ClinVar Miner

Submissions for variant NM_020822.3(KCNT1):c.1619A>G (p.Gln540Arg)

gnomAD frequency: 0.00001  dbSNP: rs1446587740
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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 RCV001294406 SCV001483284 uncertain significance Developmental and epileptic encephalopathy, 14; Autosomal dominant nocturnal frontal lobe epilepsy 5 2022-11-22 criteria provided, single submitter clinical testing 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. Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated. ClinVar contains an entry for this variant (Variation ID: 998535). This variant has not been reported in the literature in individuals affected with KCNT1-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces glutamine, which is neutral and polar, with arginine, which is basic and polar, at codon 540 of the KCNT1 protein (p.Gln540Arg).
Ambry Genetics RCV002543027 SCV003549999 uncertain significance Inborn genetic diseases 2021-01-26 criteria provided, single submitter clinical testing The c.1619A>G (p.Q540R) alteration is located in exon 16 (coding exon 16) of the KCNT1 gene. This alteration results from a A to G substitution at nucleotide position 1619, causing the glutamine (Q) at amino acid position 540 to be replaced by an arginine (R). The p.Q540R alteration is predicted to be tolerated by in silico analysis. Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.

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