Congenital limb malformation

Summary

Congenital limb malformation (MONDO:0019054) is a disease (an umbrella term covering 107 Mondo subtypes) with 1 cohort gene.

At a glance

• Umbrella term: 107 Mondo subtypes
• Cohort genes: 1
• ClinVar variants: 1

Clinical features

No curated clinical features (Orphanet) for this disease.

Identifiers

Disease identifiers

Field	Value
Canonical name	congenital limb malformation
Mondo ID	MONDO:0019054
Orphanet	68378
Is cancer (heuristic)	no

Also known as: congenital limb malformation

Data availability: 1 ClinVar variant.

Disease family

An umbrella term covering 107 Mondo subtypes.

Classification path: disease › human disease › disease by developmental or physiological process › disorder of development or morphogenesis › developmental defect during embryogenesis › congenital limb malformation

Related subtypes (51): disorder of sexual differentiation, hereditary neurocutaneous angioma, nevoid basal cell carcinoma syndrome, angioosteohypertrophic syndrome, Larsen syndrome, schwannomatosis, linear nevus sebaceous syndrome, lethal Larsen-like syndrome, pseudodiastrophic dysplasia, focal dermal hypoplasia, microtia, neurofibromatosis-Noonan syndrome, Becker nevus syndrome, Legius syndrome, bone fragility with contractures, arterial rupture, and deafness, blindness - scoliosis - arachnodactyly syndrome, cutis laxa - Marfanoid syndrome, Maffucci syndrome, hydrops fetalis, ankyloblepharon filiforme-imperforate anus syndrome, developmental anomaly of metabolic origin, progeroid syndrome, facial cleft, Desbuquois dysplasia, cysts and fistulae of the face and oral cavity, macroglossia, middle ear anomaly, cleft palate, cutis laxa, infectious embryofetopathy, toxic or drug-related embryofetopathy, hemihyperplasia-multiple lipomatosis syndrome, phakomatosis pigmentokeratotica, phakomatosis pigmentovascularis, PTEN hamartoma tumor syndrome, marfanoid habitus-inguinal hernia-advanced bone age syndrome, neurofibromatosis type 1, multiple congenital anomalies/dysmorphic syndrome, hereditary hemorrhagic telangiectasia, urogenital tract malformation, congenital anomaly of kidney and urinary tract, anotia, central nervous system malformation, Ehlers-Danlos syndrome, X-linked external auditory canal atresia-dilated internal auditory canal-facial dysmorphism syndrome, joint laxity, short stature, and myopia, diaphragmatic malformation, abdominal wall malformation, port-wine nevi-mega cisterna magna-hydrocephalus syndrome, conjoined twins, TP63-related ectodermal dysplasia spectrum with limb and orofacial malformations

