025neuroimagingofkoolende pages 2-8, john2023expandingthespeech pages 2-2)
  • Intragenic KANSL1 variants: predominately truncating/frameshift/splice; exon deletions also observed in a large cohort (john2023expandingthespeech pages 3-4)
  • Missense/VUS interpretation: 2024 episignature work provides a framework for classifying missense variants (p.Thr887Met vs p.Gly900Glu) using blood methylation signatures (awamleh2024anewblood pages 3-5)

4.3 Genotype–phenotype correlations

  • Large cohorts reported no significant clinical differences between 17q21.31 deletion and KANSL1 intragenic variant groups (colin2023genidaaparticipatory pages 2-3, john2023expandingthespeech pages 3-4).

4.4 Epigenetic information (2024–key development)

A 2024 European Journal of Human Genetics study identified a blood DNA methylation episignature of 456 CpG sites for KdVS and used an SVM classifier to support diagnosis and classify KANSL1 VUS (awamleh2024anewblood pages 1-2, awamleh2024anewblood pages 2-3).


5. Environmental Information

No specific environmental contributors, protective factors, or infectious triggers were supported by the retrieved KdVS-focused evidence.


6. Mechanism / Pathophysiology

6.1 Core mechanistic chain (evidence-backed)

KANSL1 haploinsufficiency → dysregulated chromatin/NSL complex function and H4K16 acetylation → transcriptional dysregulation of autophagy machinery and cellular homeostasis → oxidative stress, impaired lysosomal/autophagic clearance and synaptic dysfunction → neurodevelopmental phenotype; plus cardiac dysfunction in mouse models. (linda2022imbalancedautophagycauses pages 1-3, li2022kansl1haploinsufficiencyimpairs pages 1-2)

6.2 Autophagy/lysosome and oxidative stress (human neuronal models)

In KANSL1-deficient human iPSC-derived neurons, decreased SOD1 leads to increased oxidative stress and autophagosome accumulation; autophagosomes accumulate at excitatory synapses with reduced synaptic density and reduced AMPA receptor-mediated transmission, impairing network activity. Antioxidant/oxidative stress reduction rescued autophagosomes and neuronal function. (linda2022imbalancedautophagycauses pages 1-3)

Direct abstract quotes (primary literature): - “In KANSL1-deficient neurons, autophagosome accumulation at excitatory synapses resulted in reduced synaptic density, reduced GRIA/AMPA receptor-mediated transmission and impaired neuronal network activity.” (linda2022imbalancedautophagycauses pages 1-3) - “By pharmacologically reducing oxidative stress, we could rescue the aberrant autophagosome formation as well as synaptic and neuronal network activity in KANSL1-deficient neurons.” (linda2022imbalancedautophagycauses pages 1-3)

6.3 Autophagosome–lysosome fusion and mitophagy (mouse model)

A Nature Communications mouse study identified KANSL1 as essential for autophagy and showed KANSL1 modulates autophagosome–lysosome fusion via transcriptional regulation of STX17. Kansl1+/− mice show impaired clearance of damaged mitochondria, increased ROS, and neuronal/cardiac dysfunction; 13-cis retinoic acid reversed mitophagic defects and neurobehavioral abnormalities. (li2022kansl1haploinsufficiencyimpairs pages 1-2)

6.4 Suggested ontology terms

  • GO Biological Process (examples): autophagy (GO:0006914), mitophagy (GO:0000422), autophagosome maturation (GO:0097352), lysosome organization (GO:0007040), oxidative stress response (GO:0006979), synapse organization (GO:0050808)
  • Cell Ontology (CL) (examples): excitatory neuron (CL:0008030), neural progenitor cell (CL:0000047), cardiomyocyte (CL:0000746)
  • UBERON (examples): brain (UBERON:0000955), hippocampus (UBERON:0001954), heart (UBERON:0000948)

