Spondylometaphyseal dysplasia with corneal dystrophy (SMDCD; OMIM #618961) is an ultra-rare autosomal recessive skeletal dysplasia described in two Emirati first cousins and caused by a homozygous hypomorphic variant in PLCB3, encoding phospholipase C beta 3. The enzyme hydrolyses phosphatidylinositol 4,5-bisphosphate to inositol 1,4,5-trisphosphate and diacylglycerol, so its impairment is a defect of phosphoinositide signalling rather than of a structural matrix protein. Affected infants are born preterm with profound limb shortening involving both proximal and distal segments, a narrow chest, and bilateral corneal clouding evident within days of birth; radiographs show short long bones with wide metaphyses, anterior vertebral beaking, and square short iliac bones. Intellectual disability is severe. The disease variant p.A878S sits in the Ha2' element of the proximal C-terminal domain, disrupts its binding to the catalytic core, and destabilises the protein; patient fibroblasts accumulate the substrate PIP2 and show a disorganised F-actin cytoskeleton strikingly similar to that of Lowe syndrome fibroblasts, which are also phosphoinositide-signalling mutants. SMDCD is one of only three spondylometaphyseal dysplasias with eye involvement, and the only one affecting the cornea rather than the retina.
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Conditions with similar clinical presentations that must be differentiated from Spondylometaphyseal Dysplasia with Corneal Dystrophy:
name: Spondylometaphyseal Dysplasia with Corneal Dystrophy
creation_date: "2026-08-27T00:00:00Z"
category: Mendelian
description: >-
Spondylometaphyseal dysplasia with corneal dystrophy (SMDCD; OMIM #618961) is an
ultra-rare autosomal recessive skeletal dysplasia described in two Emirati first
cousins and caused by a homozygous hypomorphic variant in PLCB3, encoding
phospholipase C beta 3. The enzyme hydrolyses phosphatidylinositol
4,5-bisphosphate to inositol 1,4,5-trisphosphate and diacylglycerol, so its
impairment is a defect of phosphoinositide signalling rather than of a structural
matrix protein. Affected infants are born preterm with profound limb shortening
involving both proximal and distal segments, a narrow chest, and bilateral corneal
clouding evident within days of birth; radiographs show short long bones with wide
metaphyses, anterior vertebral beaking, and square short iliac bones. Intellectual
disability is severe. The disease variant p.A878S sits in the Ha2' element of the
proximal C-terminal domain, disrupts its binding to the catalytic core, and
destabilises the protein; patient fibroblasts accumulate the substrate PIP2 and
show a disorganised F-actin cytoskeleton strikingly similar to that of Lowe
syndrome fibroblasts, which are also phosphoinositide-signalling mutants. SMDCD is
one of only three spondylometaphyseal dysplasias with eye involvement, and the
only one affecting the cornea rather than the retina.
disease_term:
preferred_term: spondylometaphyseal dysplasia with corneal dystrophy
term:
id: MONDO:0030074
label: spondylometaphyseal dysplasia with corneal dystrophy
synonyms:
- SMDCD
- PLCB3-related spondylometaphyseal dysplasia
- Spondylometaphyseal dysplasia with corneal dystrophy and developmental delay
parents:
- Skeletal Dysplasia
classifications:
isds_skeletal_category:
- classification_value: spondylometaphyseal_dysplasias
notes: >-
ISDS Nosology of Genetic Skeletal Disorders, 2023 revision (Unger et al.,
PMID:36779427), Table 1 group 12 "Spondylometaphyseal dysplasias (SMD)",
entry NOS 12-0050, listed as "Spondylometaphyseal dysplasia with corneal
dystrophy, PLCB3-related" (AR, PLCB3, MIM 618961). This is one of the two
group-12 entries absent from dismech's own prose description of the group
before this curation, the other being NOS 12-0060 (HHAT).
prevalence:
- population: Worldwide
measure_type: CASES_IN_LITERATURE
prevalence_class: ULTRA_RARE
rate_per_100000: 0.0
notes: >-
Two affected first cousins from one consanguineous Emirati family constitute the
entire published caseload. Skeletal dysplasias as a class are relatively common
in the United Arab Emirates at 9.46 per 10,000 births, which is the ascertainment
context in which this family was recognised, but no estimate exists for this
disorder specifically; rate_per_100000 is recorded as 0.0 only to mark that the
true rate is far below the resolution of any published survey.
evidence:
- reference: PMID:29122926
reference_title: Defect in phosphoinositide signalling through a homozygous variant in PLCB3 causes a new form of spondylometaphyseal dysplasia with corneal dystrophy.
supports: SUPPORT
evidence_source: HUMAN_CLINICAL
snippet: >-
we report the clinical and molecular delineation of a new form of syndromic
autosomal recessive spondylometaphyseal dysplasia (SMD) in two Emirati first
cousins
explanation: >-
Establishes that the entire described cohort is two related individuals from a
single family.
inheritance:
- name: Autosomal Recessive
inheritance_term:
preferred_term: Autosomal recessive inheritance
term:
id: HP:0000007
label: Autosomal recessive inheritance
description: >-
SMDCD is autosomal recessive. Both affected cousins are homozygous for
PLCB3 c.2632G>T; all four parents and all healthy siblings are heterozygous, and
homozygosity mapping under a recessive model with complete penetrance is what
localised the locus to 11q12.1-q13.1.
evidence:
- reference: PMID:29122926
reference_title: Defect in phosphoinositide signalling through a homozygous variant in PLCB3 causes a new form of spondylometaphyseal dysplasia with corneal dystrophy.
supports: SUPPORT
evidence_source: HUMAN_CLINICAL
snippet: >-
Only the patients (IV-1 and IV-3) were found to be homozygous for these
variants, while all healthy individuals were heterozygous
explanation: >-
Segregation consistent with autosomal recessive inheritance in an extended
consanguineous pedigree.
genetic:
- name: Homozygous PLCB3 c.2632G>T (p.Ala878Ser)
gene_term:
preferred_term: PLCB3
term:
id: hgnc:9056
label: PLCB3
association: Causative
relationship_type: CAUSATIVE
variant_origin: GERMLINE
features: >-
A single homozygous missense allele, PLCB3 NM_000932.2:c.2632G>T (p.Ala878Ser),
at 11q13. The substituted alanine is highly conserved at both DNA and protein
level across vertebrates and affects all three coding isoforms of PLCB3. The
variant is absent from 200 ethnically matched control chromosomes and from dbSNP
and EVS, with a heterozygous minor allele frequency of 1.824e-05 in ExAC.
