Autosomal recessive omodysplasia

disease
On this page

Also known as micromelic dysplasia congenita with dislocation of radiusmicromelic dysplasia-dislocation of radius syndromeOMOD1omodysplasia 1omodysplasia autosomal recessiveomodysplasia generalised formomodysplasia generalized formomodysplasia type 1omodysplasia, autosomal recessiveomodysplasia, generalised form

Summary

Autosomal recessive omodysplasia (MONDO:0009779) is a disease caused by GPC6 (GenCC Strong), with 2 cohort genes.

At a glance

  • Prevalence: <1 / 1 000 000 (Worldwide) [Orphanet-validated]
  • Causal gene: GPC6 (GenCC Strong)
  • Cohort genes: 2
  • ClinVar variants: 132
  • Phenotypes (HPO): 24

Clinical features

Epidemiology

Prevalence records

2 prevalence record(s), Orphanet:

TypeClassValueGeographyValidation
Cases/families23WorldwideValidated
Point prevalence<1 / 1 000 000WorldwideValidated

Signs & symptoms

Clinical features (HPO)

24 HPO clinical features (Orphanet curated; top 24 by frequency):

HPO IDTermFrequency
HP:0000343Long philtrumVery frequent (80-99%)
HP:0000358Posteriorly rotated earsVery frequent (80-99%)
HP:0000369Low-set earsVery frequent (80-99%)
HP:0000463Anteverted naresVery frequent (80-99%)
HP:0000944Abnormal metaphysis morphologyVery frequent (80-99%)
HP:0002007Frontal bossingVery frequent (80-99%)
HP:0002818Abnormal morphology of the radiusVery frequent (80-99%)
HP:0003042Elbow dislocationVery frequent (80-99%)
HP:0004322Short statureVery frequent (80-99%)
HP:0005025Hypoplastic distal humeriVery frequent (80-99%)
HP:0005280Depressed nasal bridgeVery frequent (80-99%)
HP:0008905RhizomeliaVery frequent (80-99%)
HP:0000028CryptorchidismFrequent (30-79%)
HP:0000347MicrognathiaFrequent (30-79%)
HP:0002823Abnormality of femur morphologyFrequent (30-79%)
HP:0002983MicromeliaFrequent (30-79%)
HP:0003027MesomeliaFrequent (30-79%)
HP:0001059PterygiumOccasional (5-29%)
HP:0001249Intellectual disabilityOccasional (5-29%)
HP:0001363CraniosynostosisOccasional (5-29%)
HP:0003196Short noseOccasional (5-29%)
HP:0010880Increased nuchal translucencyOccasional (5-29%)
HP:0030680Abnormal cardiovascular system morphologyOccasional (5-29%)
HP:0100790HerniaOccasional (5-29%)

Identifiers

Disease identifiers

FieldValue
Canonical nameautosomal recessive omodysplasia
Mondo IDMONDO:0009779
OMIM258315
Orphanet93329
DOIDDOID:0080844
ICD-11350802889
SNOMED CT725166005
UMLSC1850318
MedGen340513
GARD0004076
Is cancer (heuristic)no

Also known as: autosomal recessive omodysplasia · micromelic dysplasia congenita with dislocation of radius · micromelic dysplasia-dislocation of radius syndrome · OMOD1 · omodysplasia 1 · omodysplasia autosomal recessive · omodysplasia generalised form · omodysplasia generalized form · omodysplasia type 1 · omodysplasia, autosomal recessive · omodysplasia, generalised form

Data availability: 132 ClinVar variants · 5 GenCC gene-disease records.

Disease family

Classification path: disease › human disease › disease by etiologic mechanism › disease of genetic or genomic mechanism › hereditary disease › autosomal genetic disease › autosomal recessive diseaseautosomal recessive omodysplasia

