Limb-mammary syndrome

Summary

Limb-mammary syndrome (MONDO:0011334) is a disease caused by TP63 (GenCC Definitive), with 1 cohort gene.

At a glance

• Prevalence: <1 / 1 000 000 (Worldwide) [Orphanet-validated]
• Causal gene: TP63 (GenCC Definitive)
• Cohort genes: 1
• ClinVar variants: 85
• Phenotypes (HPO): 32

Clinical features

Epidemiology

Prevalence records

2 prevalence record(s), Orphanet:

Type	Class	Value	Geography	Validation
Cases/families		38	Worldwide	Validated
Point prevalence	<1 / 1 000 000		Worldwide	Validated

Signs & symptoms

Clinical features (HPO)

32 HPO clinical features (Orphanet curated; top 32 by frequency):

HPO ID	Term	Frequency
HP:0000564	Lacrimal duct atresia	Frequent (30-79%)
HP:0001092	Absent lacrimal punctum	Frequent (30-79%)
HP:0002557	Hypoplastic nipples	Frequent (30-79%)
HP:0002561	Absent nipple	Frequent (30-79%)
HP:0012814	Bilateral breast hypoplasia	Frequent (30-79%)
HP:0100783	Breast aplasia	Frequent (30-79%)
HP:0000175	Cleft palate	Occasional (5-29%)
HP:0000193	Bifid uvula	Occasional (5-29%)
HP:0000498	Blepharitis	Occasional (5-29%)
HP:0000668	Hypodontia	Occasional (5-29%)
HP:0000958	Dry skin	Occasional (5-29%)
HP:0000966	Hypohidrosis	Occasional (5-29%)
HP:0001159	Syndactyly	Occasional (5-29%)
HP:0001770	Toe syndactyly	Occasional (5-29%)
HP:0002164	Nail dysplasia	Occasional (5-29%)
HP:0004209	Clinodactyly of the 5th finger	Occasional (5-29%)
HP:0007717	Chronic irritative conjunctivitis	Occasional (5-29%)
HP:0011819	Submucous cleft soft palate	Occasional (5-29%)
HP:0011939	3-4 finger cutaneous syndactyly	Occasional (5-29%)
HP:0012165	Oligodactyly	Occasional (5-29%)
HP:0410005	Cleft hard palate	Occasional (5-29%)
HP:0410030	Cleft lip	Occasional (5-29%)
HP:0000151	Aplasia of the uterus	Very rare (<1-4%)
HP:0000272	Malar flattening	Very rare (<1-4%)
HP:0000411	Protruding ear	Very rare (<1-4%)
HP:0000786	Primary amenorrhea	Very rare (<1-4%)
HP:0001480	Freckling	Very rare (<1-4%)
HP:0001596	Alopecia	Very rare (<1-4%)
HP:0003765	Psoriasiform dermatitis	Very rare (<1-4%)
HP:0007565	Multiple cafe-au-lait spots	Very rare (<1-4%)
HP:0010463	Aplasia of the ovary	Very rare (<1-4%)
HP:0045075	Sparse eyebrow	Very rare (<1-4%)

Identifiers

Disease identifiers

Field	Value
Canonical name	limb-mammary syndrome
Mondo ID	MONDO:0011334
MeSH	C535903
OMIM	603543
Orphanet	69085
ICD-11	1958986288
SNOMED CT	721972001
UMLS	C1863753
MedGen	355051
GARD	0010051
Is cancer (heuristic)	no

Also known as: limb-mammary syndrome · LMS · mammary hypoplasia, ectrodactyly, and other hand/foot anomalies

Data availability: 85 ClinVar variants · 2 GenCC gene-disease records.