Structural modelling on the Gq-alpha-PLCbeta3 complex places it in the Ha2'
element of the proximal C-terminal domain.
evidence:
- reference: PMID:29122926
reference_title: Defect in phosphoinositide signalling through a homozygous variant in PLCB3 causes a new form of spondylometaphyseal dysplasia with corneal dystrophy.
supports: SUPPORT
evidence_source: HUMAN_CLINICAL
snippet: >-
The identified variant (c.2632G>T) substitutes a serine for a highly conserved
alanine within the Ha2' element of the proximal C-terminal domain.
explanation: Names the allele and its structural location within the protein.
- reference: PMID:29122926
reference_title: Defect in phosphoinositide signalling through a homozygous variant in PLCB3 causes a new form of spondylometaphyseal dysplasia with corneal dystrophy.
supports: SUPPORT
evidence_source: HUMAN_CLINICAL
snippet: >-
This variant affects all three different coding isoforms of PLCB3, and this
position is highly conserved at the DNA and protein levels between vertebrates
and mammalians
explanation: >-
Conservation and isoform coverage are the population-genetic arguments for
pathogenicity in a single-family report.
pathophysiology:
- name: Homozygous PLCB3 p.Ala878Ser
biological_scale: MOLECULAR
description: >-
A conserved alanine in the Ha2' element of the proximal C-terminal domain is
replaced by serine. The Ha2' element normally docks onto the catalytic core; the
substitution disrupts that interaction.
genes:
- preferred_term: PLCB3
term:
id: hgnc:9056
label: PLCB3
evidence:
- reference: PMID:29122926
reference_title: Defect in phosphoinositide signalling through a homozygous variant in PLCB3 causes a new form of spondylometaphyseal dysplasia with corneal dystrophy.
supports: SUPPORT
evidence_source: HUMAN_CLINICAL
snippet: >-
The identified variant (c.2632G>T) substitutes a serine for a highly conserved
alanine within the Ha2' element of the proximal C-terminal domain.
explanation: The initiating molecular lesion.
downstream:
- target: Destabilised Phospholipase C Beta 3 with Reduced Activity
causal_link_type: DIRECT
description: >-
Loss of the Ha2'-to-catalytic-core interaction destabilises the protein and
reduces its enzymatic activity. The allele is hypomorphic rather than null,
which matters because targeted disruption of Plcb3 in mouse is embryonic
lethal.
evidence:
- reference: PMID:29122926
reference_title: Defect in phosphoinositide signalling through a homozygous variant in PLCB3 causes a new form of spondylometaphyseal dysplasia with corneal dystrophy.
supports: SUPPORT
evidence_source: IN_VITRO
snippet: >-
This disrupts binding of the Ha2' element to the catalytic core and
destabilises PLCB3.
explanation: >-
Establishes protein destabilisation as the direct consequence of the
substitution.
- name: Destabilised Phospholipase C Beta 3 with Reduced Activity
biological_scale: MOLECULAR
description: >-
PLCB3 catalyses production of diacylglycerol and inositol 1,4,5-trisphosphate
from phosphatidylinositol 4,5-bisphosphate, and is activated by G-protein
alpha-q and alpha-11 subunits and by beta-gamma subunits. The p.A878S protein is
destabilised and hypomorphic, so signalling downstream of Gq-coupled receptors is
attenuated and the substrate is not consumed.
molecular_functions:
- preferred_term: phospholipase C activity
modifier: DECREASED
term:
id: GO:0004629
label: C-type glycerophospholipase activity
evidence:
- reference: PMID:29122926
reference_title: Defect in phosphoinositide signalling through a homozygous variant in PLCB3 causes a new form of spondylometaphyseal dysplasia with corneal dystrophy.
supports: SUPPORT
evidence_source: IN_VITRO
snippet: >-
the identified PLCB3:NM_000932:c.2632G>T variant destabilises the protein and
reduces its enzymatic activity, leading to PIP2 accumulation
explanation: >-
Links the destabilisation directly to reduced catalysis and to substrate
accumulation.
downstream:
- target: Accumulation of Phosphatidylinositol 4,5-Bisphosphate
causal_link_type: DIRECT
description: >-
With the hydrolysing enzyme impaired, its substrate builds up. This was
measured directly in patient fibroblasts by anti-PtdIns(4,5)P2
immunofluorescence.
evidence:
- reference: PMID:29122926
reference_title: Defect in phosphoinositide signalling through a homozygous variant in PLCB3 causes a new form of spondylometaphyseal dysplasia with corneal dystrophy.
supports: SUPPORT
evidence_source: IN_VITRO
snippet: >-
Here we show that this hypomorphic variant leads to elevated levels of PIP2
in patient fibroblasts, causing disorganisation of the F-actin cytoskeleton.
explanation: >-
Substrate accumulation demonstrated in patient-derived cells, together with
its cytoskeletal consequence.