Related subtypes (218): immunodeficiency-centromeric instability-facial anomalies syndrome, hypercalcemia, infantile, Ochoa syndrome, autosomal recessive Ehlers-Danlos syndrome, vascular type, hydrolethalus syndrome, 3-M syndrome, isolated hyperchlorhidrosis, dacryocystitis-osteopoikilosis syndrome, Hutchinson-Gilford progeria syndrome, achalasia microcephaly syndrome, acrorenal syndrome, autosomal recessive, beta-ketothiolase deficiency, autosomal recessive Alport syndrome, Alstrom syndrome, microphthalmia with limb anomalies, camptodactyly-arthropathy-coxa vara-pericarditis syndrome, Behr syndrome, bifid nose, autosomal recessive, Bloom syndrome, Bowen-Conradi syndrome, camptodactyly with fibrous tissue hyperplasia and skeletal dysplasia, heart defects-limb shortening syndrome, autosomal recessive palmoplantar keratoderma and congenital alopecia, COFS syndrome, craniometaphyseal dysplasia, autosomal recessive, Fraser syndrome, cystic fibrosis, polycystic lipomembranous osteodysplasia with sclerosing leukoencephaly, persistent hyperplastic primary vitreous, autosomal recessive, Donnai-Barrow syndrome, Schöpf-Schulz-Passarge syndrome, cleft lip/palate-ectodermal dysplasia syndrome, Ellis-van Creveld syndrome, Wolcott-Rallison syndrome, autosomal recessive faciodigitogenital syndrome, acromesomelic dysplasia 2B, brittle cornea syndrome, triple-A syndrome, autosomal recessive humeroradial synostosis, multinucleated neurons-anhydramnios-renal dysplasia-cerebellar hypoplasia-hydranencephaly syndrome, hydrocephalus, nonsyndromic, autosomal recessive 1, autosomal recessive hydrocephalus due to congenital stenosis of aqueduct of Sylvius, hypertelorism, microtia, facial clefting syndrome, hypoparathyroidism-retardation-dysmorphism syndrome, Vici syndrome, Johanson-Blizzard syndrome, autosomal recessive Kenny-Caffey syndrome, Papillon-Lefevre disease, Haim-Munk syndrome, Laurence-Moon syndrome, Donohue syndrome, lipase deficiency, combined, autosomal recessive familial Mediterranean fever, thiamine-responsive megaloblastic anemia syndrome, cartilage-hair hypoplasia, Nijmegen breakage syndrome, pseudo-TORCH syndrome, Galloway-Mowat syndrome, mulibrey nanism, myotonia congenita, autosomal recessive, Schwartz-Jampel syndrome, proteosome-associated autoinflammatory syndrome, Netherton syndrome, Niemann-Pick disease type A, oculodentodigital dysplasia, autosomal recessive, odonto-onycho-dermal dysplasia, osteoporosis-pseudoglioma syndrome, Shwachman-Diamond syndrome, phenylketonuria, Bjornstad syndrome, Laron syndrome, autosomal recessive polycystic kidney disease, autosomal recessive inherited pseudoxanthoma elasticum, autosomal recessive multiple pterygium syndrome, rapadilino syndrome, short-rib thoracic dysplasia 9 with or without polydactyly, autosomal recessive Robinow syndrome, Sjogren-Larsson syndrome, scapuloperoneal spinal muscular atrophy, autosomal recessive, spondyloepiphyseal dysplasia tarda, autosomal recessive, inherited threoninemia, Pendred syndrome, autosomal recessive spondylocostal dysostosis, Werner syndrome, ABCD syndrome, Naxos disease, autosomal recessive amelia, human HOXA1 syndromes, sickle cell disease, autosomal recessive proximal renal tubular acidosis, hyper-IgM syndrome type 2, temtamy preaxial brachydactyly syndrome, TH-deficient dopa-responsive dystonia, craniosynostosis syndrome, autosomal recessive, Niemann-Pick disease type B, skin fragility-woolly hair-palmoplantar keratoderma syndrome, CoQ-responsive OXPHOS deficiency, familial adenomatous polyposis 2, Pierson syndrome, palmoplantar keratoderma-XX sex reversal-predisposition to squamous cell carcinoma syndrome, cardiomyopathy-hypotonia-lactic acidosis syndrome, PHARC syndrome, Kahrizi syndrome, cutis laxa with severe pulmonary, gastrointestinal and urinary anomalies, congenital prothrombin deficiency, immunodeficiency 31B, dyskeratosis congenita, autosomal recessive 2, dyskeratosis congenita, autosomal recessive 3, Nestor-Guillermo progeria syndrome, leukoencephalopathy with calcifications and cysts, mitochondrial pyruvate carrier deficiency, branched-chain keto acid dehydrogenase kinase deficiency, dyskeratosis congenita, autosomal recessive 5, hypohidrosis-enamel hypoplasia-palmoplantar keratoderma-intellectual disability syndrome, alacrima, achalasia, and intellectual disability syndrome, hyperlipoproteinemia, type 1D, microcephaly and chorioretinopathy 2, congenital stationary night blindness 1G, combined oxidative phosphorylation deficiency 29, hypermanganesemia with dystonia 2, growth