ClinVar Miner

Submissions for variant NM_020822.3(KCNT1):c.3431C>G (p.Ser1144Cys)

gnomAD frequency: 0.00001  dbSNP: rs766557144
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV001212182 SCV001383758 uncertain significance Developmental and epileptic encephalopathy, 14; Autosomal dominant nocturnal frontal lobe epilepsy 5 2023-02-18 criteria provided, single submitter clinical testing This sequence change replaces serine, which is neutral and polar, with cysteine, which is neutral and slightly polar, at codon 1144 of the KCNT1 protein (p.Ser1144Cys). The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This variant has not been reported in the literature in individuals affected with KCNT1-related conditions. ClinVar contains an entry for this variant (Variation ID: 942238). 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 KCNT1 protein function. 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.
PreventionGenetics, part of Exact Sciences RCV003973143 SCV004788172 uncertain significance KCNT1-related condition 2023-10-18 criteria provided, single submitter clinical testing The KCNT1 c.3431C>G variant is predicted to result in the amino acid substitution p.Ser1144Cys. To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.015% of alleles in individuals of African descent in gnomAD (http://gnomad.broadinstitute.org/variant/9-138678296-C-G). At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence.

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