- name: Accumulation of Phosphatidylinositol 4,5-Bisphosphate
biological_scale: MOLECULAR
description: >-
PIP2 is elevated in patient fibroblasts. PIP2 is not merely a signalling
precursor but a direct regulator of actin-binding proteins at the plasma
membrane, which is the route by which a signalling-enzyme defect becomes a
structural cytoskeletal defect.
biological_processes:
- preferred_term: phosphatidylinositol-mediated signaling
modifier: DECREASED
term:
id: GO:0048015
label: phosphatidylinositol-mediated signaling
evidence:
- reference: PMID:29122926
reference_title: Defect in phosphoinositide signalling through a homozygous variant in PLCB3 causes a new form of spondylometaphyseal dysplasia with corneal dystrophy.
supports: SUPPORT
evidence_source: IN_VITRO
snippet: >-
Here we show that this hypomorphic variant leads to elevated levels of PIP2 in
patient fibroblasts, causing disorganisation of the F-actin cytoskeleton.
explanation: Measures the substrate accumulation in patient material.
downstream:
- target: F-Actin Cytoskeletal Disorganisation
causal_link_type: DIRECT
description: >-
Excess PIP2 disorganises the actin cytoskeleton. The phenotype is the same one
seen in Lowe syndrome fibroblasts, where the defect is in a different
phosphoinositide-metabolising enzyme, which is the convergence argument that
makes the link mechanistic rather than incidental.
evidence:
- reference: PMID:29122926
reference_title: Defect in phosphoinositide signalling through a homozygous variant in PLCB3 causes a new form of spondylometaphyseal dysplasia with corneal dystrophy.
supports: SUPPORT
evidence_source: IN_VITRO
snippet: >-
This phenotype is strikingly similar to Lowe syndrome (MIM 309000)
fibroblasts, which also display actin abnormalities due to defects in
phosphoinositide signalling.
explanation: >-
The convergence with an independent phosphoinositide disorder supports the
causal reading of the actin phenotype.
- name: F-Actin Cytoskeletal Disorganisation
biological_scale: CELLULAR
description: >-
Patient fibroblasts are significantly larger than controls, with a weaker F-actin
network and a more punctate appearance, scored blind to genotype using an
established four-pattern classification of stress-fibre number and length. How
this cellular phenotype produces a growth-plate lesion, a corneal opacity, and
developmental delay is not established.
cell_types:
- preferred_term: fibroblast
term:
id: CL:0000057
label: fibroblast
cellular_components:
- preferred_term: actin filament
term:
id: GO:0005884
label: actin filament
biological_processes:
- preferred_term: actin cytoskeleton organization
modifier: ABNORMAL
term:
id: GO:0030036
label: actin cytoskeleton organization
evidence:
- reference: PMID:29122926
reference_title: Defect in phosphoinositide signalling through a homozygous variant in PLCB3 causes a new form of spondylometaphyseal dysplasia with corneal dystrophy.
supports: SUPPORT
evidence_source: IN_VITRO
snippet: >-
Patient fibroblasts are significantly larger with a weaker F-actin network and
more punctuate appearance.
explanation: The measured cellular phenotype in patient-derived cells.
downstream:
- target: Spondylometaphyseal Skeletal Dysplasia
causal_link_type: INDIRECT_UNKNOWN_INTERMEDIATES
description: >-
The skeletal lesion is attributed to disturbed phosphoinositide signalling
during skeletal development, supported by expression of Plcb3 in bone,
cartilage, and neural crest in zebrafish and by abnormal skeletal patterning
with malformed facial and thoracic bones in zebrafish plcb3 null mutants. The
intervening steps in human cartilage have not been demonstrated.
evidence:
- reference: PMID:29122926
reference_title: Defect in phosphoinositide signalling through a homozygous variant in PLCB3 causes a new form of spondylometaphyseal dysplasia with corneal dystrophy.
supports: SUPPORT
directness: INDIRECT
evidence_source: MODEL_ORGANISM
snippet: >-
Plcb3 null mutants in zebra fish showed abnormal skeletal patterning with
malformed facial and thoracic bones.
explanation: >-
A model-organism result establishing that Plcb3 loss disturbs skeletal
patterning, without showing the mechanism in human cartilage.
- target: Severe Developmental Delay
causal_link_type: INDIRECT_UNKNOWN_INTERMEDIATES
description: >-
Severe global developmental delay is part of the syndrome and PLCB3 is most
highly expressed in brain, but no step between the phosphoinositide defect and
the neurodevelopmental phenotype has been demonstrated. Prematurity and chronic
respiratory failure are uncontrolled confounders in both reported children.
- target: Hypertelorism with Depressed Nasal Bridge
causal_link_type: INDIRECT_UNKNOWN_INTERMEDIATES
description: >-
A consistent facial gestalt across both affected cousins. Facial morphogenesis
is neural-crest-dependent and zebrafish plcb3 is expressed in neural crest, but
the connection is an inference from expression rather than a demonstrated
mechanism.
- target: Patent Ductus Arteriosus
causal_link_type: UNKNOWN
description: >-
A large patent ductus arteriosus occurred in both affected children. Both were
also born preterm — at 29 and 27 weeks — and prematurity alone is a sufficient
explanation for a persistent duct, so this edge is left with directness
UNKNOWN rather than asserted as part of the syndrome.
- target: Corneal Dystrophy
causal_link_type: INDIRECT_UNKNOWN_INTERMEDIATES
description: >-
The corneal opacity is present within days of birth and is confined to the
cornea, with normal retinas, optic nerves, vitreous, and posterior lens on
ophthalmological and B-scan assessment. No mechanism connecting the
phosphoinositide defect to corneal stromal transparency has been proposed.
evidence:
- reference: PMID:29122926
reference_title: Defect in phosphoinositide signalling through a homozygous variant in PLCB3 causes a new form of spondylometaphyseal dysplasia with corneal dystrophy.
supports: SUPPORT
directness: INDIRECT
evidence_source: HUMAN_CLINICAL
snippet: >-
Opthalmological examination revealed bilateral corneal haziness with normal
retinas.
explanation: >-
Establishes that the eye lesion is corneal and anterior-segment specific, but
supplies no mechanism, hence the unknown-intermediates grading.
- name: Spondylometaphyseal Skeletal Dysplasia
biological_scale: ORGANISM
description: >-
Profound limb shortening involving both proximal and distal segments, with short
fingers and toes and a narrow chest. Radiographs show short long bones with wide
metaphyses and coarse metaphyseal trabeculae, cupping of the distal radius and
ulna, uncalcified distal femoral and proximal tibial epiphyses in the neonate,
short ribs with a wide anterior aspect, anterior beaking of the lumbar and
thoracic vertebrae with wide intervertebral spaces, and almost square, short iliac
bones with medial projections. The iliac shape was close enough to Schneckenbecken
dysplasia that SLC35D1 was sequenced and excluded before the locus was mapped.
evidence:
- reference: PMID:29122926
reference_title: Defect in phosphoinositide signalling through a homozygous variant in PLCB3 causes a new form of spondylometaphyseal dysplasia with corneal dystrophy.
supports: SUPPORT
evidence_source: HUMAN_CLINICAL
snippet: >-
Skeletal survey (figure 1B) showed short long bones with wide metaphyses and
some coarse trabecule at the metaphyses.
explanation: The primary radiographic description of the skeletal lesion.