retardation, intellectual developmental disorder, hypotonia, and hepatopathy, gnb5-related intellectual disability-cardiac arrhythmia syndrome, autosomal recessive spastic paraplegia type 78, autosomal recessive limb-girdle muscular dystrophy, Bardet-Biedl syndrome, autosomal recessive cerebellar ataxia, neuronopathy, distal hereditary motor, autosomal recessive, UV-sensitive syndrome, Ehlers-Danlos syndrome, kyphoscoliotic type 1, Cockayne syndrome, hyperphenylalaninemia due to tetrahydrobiopterin deficiency, leukoencephalopathy-palmoplantar keratoderma syndrome, autosomal recessive hypohidrotic ectodermal dysplasia, Warburg micro syndrome, autosomal recessive primary microcephaly, autosomal recessive progressive external ophthalmoplegia, Meier-Gorlin syndrome, autosomal recessive sideroblastic anemia, autosomal recessive intermediate Charcot-Marie-Tooth disease, Perrault syndrome, autosomal recessive hypophosphatemic rickets, de Barsy syndrome, leukocyte adhesion deficiency, Senior-Loken syndrome, autosomal recessive spastic ataxia, childhood-onset autosomal recessive myopathy with external ophthalmoplegia, autosomal recessive cerebral atrophy, GM3 synthase deficiency, autosomal recessive distal renal tubular acidosis, pigmentation defects-palmoplantar keratoderma-skin carcinoma syndrome, autosomal recessive brachyolmia, Aicardi-Goutieres syndrome, homocystinuria without methylmalonic aciduria, Niemann-Pick disease type C, nephronophthisis, autosomal recessive osteopetrosis, peroxisome biogenesis disorder, congenital non-bullous ichthyosiform erythroderma, Seckel syndrome, Usher syndrome, autosomal recessive cutis laxa type 1, autosomal recessive cutis laxa type 2, hearing loss, autosomal recessive, microcephaly, growth restriction, and increased sister chromatid exchange 2, encephalopathy, progressive, early-onset, with brain edema and/or leukoencephalopathy, 1, congenital vertebral-cardiac-renal anomalies syndrome, hair defect with photosensitivity and intellectual disability syndrome, autosomal recessive severe congenital neutropenia, severe combined immunodeficiency due to CARMIL2 deficiency, extraoral halitosis due to methanethiol oxidase deficiency, neurodevelopmental disorder with microcephaly, impaired language, epilepsy, and gait abnormalities, mitochondrial complex 2 deficiency, nuclear type 3, mitochondrial complex 2 deficiency, nuclear type 4, mismatch repair cancer syndrome, spondyloepimetaphyseal dysplasia with joint laxity, type 3, Kilquist syndrome, Duane anomaly-myopathy-scoliosis syndrome, autosomal recessive axonal charcot-marie-tooth disease due to copper metabolism defect, immune dysregulation-inflammatory bowel disease-arthritis-recurrent infections-lymphopenia syndrome, optic atrophy-ataxia-peripheral neuropathy-global developmental delay syndrome, congenital myopathy with reduced type 2 muscle fibers, NAD(P)HX dehydratase deficiency, autosomal recessive ocular albinism, ichthyosis linearis circumflexa, eosinophil peroxidase deficiency, hyperphenylalaninemia due to DNAJC12 deficiency, autosomal recessive epidermolytic ichthyosis, Ehlers-Danlos syndrome, classic-like, 2, joint laxity, short stature, and myopia, HELIX syndrome, auditory neuropathy-optic atrophy syndrome, glycosylphosphatidylinositol biosynthesis defect 15, neurodegeneration, childhood-onset, stress-induced, with variable ataxia and seizures, SCN4A-related myopathy, autosomal recessive, Uner Tan Syndrome, nephropathic cystinosis, Imerslund-Grasbeck syndrome type 1, Imerslund-Grasbeck syndrome type 2, permanent neonatal diabetes mellitus 1, growth hormone insensitivity with immune dysregulation 1, autosomal recessive, Rajab interstitial lung disease with brain calcifications 1, Roberts-SC phocomelia syndrome, neurodevelopmental disorder with microcephaly, impaired language, and gait abnormalities, RPE65-related recessive retinopathy, GUCY2D-related recessive retinopathy, autosomal recessive titinopathy, intellectual disability, autosomal recessive, ALPL-related autosomal recessive hypophosphatasia, spastic paraplegia 18b, autosomal recessive, CEP164-related ciliopathy, RP1-related recessive retinopathy, pseudohypoaldosteronism, type IB2, autosomal recessive, pseudohypoaldosteronism, type IB3, autosomal recessive, spastic paraplegia 30B, autosomal recessive, cerebral arteriopathy, autosomal recessive, with subcortical infarcts and leukoencephalopathy 1, brain small vessel disease 2B, autosomal recessive, IMPG1-related recessive retinopathy, PROM1-related recessive retinopathy

Genetics & variants

GWAS landscape

No GWAS associations recorded — common-variant (GWAS) studies don’t cover this disease (typical for Mendelian / rare diseases). See the curated gene cohort and Mendelian overlap below.

Variant details and genetic-evidence tiers

ClinVar germline variants

132 retrieved; paginated sample, class counts are floors:

85 uncertain significance, 29 benign, 7 pathogenic, 5 likely benign, 4 conflicting classifications of pathogenicity, 2 benign/likely benign

ClinVarVariant (HGVS)GeneClassificationReview
5549NM_005708.5(GPC6):c.778del (p.Leu260fs)GPC6Pathogenicno assertion criteria provided
5550NC_000013.11:g.93997007_94063501del66495insATAAATCACTTAGAGATGTGPC6Pathogenicno assertion criteria provided
5551NC_000013.11:g.94252984_94352299del99316insCTAGPC6Pathogenicno assertion criteria provided
5553NM_005708.3(GPC6):c.712_877dupGPC6Pathogenicno assertion criteria provided
5552NM_005708.5(GPC6):c.700C>T (p.Arg234Ter)GPC6-AS2Pathogenicno assertion criteria provided
5554NM_005708.3(GPC6):c.320_711delGPC6-AS2Pathogenicno assertion criteria provided
5555NM_005708.3(GPC6):c.320_711delGPC6-AS2Pathogenicno assertion criteria provided
312551NM_005708.5(GPC6):c.1485A>T (p.Ser495=)GPC6Conflicting classifications of pathogenicitycriteria provided, conflicting classifications
312553NM_005708.5(GPC6):c.1524G>A (p.Thr508=)GPC6Conflicting classifications of pathogenicitycriteria provided, conflicting classifications
881581NM_005708.5(GPC6):c.1289+13C>TGPC6Conflicting classifications of pathogenicitycriteria provided, conflicting classifications
882731NM_005708.5(GPC6):c.1512C>T (p.Asp504=)GPC6Conflicting classifications of pathogenicitycriteria provided, conflicting classifications
1806178NM_005708.5(GPC6):c.1228G>A (p.Glu410Lys)GPC6Uncertain significancecriteria provided, single submitter
287156NM_005708.5(GPC6):c.1129G>A (p.Ala377Thr)GPC6Uncertain significancecriteria provided, multiple submitters, no conflicts
3065600NM_005708.5(GPC6):c.49C>T (p.Leu17Phe)GPC6Uncertain significancecriteria provided, single submitter
3065690NM_005708.5(GPC6):c.1193T>G (p.Val398Gly)GPC6Uncertain significancecriteria provided, single submitter
312530NM_005708.5(GPC6):c.-442C>TGPC6Uncertain significancecriteria provided, single submitter
312532NM_005708.5(GPC6):c.-307T>AGPC6Uncertain significancecriteria provided, single submitter
312534NM_005708.5(GPC6):c.-133G>TGPC6Uncertain significancecriteria provided, single submitter
312535NM_005708.5(GPC6):c.-100G>AGPC6Uncertain significancecriteria provided, single submitter
312536NM_005708.5(GPC6):c.-69C>TGPC6Uncertain significancecriteria provided, single submitter
312537NM_005708.5(GPC6):c.-23G>TGPC6Uncertain significancecriteria provided, single submitter
312538NM_005708.5(GPC6):c.49C>A (p.Leu17Ile)GPC6Uncertain significancecriteria provided, multiple submitters, no conflicts
312539NM_005708.5(GPC6):c.161-4G>TGPC6Uncertain significancecriteria provided, single submitter
312540NM_005708.5(GPC6):c.585C>T (p.Asp195=)GPC6Uncertain significancecriteria provided, single submitter
312542NM_005708.5(GPC6):c.1033A>G (p.Lys345Glu)GPC6Uncertain significancecriteria provided, single submitter
312543NM_005708.5(GPC6):c.1088G>A (p.Arg363His)GPC6Uncertain significancecriteria provided, multiple submitters, no conflicts
312544NM_005708.5(GPC6):c.1137A>C (p.Thr379=)GPC6Uncertain significancecriteria provided, single submitter
312545NM_005708.5(GPC6):c.1162A>G (p.Ile388Val)GPC6Uncertain significancecriteria provided, multiple submitters, no conflicts
312546NM_005708.5(GPC6):c.1216A>G (p.Ile406Val)GPC6Uncertain significancecriteria provided, multiple submitters, no conflicts
312552NM_005708.5(GPC6):c.1496G>A (p.Ser499Asn)GPC6Uncertain significancecriteria provided, multiple submitters, no conflicts