Disease family

Classification path: disease › human disease › disease by body system or component › syndromic disease › ectodermal dysplasia syndrome › limb-mammary syndrome

Related subtypes (119): ADULT syndrome, autosomal dominant palmoplantar keratoderma and congenital alopecia, ameloonychohypohidrotic syndrome, ankyloblepharon-ectodermal defects-cleft lip/palate syndrome, anonychia with flexural pigmentation, Böök syndrome, blepharocheilodontic syndrome, Stern-Lubinsky-Durrie syndrome, dermatopathia pigmentosa reticularis, dermo-odonto dysplasia, Rapp-Hodgkin syndrome, Clouston syndrome, ectodermal dysplasia, trichoodontoonychial type, gingival fibromatosis-hypertrichosis syndrome, hypertrichosis cubiti-short stature syndrome, Johnson neuroectodermal syndrome, Marshall syndrome, Naegeli-Franceschetti-Jadassohn syndrome, oculodentodigital dysplasia, Cronkhite-Canada syndrome, scalp-ear-nipple syndrome, tooth and nail syndrome, tricho-dento-osseous syndrome, tricho-retino-dento-digital syndrome, acrofacial dysostosis, Weyers type, Ackerman syndrome, alopecia - contractures - dwarfism - intellectual disability syndrome, AREDYLD syndrome, Barber-Say syndrome, oculoosteocutaneous syndrome, cataract-hypertrichosis-intellectual disability syndrome, autosomal recessive palmoplantar keratoderma and congenital alopecia, cerebellar ataxia-ectodermal dysplasia syndrome, cranioectodermal dysplasia, conductive deafness-ptosis-skeletal anomalies syndrome, dermatoosteolysis, Kirghizian type, Dubowitz syndrome, ectodermal dysplasia-sensorineural deafness syndrome, ectodermal dysplasia-intellectual disability-central nervous system malformation syndrome, hypohidrotic ectodermal dysplasia-hypothyroidism-ciliary dyskinesia syndrome, cleft lip/palate-ectodermal dysplasia syndrome, EEM syndrome, Ellis-van Creveld syndrome, amelocerebrohypohidrotic syndrome, GAPO syndrome, ichthyosis-alopecia-eclabion-ectropion-intellectual disability syndrome, Leukomelanoderma-infantilism-intellectual disability-hypodontia-hypotrichosis syndrome, Dahlberg-Borer-Newcomer syndrome, cartilage-hair hypoplasia, oculotrichodysplasia, pilodental dysplasia-refractive errors syndrome, Bartsocas-Papas syndrome 1, ectodermal dysplasia-blindness syndrome, Schinzel-Giedion syndrome, Teebi-Shaltout syndrome, taurodontia-absent teeth-sparse hair syndrome, odontotrichomelic syndrome, trichomegaly-retina pigmentary degeneration-dwarfism syndrome, trichoodontoonychial dysplasia, CHIME syndrome, anhidrotic ectodermal dysplasia-immunodeficiency-osteopetrosis-lymphedema syndrome, Ito hypomelanosis, contractures-ectodermal dysplasia-cleft lip/palate syndrome, incontinentia pigmenti, Toriello-Lacassie-Droste syndrome, odontomicronychial dysplasia, ectodermal dysplasia with natal teeth, Turnpenny type, hidrotic ectodermal dysplasia, Christianson-Fourie type, trichodental syndrome, congenital hypotrichosis with juvenile macular dystrophy, tricho-oculo-dermo-vertebral syndrome, odonto-tricho-ungual-digito-palmar syndrome, Fried’s tooth and nail syndrome, epidermolysis bullosa simplex due to plakophilin deficiency, arrhythmogenic cardiomyopathy with wooly hair and keratoderma, Curly hair - acral keratoderma - caries syndrome, hypotrichosis-osteolysis-periodontitis-palmoplantar keratoderma syndrome, Lelis syndrome, Fontaine progeroid syndrome, ectodermal dysplasia-syndactyly syndrome, ectodermal dysplasia 5, hair/nail type, nail and teeth abnormalities-marginal palmoplantar keratoderma-oral hyperpigmentation syndrome, ectodermal dysplasia 12, hypohidrotic/hair/tooth/nail type, cardiofaciocutaneous syndrome, choroidal atrophy-alopecia syndrome, dyskeratosis congenita, hidrotic ectodermal dysplasia, Halal type, hypertrichosis lanuginosa congenita, hypohidrotic ectodermal dysplasia, odonto-onycho dysplasia-alopecia syndrome, pili torti-onychodysplasia syndrome, chondroectodermal dysplasia with night blindness, trichorhinophalangeal syndrome, trichothiodystrophy, trichodermodysplasia-dental alterations syndrome, autosomal dominant trichoodontoonychodysplasia-syndactyly, focal facial dermal dysplasia, KID syndrome, pure hair and nail ectodermal dysplasia, circumscribed palmoplantar hypokeratosis, trichodysplasia-amelogenesis imperfecta syndrome, dermotrichic syndrome, alves Castelo dos Santos syndrome, Brunoni syndrome, ectodermal dysplasia Bartalos type, ectodermal dysplasia margarita type, ectodermal dysplasia alopecia preaxial polydactyly, ectodermal dysplasia arthrogryposis diabetes mellitus, ectodermal dysplasia blindness, ectodermal dysplasia neurosensory deafness, ectodermal dysplasia 14, hair/tooth type with or without hypohidrosis, ectodermal dysplasia 15, hypohidrotic/hair type, linear hypopigmentation and craniofacial asymmetry with acral, ocular and brain anomalies, jones hersh yusk syndrome, ectodermal dysplasia 13, hair/tooth type, arthrogryposis-ectodermal dysplasia-other anomalies syndrome, ectodermal dysplasia WNT10A related, CTSC-related disorder, ectodermal dysplasia 17 with or without limb malformations

