ClinVar Miner

Submissions for variant NM_000346.4(SOX9):c.337A>G (p.Met113Val)

dbSNP: rs2143240089
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV001658995 SCV001875122 pathogenic not provided 2021-09-03 criteria provided, single submitter clinical testing Published functional studies demonstrate M113V binding to several sites from SOX9-responsive regulatory regions was reduced compared to wildtype (Staffler et al., 2010); In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; Not observed in large population cohorts (Lek et al., 2016); This variant is associated with the following publications: (PMID: 20513132)
Invitae RCV003497930 SCV004297519 pathogenic Camptomelic dysplasia 2023-05-16 criteria provided, single submitter clinical testing For these reasons, this variant has been classified as Pathogenic. This variant disrupts the p.Met113 amino acid residue in SOX9. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 20513132, 32381727). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. 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 SOX9 protein function. ClinVar contains an entry for this variant (Variation ID: 1254813). This missense change has been observed in individual(s) with campomelic dysplasia (PMID: 20513132; Invitae). In at least one individual the variant was observed to be de novo. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces methionine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 113 of the SOX9 protein (p.Met113Val).

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