ClinVar Miner

Submissions for variant NM_025216.3(WNT10A):c.322T>C (p.Ser108Pro)

dbSNP: rs1249944381
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV002005566 SCV002277169 likely pathogenic Odonto-onycho-dermal dysplasia; Tooth agenesis, selective, 4 2024-02-19 criteria provided, single submitter clinical testing This sequence change replaces serine, which is neutral and polar, with proline, which is neutral and non-polar, at codon 108 of the WNT10A protein (p.Ser108Pro). This variant is present in population databases (no rsID available, gnomAD 0.003%). This missense change has been observed in individual(s) with clinical features of odontoonychodermal 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: 1484123). 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 not expected to disrupt WNT10A protein function with a negative predictive value of 80%. In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic.
Fulgent Genetics, Fulgent Genetics RCV005017009 SCV005647769 likely pathogenic Odonto-onycho-dermal dysplasia; SchC6pf-Schulz-Passarge syndrome; Tooth agenesis, selective, 4 2024-03-27 criteria provided, single submitter clinical testing

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