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

85 retrieved; paginated sample, class counts are floors:

48 uncertain significance, 11 conflicting classifications of pathogenicity, 10 likely benign, 7 benign/likely benign, 5 likely pathogenic, 3 pathogenic, 1 pathogenic/likely pathogenic

ClinVar	Variant (HGVS)	Gene	Classification	Review
1024583	NM_003722.5(TP63):c.1861del (p.Ser621fs)	TP63	Pathogenic	criteria provided, single submitter
6527	NM_003722.5(TP63):c.727C>T (p.Arg243Trp)	TP63	Pathogenic	criteria provided, multiple submitters, no conflicts
6534	NM_003722.5(TP63):c.1028G>A (p.Arg343Gln)	TP63	Pathogenic/Likely pathogenic	criteria provided, multiple submitters, no conflicts
6538	NM_003722.5(TP63):c.1693_1694del (p.Phe565fs)	TP63	Pathogenic	no assertion criteria provided
2434205	NM_003722.5(TP63):c.1963C>T (p.Arg655Ter)	TP63	Likely pathogenic	criteria provided, multiple submitters, no conflicts
3589070	NM_003722.5(TP63):c.345dup (p.Leu116fs)	TP63	Likely pathogenic	criteria provided, single submitter
3589074	NM_003722.5(TP63):c.1129+1G>A	TP63	Likely pathogenic	criteria provided, single submitter
4796625	NM_003722.5(TP63):c.733C>T (p.Pro245Ser)	TP63	Likely pathogenic	criteria provided, single submitter
620399	NM_003722.5(TP63):c.1927C>T (p.Arg643Ter)	TP63	Likely pathogenic	criteria provided, single submitter
1370798	NM_003722.5(TP63):c.1537G>C (p.Ala513Pro)	TP63	Conflicting classifications of pathogenicity	criteria provided, conflicting classifications
1412118	NM_003722.5(TP63):c.1814G>A (p.Arg605Gln)	TP63	Conflicting classifications of pathogenicity	criteria provided, conflicting classifications
1433359	NM_003722.5(TP63):c.1807G>C (p.Asp603His)	TP63	Conflicting classifications of pathogenicity	criteria provided, conflicting classifications
1476128	NM_003722.5(TP63):c.2003G>A (p.Arg668His)	TP63	Conflicting classifications of pathogenicity	criteria provided, conflicting classifications
1503085	NM_003722.5(TP63):c.1352C>G (p.Thr451Ser)	TP63	Conflicting classifications of pathogenicity	criteria provided, conflicting classifications
1561066	NM_003722.5(TP63):c.475C>T (p.Leu159Phe)	TP63	Conflicting classifications of pathogenicity	criteria provided, conflicting classifications
1598420	NM_003722.5(TP63):c.1367C>T (p.Pro456Leu)	TP63	Conflicting classifications of pathogenicity	criteria provided, conflicting classifications
1600102	NM_003722.5(TP63):c.1480A>G (p.Thr494Ala)	TP63	Conflicting classifications of pathogenicity	criteria provided, conflicting classifications
2721206	NM_003722.5(TP63):c.1661C>T (p.Ala554Val)	TP63	Conflicting classifications of pathogenicity	criteria provided, conflicting classifications
725955	NM_003722.5(TP63):c.84T>G (p.His28Gln)	TP63	Conflicting classifications of pathogenicity	criteria provided, conflicting classifications
899830	NM_003722.5(TP63):c.210G>C (p.Gln70His)	TP63	Conflicting classifications of pathogenicity	criteria provided, conflicting classifications
1038841	NM_003722.5(TP63):c.1121C>T (p.Thr374Met)	TP63	Uncertain significance	criteria provided, multiple submitters, no conflicts
1042494	NM_003722.5(TP63):c.1697C>T (p.Thr566Met)	TP63	Uncertain significance	criteria provided, multiple submitters, no conflicts
1314992	NM_003722.5(TP63):c.2021G>A (p.Arg674His)	TP63	Uncertain significance	criteria provided, multiple submitters, no conflicts
1370657	NM_003722.5(TP63):c.1831TCC[1] (p.Ser612del)	TP63	Uncertain significance	criteria provided, multiple submitters, no conflicts
1375700	NM_003722.5(TP63):c.1507+6_1507+7del	TP63	Uncertain significance	criteria provided, multiple submitters, no conflicts
1385690	NM_003722.5(TP63):c.1583C>A (p.Pro528Gln)	TP63	Uncertain significance	criteria provided, multiple submitters, no conflicts
1398414	NM_003722.5(TP63):c.110G>A (p.Arg37Gln)	TP63	Uncertain significance	criteria provided, multiple submitters, no conflicts
1421645	NM_003722.5(TP63):c.50C>G (p.Pro17Arg)	TP63	Uncertain significance	criteria provided, multiple submitters, no conflicts
1494162	NM_003722.5(TP63):c.1612A>G (p.Thr538Ala)	TP63	Uncertain significance	criteria provided, multiple submitters, no conflicts
1510128	NM_003722.5(TP63):c.62G>A (p.Arg21His)	TP63	Uncertain significance	criteria provided, multiple submitters, no conflicts