- reference: PMID:29122926
reference_title: Defect in phosphoinositide signalling through a homozygous variant in PLCB3 causes a new form of spondylometaphyseal dysplasia with corneal dystrophy.
supports: SUPPORT
evidence_source: HUMAN_CLINICAL
snippet: >-
The lumbar and thoracic vertebrae had beaks at their anterior aspects, and the
intervertebral spaces were wide.
explanation: >-
The vertebral component that makes this a spondylometaphyseal rather than a
purely metaphyseal dysplasia.
downstream:
- target: Profound Limb Shortening
causal_link_type: DIRECT
description: >-
Micromelia involving both proximal and distal segments, detectable on prenatal
ultrasound.
- target: Metaphyseal Widening
causal_link_type: DIRECT
description: Wide metaphyses with coarse trabeculae and distal forearm cupping.
- target: Anterior Vertebral Beaking
causal_link_type: DIRECT
description: >-
Anterior beaks on the lumbar and thoracic bodies with wide intervertebral
spaces.
- target: Severe Postnatal Growth Deficiency
causal_link_type: DIRECT
description: >-
Growth deficiency that is postnatal in onset: birth weight was above the 25th
centile in the proband, while weight and height were both far below the third
by four years.
- target: Narrow Chest with Pulmonary Hypoplasia
causal_link_type: DIRECT
description: >-
Short, anteriorly wide ribs give a narrow thorax that constrains lung growth.
This is the feature that dominates the natural history and determines survival.
- name: Corneal Dystrophy
biological_scale: ORGANISM
description: >-
Bilateral corneal clouding evident within the first days of life. In the second
cousin the corneas showed vascularised opacities with central thickened white
cream-coloured tissue and a thinner greyish periphery over an epithelialised
surface. Both children underwent corneal grafting; one experienced graft
rejection. Screening for a storage disease — white cell inclusions, urine
mucopolysaccharides and oligosaccharides — was negative, which is the standard
first differential for neonatal corneal clouding.
evidence:
- reference: PMID:29122926
reference_title: Defect in phosphoinositide signalling through a homozygous variant in PLCB3 causes a new form of spondylometaphyseal dysplasia with corneal dystrophy.
supports: SUPPORT
evidence_source: HUMAN_CLINICAL
snippet: >-
Ophthalmological evaluation showed bilateral vascularised corneal opacities
with central thickened white cream-coloured tissue and thinner greyish
periphery; the surface of the cornea was epithelised.
explanation: The detailed corneal description in the second affected cousin.
downstream:
- target: Corneal Clouding
causal_link_type: DIRECT
description: >-
Bilateral corneal opacity apparent within the first two weeks of life, with
normal retinas behind it.
phenotypes:
- category: Ophthalmologic
name: Corneal Clouding
frequency: OBLIGATE
description: >-
Bilateral corneal opacity noted within the first two weeks of life in both
affected children, with normal retinas. Definitional for the entity, and the
feature that distinguishes it from every other spondylometaphyseal dysplasia.
phenotype_term:
preferred_term: Corneal opacity
term:
id: HP:0007957
label: Corneal opacity
evidence:
- reference: PMID:29122926
reference_title: Defect in phosphoinositide signalling through a homozygous variant in PLCB3 causes a new form of spondylometaphyseal dysplasia with corneal dystrophy.
supports: SUPPORT
evidence_source: HUMAN_CLINICAL
snippet: >-
He was noted to have bilateral corneal clouding on day 12.
explanation: Documents the corneal opacity and its neonatal onset in the proband.
- category: Skeletal
name: Profound Limb Shortening
frequency: OBLIGATE
description: >-
Micromelia involving both proximal and distal segments, with short fingers and
toes, detectable on prenatal ultrasound.
phenotype_term:
preferred_term: Micromelia
term:
id: HP:0002983
label: Micromelia
evidence:
- reference: PMID:29122926
reference_title: Defect in phosphoinositide signalling through a homozygous variant in PLCB3 causes a new form of spondylometaphyseal dysplasia with corneal dystrophy.
supports: SUPPORT
evidence_source: HUMAN_CLINICAL
snippet: >-
On examination, he had short limbs, with proximal and distal segments involved.
explanation: Documents the pattern of limb shortening in the proband.
- category: Skeletal
name: Metaphyseal Widening
frequency: OBLIGATE
description: >-
Wide metaphyses with coarse trabeculae and cupping of the distal radius and ulna.
phenotype_term:
preferred_term: Metaphyseal widening
term:
id: HP:0003016
label: Metaphyseal widening
evidence:
- reference: PMID:29122926
reference_title: Defect in phosphoinositide signalling through a homozygous variant in PLCB3 causes a new form of spondylometaphyseal dysplasia with corneal dystrophy.
supports: SUPPORT
evidence_source: HUMAN_CLINICAL
snippet: >-
Skeletal survey (figure 1B) showed short long bones with wide metaphyses and
some coarse trabecule at the metaphyses.
explanation: Documents the metaphyseal component of the radiographic phenotype.
- category: Skeletal
name: Anterior Vertebral Beaking
frequency: OBLIGATE
description: >-
Anterior beaks on the lumbar and thoracic vertebral bodies with wide
intervertebral spaces — the vertebral component of the dysplasia.
phenotype_term:
preferred_term: Anterior beaking of lumbar vertebrae
term:
id: HP:0008430
label: Anterior beaking of lumbar vertebrae
evidence:
- reference: PMID:29122926
reference_title: Defect in phosphoinositide signalling through a homozygous variant in PLCB3 causes a new form of spondylometaphyseal dysplasia with corneal dystrophy.
supports: SUPPORT
evidence_source: HUMAN_CLINICAL
snippet: >-
The lumbar and thoracic vertebrae had beaks at their anterior aspects, and the
intervertebral spaces were wide.
explanation: Documents the vertebral morphology.
