ClinVar Miner

Submissions for variant NM_006514.4(SCN10A):c.3598G>A (p.Glu1200Lys)

gnomAD frequency: 0.00002  dbSNP: rs202199966
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV001886033 SCV002143530 uncertain significance Brugada syndrome 2021-02-18 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. 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 SCN10A protein function. This variant has not been reported in the literature in individuals with SCN10A-related conditions. This variant is not present in population databases (ExAC no frequency). This sequence change replaces glutamic acid with lysine at codon 1200 of the SCN10A protein (p.Glu1200Lys). The glutamic acid residue is highly conserved and there is a small physicochemical difference between glutamic acid and lysine.
Ambry Genetics RCV003303269 SCV003999214 uncertain significance Cardiovascular phenotype 2023-04-27 criteria provided, single submitter clinical testing The p.E1200K variant (also known as c.3598G>A), located in coding exon 20 of the SCN10A gene, results from a G to A substitution at nucleotide position 3598. The glutamic acid at codon 1200 is replaced by lysine, an amino acid with similar properties. This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. The evidence for this gene-disease relationship is limited; therefore, the clinical significance of this alteration is unclear.
GeneDx RCV005232696 SCV005875024 uncertain significance not provided 2024-08-26 criteria provided, single submitter clinical testing Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Has not been previously published as pathogenic or benign to our knowledge

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