TP63

protein-coding

tumor protein p63, the group of MicroRNA protein coding host genes

Gene summary

This gene encodes a member of the p53 family of transcription factors. The functional domains of p53 family proteins include an N-terminal transactivation domain, a central DNA-binding domain and an oligomerization domain. Alternative splicing of this gene and the use of alternative promoters results in multiple transcript variants encoding different isoforms that vary in their functional properties. These isoforms function during skin development and maintenance, adult stem/progenitor cell regulation, heart development and premature aging. Some isoforms have been found to protect the germline by eliminating oocytes or testicular germ cells that have suffered DNA damage. Mutations in this gene are associated with ectodermal dysplasia, and cleft lip/palate syndrome 3 (EEC3); split-hand/foot malformation 4 (SHFM4); ankyloblepharon-ectodermal defects-cleft lip/palate; ADULT syndrome (acro-dermato-ungual-lacrimal-tooth); limb-mammary syndrome; Rap-Hodgkin syndrome (RHS); and orofacial cleft 8. [provided by RefSeq, Aug 2016]

Previous symbols:
  • TP73L
  • TP53L
  • TP53CP

MANE transcript

NM_003722.5

Inheritance

AD

ClinVar variants

P:141U:274B:187

Top phenotype

Split-hand/foot malformation 4; Ectrodactyly, ectodermal dysplasia, and cleft lip/palate syndrome 3; Limb-mammary syndrome; Rapp-Hodgkin syndrome; ADULT syndrome; Ankyloblepharon-ectodermal defects-cleft lip/palate; Orofacial cleft 8; Premature ovarian failure 21

gnomAD constraint

pLI —, LoF o/e 0.13

Max pathogenic AF

—

Genomic locus

chr3:189,631,389-189,897,276

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~265.9 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

Rapp-Hodgkin syndromeDEFINITIVE

Inheritance Pattern: AD

Disease ID:MONDO:0007508

Submitter: G2P

ectrodactyly, ectodermal dysplasia, and cleft lip-palate syndrome 3DEFINITIVE

Inheritance Pattern: AD

Disease ID:MONDO:0011428

Submitter: Ambry Genetics

ectrodactyly, ectodermal dysplasia, and cleft lip-palate syndrome 3STRONG

Inheritance Pattern: AD

Disease ID:MONDO:0011428

Submitter: Labcorp Genetics (formerly Invitae)

limb-mammary syndromeSUPPORTIVE

Inheritance Pattern: AD

Disease ID:MONDO:0011334

Submitter: Orphanet

TP63-related ectodermal dysplasia spectrum with limb and orofacial malformationsSTRONG

Inheritance Pattern: AD

Disease ID:MONDO:1040001

Submitter: PanelApp Australia

ectrodactyly, ectodermal dysplasia, and cleft lip-palate syndrome 3DEFINITIVE

Inheritance Pattern: AD

Disease ID:MONDO:0011428

Submitter: ClinGen

TP63 was first reported in relation to AD TP63-related ectodermal dysplasia spectrum with limb and orofacial malformations in 1999 (Celli et al., PMID: 10535733). TP63-related ectodermal dysplasia spectrum with limb and orofacial malformations is characterized by variable ectodermal dysplasia, limb defects, and orofacial clefting. Per criteria outlined by the ClinGen Lumping and Splitting Working Group, we found no difference in inheritance pattern and phenotypic variability. Therefore, the following disease entities, EEC3 syndrome (MIM:604292), ADULT syndrome (MIM:103285), AEC syndrome (MIM:106260), Rapp-Hodgkin syndrome (MIM:129400), Limb-mammary syndrome (MIM:603543), Split-hand/foot malformation 4 (MIM:605289), and Orofacial cleft 8 (MIM:618149), have been lumped into one disease entity, TP63-related ectodermal dysplasia spectrum with limb and orofacial malformations. However, Premature ovarian failure 21 (MIM:620311) was split out due to phenotypic differences and will be curated by a different GCEP. 21 variants (16 missense, 4 frameshift, and 1 nonsense) that have been reported in 21 probands in 9 publications (PMIDs: 10535733, 11159940, 11462173, 20491771, 21204238, 22574117, 29500247, 33622322, 37920856) are included in this curation. More evidence is available in the literature, but the maximum score for genetic evidence (12 pts.) has been reached. The mechanism of pathogenicity at this time is unknown. This gene-disease relationship is also supported by animal models, functional alteration, protein-protein interactions, and expression studies (PMIDs: 10227294, 22247000, 19353588, 20855944, 21965674). In summary, there is definitive evidence supporting the relationship between TP63 and AD TP63-related ectodermal dysplasia spectrum with limb and orofacial malformations. This has been repeatedly demonstrated in both the research and clinical diagnostic settings, and has been upheld over time.This classification was approved by the ClinGen Craniofacial Malformation GCEP on the meeting date October 17th, 2024 (SOP Version 11).