Genes & proteins

Mendelian disease overlap and somatic drivers

GenCC: 5 · Orphanet: 1 · OMIM-shared: 0 · Dual-evidence (GWAS+Mendelian): 0

GenCC gene–disease validity (cohort genes)

the Disease column is the GenCC-asserted condition — a cohort gene’s strongest validity may be for a related predisposition syndrome.

GeneClassificationInheritanceDiseaseRecords
GPC6StrongAutosomal recessiveautosomal recessive omodysplasia5

Orphanet rare-disease linkage (cohort genes)

GeneOrphanet IDRare disease
GPC6Orphanet:93329Autosomal recessive omodysplasia

Cohort genes → proteins

2 cohort genes, 1 distinct canonical proteins.

Evidence partition

SubsetGenes
multi_evidence2

Cohort genes (full)

SymbolHGNCEnsemblUniProtNameEvidence
GPC6HGNC:4454ENSG00000183098Q9Y625Glypican-6gencc,clinvar
GPC6-AS2HGNC:39910ENSG00000224394GPC6 antisense RNA 2clinvar

Cohort function summary

Lead sentence per gene, UniProt-curated.

SymbolProtein nameFunction (lead sentence)
GPC6Glypican-6Cell surface proteoglycan that bears heparan sulfate.

Protein-family classification

Druggable: 0 · Difficult: 0 · Unknown: 2 · Druggable fraction: 0.0

Family distribution

Cohort families vs a genome-wide background (hypergeometric, BH-FDR; fold = observed/expected). Counts kept; sorted by enrichment, so the catch-all Other/Unknown bucket no longer leads.

FamilyGenesFoldFDR
Other/Unknown21.8×0.312

Per-gene assignment

SymbolFamilyDruggable?ECInterPro (top 3)
GPC6Other/UnknownnoGlypican, Glypican_CS
GPC6-AS2Other/Unknownno

Expression context

Cohort genes with no expression data: 0.

1 cohort gene are a single-cell marker in ≥1 SCXA experiment.

Breadth distribution (Bgee present_calls)

BucketGenes
narrow (1-5 tissues)0
moderate (6-20)0
broad (>20)2
unknown0

Top tissues across cohort

TissueCohort genes
cartilage tissue1
tibia1
vena cava1
adrenal gland1
adrenal tissue1
male germ line stem cell (sensu Vertebrata) in testis1

Per-gene tissue summary (top 30)

SymbolBgee breadthFANTOM5 breadthSCXATop tissues
GPC6217ubiquitousmarkercartilage tissue, tibia, vena cava
GPC6-AS281yesmale germ line stem cell (sensu Vertebrata) in testis, adrenal tissue, adrenal gland

Protein interactions among cohort

Intra-cohort edges: 0.

