ClinVar Miner

Submissions for variant NM_025216.3(WNT10A):c.1034T>C (p.Phe345Ser)

dbSNP: rs1553623335
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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 RCV000559209 SCV000638461 uncertain significance Odonto-onycho-dermal dysplasia; Tooth agenesis, selective, 4 2024-10-28 criteria provided, single submitter clinical testing This sequence change replaces phenylalanine, which is neutral and non-polar, with serine, which is neutral and polar, at codon 345 of the WNT10A protein (p.Phe345Ser). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individual(s) with clinical features of odontoonychodermal dysplasia (internal data). ClinVar contains an entry for this variant (Variation ID: 464178). Invitae Evidence Modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) indicates that this missense variant is expected to disrupt WNT10A protein function with a positive predictive value of 80%. This variant disrupts the p.Phe345 amino acid residue in WNT10A. Other variant(s) that disrupt this residue have been observed in individuals with WNT10A-related conditions (PMID: 28976000), which suggests that this may be a clinically significant amino acid residue. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.
GeneDx RCV004760569 SCV005372392 likely pathogenic not provided 2023-06-13 criteria provided, single submitter clinical testing In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 36294409)

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