ClinVar Miner

Submissions for variant NM_001112741.2(KCNC1):c.1538C>T (p.Ala513Val)

gnomAD frequency: 0.00001  dbSNP: rs1485166517
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Total submissions: 1
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV001208247 SCV001379625 likely pathogenic Progressive myoclonic epilepsy type 7 2023-12-22 criteria provided, single submitter clinical testing This sequence change replaces alanine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 513 of the KCNC1 protein (p.Ala513Val). This variant is present in population databases (no rsID available, gnomAD 0.002%). This missense change has been observed in individual(s) with clinical features of KCNC1-related conditions (PMID: 31353855). In at least one individual the variant was observed to be de novo. ClinVar contains an entry for this variant (Variation ID: 938939). 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 KCNC1 protein function with a negative predictive value of 95%. Experimental studies have shown that this missense change affects KCNC1 function (PMID: 34232791). 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.

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