TP63
protein-codingtumor 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]
- TP73L
- TP53L
- TP53CP
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~265.9 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AD
Disease ID:MONDO:0007508
Submitter: G2P
Inheritance Pattern: AD
Disease ID:MONDO:0011428
Submitter: Ambry Genetics
Inheritance Pattern: AD
Disease ID:MONDO:0011428
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AD
Disease ID:MONDO:0011334
Submitter: Orphanet
Inheritance Pattern: AD
Disease ID:MONDO:1040001
Submitter: PanelApp Australia
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).
Inheritance Pattern: AD
Disease ID:MONDO:0011535
Submitter: Illumina
Inheritance Pattern: AD
Disease ID:MONDO:0007508
Submitter: G2P
Inheritance Pattern: AD
Disease ID:MONDO:0007124
Submitter: G2P
Inheritance Pattern: AD
Disease ID:MONDO:0007072
Submitter: Orphanet
Inheritance Pattern: AD
Disease ID:MONDO:0010004
Submitter: Orphanet
Inheritance Pattern: AD
Disease ID:MONDO:0016576
Submitter: Orphanet
Inheritance Pattern: AD
Disease ID:MONDO:0957216
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AD
Disease ID:MONDO:0957216
Submitter: Ambry Genetics
Inheritance Pattern: AD
Disease ID:MONDO:0011334
Submitter: G2P
Inheritance Pattern: AD
Disease ID:MONDO:0007072
Submitter: G2P
Clinical Genomic Database (CGD)
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
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to TP63 variants in ClinVar
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.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 5 | 152 | 3 | 160 | ||
| missense | 31 | 63 | 265 | 29 | 2 | 390 |
| nonsense | 9 | 6 | 2 | 17 | ||
| start loss | 1 | 1 | ||||
| frameshift | 16 | 9 | 1 | 26 | ||
| splice donor/acceptor (+/-2bp) | 4 | 2 | 1 | 1 | 8 | |
| Total | 60 | 81 | 274 | 182 | 5 | 602 |
Highest pathogenic variant AF is 0.00001315703
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_003713.3 | 14 | MANE Select | |
| Ensembl | ENSP00000264731.3 | 14 | MANE Select | |
| RefSeq | NP_001108450.1 | 13 | Standard | |
| RefSeq | NP_001108451.1 | 11 | Standard |
Model Organisms & Knockout Phenotypes
Observed phenotypic effects in mouse and zebrafish models
| Gene / Model | Organism | Observed Phenotype |
|---|---|---|
| tp63 | Danio 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:
- 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-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 2.21 | 290 | 417 | 0.696 | 0.0000262 | 4505 |
| Missense (PolyPhen) | 78 | 179.41 | 0.43477 | 1883 | ||
| Synonymous | -0.994 | 170 | 154 | 1.10 | 0.0000103 | 1302 |
| Loss of Function | 5.08 | 5 | 39.4 | 0.127 | 0.00000237 | 393 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.000062 | 0.000062 | rare |
| Latino/Admixed American | 0.000029 | 0.000029 | rare |
| Ashkenazi Jewish | 0.0012 | 0.0012 | notable |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0.00028 | 0.00028 | rare |
| European (Non-Finnish) | 0.000035 | 0.000035 | rare |
| South Asian | 0.000098 | 0.000098 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- 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
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |