ClinVar Miner

Submissions for variant NM_025216.3(WNT10A):c.311G>A (p.Arg104His)

gnomAD frequency: 0.00002  dbSNP: rs374910216
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV001047681 SCV001211658 pathogenic Odonto-onycho-dermal dysplasia; Tooth agenesis, selective, 4 2023-11-27 criteria provided, single submitter clinical testing This sequence change replaces arginine, which is basic and polar, with histidine, which is basic and polar, at codon 104 of the WNT10A protein (p.Arg104His). This variant is present in population databases (rs374910216, gnomAD 0.01%). This missense change has been observed in individual(s) with clinical features of tricho-odonto-onycho-dermal dysplasia (Invitae). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. ClinVar contains an entry for this variant (Variation ID: 633837). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt WNT10A protein function with a positive predictive value of 80%. This variant disrupts the p.Arg104 amino acid residue in WNT10A. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 30974434; Invitae). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. For these reasons, this variant has been classified as Pathogenic.
GeneDx RCV001546388 SCV001765894 uncertain significance not provided 2021-01-13 criteria provided, single submitter clinical testing In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; This variant is associated with the following publications: (PMID: 31652981)
Revvity Omics, Revvity RCV001546388 SCV002017946 likely pathogenic not provided 2020-12-08 criteria provided, single submitter clinical testing
Institute of Human Genetics, University of Ulm RCV000782362 SCV000920801 pathogenic Tooth agenesis, selective, 4 2018-04-11 no assertion criteria provided research

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