7. Anatomical Structures Affected

From cohort data, the primary impacted system is the nervous system, with frequent multisystem involvement: - CNS/neurodevelopment: developmental delay, ID, seizures; imaging anomalies in a subset (john2023expandingthespeech pages 2-2) - Cardiac: ASD/VSD and other defects in substantial fractions (colin2023genidaaparticipatory pages 3-4, john2023expandingthespeech pages 2-2) - Renal/urogenital: relatively common (colin2023genidaaparticipatory pages 3-4) - Musculoskeletal: hypermobility/scoliosis, etc. (colin2023genidaaparticipatory pages 7-9)


8. Temporal Development

  • Onset: typically congenital/early childhood, reflected in early hypotonia and feeding difficulties (colin2023genidaaparticipatory pages 3-4)
  • Motor milestone timing (median): sitting 10.7 mo, standing 17.5 mo, walking 23.4 mo (colin2023genidaaparticipatory pages 3-4)
  • Seizure onset: mean 3.4y; median 2.0y (colin2023genidaaparticipatory pages 7-9)
  • Developmental course: registry modeling indicates positive trajectory for speech/language and relatively good reading ability over time (colin2023genidaaparticipatory pages 1-2)

9. Inheritance and Population

9.1 Epidemiology

  • Estimated prevalence: approximately 1:55,000 births for the 17q21.31 deletion (houser2025neuroimagingofkoolende pages 2-8, prat2021ocularmanifestationsand pages 4-4)

9.2 Population demographics

  • No sex predilection suggested by near-equal male/female distribution in GenIDA and other sources (colin2023genidaaparticipatory pages 3-4)

10. Diagnostics

10.1 Genetic testing (current practice)

Diagnosis is molecular and includes: - Chromosomal microarray (CMA) to detect 17q21.31 deletions - Single-gene testing / multigene panels for KANSL1 variants - Broader genomic approaches when phenotype is atypical (houser2025neuroimagingofkoolende pages 2-8)

10.2 Omics-based diagnostics (major 2024 development)

A 2024 study developed a blood DNA methylation episignature (456 CpGs) and demonstrated diagnostic utility for classification of KANSL1 VUS and atypical cases, with validation case scores 75–92% vs controls 0–13%. (awamleh2024anewblood pages 2-3, awamleh2024anewblood pages 1-2)

Direct abstract quote (Awamleh 2024): “In this study, we identified a robust DNAm signature of 456 significant CpG sites…” (awamleh2024anewblood pages 1-2)

10.3 Differential diagnosis

Differential diagnoses are not systematically enumerated in the retrieved evidence; however, KdVS is placed among syndromic neurodevelopmental disorders with overlapping features, and facial/speech phenotyping tools are used in the broader field (e.g., NDD cohorts referenced indirectly). Evidence in this run is insufficient to list a complete differential.


11. Outcome/Prognosis

  • Natural history: improvements in speech/language over time and continuing gains beyond childhood are supported by registry modeling and cohort interpretation (colin2023genidaaparticipatory pages 1-2, john2023expandingthespeech pages 1-2).
  • Life expectancy / mortality: Not found in retrieved evidence.

12. Treatment

12.1 Current standard management (real-world implementation)

There is no curative therapy described in clinical summaries; management is symptomatic and multidisciplinary, including physiotherapy for motor delays, speech/feeding therapy, and educational supports, with multispecialty monitoring (houser2025neuroimagingofkoolende pages 2-8).

Speech/language recommendations (2023 cohort) emphasize early AAC and ongoing targeted therapy across development. (john2023expandingthespeech pages 1-2)

12.2 Epilepsy management (real-world observational data)

Caregiver-reported medication effectiveness in GenIDA suggested reported efficacy for valproate (83%) and levetiracetam (67% good efficacy among reporters), with additional reported effectiveness of valproate and oxcarbazepine at cohort level. (colin2023genidaaparticipatory pages 7-9, colin2023genidaaparticipatory pages 1-2)

12.3 Experimental / translational therapeutic leads

  • Mouse model pharmacologic rescue: FDA-approved 13-cis retinoic acid reversed mitophagic defects and neurobehavioral abnormalities in Kansl1+/− mice (li2022kansl1haploinsufficiencyimpairs pages 1-2).
  • Human neuronal model rescue: pharmacologic reduction of oxidative stress rescued autophagosome accumulation and synaptic/network activity (linda2022imbalancedautophagycauses pages 1-3).

12.4 Trial readiness and research infrastructure (expert/authoritative perspective)

A 2024 review describing the KdVS Foundation’s strategy emphasizes models, registries, natural history, and translational funding, with a stated goal of a first clinical trial in late 2026. (pfalzer2024koolendevriessyndrome pages 2-3)

12.5 MAXO term suggestions (examples)

  • Physical therapy (MAXO:0000011)
  • Speech therapy (MAXO:0000016)
  • Feeding therapy / nutritional support (MAXO:0000082; descriptive)
  • Anticonvulsant therapy (MAXO:0000749)

13. Prevention

Primary prevention is not applicable to the de novo genetic cause, but genetic counseling is relevant given the autosomal dominant, typically de novo etiology. (houser2025neuroimagingofkoolende pages 2-8, saxena2021koolen‐devriessyndrome pages 2-4)


14. Other Species / Natural Disease

No evidence of naturally occurring KdVS-equivalent disease in non-human species was retrieved. KANSL1 is conserved and studied in model organisms, but veterinary natural disease evidence is not available in the retrieved texts.


15. Model Organisms

  • Mouse model (Kansl1+/−): links KANSL1 to autophagosome–lysosome fusion, mitophagy/ROS, and neuronal/cardiac dysfunction; provides a preclinical pharmacologic rescue (13-cis retinoic acid). (li2022kansl1haploinsufficiencyimpairs pages 1-2)
  • Human iPSC-derived neuron models: show oxidative stress/autophagy imbalance and synaptic transmission/network deficits with rescue by reducing oxidative stress. (linda2022imbalancedautophagycauses pages 1-3)

Evidence Gaps (limitations of this run)

  • MONDO, Orphanet, MeSH, ICD-10/11 codes were not extractable from the retrieved full-text chunks and thus cannot be cited here.
  • Mortality/life expectancy statistics and formal clinical diagnostic criteria (beyond molecular testing) were not found in the retrieved evidence.
  • Comprehensive differential diagnosis lists and environmental modifiers were not supported by the current evidence set.

High-utility Summary Table

The following artifact condenses the key actionable facts (identifiers, genetics, prevalence, phenotype frequencies, and 2024 diagnostic episignature metrics) with URLs and publication dates.

Category Data point Value/description Source (author/year/journal) URL Pub date
Disease information Primary disease name Koolen-de Vries syndrome (KdVS); rare multisystem neurodevelopmental disorder caused by 17q21.31 deletion including KANSL1 or heterozygous intragenic KANSL1 pathogenic variant (colin2023genidaaparticipatory pages 2-3, houser2025neuroimagingofkoolende pages 2-8) Colin et al. 2023, Genetics in Medicine Open; Houser et al. 2025, Cureus https://doi.org/10.1016/j.gimo.2023.100817; https://doi.org/10.7759/cureus.79194 2023-01; 2025-02
Disease information Key identifier OMIM 610443 (reported in GenIDA KdVS cohort excerpt) (colin2023genidaaparticipatory pages 2-3) Colin et al. 2023, Genetics in Medicine Open https://doi.org/10.1016/j.gimo.2023.100817 2023-01
Disease information Common synonyms 17q21.31 microdeletion syndrome; KANSL1-related intellectual disability syndrome (colin2023genidaaparticipatory pages 2-3, farne2022koolen‐devriessyndrome pages 10-12) Colin et al. 2023, Genetics in Medicine Open; Farnè et al. 2022, Am J Med Genet A https://doi.org/10.1016/j.gimo.2023.100817; https://doi.org/10.1002/ajmg.a.62536 2023-01; 2022-10
Genetic etiology Typical recurrent deletion Typical recurrent 17q21.31 deletion ~500–650 kb; cohort wording also notes recurrent deletion spanning ~43.7–44.25 Mb region (john2023expandingthespeech pages 3-4, houser2025neuroimagingofkoolende pages 2-8) St John et al. 2023, Eur J Hum Genet; Houser et al. 2025, Cureus https://doi.org/10.1038/s41431-022-01230-7; https://doi.org/10.7759/cureus.79194 2023-12; 2025-02
Genetic etiology Deletion vs sequence variant proportion About 60% due to heterozygous 17q21.31 deletion and 40% due to KANSL1 sequence variants in one review excerpt (houser2025neuroimagingofkoolende pages 2-8) Houser et al. 2025, Cureus https://doi.org/10.7759/cureus.79194 2025-02
Genetic etiology GenIDA genotype counts In GenIDA cohort, 157 individuals with 17q21.31 deletion and 40 with pathogenic KANSL1 variant; no major clinical differences detected between groups (colin2023genidaaparticipatory pages 2-3) Colin et al. 2023, Genetics in Medicine Open https://doi.org/10.1016/j.gimo.2023.100817 2023-01
Genetic etiology 2023 speech cohort genotype counts In speech/language cohort (n=81), 56/81 (69.1%) had typical 17q21.31 deletion and 19/81 had KANSL1-only sequence variants; no group score differences reported between deletion and KANSL1-variant groups (john2023expandingthespeech pages 2-2, john2023expandingthespeech pages 3-4) St John et al. 2023, Eur J Hum Genet https://doi.org/10.1038/s41431-022-01230-7 2023-12
Genetic etiology Variant classes observed Predominantly loss-of-function intragenic variants: truncating, frameshift, splice-site, small intragenic exon deletion; 2024 episignature study also discusses missense/nonsense/frameshift/deletion-insertion/mosaic variants for classification (john2023expandingthespeech pages 3-4, awamleh2024anewblood pages 3-5) St John et al. 2023, Eur J Hum Genet; Awamleh et al. 2024, Eur J Hum Genet https://doi.org/10.1038/s41431-022-01230-7; https://doi.org/10.1038/s41431-024-01538-6 2023-12; 2024-01
Inheritance/epidemiology Inheritance pattern Autosomal dominant; typically de novo disease mechanism highlighted in KdVS descriptions (houser2025neuroimagingofkoolende pages 2-8, prat2021ocularmanifestationsand pages 4-4, saxena2021koolen‐devriessyndrome pages 2-4) Houser et al. 2025, Cureus; Prat et al. 2021, Ophthalmic Genetics; Saxena et al. 2021, Am J Med Genet A https://doi.org/10.7759/cureus.79194; https://doi.org/10.1080/13816810.2020.1868012; https://doi.org/10.1002/ajmg.a.62008 2025-02; 2021-01; 2021-12