Genes & proteins

Mendelian disease overlap and somatic drivers

GenCC: 16 · Orphanet: 9 · 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.

Gene	Classification	Inheritance	Disease	Records
TP63	Definitive	Autosomal dominant	limb-mammary syndrome	16

Orphanet rare-disease linkage (cohort genes)

Gene	Orphanet ID	Rare disease
TP63	Orphanet:1072	Ankyloblepharon filiforme adnatum-cleft palate syndrome
TP63	Orphanet:141291	Cleft lip and alveolus
TP63	Orphanet:1896	EEC syndrome
TP63	Orphanet:199302	Isolated cleft lip
TP63	Orphanet:199306	Cleft lip/palate
TP63	Orphanet:2440	Isolated split hand-split foot malformation
TP63	Orphanet:69085	Limb-mammary syndrome
TP63	Orphanet:93930	Classic bladder exstrophy
TP63	Orphanet:978	ADULT 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
TP63	HGNC:15979	ENSG00000073282	Q9H3D4	Tumor protein 63	gencc,clinvar

Cohort function summary

Lead sentence per gene, UniProt-curated.

Symbol	Protein name	Function (lead sentence)
TP63	Tumor protein 63	Acts as a sequence specific DNA binding transcriptional activator or repressor.

Protein-family classification

Druggable: 0 · Difficult: 1 · Unknown: 0 · 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
Transcription factor	1	8.3×	0.121

Per-gene assignment

Symbol	Family	Druggable?	EC	InterPro (top 3)
TP63	Transcription factor	no		SAM, p53_tumour_suppressor, p53-like_TF_DNA-bd_sf

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
skin of hip	1
upper arm skin	1
upper leg skin	1

Per-gene tissue summary (top 30)

Symbol	Bgee breadth	FANTOM5 breadth	SCXA	Top tissues
TP63	207	broad	marker	upper leg skin, skin of hip, upper arm skin

Protein interactions among cohort

Intra-cohort edges: 0.