split hand-foot malformation 4MODERATE

Inheritance Pattern: AD

Disease ID:MONDO:0011535

Submitter: Illumina

Rapp-Hodgkin syndromeDEFINITIVE

Inheritance Pattern: AD

Disease ID:MONDO:0007508

Submitter: G2P

ankyloblepharon-ectodermal defects-cleft lip/palate syndromeDEFINITIVE

Inheritance Pattern: AD

Disease ID:MONDO:0007124

Submitter: G2P

ADULT syndromeSUPPORTIVE

Inheritance Pattern: AD

Disease ID:MONDO:0007072

Submitter: Orphanet

EEC syndromeSUPPORTIVE

Inheritance Pattern: AD

Disease ID:MONDO:0010004

Submitter: Orphanet

split hand-foot malformationSUPPORTIVE

Inheritance Pattern: AD

Disease ID:MONDO:0016576

Submitter: Orphanet

premature ovarian failure 21STRONG

Inheritance Pattern: AD

Disease ID:MONDO:0957216

Submitter: Labcorp Genetics (formerly Invitae)

premature ovarian failure 21MODERATE

Inheritance Pattern: AD

Disease ID:MONDO:0957216

Submitter: Ambry Genetics

limb-mammary syndromeDEFINITIVE

Inheritance Pattern: AD

Disease ID:MONDO:0011334

Submitter: G2P

ADULT syndromeDEFINITIVE

Inheritance Pattern: AD

Disease ID:MONDO:0007072

Submitter: G2P

Clinical Genomic Database (CGD)

Split-hand/foot malformation 4; Ectrodactyly, ectodermal dysplasia, and cleft lip/palate syndrome 3; Limb-mammary syndrome; Rapp-Hodgkin syndrome; ADULT syndrome; Ankyloblepharon-ectodermal defects-cleft lip/palate; Orofacial cleft 8; Premature ovarian failure 21AD

Manifestation: Audiologic/Otolaryngologic; Craniofacial; Dental; Dermatologic; Endocrine; Gastrointestinal; Genitourinary; Musculoskeletal; Obstetric

Intervention: General

Rationale: Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing

Refs: 5713637; 946410; 3366140; 9443880; 10535733; 9973291; 10886756; 10839977; 11528512; 11159940; 11462173; 11929852; 12838557; 12939657; 14684701; 12766194; 15200513; 16688749; 16740912; 17041931; 16724007; 17609671; 17431922; 18627043; 19239083; 18603493; 19697430; 19353643; 19676059; 19530185; 21204238; 21990121; 22065540; 22065614; 22069181; 22430731; 22574117; 22607287; 22740388; 29500247; 30924587; 35801529; 36856110Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to TP63 variants in ClinVar

26 Conditions Cataloged
TP63-Related Spectrum DisordersTotal: 507
not providedTotal: 174
Ectrodactyly, ectodermal dysplasia, and cleft lip-palate syndrome 3Total: 138
Orofacial cleft 8Total: 114
Split hand-foot malformation 4Total: 97
Rapp-Hodgkin syndromeTotal: 96
ADULT syndromeTotal: 94
Ankyloblepharon-ectodermal defects-cleft lip/palate syndromeTotal: 92