Subtypes (107): Adams-Oliver syndrome, ADULT syndrome, Hypoglossia-hypodactyly syndrome, ankyloblepharon-ectodermal defects-cleft lip/palate syndrome, Cooks syndrome, Townes-Brocks syndrome, brachydactyly-arterial hypertension syndrome, brachydactyly-preaxial hallux varus syndrome, fibular aplasia-ectrodactyly syndrome, Brachymorphism-onychodysplasia-dysphalangism syndrome, brachytelephalangy-dysmorphism-Kallmann syndrome, femoral-facial syndrome, laurin-Sandrow syndrome, Emery-Nelson syndrome, hand-foot-genital syndrome, IVIC syndrome, Leri pleonosteosis, OSLAM syndrome, pelvis-shoulder dysplasia, phocomelia-ectrodactyly-deafness-sinus arrhythmia syndrome, Poland syndrome, crossed polysyndactyly, postaxial tetramelic oligodactyly, radio-renal syndrome, scalp defects-postaxial polydactyly syndrome, splenogonadal fusion-limb defects-micrognathia syndrome, Karsch-Neugebauer syndrome, symphalangism with multiple anomalies of hands and feet, proximal symphalangism, tarsal-carpal coalition syndrome, extensor tendons of finger anomalies, tetramelic monodactyly, thumb stiffness-brachydactyly-intellectual disability syndrome, tibia, hypoplasia or aplasia of, with polydactyly, Say-field-Coldwell syndrome, triphalangeal thumbs-brachyectrodactyly syndrome, humerus trochlea aplasia, Aphalangy-hemivertebrae-urogenital-intestinal dysgenesis syndrome, camptodactyly syndrome, Guadalajara type 2, Cenani-Lenz syndactyly syndrome, split hand-foot malformation 1 with sensorineural hearing loss, EEM syndrome, ectrodactyly-polydactyly syndrome, lethal faciocardiomelic dysplasia, femur-fibula-ulna complex, Gollop-Wolfgang complex, acromesomelic dysplasia 2B, Fuhrmann syndrome, hallux varus-preaxial polysyndactyly syndrome, Keutel syndrome, absence deformity of leg-cataract syndrome, intellectual disability-spasticity-ectrodactyly syndrome, fibular aplasia, tibial campomelia, and oligosyndactyly syndrome, pelviscapular dysplasia, radioulnar synostosis-developmental delay-hypotonia syndrome, rapadilino syndrome, EEC syndrome, Sugarman brachydactyly, tetraamelia-multiple malformations syndrome, thrombocytopenia-absent radius syndrome, phocomelia, Schinzel type, ulna hypoplasia-intellectual disability syndrome, syndactyly-telecanthus-anogenital and renal malformations syndrome, Mononen-Karnes-Senac syndrome, absent radius-anogenital anomalies syndrome, ulnar hypoplasia-split foot syndrome, aphalangy-syndactyly-microcephaly syndrome, 2q37 microdeletion syndrome, absent tibia-polydactyly-arachnoid cyst syndrome, skeletal dysplasia-epilepsy-short stature syndrome, autosomal recessive amelia, temtamy preaxial brachydactyly syndrome, radio-ulnar synostosis-amegakaryocytic thrombocytopenia syndrome, acropectoral syndrome, familial digital arthropathy-brachydactyly, Duane-radial ray syndrome, ulnar/fibula ray defect-brachydactyly syndrome, intellectual disability-brachydactyly-Pierre Robin syndrome, Al-Gazali syndrome, cocoon syndrome, mammary-digital-nail syndrome, syndactyly-camptodactyly and clinodactyly of fifth fingers-bifid toes syndrome, postaxial polydactyly-anterior pituitary anomalies-facial dysmorphism syndrome, split-foot malformation-mesoaxial polydactyly syndrome, TELO2-related intellectual disability-neurodevelopmental disorder, arthrogryposis syndrome, radial deficiency-tibial hypoplasia syndrome, camptodactyly-taurinuria syndrome, fibular dimelia-diplopodia syndrome, shoulder and thorax deformity-congenital heart disease syndrome, Cornelia de Lange syndrome, familial clubfoot with or without associated lower limb anomalies, heart-hand syndrome, hyperphosphatasia-intellectual disability syndrome, limb transversal defect-cardiac anomaly syndrome, triphalangeal thumb-polysyndactyly syndrome, multiple synostoses syndrome, hereditary thrombocytosis with transverse limb defect, thalidomide embryopathy, tibial aplasia-ectrodactyly syndrome, microcephaly-brachydactyly-kyphoscoliosis syndrome, acrofacial dysostosis, caudal regression-sirenomelia spectrum, Rubinstein-Taybi syndrome, acrocephalosyndactyly, congenital progressive bone marrow failure-B-cell immunodeficiency-skeletal dysplasia syndrome, omphalocele-diaphragmatic hernia-cardiovascular anomalies-radial ray defect syndrome

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

1 retrieved; paginated sample, class counts are floors:

1 uncertain significance

ClinVar	Variant (HGVS)	Gene	Classification	Review
4075173	NM_022458.4(LMBR1):c.901CTT[1] (p.Leu302del)	LMBR1	Uncertain significance	criteria provided, single submitter

Genes & proteins

Mendelian disease overlap and somatic drivers

GenCC: 0 · Orphanet: 6 · OMIM-shared: 0 · Dual-evidence (GWAS+Mendelian): 0

Orphanet rare-disease linkage (cohort genes)

Gene	Orphanet ID	Rare disease
LMBR1	Orphanet:2378	Laurin-Sandrow syndrome
LMBR1	Orphanet:931	Isolated acheiropodia
LMBR1	Orphanet:93321	Isolated radial hemimelia
LMBR1	Orphanet:93336	Polydactyly of a triphalangeal thumb
LMBR1	Orphanet:93405	Syndactyly type 4
LMBR1	Orphanet:988	Tibial hemimelia-polysyndactyly-triphalangeal thumb syndrome

Cohort genes → proteins

1 cohort genes, 1 distinct canonical proteins.

Evidence partition

Subset	Genes
multi_evidence	1

Cohort genes (full)

Symbol	HGNC	Ensembl	UniProt	Name	Evidence
LMBR1	HGNC:13243	ENSG00000105983	Q8WVP7	Limb region 1 protein homolog	clinvar

Cohort function summary

Lead sentence per gene, UniProt-curated.

Symbol	Protein name	Function (lead sentence)
LMBR1	Limb region 1 protein homolog	Putative membrane receptor.

Protein-family classification

Druggable: 0 · Difficult: 0 · Unknown: 1 · 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.

Family	Genes	Fold	FDR
Other/Unknown	1	1.8×	0.558

Per-gene assignment

Symbol	Family	Druggable?	EC	InterPro (top 3)
LMBR1	Other/Unknown	no		LMBR1-like_membr_prot, LIMR

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)

Bucket	Genes
narrow (1-5 tissues)	0
moderate (6-20)	0
broad (>20)	1
unknown	0

Top tissues across cohort

Tissue	Cohort genes
adrenal tissue	1
calcaneal tendon	1
sural nerve	1

Per-gene tissue summary (top 30)

Symbol	Bgee breadth	FANTOM5 breadth	SCXA	Top tissues
LMBR1	249	ubiquitous	marker	adrenal tissue, sural nerve, calcaneal tendon

Protein interactions among cohort

Intra-cohort edges: 0.

Hub genes (top 10 by interactor count)

Symbol	Interactor count
LMBR1	977

Structural data

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

AlphaFold-only cohort genes (top 30 by pLDDT)

Symbol	UniProt	pLDDT
LMBR1	Q8WVP7	79.49

Function

Pathway analysis

Distinct Reactome pathways touched by cohort: 0. Enrichment computed across 1 evidence-associated genes (0 with Reactome annotation).

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 term	Cohort genes	Fold	FDR	Sample cohort genes
embryonic digit morphogenesis	1	300.9×	0.007	LMBR1
signal transduction	1	16.1×	0.062	LMBR1

Therapeutics

Drug target analysis

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

Druggability breadth: 0 of 1 evidence-associated genes (0%) have a ChEMBL target (buckets above are over the deeply-mined display cohort).

Top cohort targets by molecule count

Symbol	Molecules	Max phase
LMBR1	0	0

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):

Tier	Definition	Genes	Symbols
A	Approved (phase 4 drug)	0
B	Phased (≥1) drug, not yet approved	0
C	Druggable family + PDB, no drug	0
D	Druggable family + AlphaFold only, no drug	0
E	Difficult family or no structure, no drug	1	LMBR1

Undrugged target profiles

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

Symbol	ChEMBL assays	Drugged partners (top 3)
LMBR1	0	—

Clinical trials & evidence

Clinical trials

Clinical trials: 0.