WNT10A

protein-coding

Wnt 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

NM_025216.3

Inheritance

AR, SD, AD

ClinVar variants

P:130U:177B:255

Top phenotype

Odontoonychodermal dysplasia; Schopf-Schulz-Passarge syndrome; Tooth agenesis, selective, 4

gnomAD constraint

pLI —, LoF o/e 0.88

Max pathogenic AF

—

Genomic locus

chr2:218,880,852-218,899,581

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~18.7 kb
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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

autosomal recessive hypohidrotic ectodermal dysplasiaSUPPORTIVE

Inheritance Pattern: AR

Disease ID:MONDO:0016619

Submitter: Orphanet

odonto-onycho-dermal dysplasiaSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0009773

Submitter: Labcorp Genetics (formerly Invitae)

ectodermal dysplasia WNT10A relatedDEFINITIVE

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).

ectodermal dysplasia WNT10A relatedSTRONG

Inheritance Pattern: AD

Disease ID:MONDO:0100358

Submitter: PanelApp Australia

ectodermal dysplasia WNT10A relatedSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0100358

Submitter: PanelApp Australia

tooth agenesisSUPPORTIVE

Inheritance Pattern: AD

Disease ID:MONDO:0005486

Submitter: Orphanet

odonto-onycho-dermal dysplasiaSUPPORTIVE

Inheritance Pattern: AR

Disease ID:MONDO:0009773

Submitter: Orphanet

tooth agenesis, selective, 4STRONG

Inheritance Pattern: AD

Disease ID:MONDO:0007881

Submitter: Labcorp Genetics (formerly Invitae)

ectodermal dysplasia WNT10A relatedDEFINITIVE

Inheritance Pattern: SD

Disease ID:MONDO:0100358

Submitter: Natera

Schöpf-Schulz-Passarge syndromeSUPPORTIVE

Inheritance Pattern: AD

Disease ID:MONDO:0009145

Submitter: Orphanet

ectodermal dysplasia WNT10A relatedDEFINITIVE

Inheritance Pattern: SD

Disease ID:MONDO:0100358

Submitter: Illumina

Clinical Genomic Database (CGD)

Odontoonychodermal dysplasia; Schopf-Schulz-Passarge syndrome; Tooth agenesis, selective, 4AR

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

Refs: 4281327; 6837628; 15316967; 17847007; 19471313; 19559398; 20163410; 20418069; 21143469; 21484994; 21834823; 24449199Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to WNT10A variants in ClinVar

16 Conditions Cataloged
Tooth agenesis, selective, 4Total: 482
Odonto-onycho-dermal dysplasiaTotal: 481
Sch�pf-Schulz-Passarge syndromeTotal: 149
Inborn genetic diseasesTotal: 71
not providedTotal: 61
WNT10A-related disorderTotal: 25
not specifiedTotal: 14
Ectodermal dysplasia WNT10A relatedTotal: 3

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.

EffectPLPVUSLBBSum
synonymous
5
clinvar
235
clinvar
2
clinvar
242
missense
3
clinvar
34
clinvar
171
clinvar
16
clinvar
2
clinvar
226
nonsense
20
clinvar
15
clinvar
1
clinvar
36
start loss
1
clinvar
4
clinvar
5
frameshift
37
clinvar
11
clinvar
48
splice donor/acceptor (+/-2bp)
2
clinvar
3
clinvar
5
Total63671772514562

Highest pathogenic variant AF is 0.0014087509

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 10 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_025216.3RefSeqNP_079492.24MANE Select
ENST00000258411.8EnsemblENSP00000258411.34MANE Select
ENST00000458582.1EnsemblENSP00000388812.12Standard
ENST00000865256.1EnsemblENSP00000535315.14Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / ModelOrganismObserved Phenotype
wnt10aDanio 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: gnomAD

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-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense-0.4492812611.080.00001482659
Missense (PolyPhen)115114.891.00091241
Synonymous-0.09731131121.010.00000649871
Loss of Function0.4581416.00.8769.50e-7142

Population LoF Frequency

PopulationCAFp-valueStatus
African0.000490.00049rare
Latino/Admixed American0.0000580.000058rare
Ashkenazi Jewish00.0absent
East Asian0.000440.00044rare
Finnish0.0000920.000092rare
European (Non-Finnish)0.00140.0014notable
South Asian0.0000680.000065rare
Other0.000330.00033rare

dbNSFP Gene Annotations

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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