ClinVar Miner

Submissions for variant NM_025216.3(WNT10A):c.337C>T (p.Arg113Cys)

gnomAD frequency: 0.00080  dbSNP: rs141074983
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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000413047 SCV000490882 likely pathogenic not provided 2024-08-21 criteria provided, single submitter clinical testing Considered a low penetrance variant for autosomal dominant and recessive inherited tooth agenesis (PMID: 31433103); this variant has been observed in at least one homozygous individual in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 23167694, 23991204, 24449199, 31589614, 33034246, 36294409, 36250548, 25545742, 31433103, 35999385)
Labcorp Genetics (formerly Invitae), Labcorp RCV001080960 SCV001106314 likely benign Odonto-onycho-dermal dysplasia; Tooth agenesis, selective, 4 2025-01-14 criteria provided, single submitter clinical testing
MGZ Medical Genetics Center RCV000991159 SCV002579111 likely pathogenic Tooth agenesis, selective, 4 2022-06-13 criteria provided, single submitter clinical testing
Institute for Clinical Genetics, University Hospital TU Dresden, University Hospital TU Dresden RCV000413047 SCV004026391 uncertain significance not provided 2023-05-22 criteria provided, single submitter clinical testing PP3
PreventionGenetics, part of Exact Sciences RCV004530509 SCV004120619 likely pathogenic WNT10A-related disorder 2023-05-09 criteria provided, single submitter clinical testing The WNT10A c.337C>T variant is predicted to result in the amino acid substitution p.Arg113Cys. This variant has been reported in the homozygous, compound heterozygous, and heterozygous states in multiple individuals with tooth agenesis (Arte et al. 2013. PubMed ID: 23991204; Mostowska et al. 2014. PubMed ID: 25545742). Functional study showed that this variant decreased WNT signaling, although some activity was retained (Zeng et al. 2020. PubMed ID: 33034246). This variant is reported in 0.66% of alleles in individuals of European (Finnish) descent in gnomAD (http://gnomad.broadinstitute.org/variant/2-219747106-C-T). This variant is interpreted as likely pathogenic.
Reproductive Health Research and Development, BGI Genomics RCV000991159 SCV001142326 likely pathogenic Tooth agenesis, selective, 4 2020-01-06 no assertion criteria provided curation NM_025216.2:c.337C>T in the WNT10A gene has an allele frequency of 0.007 in European (Finnish) subpopulation in the gnomAD database. This variant has been reported previously in the homozygous, reportedly compound heterozygous, and heterozygous state in multiple individuals with tooth agenesis (PMID: 23991204). Pathogenic computational verdict because pathogenic predictions from DANN, DEOGEN2, EIGEN, FATHMM-MKL, M-CAP, MVP, MutationAssessor, MutationTaster, REVEL and SIFT. Taken together, we interprete this variant as Pathogenic/Likely pathogenic. ACMG/AMP Criteria applied: PP3; PP4; PM3_Strong.

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