ClinVar Miner

Submissions for variant NM_004519.4(KCNQ3):c.1531A>G (p.Met511Val)

dbSNP: rs200219106
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000278507 SCV000329372 uncertain significance not specified 2016-05-20 criteria provided, single submitter clinical testing The M511V variant has not been published as a pathogenic variant, nor has it been reported as a benign variant to our knowledge. The M511V variant is a conservative amino acid substitution, which is not likely to impact secondary protein structure as these residues share similar properties. This substitution occurs at a position where amino acids with similar properties to Methionine are tolerated across species. However, M511V was not observed in approximately 6,500 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations. In silico analysis is inconsistent in its predictions as to whether or not the variant is damaging to the protein structure/function. Therefore, based on the currently available information, it is unclear whether this variant is a pathogenic variant or a rare benign variant.
Mayo Clinic Laboratories, Mayo Clinic RCV002261027 SCV002540967 uncertain significance not provided 2021-07-23 criteria provided, single submitter clinical testing
Invitae RCV003748215 SCV004529001 uncertain significance Benign neonatal seizures 2023-12-12 criteria provided, single submitter clinical testing This sequence change replaces methionine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 511 of the KCNQ3 protein (p.Met511Val). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with KCNQ3-related conditions. ClinVar contains an entry for this variant (Variation ID: 279819). 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 KCNQ3 protein function with a negative predictive value of 80%. 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.

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