- category: Respiratory
name: Narrow Chest with Pulmonary Hypoplasia
frequency: OBLIGATE
description: >-
A narrow thorax with short, anteriorly wide ribs. Both children were floppy at
birth, required intubation and ventilation, and developed chronic lung disease;
one needed a tracheostomy and continuous oxygen, the other had pulmonary
hypertension and died at eight months of septic shock. The respiratory
consequence of the thoracic dysplasia dominates the natural history.
phenotype_term:
preferred_term: Pulmonary hypoplasia
term:
id: HP:0002089
label: Pulmonary hypoplasia
evidence:
- reference: PMID:29122926
reference_title: Defect in phosphoinositide signalling through a homozygous variant in PLCB3 causes a new form of spondylometaphyseal dysplasia with corneal dystrophy.
supports: SUPPORT
evidence_source: HUMAN_CLINICAL
snippet: >-
The baby had a stormy neonatal period and was difficult to wean off the
ventilator due to the narrow chest and hypoplastic lungs.
explanation: >-
Attributes the ventilator dependence directly to the thoracic and pulmonary
hypoplasia.
- category: Neurologic
name: Severe Developmental Delay
frequency: OBLIGATE
description: >-
Severe global developmental delay. At six years the surviving proband could roll
over and sit unsupported but not bear weight, was wheelchair-bound, and had no
speech or meaningful babbling despite being able to hear and understand words.
phenotype_term:
preferred_term: Global developmental delay
term:
id: HP:0001263
label: Global developmental delay
severity: SEVERE
evidence:
- reference: PMID:29122926
reference_title: Defect in phosphoinositide signalling through a homozygous variant in PLCB3 causes a new form of spondylometaphyseal dysplasia with corneal dystrophy.
supports: SUPPORT
evidence_source: HUMAN_CLINICAL
snippet: >-
Currently, he is 6 years old with severe developmental delay.
explanation: Documents the severity of the developmental phenotype at age six.
- category: Cardiovascular
name: Patent Ductus Arteriosus
frequency: VERY_FREQUENT
description: >-
A large patent ductus arteriosus in both affected children, requiring surgical
correction in one and producing a left-to-right shunt in the other.
phenotype_term:
preferred_term: Patent ductus arteriosus
term:
id: HP:0001643
label: Patent ductus arteriosus
evidence:
- reference: PMID:29122926
reference_title: Defect in phosphoinositide signalling through a homozygous variant in PLCB3 causes a new form of spondylometaphyseal dysplasia with corneal dystrophy.
supports: SUPPORT
evidence_source: HUMAN_CLINICAL
snippet: >-
Echocardiography showed a large patent ductus arteriosus, which eventually
required surgical correction.
explanation: >-
Documents the cardiac lesion in the proband; both children were preterm, so
prematurity is a confounder for this feature specifically.
- category: Craniofacial
name: Hypertelorism with Depressed Nasal Bridge
frequency: VERY_FREQUENT
description: >-
Hypertelorism, prominent eyes, a depressed nasal bridge, and a short upturned
nose in both affected children.
phenotype_term:
preferred_term: Hypertelorism
term:
id: HP:0000316
label: Hypertelorism
evidence:
- reference: PMID:29122926
reference_title: Defect in phosphoinositide signalling through a homozygous variant in PLCB3 causes a new form of spondylometaphyseal dysplasia with corneal dystrophy.
supports: SUPPORT
evidence_source: HUMAN_CLINICAL
snippet: >-
There was hypertelorism, prominent eyes, depressed nasal bridge and short
upturned nose.
explanation: The facial phenotype as recorded in the proband.
- category: Growth
name: Severe Postnatal Growth Deficiency
frequency: OBLIGATE
description: >-
Postnatal growth deficiency. At four years the proband weighed 14 kg and measured
85 cm, both well below the third centile, despite a birth weight above the 25th.
phenotype_term:
preferred_term: Severe short stature
term:
id: HP:0003510
label: Severe short stature
evidence:
- reference: PMID:29122926
reference_title: Defect in phosphoinositide signalling through a homozygous variant in PLCB3 causes a new form of spondylometaphyseal dysplasia with corneal dystrophy.
supports: SUPPORT
evidence_source: HUMAN_CLINICAL
snippet: >-
They displayed postnatal growth deficiency causing profound limb shortening
with proximal and distal segments involvement, narrow chest, radiological
abnormalities involving the spine, pelvis and metaphyses, corneal clouding and
intellectual disability.
explanation: >-
The summary clinical description, establishing postnatal growth deficiency
alongside the other core features.
progression:
- phase: Neonatal
age_range: Birth to 1 month
notes: >-
Both children were born preterm — at 29 and 27 weeks — and were floppy at birth,
requiring intubation and ventilation. Prenatal ultrasound had shown short limbs
and a narrow thorax in the proband. Corneal clouding was apparent within the
first two weeks.
evidence:
- reference: PMID:29122926
reference_title: Defect in phosphoinositide signalling through a homozygous variant in PLCB3 causes a new form of spondylometaphyseal dysplasia with corneal dystrophy.
supports: SUPPORT
evidence_source: HUMAN_CLINICAL
snippet: >-
Prenatal ultrasound revealed short limbs and narrow thorax. The baby was floppy
at birth and required intubation and ventilation.
explanation: Documents the prenatal detection and the neonatal respiratory course.
- phase: Infancy and childhood
age_range: 1 month onward
notes: >-
Chronic lung disease with respiratory failure, requiring tracheostomy and
continuous oxygen in the surviving child, plus gastrostomy for chronic reflux and
repeated aspiration pneumonia. Corneal grafting was performed in both children.