Inheritance/epidemiology Estimated prevalence Estimated prevalence for 17q21.31 deletion approximately 1:55,000 births (houser2025neuroimagingofkoolende pages 2-8, prat2021ocularmanifestationsand pages 4-4) Houser et al. 2025, Cureus; Prat et al. 2021, Ophthalmic Genetics https://doi.org/10.7759/cureus.79194; https://doi.org/10.1080/13816810.2020.1868012 2025-02; 2021-01
Epidemiology Sex distribution in GenIDA 116 males / 121 females; mean age 14.0 years in GenIDA cohort (colin2023genidaaparticipatory pages 3-4) Colin et al. 2023, Genetics in Medicine Open https://doi.org/10.1016/j.gimo.2023.100817 2023-01
Epidemiology Sex/age in speech cohort 35 female / 46 male; age 1.5–40.2 years, mean 9 years 10 months (john2023expandingthespeech pages 2-2) St John et al. 2023, Eur J Hum Genet https://doi.org/10.1038/s41431-022-01230-7 2023-12
Phenotypes (GenIDA 2023) Prenatal/perinatal problems 77.9% (colin2023genidaaparticipatory pages 3-4) Colin et al. 2023, Genetics in Medicine Open https://doi.org/10.1016/j.gimo.2023.100817 2023-01
Phenotypes (GenIDA 2023) Hypotonia 61.5% (colin2023genidaaparticipatory pages 3-4) Colin et al. 2023, Genetics in Medicine Open https://doi.org/10.1016/j.gimo.2023.100817 2023-01
Phenotypes (GenIDA 2023) Feeding difficulties 60.2% (colin2023genidaaparticipatory pages 3-4) Colin et al. 2023, Genetics in Medicine Open https://doi.org/10.1016/j.gimo.2023.100817 2023-01
Phenotypes (GenIDA 2023) Intellectual disability Formal ID diagnosis in 89.2%; severity: mild 16.9%, moderate 60.2%, severe 2.4%, profound 20.5% (colin2023genidaaparticipatory pages 3-4) Colin et al. 2023, Genetics in Medicine Open https://doi.org/10.1016/j.gimo.2023.100817 2023-01
Phenotypes (GenIDA 2023) Epilepsy 47.3% (97/204) with epilepsy/seizures (colin2023genidaaparticipatory pages 6-7, colin2023genidaaparticipatory pages 3-4) Colin et al. 2023, Genetics in Medicine Open https://doi.org/10.1016/j.gimo.2023.100817 2023-01
Phenotypes (GenIDA 2023) Seizure types among seizure cases Tonic-clonic 38.1%, absence 28.9%, complex partial 22.7%, nocturnal 21.6%, febrile convulsions 19.6%, infantile spasms 14.4%, atonic 9.3% (colin2023genidaaparticipatory pages 6-7) Colin et al. 2023, Genetics in Medicine Open https://doi.org/10.1016/j.gimo.2023.100817 2023-01
Phenotypes (GenIDA 2023) Age at first seizure Average 3.4 years, median 2.0 years (colin2023genidaaparticipatory pages 7-9) Colin et al. 2023, Genetics in Medicine Open https://doi.org/10.1016/j.gimo.2023.100817 2023-01
Phenotypes (GenIDA 2023) Speech/language delay 73.6% in children >2 years; first words average 2.2 years (colin2023genidaaparticipatory pages 3-4) Colin et al. 2023, Genetics in Medicine Open https://doi.org/10.1016/j.gimo.2023.100817 2023-01
Phenotypes (GenIDA 2023) Motor milestone delay Median sit 10.7 mo, stand 17.5 mo, walk 23.4 mo (colin2023genidaaparticipatory pages 3-4) Colin et al. 2023, Genetics in Medicine Open https://doi.org/10.1016/j.gimo.2023.100817 2023-01
Phenotypes (GenIDA 2023) Musculoskeletal findings Joint laxity 50.0%, scoliosis 25.5%, hip dislocation/dysplasia 18.0%, pes planus 22.0%; musculoskeletal anomalies overall 75.5% in later excerpt (colin2023genidaaparticipatory pages 3-4, colin2023genidaaparticipatory pages 7-9) Colin et al. 2023, Genetics in Medicine Open https://doi.org/10.1016/j.gimo.2023.100817 2023-01
Phenotypes (GenIDA 2023) Sleep disorders 42.6% (colin2023genidaaparticipatory pages 3-4) Colin et al. 2023, Genetics in Medicine Open https://doi.org/10.1016/j.gimo.2023.100817 2023-01
Phenotypes (GenIDA 2023) Dental problems 65.1% (colin2023genidaaparticipatory pages 3-4) Colin et al. 2023, Genetics in Medicine Open https://doi.org/10.1016/j.gimo.2023.100817 2023-01
Phenotypes (GenIDA 2023) Cardiac anomalies Atrial septal defect 18.9%; ventricular septal defect 10.9% (colin2023genidaaparticipatory pages 3-4, colin2023genidaaparticipatory pages 6-7) Colin et al. 2023, Genetics in Medicine Open https://doi.org/10.1016/j.gimo.2023.100817 2023-01
Phenotypes (GenIDA 2023) Renal/urogenital issues Approximately 38.3%; male cryptorchidism 22.6% (colin2023genidaaparticipatory pages 3-4, colin2023genidaaparticipatory pages 7-9) Colin et al. 2023, Genetics in Medicine Open https://doi.org/10.1016/j.gimo.2023.100817 2023-01
Phenotypes (GenIDA 2023) Vision/hearing Hypermetropia 38.8%, strabismus 34.7%; hearing problems 40.8%, deafness 12.2% (colin2023genidaaparticipatory pages 6-7) Colin et al. 2023, Genetics in Medicine Open https://doi.org/10.1016/j.gimo.2023.100817 2023-01
Phenotypes (GenIDA 2023) Respiratory issues Respiratory issues 39.8%; laryngomalacia 15.4%; tracheomalacia 8.5%; asthma 16.4%; recurrent pneumonia noted in 13 persons (colin2023genidaaparticipatory pages 6-7, colin2023genidaaparticipatory pages 7-9, colin2023genidaaparticipatory pages 1-2) Colin et al. 2023, Genetics in Medicine Open https://doi.org/10.1016/j.gimo.2023.100817 2023-01
Phenotypes (GenIDA 2023) Behavioral profile Behavioral problems 54.8%; repetitive behaviors 35.2%, attention deficit 32.7%, anxiety 31.2%, obsessive behavior 29.6%, hyperactivity 27.6%; sociable with familiar adults 98.1% and children 88.6% (colin2023genidaaparticipatory pages 6-7, colin2023genidaaparticipatory pages 7-9) Colin et al. 2023, Genetics in Medicine Open https://doi.org/10.1016/j.gimo.2023.100817 2023-01
Phenotypes (EJHG speech cohort 2023) Developmental delay 78/81 (96.3%) (john2023expandingthespeech pages 2-2) St John et al. 2023, Eur J Hum Genet https://doi.org/10.1038/s41431-022-01230-7 2023-12
Phenotypes (EJHG speech cohort 2023) Dysmorphic features 73/81 (90.1%); pear-shaped bulbous nose 48/81 (59.3%) (john2023expandingthespeech pages 2-2) St John et al. 2023, Eur J Hum Genet https://doi.org/10.1038/s41431-022-01230-7 2023-12
Phenotypes (EJHG speech cohort 2023) Intellectual disability Among assessed individuals (n=56), 49/56 (87.5%) had ID; 51.8% moderate, 19.6% severe (john2023expandingthespeech pages 2-2) St John et al. 2023, Eur J Hum Genet https://doi.org/10.1038/s41431-022-01230-7 2023-12
Phenotypes (EJHG speech cohort 2023) Structural brain anomalies 33/62 (53.2%) with imaging had structural brain anomalies (john2023expandingthespeech pages 2-2) St John et al. 2023, Eur J Hum Genet https://doi.org/10.1038/s41431-022-01230-7 2023-12
Phenotypes (EJHG speech cohort 2023) Epilepsy/seizures 29/81 (35.8%) (john2023expandingthespeech pages 2-2) St John et al. 2023, Eur J Hum Genet https://doi.org/10.1038/s41431-022-01230-7 2023-12
Phenotypes (EJHG speech cohort 2023) Hearing loss 24/81 (29.6%), often moderate and conductive (john2023expandingthespeech pages 2-2) St John et al. 2023, Eur J Hum Genet https://doi.org/10.1038/s41431-022-01230-7 2023-12