Hub genes (top 10 by interactor count)

Symbol	Interactor count
TP63	2,893

Structural data

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

Cohort genes with PDB structures (top 30)

Symbol	UniProt	PDB entries
TP63	Q9H3D4	26

Function

Pathway analysis

Distinct Reactome pathways touched by cohort: 12. Enrichment computed across 1 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.

Pathway	Cohort genes	Fold	FDR	Sample cohort genes
Activation of PUMA and translocation to mitochondria	1	1142.0×	0.003	TP63
TP53 Regulates Transcription of Caspase Activators and Caspases	1	951.7×	0.003	TP63
TP53 Regulates Transcription of Death Receptors and Ligands	1	951.7×	0.003	TP63
Regulation of TP53 Activity through Association with Co-factors	1	815.7×	0.003	TP63
TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain	1	761.3×	0.003	TP63
Developmental Lineage of Mammary Stem Cells	1	761.3×	0.003	TP63
TP53 Regulates Transcription of Genes Involved in Cytochrome C Release	1	543.8×	0.003	TP63
Developmental Lineage of Mammary Gland Myoepithelial Cells	1	543.8×	0.003	TP63
Developmental Lineage of Mammary Gland Luminal Epithelial Cells	1	456.8×	0.003	TP63
Pyroptosis	1	423.0×	0.003	TP63
Differentiation of Keratinocytes in Interfollicular Epidermis in Mammalian Skin	1	278.5×	0.004	TP63
TP53 Regulates Metabolic Genes	1	129.8×	0.008	TP63

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
ectoderm and mesoderm interaction	1	16852.0×	0.001	TP63
epidermal cell division	1	16852.0×	0.001	TP63
cloacal septation	1	8426.0×	0.001	TP63
squamous basal epithelial stem cell differentiation involved in prostate gland acinus development	1	8426.0×	0.001	TP63
positive regulation of somatic stem cell population maintenance	1	8426.0×	0.001	TP63
regulation of epidermal cell division	1	5617.3×	0.001	TP63
female genitalia morphogenesis	1	5617.3×	0.001	TP63
negative regulation of mesoderm development	1	5617.3×	0.001	TP63
prostatic bud formation	1	4213.0×	0.001	TP63
polarized epithelial cell differentiation	1	2808.7×	0.002	TP63
negative regulation of keratinocyte differentiation	1	1685.2×	0.003	TP63
positive regulation of fibroblast apoptotic process	1	1685.2×	0.003	TP63
epithelial cell development	1	1532.0×	0.003	TP63
skin morphogenesis	1	1404.3×	0.003	TP63
negative regulation of intracellular estrogen receptor signaling pathway	1	1123.5×	0.003	TP63
positive regulation of cell cycle G1/S phase transition	1	1123.5×	0.003	TP63
establishment of planar polarity	1	1053.2×	0.003	TP63
positive regulation of keratinocyte proliferation	1	991.3×	0.003	TP63
sympathetic nervous system development	1	936.2×	0.003	TP63
cranial skeletal system development	1	936.2×	0.003	TP63
post-anal tail morphogenesis	1	732.7×	0.003	TP63
proximal/distal pattern formation	1	648.1×	0.003	TP63
negative regulation of cellular senescence	1	648.1×	0.003	TP63
protein tetramerization	1	624.1×	0.003	TP63
embryonic hindlimb morphogenesis	1	581.1×	0.003	TP63
keratinocyte proliferation	1	581.1×	0.003	TP63
positive regulation of apoptotic signaling pathway	1	581.1×	0.003	TP63
positive regulation of stem cell proliferation	1	526.6×	0.003	TP63
hair follicle morphogenesis	1	495.6×	0.003	TP63
embryonic forelimb morphogenesis	1	495.6×	0.003	TP63

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
TP63	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	TP63

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)
TP63	0	—

Clinical trials & evidence

Clinical trials

Clinical trials: 0.