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_003722.5. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

EffectPLPVUSLBBSum
synonymous
5
clinvar
152
clinvar
3
clinvar
160
missense
31
clinvar
63
clinvar
265
clinvar
29
clinvar
2
clinvar
390
nonsense
9
clinvar
6
clinvar
2
clinvar
17
start loss
1
clinvar
1
frameshift
16
clinvar
9
clinvar
1
clinvar
26
splice donor/acceptor (+/-2bp)
4
clinvar
2
clinvar
1
clinvar
1
clinvar
8
Total60812741825602

Highest pathogenic variant AF is 0.00001315703

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 29 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_003722.5RefSeqNP_003713.314MANE Select
ENST00000264731.8EnsemblENSP00000264731.314MANE Select
NM_001114978.2RefSeqNP_001108450.113Standard
NM_001114979.2RefSeqNP_001108451.111Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / ModelOrganismObserved Phenotype
tp63Danio rerio

Structure: peridermal cell

Quality: increased size

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

  • MicroRNAs in cancer - Homo sapiens (human)
  • TP53 Network
  • Apoptosis
  • Hair Follicle Development- Induction (Part 1 of 3)
  • Apoptotic Signaling Pathway

Biological Process

  • negative regulation of transcription by RNA polymerase II
  • replicative cell aging
  • skeletal system development
  • establishment of planar polarity
  • epithelial cell development

Molecular Function

  • DNA-binding transcription factor activity, RNA polymerase II-specific
  • DNA-binding transcription activator activity, RNA polymerase II-specific
  • p53 binding
  • DNA binding
  • chromatin binding

Cellular Component

  • nuclear chromatin
  • nucleus
  • nucleoplasm
  • cytoplasm
  • mitochondrion

gnomAD Constraint

Source: gnomAD

Gene type
protein_coding
Transcript type
protein_coding
Transcript
ENST00000264731
Coding exons
14
Length
265864
Individuals with no LoFs
125721
Homozygous LoFs
0
Heterozygous LoFs
27
Defined
125748
p
0.000107
Z-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense2.212904170.6960.00002624505
Missense (PolyPhen)78179.410.434771883
Synonymous-0.9941701541.100.00001031302
Loss of Function5.08539.40.1270.00000237393

Population LoF Frequency

PopulationCAFp-valueStatus
African0.0000620.000062rare
Latino/Admixed American0.0000290.000029rare
Ashkenazi Jewish0.00120.0012notable
East Asian00.0absent
Finnish0.000280.00028rare
European (Non-Finnish)0.0000350.000035rare
South Asian0.0000980.000098rare
Other00.0absent

