WNT10A
protein-codingWnt family member 10A, the group of Wnt family
Gene summary
The WNT gene family consists of structurally related genes which encode secreted signaling proteins. These proteins have been implicated in oncogenesis and in several developmental processes, including regulation of cell fate and patterning during embryogenesis. This gene is a member of the WNT gene family. It is strongly expressed in the cell lines of promyelocytic leukemia and Burkitt's lymphoma. In addition, it and another family member, the WNT6 gene, are strongly coexpressed in colorectal cancer cell lines. The gene overexpression may play key roles in carcinogenesis through activation of the WNT-beta-catenin-TCF signaling pathway. This gene and the WNT6 gene are clustered in the chromosome 2q35 region. [provided by RefSeq, Jul 2008]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~18.7 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AR
Disease ID:MONDO:0016619
Submitter: Orphanet
Inheritance Pattern: AR
Disease ID:MONDO:0009773
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: SD
Disease ID:MONDO:0100358
Submitter: ClinGen
The WNT10A gene is located on chromosome 2 at 2q35 and encodes the Wnt Family Member 10A protein, a secreted signaling protein that binds the frizzled family of seven transmembrane receptors. WNT10A was first reported in relation to semi-dominant ectodermal dysplasia WNT10A-related in 2009 (Bohring et al., PMID: 19559398). This form of ectodermal dysplasia exhibits alterations in ectoderm-derived features including hair, nails, teeth, and sweat glands. Common features include hypodontia, anodontia, hyperkeratosis, hypohidrosis, anhidrosis, and hypotrichosis. Per criteria outlined by the ClinGen Lumping and Splitting Working Group, we found no difference in molecular mechanism(s) or phenotypic variability. Therefore, the disease entities odontoonychodermal dysplasia (OMIM: 257980), Schopf-Schulz-Passarge syndrome (OMIM: 224750), and Tooth agenesis, selective, 4 (OMIM: 150400) have been lumped into one disease entity, Ectodermal dysplasia WNT10A related (MONDO: 0100358) . At least 7 variants (including 3 missense, 1 frameshift, and 3 nonsense variants) have been reported in 9 probands in 7 publications (PMID: 19559398; Cluzeau et al., 2011, PMID: 20979233; Plaisancié et al., 2013, PMID: 23401279; Van den Boogaard et al., 2012, PMID: 22581971; Krøigård et al., 2016, PMID: 26964878; Martínez-Romero et al., 2019, PMID: 31796081; Ismail et al., 2019, PMID: 31468502) and are included in this curation. Several recurrent variants were identified including c.321C>A (p.Cys107Ter) and c.682T>A (p.Phe228Ile), which were both found in a heterozygous and homozygous state in individuals exhibiting the spectrum of associated phenotype (PMIDs: 19559398; Vink et al., 2014, PMID: 24398796; Plaisancié et al., 2013, PMID: 23401279). More evidence is available in the literature, but the maximum score for genetic evidence (12 pts.) has been reached. This gene-disease relationship is also supported by zebrafish and mouse models (Yang et al., 2015, PMID: 25629078; Yuan et al., 2017, PMID: 29178643). In summary, WNT10A is definitively associated with semi-dominant ectodermal dysplasia WNT10A related. 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 Syndromic Disorders Gene Curation Expert Panel on the meeting date 08.20.2021 (SOP Version 8).
Inheritance Pattern: AD
Disease ID:MONDO:0100358
Submitter: PanelApp Australia
Inheritance Pattern: AR
Disease ID:MONDO:0100358
Submitter: PanelApp Australia
Inheritance Pattern: AD
Disease ID:MONDO:0005486
Submitter: Orphanet
Inheritance Pattern: AR
Disease ID:MONDO:0009773
Submitter: Orphanet
Inheritance Pattern: AD
Disease ID:MONDO:0007881
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: SD
Disease ID:MONDO:0100358
Submitter: Natera
Inheritance Pattern: AD
Disease ID:MONDO:0009145
Submitter: Orphanet
Inheritance Pattern: SD
Disease ID:MONDO:0100358
Submitter: Illumina
Clinical Genomic Database (CGD)
Manifestation: Dental; Dermatologic
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 WNT10A variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_025216.3. 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 | 235 | 2 | 242 | ||
| missense | 3 | 34 | 171 | 16 | 2 | 226 |
| nonsense | 20 | 15 | 1 | 36 | ||
| start loss | 1 | 4 | 5 | |||
| frameshift | 37 | 11 | 48 | |||
| splice donor/acceptor (+/-2bp) | 2 | 3 | 5 | |||
| Total | 63 | 67 | 177 | 251 | 4 | 562 |
Highest pathogenic variant AF is 0.0014087509
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_079492.2 | 4 | MANE Select | |
| Ensembl | ENSP00000258411.3 | 4 | MANE Select | |
| Ensembl | ENSP00000388812.1 | 2 | Standard | |
| Ensembl | ENSP00000535315.1 | 4 | Standard |
Model Organisms & Knockout Phenotypes
Observed phenotypic effects in mouse and zebrafish models
| Gene / Model | Organism | Observed Phenotype |
|---|---|---|
| wnt10a | Danio rerio | Structure: cranial cartilage Quality: morphology abnormal |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Gastric cancer - Homo sapiens (human)
- mTOR signaling pathway - Homo sapiens (human)
- Cushing,s syndrome - Homo sapiens (human)
- Breast cancer - Homo sapiens (human)
- HTLV-I infection - Homo sapiens (human)
Biological Process
- hair follicle development
- regulation of signaling receptor activity
- positive regulation of gene expression
- neural crest cell differentiation
- Wnt signaling pathway
Molecular Function
- frizzled binding
- receptor ligand activity
Cellular Component
- extracellular region
- extracellular space
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000258411
- Coding exons
- 4
- Length
- 19219
- Individuals with no LoFs
- 125560
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 187
- Defined
- 125747
- p
- 0.000744
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.449 | 281 | 261 | 1.08 | 0.0000148 | 2659 |
| Missense (PolyPhen) | 115 | 114.89 | 1.0009 | 1241 | ||
| Synonymous | -0.0973 | 113 | 112 | 1.01 | 0.00000649 | 871 |
| Loss of Function | 0.458 | 14 | 16.0 | 0.876 | 9.50e-7 | 142 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00049 | 0.00049 | rare |
| Latino/Admixed American | 0.000058 | 0.000058 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00044 | 0.00044 | rare |
| Finnish | 0.000092 | 0.000092 | rare |
| European (Non-Finnish) | 0.0014 | 0.0014 | notable |
| South Asian | 0.000068 | 0.000065 | rare |
| Other | 0.00033 | 0.00033 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Ligand for members of the frizzled family of seven transmembrane receptors (Probable). Functions in the canonical Wnt/beta-catenin signaling pathway (By similarity). Plays a role in normal ectoderm development (PubMed:17847007, PubMed:28589954). Required for normal tooth development (PubMed:17847007, PubMed:29178643, PubMed:28589954). Required for normal postnatal development and maintenance of tongue papillae and sweat ducts (PubMed:28589954). Required for normal proliferation of basal cells in tongue filiform papillae, plantar epithelium and sweat ducts. Required for normal expression of keratins in tongue papillae (By similarity). Required for normal expression of KRT9 in foot plant epithelium (PubMed:28589954). Required for normal hair follicle function (PubMed:28589954). {ECO:0000250|UniProtKB:P70701, ECO:0000269|PubMed:17847007, ECO:0000269|PubMed:28589954, ECO:0000269|PubMed:29178643, ECO:0000305}.;
- Disease
- DISEASE: Odonto-onycho-dermal dysplasia (OODD) [MIM:257980]: A rare autosomal recessive ectodermal dysplasia characterized by dry hair, severe hypodontia, smooth tongue with marked reduction of fungiform and filiform papillae, onychodysplasia, keratoderma and hyperhidrosis of palms and soles, and hyperkeratosis of the skin. {ECO:0000269|PubMed:17847007, ECO:0000269|PubMed:19471313, ECO:0000269|PubMed:19559398, ECO:0000269|PubMed:24458874, ECO:0000269|PubMed:28589954}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Schopf-Schulz-Passarge syndrome (SSPS) [MIM:224750]: A rare ectodermal dysplasia, characterized chiefly by cysts of the eyelid margins, palmoplantar keratoderma, hypodontia, hypotrichosis and nail dystrophy. Multiple eyelid apocrine hidrocystomas are the hallmark of this condition, although they usually appear in adulthood. The concomitant presence of eccrine syringofibroadenoma in most patients and of other adnexal skin tumors in some affected subjects indicates that Schopf-Schulz- Passarge syndrome is a genodermatosis with skin appendage neoplasms. {ECO:0000269|PubMed:19559398, ECO:0000269|PubMed:21143469}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Tooth agenesis, selective, 4 (STHAG4) [MIM:150400]: A form of selective tooth agenesis, a common anomaly characterized by the congenital absence of one or more teeth. Selective tooth agenesis without associated systemic disorders has sometimes been divided into 2 types: oligodontia, defined as agenesis of 6 or more permanent teeth, and hypodontia, defined as agenesis of less than 6 teeth. The number in both cases does not include absence of third molars (wisdom teeth). In STHAG4, the upper lateral incisors are absent or peg-shaped. Some STHAG4 patients manifest mild features of ectodermal dysplasia, including sparse hair, sparse eyebrows, short eyelashes, abnormalities of the nails, sweating anomalies and dry skin. STHAG4 inheritance is autosomal dominant or autosomal recessive. {ECO:0000269|PubMed:20979233, ECO:0000269|PubMed:21484994, ECO:0000269|PubMed:22581971, ECO:0000269|PubMed:23401279, ECO:0000269|PubMed:24311251, ECO:0000269|PubMed:24449199, ECO:0000269|PubMed:27657131, ECO:0000269|PubMed:29178643}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Recessive Scores
- pRec
- 0.203
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.501
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |