rs121908120

This is a variant in the WNT10A gene that changes a phenylalanine to an isoleucine.

GWAS Catalog Trait Associations (16)

Genome-wide significant associations (p < 5×10⁻⁸) from the NHGRI-EBI GWAS Catalog.

galanin peptides measurement

Allele A
OR 0.20
p 9.0e-47
N 47,745
Large GWAS
European

tooth agenesis

Jonsson L et al. Rare and Common Variants Conferring Risk of Tooth Agenesis. Journal of Dental Research 97(5):515-522 (2018)
Allele A
OR 3.25
p 2.0e-40
N 340,498
Large GWAS
multi-ancestry

corneal resistance factor

Allele T
OR 0.34
p 1.0e-34
N 76,029
Large GWAS
European

Epidermal Inclusion Cyst

Verma A et al. Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program. Science (new York, N.y.) 385(6706):eadj1182 (2024)
Allele T
OR 0.40
p 2.0e-28
N 420,570
Major Consortium StudyLarge GWAS
European

cystatin-M measurement

Allele A
OR 0.14
p 8.0e-24
N 47,745
Large GWAS
European

dental caries, dentures

Allele A
OR 0.08
p 2.0e-22
N 487,823
Large GWAS
multi-ancestry

dentures

Allele A
OR 0.16
p 2.0e-20
N 461,031
Large GWAS
European

kallikrein-8 measurement

Allele A
OR 0.14
p 1.0e-18
N 47,745
Large GWAS
European

poly(U)-specific endoribonuclease measurement

Allele A
OR 0.12
p 5.0e-18
N 47,745
Large GWAS
European

level of serine protease inhibitor Kazal-type 5 in blood

Allele A
OR 0.12
p 6.0e-16
N 47,745
Large GWAS
European

ClinVar annotation

Pathogenic★★★
39 submitters29 publications

Ectodermal dysplasia; Ectodermal dysplasia WNT10A related; Hypohidrotic ectodermal dysplasia (HED); Inborn genetic diseases; Odonto-onycho-dermal dysplasia; SchC6pf-Schulz-Passarge syndrome; See cases; Tooth agenesis; Tooth agenesis, selective, 4 (STHAG4); WNT10A-related disorder

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Research that mentions this SNP (2)

Disease variants in genomes of 44 centenarians
Case reportN=44Yun Freudenberg‐Hua et al.(2014)· Molecular Genetics &amp; Genomic Medicine

Whole genome sequencing of 44 Ashkenazi Jewish centenarians identified 216 coding variants annotated as pathogenic or likely pathogenic in ClinVar. The study found 130 rare variants (MAF <5%) reported to cause degenerative, neoplastic, and cardiac diseases with various inheritance patterns. Notably, several carriers had no clinical manifestations despite carrying variants linked to serious diseases (e.g., an APOE ε4 homozygote without Alzheimer's disease, a UBQLN2 P525S carrier without ALS). These findings suggest incomplete penetrance and reduced clinical significance for many reported disease mutations.

Traits studied:Aging and longevityAlzheimer's diseaseAmyotrophic lateral sclerosisBecker muscular dystrophyBrugada syndromeCancer/NeoplasmCardiac arrhythmiaCardiomyopathyDeafnessDementia with Lewy bodiesDiabetesDuchenne muscular dystrophyEhlers-Danlos syndromeGaucher diseaseGlaucomaHypercholesterolemiaIchthyosisKeratoconusLong QT syndromeObesityParkinson's diseasePremature ovarian failureRetinitis pigmentosa
WNT10A and isolated hypodontia
Case reportPiranit Kantaputra et al.(2011)· American Journal of Medical Genetics Part A

A family report of isolated hypodontia (missing and small teeth) caused by two WNT10A missense mutations: c.682T>A (p.Phe228Ile) and c.649G>A (p.Asp217Asn). The father and oldest son carried the first mutation, the mother and second son carried the second mutation, and the youngest son was a compound heterozygote. No other features of ectodermal dysplasia were observed, demonstrating that WNT10A mutations can cause isolated hypodontia without systemic manifestations.

Traits studied:HypodontiaIsolated hypodontiaMicrodontiaMissing teeth

About WNT10A

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]

View all WNT10A variants →

Gene information from NCBI Gene. Variant classifications from ClinVar.

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