One died at eight months of septic shock with pulmonary hypertension; the other
was alive at six years, wheelchair-bound with severe developmental delay.
evidence:
- reference: PMID:29122926
reference_title: Defect in phosphoinositide signalling through a homozygous variant in PLCB3 causes a new form of spondylometaphyseal dysplasia with corneal dystrophy.
supports: SUPPORT
evidence_source: HUMAN_CLINICAL
snippet: >-
He died at the age of 8 months of septic shock.
explanation: Records the fatal outcome in the second affected cousin.
diagnosis:
- name: Neonatal Corneal Clouding with a Skeletal Dysplasia
diagnosis_term:
preferred_term: eye examination
term:
id: NCIT:C38060
label: Eye Examination
description: >-
The combination that should prompt this diagnosis is neonatal corneal clouding
with a spondylometaphyseal skeletal survey. Because that combination is
classically a lysosomal storage disorder, storage screening comes first and was
negative in both children — white cell inclusions, urine mucopolysaccharides, and
urine oligosaccharides.
evidence:
- reference: PMID:29122926
reference_title: Defect in phosphoinositide signalling through a homozygous variant in PLCB3 causes a new form of spondylometaphyseal dysplasia with corneal dystrophy.
supports: SUPPORT
evidence_source: HUMAN_CLINICAL
snippet: >-
Basic screening for storage disease including white blood cell inclusions,
urine mucopolysaccharides and oligosaccharides was negative.
explanation: Documents the storage-disease exclusion that precedes the genetic diagnosis.
- name: PLCB3 Sequencing
diagnosis_term:
preferred_term: genetic testing
term:
id: NCIT:C15709
label: Genetic Testing
description: >-
Biallelic PLCB3 variants confirm the diagnosis. With one family reported, the
evidence base for interpreting a novel PLCB3 allele is thin; the founding report
reached its assignment only after excluding three other homozygous variants in
the same linkage interval by functional assay, which is a reminder of how weak
homozygosity mapping alone is in a single consanguineous pedigree.
evidence:
- reference: PMID:29122926
reference_title: Defect in phosphoinositide signalling through a homozygous variant in PLCB3 causes a new form of spondylometaphyseal dysplasia with corneal dystrophy.
supports: SUPPORT
evidence_source: HUMAN_CLINICAL
snippet: >-
Based on these experiments we considered the variants in FEN1, INCENP and
PRPF19 unlikely to be the cause of our patients
explanation: >-
Three competing homozygous candidates in the same interval had to be excluded
functionally before PLCB3 could be assigned.
differential_diagnoses:
- name: Mucopolysaccharidoses and Other Lysosomal Storage Disorders
description: >-
Neonatal corneal clouding with a dysostotic skeletal survey is the classic
presentation of a storage disorder, and both affected children were screened for
one before the genetic diagnosis was reached. Anterior vertebral beaking in
particular is a recognised storage-disease sign, which makes the radiographic
overlap substantial.
evidence:
- reference: PMID:29122926
reference_title: Defect in phosphoinositide signalling through a homozygous variant in PLCB3 causes a new form of spondylometaphyseal dysplasia with corneal dystrophy.
supports: SUPPORT
evidence_source: HUMAN_CLINICAL
snippet: >-
Basic screening for storage disease including white blood cell inclusions,
urine mucopolysaccharides and oligosaccharides was negative.
explanation: >-
The storage differential was actively pursued in the reported family, which is
why it belongs here.
- name: Schneckenbecken Dysplasia
description: >-
The square, short iliac bones with medial projections resembled those of
Schneckenbecken dysplasia closely enough that SLC35D1 was sequenced and excluded
before the linkage analysis. Schneckenbecken dysplasia sits in ISDS group 14
(severe spondylodysplastic dysplasias), so this is also a differential across
nosology groups.
evidence:
- reference: PMID:29122926
reference_title: Defect in phosphoinositide signalling through a homozygous variant in PLCB3 causes a new form of spondylometaphyseal dysplasia with corneal dystrophy.
supports: SUPPORT
evidence_source: HUMAN_CLINICAL
snippet: >-
Given that the radiological features, particularly the shape of ilium, were
similar to Schneckenbecken dysplasia (OMIM 269250), we sequenced SLC35D1 but
did not find any pathogenic variants
explanation: Documents the specific radiographic mimicry and its molecular exclusion.
- name: Spondylometaphyseal Dysplasias with Retinal Involvement
description: >-
Only two other spondylometaphyseal dysplasias involve the eye, and both affect
the retina rather than the cornea: SMD with cone-rod dystrophy (PCYT1A) and axial
SMD with retinal degeneration. An anterior-segment lesion with normal retinas
therefore separates SMDCD from both at the bedside.
evidence:
- reference: PMID:29122926
reference_title: Defect in phosphoinositide signalling through a homozygous variant in PLCB3 causes a new form of spondylometaphyseal dysplasia with corneal dystrophy.
supports: SUPPORT
evidence_source: HUMAN_CLINICAL
snippet: >-
Ophthalmological abnormalities have been reported in only two types of SMDs:
SMD cone rod dystrophy (SMDCRD, MIM 608940)
explanation: >-
Establishes that eye involvement in the SMD group was previously confined to
two retinal disorders, which is what makes the corneal phenotype diagnostic.
treatments:
- name: Corneal Grafting
description: >-
Both affected children underwent bilateral corneal grafting — one at six months,
followed by tarsorrhaphy and keratoplasty. Outcomes were mixed: the second child
experienced graft rejection, and the surviving proband still had blurred vision
from corneal opacities at six years.
treatment_term:
preferred_term: surgical procedure
term:
id: NCIT:C15329
label: Surgical Procedure
therapeutic_modality: SURGERY
target_mechanisms:
- target: Corneal Dystrophy
treatment_effect: MODULATES
description: >-
Grafting replaces the opacified tissue but does not address the underlying
signalling defect, and the reported outcomes suggest the benefit is partial and
not durable in every case.
evidence:
- reference: PMID:29122926
reference_title: Defect in phosphoinositide signalling through a homozygous variant in PLCB3 causes a new form of spondylometaphyseal dysplasia with corneal dystrophy.
supports: SUPPORT
directness: INDIRECT
evidence_source: HUMAN_CLINICAL
snippet: >-
He had corneal grafting of the right eye followed by the left eye, but he
experienced graft rejection.
explanation: >-
Graft rejection in one of the two treated children is why the effect is
recorded as partial.
evidence:
- reference: PMID:29122926
reference_title: Defect in phosphoinositide signalling through a homozygous variant in PLCB3 causes a new form of spondylometaphyseal dysplasia with corneal dystrophy.
supports: SUPPORT
evidence_source: HUMAN_CLINICAL
snippet: >-
The child had bilateral corneal grafting at the age of 6 months followed by
tarsorrhaphy and keratoplasty.
explanation: Documents the intervention actually performed.
- name: Respiratory Support
description: >-
Intubation and ventilation from birth, progressing to tracheostomy and continuous
supplemental oxygen for chronic respiratory failure. This is the dominant care
burden and the determinant of survival.
treatment_term:
preferred_term: supportive care
term:
id: NCIT:C15747
label: Supportive Care
therapeutic_modality: DEVICE
evidence:
- reference: PMID:29122926
reference_title: Defect in phosphoinositide signalling through a homozygous variant in PLCB3 causes a new form of spondylometaphyseal dysplasia with corneal dystrophy.
supports: SUPPORT
evidence_source: HUMAN_CLINICAL
snippet: >-
He is developmentally delayed and has chronic lung disease with chronic
respiratory failure requiring a tracheostomy and continuous oxygen
supplementation.
explanation: Documents the respiratory support required in the surviving child.
- name: Nutritional Support via Gastrostomy
description: >-
Gastrostomy feeding was required in the surviving child for chronic
gastro-oesophageal reflux with repeated aspiration pneumonia.
treatment_term:
preferred_term: Nutritional Support
term:
id: NCIT:C15433
label: Nutritional Support
therapeutic_modality: DEVICE
evidence:
- reference: PMID:29122926
reference_title: Defect in phosphoinositide signalling through a homozygous variant in PLCB3 causes a new form of spondylometaphyseal dysplasia with corneal dystrophy.
supports: SUPPORT
evidence_source: HUMAN_CLINICAL
snippet: >-
He also has a gastrostomy tube to counteract chronic gastro-oesophageal reflux
and repeated aspiration pneumonia.
explanation: Documents the feeding intervention actually performed.
- name: Genetic Counseling
description: >-
Autosomal recessive inheritance in a consanguineous family carries a 25 percent
recurrence risk, and the two affected children are cousins, so the risk extends
across the wider pedigree. Carrier testing for the familial allele is
straightforward once identified.
treatment_term:
preferred_term: genetic counseling
term:
id: NCIT:C15240
label: Genetic Counseling
therapeutic_modality: OTHER
evidence:
- reference: PMID:29122926
reference_title: Defect in phosphoinositide signalling through a homozygous variant in PLCB3 causes a new form of spondylometaphyseal dysplasia with corneal dystrophy.
supports: SUPPORT
evidence_source: HUMAN_CLINICAL
snippet: >-
Here, we report a consanguineous family from UAE with a new autosomal recessive
(AR) SMD associated with intellectual disability and corneal dystrophy (SMDCD)
caused by a homozygous variant in PLCB3.
explanation: >-
Establishes the consanguineous recessive family structure that makes
recurrence-risk counselling and cascade carrier testing the relevant action.
experimental_models:
- name: SMDCD patient-derived dermal fibroblasts
experimental_model_type: PRIMARY_CELL_CULTURE
description: >-
Primary adherent fibroblasts from a skin biopsy of patient IV-1, assayed for
PLCB3 protein level by immunoblot, for PIP2 by anti-PtdIns(4,5)P2
immunofluorescence, and for F-actin organisation by phalloidin staining scored
blind to genotype against a published four-pattern classification, with
cytochalasin D as a cytoskeletal control.
cell_source: Patient-derived (skin biopsy)
culture_system: Two-dimensional monolayer culture on coverslips
modeled_mechanisms:
- target: F-Actin Cytoskeletal Disorganisation
relationship: RECAPITULATES
fidelity: MODERATE
description: >-
The patient fibroblast is the only human cellular system reported for this
disorder and carries both the substrate-accumulation and the cytoskeletal
findings.
limitations: >-
Dermal fibroblasts are not chondrocytes, corneal keratocytes, or neurons, and
none of the three affected tissues has been modelled. The cellular phenotype is
therefore a demonstration that the allele is functionally consequential rather
than a model of any of the disease's organ lesions.
readouts:
- name: Anti-PtdIns(4,5)P2 immunofluorescence
target: F-Actin Cytoskeletal Disorganisation
direction: INCREASED
interpretation: >-
Elevated PIP2 in patient cells is the direct evidence that the variant
impairs substrate turnover in vivo.
- name: F-actin stress-fibre pattern score
target: F-Actin Cytoskeletal Disorganisation
direction: ALTERED
interpretation: >-
Blinded scoring of stress-fibre number and length shifts towards the weaker
patterns in patient cells.
evidence:
- reference: PMID:29122926
reference_title: Defect in phosphoinositide signalling through a homozygous variant in PLCB3 causes a new form of spondylometaphyseal dysplasia with corneal dystrophy.
supports: SUPPORT
evidence_source: IN_VITRO
snippet: >-
Here we show that this hypomorphic variant leads to elevated levels of PIP2
in patient fibroblasts, causing disorganisation of the F-actin cytoskeleton.
explanation: >-
States both readouts and the causal claim the model is used to support.
discussions:
- discussion_id: smdcd_single_family_evidence_base
kind: KNOWLEDGE_GAP
status: OPEN
attaches_to:
- disease#Spondylometaphyseal Dysplasia with Corneal Dystrophy
prompt: >-
Is SMDCD an established gene-disease relationship, given that it rests on one
homozygous missense allele in two cousins from a single family?
rationale: >-
Every clinical and molecular statement about this disorder comes from one report
of one consanguineous pedigree. The linkage interval spanned 19.3 Mb and 487
genes, and four homozygous candidate variants survived filtering; PLCB3 was
selected partly on the prior that phospholipid-metabolism genes such as PLCB4 and
PCYT1A cause bone dysplasia, and the three competitors were excluded by functional
assays rather than by independent genetic replication. The functional work is
good, but no second family has been published, so the relationship has not been
replicated in the way a gene-disease assertion normally requires. The ISDS
nosology nonetheless lists it as a distinct entity, which this entry follows while
recording the limitation.
evidence:
- reference: PMID:29122926
reference_title: Defect in phosphoinositide signalling through a homozygous variant in PLCB3 causes a new form of spondylometaphyseal dysplasia with corneal dystrophy.
supports: SUPPORT
evidence_source: HUMAN_CLINICAL
snippet: >-
Whole genome homozygosity mapping localised the genetic cause to 11q12.1-q13.1,
a region spanning 19.32 Mb with ~490 genes.
explanation: >-
The size of the linkage interval is what makes independent replication, rather
than functional exclusion of competitors, the missing evidence.
- reference: PMID:29122926
reference_title: Defect in phosphoinositide signalling through a homozygous variant in PLCB3 causes a new form of spondylometaphyseal dysplasia with corneal dystrophy.
supports: SUPPORT
directness: INDIRECT
evidence_source: HUMAN_CLINICAL
snippet: >-
Pathogenic variants in genes involved in phospholipid metabolism, such as PLCB4
and PCYT1A, are known to cause bone dysplasia with or without eye anomalies,
which led us to select PLCB3 as a strong candidate.
explanation: >-
Candidate selection was partly driven by a pathway prior, which is a legitimate
heuristic but not independent evidence.
proposed_experiments:
- experiment_id: exp_smdcd_independent_replication
name: Seek independent PLCB3 families through matchmaking
description: >-
Submit the PLCB3 phenotype to GeneMatcher and equivalent matchmaking services
and to skeletal dysplasia consortia, and reanalyse unsolved neonatal
corneal-clouding-plus-skeletal-dysplasia exomes for biallelic PLCB3 variants.
would_support:
- pathophysiology#Homozygous PLCB3 p.Ala878Ser
supporting_outcome:
- >-
A second unrelated family with biallelic PLCB3 variants and a matching
phenotype would convert the assertion from single-family to replicated.
would_refute:
- pathophysiology#Homozygous PLCB3 p.Ala878Ser
refuting_outcome:
- >-
Identification of a pathogenic variant in one of the other candidate genes in
the interval in a second family with the same phenotype would reopen the gene
assignment.
- discussion_id: smdcd_actin_to_organ_lesion_gap
kind: KNOWLEDGE_GAP
status: OPEN
attaches_to:
- pathophysiology#F-Actin Cytoskeletal Disorganisation
prompt: >-
How does a fibroblast actin phenotype account for a growth-plate dysplasia, a
corneal opacity, and severe developmental delay?
rationale: >-
The mechanism is demonstrated as far as the fibroblast and stops there. Three
distinct organ lesions are attributed to it, in tissues that were never assayed.
Zebrafish plcb3 nulls give some support for the skeletal branch, but mouse Plcb3
disruption is embryonic lethal and further knockout models gave discordant
results that the authors attribute to how the gene was disrupted — so there is no
settled animal model either. The corneal branch is the weakest: nothing connects
phosphoinositide signalling to corneal stromal transparency, and the opacity is
present within days of birth, implying a developmental rather than a degenerative
process.
evidence:
- reference: PMID:29122926
reference_title: Defect in phosphoinositide signalling through a homozygous variant in PLCB3 causes a new form of spondylometaphyseal dysplasia with corneal dystrophy.
supports: SUPPORT
directness: INDIRECT
evidence_source: MODEL_ORGANISM
snippet: >-
In mice, targeted disruption of plcb3 results in embryonic lethality.
explanation: >-
The lethality of the mouse null is why no mammalian model of the organ lesions
exists.
- reference: PMID:29122926
reference_title: Defect in phosphoinositide signalling through a homozygous variant in PLCB3 causes a new form of spondylometaphyseal dysplasia with corneal dystrophy.
supports: SUPPORT
directness: INDIRECT
evidence_source: MODEL_ORGANISM
snippet: >-
However, further Plcb3 knockout models showed discordant results.
explanation: >-
Discordance between knockout models means the existing animal evidence cannot
arbitrate the organ mechanisms.
proposed_experiments:
- experiment_id: exp_smdcd_hypomorphic_knockin_and_tissue_models
name: Hypomorphic Plcb3 knock-in and human tissue-specific models
description: >-
Generate a knock-in carrying the human p.A878S hypomorph rather than a null, so
that animals survive, and phenotype the growth plate, cornea, and brain.
Complement with patient iPSC-derived chondrocytes and corneal keratocytes
assayed for PIP2, actin organisation, and tissue-specific differentiation.
would_support:
- pathophysiology#Corneal Dystrophy
supporting_outcome:
- >-
Corneal opacity and a spondylometaphyseal skeletal phenotype in hypomorphic
animals would establish that the single allele accounts for the organ lesions.
would_refute:
- pathophysiology#F-Actin Cytoskeletal Disorganisation
refuting_outcome:
- >-
Normal actin organisation in patient-derived chondrocytes and keratocytes
despite the skeletal and corneal phenotypes would show the fibroblast actin
finding is not the operative mechanism in the affected tissues.
references:
- reference: PMID:36779427
title: "Nosology of genetic skeletal disorders: 2023 revision."
findings: []
clinical_trials: []
datasets: []
notes: >-
Curated as part of filling ISDS Nosology group 12 (Spondylometaphyseal
dysplasias), which was unpopulated when this work began. SMDCD is NOS 12-0050 in the 2023
revision and was one of the two group-12 members that the schema's own
description of the group did not name before this curation. The whole entry rests on a single family, which is
recorded explicitly as an open discussion rather than being smoothed over: the
functional work in patient fibroblasts is solid, but the gene-disease relationship
has not been independently replicated. Downstream edges from the cellular node to
the three organ lesions are graded INDIRECT_UNKNOWN_INTERMEDIATES for the same
reason.