Phenotypes (EJHG speech cohort 2023) Cardiac/musculoskeletal/sleep Cardiac defects 32/81 (39.5%); musculoskeletal problems 32/81 (39.5%); sleep disturbances 33/81 (40.7%) (john2023expandingthespeech pages 2-2) St John et al. 2023, Eur J Hum Genet https://doi.org/10.1038/s41431-022-01230-7 2023-12
Phenotypes (EJHG speech cohort 2023) Other systemic features Dental problems 36/72 (50.0%); renal/urogenital complications 25/81 (30.9%); GI concerns 24/81 (29.6%); mental health problems 23/81 (28.4%); cryptorchidism 21/46 (45.7%) of males (john2023expandingthespeech pages 2-2) St John et al. 2023, Eur J Hum Genet https://doi.org/10.1038/s41431-022-01230-7 2023-12
Phenotypes (EJHG speech cohort 2023) Verbal status 62/81 (76.5%) verbal; minimally verbal participants used AAC successfully (john2023expandingthespeech pages 1-2) St John et al. 2023, Eur J Hum Genet https://doi.org/10.1038/s41431-022-01230-7 2023-12
Phenotypes (EJHG speech cohort 2023) Motor speech disorders Apraxia in 39/61 (63.9%) verbal participants; dysarthria in 28/61 (45.9%) (john2023expandingthespeech pages 1-2) St John et al. 2023, Eur J Hum Genet https://doi.org/10.1038/s41431-022-01230-7 2023-12
Phenotypes (EJHG speech cohort 2023) Stuttering 36/47 (76.6%) of verbal participants; described as late-onset and fluctuating (john2023expandingthespeech pages 1-2) St John et al. 2023, Eur J Hum Genet https://doi.org/10.1038/s41431-022-01230-7 2023-12
Diagnostics / omics 2024 blood DNAm episignature cohort Whole-blood DNAm profiled in 13 individuals with KANSL1 variants, 4 with 17q21.31 microdeletions, and 21 controls using Illumina EPIC array (awamleh2024anewblood pages 1-2) Awamleh et al. 2024, Eur J Hum Genet https://doi.org/10.1038/s41431-024-01538-6 2024-01
Diagnostics / omics 2024 episignature size Robust blood DNA methylation signature of 456 significant CpG sites (awamleh2024anewblood pages 1-2, awamleh2024anewblood pages 2-3) Awamleh et al. 2024, Eur J Hum Genet https://doi.org/10.1038/s41431-024-01538-6 2024-01
Diagnostics / omics Discovery and validation Discovery cohort n=8 KdVS cases; independent validation cohort n=8; validation SVM scores for KdVS cases 75–92% vs controls 0–13% (awamleh2024anewblood pages 5-7, awamleh2024anewblood pages 2-3, awamleh2024anewblood pages 7-8) Awamleh et al. 2024, Eur J Hum Genet https://doi.org/10.1038/s41431-024-01538-6 2024-01
Diagnostics / omics Variant classification utility Used to classify 2 KANSL1 VUS and 4 atypical-presentation variants; one missense p.Thr887Met scored KdVS-like (~72%), while p.Gly900Glu scored control-like (~4.7%) (awamleh2024anewblood pages 3-5, awamleh2024anewblood pages 1-2, awamleh2024anewblood pages 7-8) Awamleh et al. 2024, Eur J Hum Genet https://doi.org/10.1038/s41431-024-01538-6 2024-01
Diagnostics / omics Microdeletion vs sequence variant DNAm difference No significant DNAm difference between 17q21.31 microdeletion carriers and KANSL1 sequence-variant carriers (adjusted p = 0.34) (awamleh2024anewblood pages 2-3) Awamleh et al. 2024, Eur J Hum Genet https://doi.org/10.1038/s41431-024-01538-6 2024-01

Table: This table condenses the most actionable disease-level facts for Koolen-de Vries syndrome, including identifiers, causal genetics, prevalence, major 2023 cohort phenotype frequencies, and the 2024 DNA methylation episignature findings. It is useful as a quick-reference artifact for knowledge-base population and evidence-backed summarization.

References

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