dbNSFP Gene Annotations

Source: dbNSFP

Function
FUNCTION: Acts as a sequence specific DNA binding transcriptional activator or repressor. The isoforms contain a varying set of transactivation and auto-regulating transactivation inhibiting domains thus showing an isoform specific activity. Isoform 2 activates RIPK4 transcription. May be required in conjunction with TP73/p73 for initiation of p53/TP53 dependent apoptosis in response to genotoxic insults and the presence of activated oncogenes. Involved in Notch signaling by probably inducing JAG1 and JAG2. Plays a role in the regulation of epithelial morphogenesis. The ratio of DeltaN-type and TA*-type isoforms may govern the maintenance of epithelial stem cell compartments and regulate the initiation of epithelial stratification from the undifferentiated embryonal ectoderm. Required for limb formation from the apical ectodermal ridge. Activates transcription of the p21 promoter. {ECO:0000269|PubMed:11641404, ECO:0000269|PubMed:12374749, ECO:0000269|PubMed:12446779, ECO:0000269|PubMed:12446784, ECO:0000269|PubMed:20123734, ECO:0000269|PubMed:22197488, ECO:0000269|PubMed:9774969}.;
Disease
DISEASE: Acro-dermato-ungual-lacrimal-tooth syndrome (ADULT syndrome) [MIM:103285]: A form of ectodermal dysplasia. Ectodermal dysplasia defines a heterogeneous group of disorders due to abnormal development of two or more ectodermal structures. ADULT syndrome involves ectrodactyly, syndactyly, finger- and toenail dysplasia, hypoplastic breasts and nipples, intensive freckling, lacrimal duct atresia, frontal alopecia, primary hypodontia and loss of permanent teeth. ADULT syndrome differs significantly from EEC3 syndrome by the absence of facial clefting. Inheritance is autosomal dominant. {ECO:0000269|PubMed:11929852}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Ankyloblepharon-ectodermal defects-cleft lip/palate (AEC) [MIM:106260]: An autosomal dominant condition characterized by congenital ectodermal dysplasia with coarse, wiry, sparse hair, dystrophic nails, slight hypohidrosis, scalp infections, ankyloblepharon filiform adnatum, maxillary hypoplasia, hypodontia and cleft lip/palate. {ECO:0000269|PubMed:11159940}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Ectrodactyly, ectodermal dysplasia, and cleft lip/palate syndrome 3 (EEC3) [MIM:604292]: A form of ectodermal dysplasia, a heterogeneous group of disorders due to abnormal development of two or more ectodermal structures. It is an autosomal dominant syndrome characterized by ectrodactyly of hands and feet, ectodermal dysplasia and facial clefting. {ECO:0000269|PubMed:10535733, ECO:0000269|PubMed:10839977, ECO:0000269|PubMed:11462173, ECO:0000269|PubMed:12838557}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Split-hand/foot malformation 4 (SHFM4) [MIM:605289]: A limb malformation involving the central rays of the autopod and presenting with syndactyly, median clefts of the hands and feet, and aplasia and/or hypoplasia of the phalanges, metacarpals, and metatarsals. Some patients have been found to have mental retardation, ectodermal and craniofacial findings, and orofacial clefting. {ECO:0000269|PubMed:10839977, ECO:0000269|PubMed:11462173}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Limb-mammary syndrome (LMS) [MIM:603543]: Characterized by ectrodactyly, cleft palate and mammary-gland abnormalities. {ECO:0000269|PubMed:11462173}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Note=Defects in TP63 are a cause of cervical, colon, head and neck, lung and ovarian cancers.; DISEASE: Ectodermal dysplasia, Rapp-Hodgkin type (EDRH) [MIM:129400]: A form of ectodermal dysplasia, a heterogeneous group of disorders due to abnormal development of two or more ectodermal structures. Characterized by the combination of anhidrotic ectodermal dysplasia, cleft lip, and cleft palate. The clinical syndrome is comprised of a characteristic facies (narrow nose and small mouth), wiry, slow-growing, and uncombable hair, sparse eyelashes and eyebrows, obstructed lacrimal puncta/epiphora, bilateral stenosis of external auditory canals, microsomia, hypodontia, cone-shaped incisors, enamel hypoplasia, dystrophic nails, and cleft lip/cleft palate. {ECO:0000269|PubMed:12766194, ECO:0000269|PubMed:12939657, ECO:0000269|PubMed:15200513, ECO:0000269|PubMed:16740912}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Non-syndromic orofacial cleft 8 (OFC8) [MIM:129400]: A birth defect consisting of cleft lips with or without cleft palate. Cleft lips are associated with cleft palate in two-third of cases. A cleft lip can occur on one or both sides and range in severity from a simple notch in the upper lip to a complete opening in the lip extending into the floor of the nostril and involving the upper gum. Note=The disease is caused by mutations affecting the gene represented in this entry.;

Recessive Scores

pRec
0.571

Intolerance Scores

LoFtool
0.00668
RVIS EVS
-0.91
RVIS percentile EVS
9.96

Essentials

Essential (CRISPR)
N
Essential (CRISPR2)
N
Essential (gene trap)
N
Indispensability pred.
E
Indispensability score
0.866

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
For research and educational, non-commercial use only. Not for clinical or diagnostic use. GeneBe does not provide medical advice. Data use for AI modeling is prohibited: if used, the cost is $0.001 per byte of downloaded uncompressed data.