Hub genes (top 10 by interactor count)

SymbolInteractor count
GPC61,237
GPC6-AS20

Structural data

PDB: 0 · AlphaFold-only: 1 · No structure: 1

AlphaFold-only cohort genes (top 30 by pLDDT)

SymbolUniProtpLDDT
GPC6Q9Y62582.67

Function

Pathway analysis

Distinct Reactome pathways touched by cohort: 16. Enrichment computed across 2 evidence-associated genes (1 with Reactome annotation).

Pathways by enrichment

Over-representation of cohort genes vs the genome-wide background (hypergeometric test, Benjamini-Hochberg FDR; fold = observed/expected over 1 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.

PathwayCohort genesFoldFDRSample cohort genes
Defective EXT2 causes exostoses 21815.7×0.004GPC6
Defective EXT1 causes exostoses 1, TRPS2 and CHDS1815.7×0.004GPC6
Attachment and Entry1601.0×0.004GPC6
Defective B4GALT7 causes EDS, progeroid type1571.0×0.004GPC6
Defective B3GAT3 causes JDSSDHD1571.0×0.004GPC6
Defective B3GALT6 causes EDSP2 and SEMDJL11571.0×0.004GPC6
HS-GAG degradation1496.5×0.004GPC6
Respiratory syncytial virus (RSV) attachment and entry1496.5×0.004GPC6
Initiation of coagulation cascade1475.8×0.004GPC6
Glycosaminoglycan-protein linkage region biosynthesis1393.8×0.004GPC6
HS-GAG biosynthesis1346.1×0.004GPC6
Dengue Virus Attachment and Entry1259.6×0.005GPC6
Retinoid metabolism and transport1248.3×0.005GPC6
Regulation of clotting cascade1233.1×0.005GPC6
RSV-host interactions1156.4×0.007GPC6
Dengue Virus-Host Interactions145.7×0.022GPC6

GO biological processes by enrichment

Over-representation of cohort genes vs the genome-wide background (hypergeometric test, Benjamini-Hochberg FDR; fold = observed/expected over 1 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.

GO termCohort genesFoldFDRSample cohort genes
regulation of neurotransmitter receptor localization to postsynaptic specialization membrane1887.0×0.003GPC6
regulation of signal transduction1267.5×0.006GPC6
cell migration161.5×0.016GPC6

Therapeutics

Drug target analysis

Approved (phase 4): 0 · Phase ≥3: 0 · Phased (≥1): 0 · Undrugged: 2

Druggability breadth: 0 of 2 evidence-associated genes (0%) have a ChEMBL target (buckets above are over the deeply-mined display cohort).

Top cohort targets by molecule count

SymbolMoleculesMax phase
GPC600
GPC6-AS200

Bioactivity and enzyme data

Enzyme cohort genes (≥1 EC): 0.

Pharmacogenomics

Cohort genes with a PharmGKB record: 1; with CPIC/DPWG dosing guidelines: 0.

No cohort gene has a CPIC/DPWG genotype-guided dosing guideline (PharmGKB).

Chemical tractability of cohort targets

0 approved/phased compounds have measured bioactivity against a cohort gene (and aren’t yet in disease-level trials). This is a research / tractability signal, NOT a therapeutic recommendation — a bioactivity row often reflects off-target or screening binding (e.g. promiscuous kinase inhibitors against a cohort kinase), implying no disease mechanism.

Druggability pyramid

Cohort genes binned by druggability tier (high → low):

TierDefinitionGenesSymbols
AApproved (phase 4 drug)0
BPhased (≥1) drug, not yet approved0
CDruggable family + PDB, no drug0
DDruggable family + AlphaFold only, no drug0
EDifficult family or no structure, no drug2GPC6, GPC6-AS2

Undrugged target profiles

2 cohort genes are undrugged. Ranked by ‘starting-point quality’ (assay depth + drugged-partner adjacency).

SymbolChEMBL assaysDrugged partners (top 3)
GPC60
GPC6-AS20

Clinical trials & evidence

Clinical trials

Clinical trials: 0.