ClinVar Miner

Submissions for variant NM_003098.3(SNTA1):c.1205G>A (p.Arg402Gln)

gnomAD frequency: 0.00002  dbSNP: rs771369802
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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Illumina Laboratory Services, Illumina RCV000259983 SCV000433491 uncertain significance Congenital long QT syndrome 2016-06-14 criteria provided, single submitter clinical testing
Illumina Laboratory Services, Illumina RCV000317445 SCV000433492 uncertain significance Long QT syndrome 12 2018-01-12 criteria provided, single submitter clinical testing This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease.
Labcorp Genetics (formerly Invitae), Labcorp RCV001342404 SCV001536332 uncertain significance Long QT syndrome 2020-10-05 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 sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site, but this prediction has not been confirmed by published transcriptional studies. 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, but these predictions have not been confirmed by published functional studies and their clinical significance is uncertain. This variant has not been reported in the literature in individuals with SNTA1-related conditions. ClinVar contains an entry for this variant (Variation ID: 338213). This variant is present in population databases (rs771369802, ExAC 0.006%). This sequence change replaces arginine with glutamine at codon 402 of the SNTA1 protein (p.Arg402Gln). The arginine residue is weakly conserved and there is a small physicochemical difference between arginine and glutamine.
GeneDx RCV001770272 SCV002002062 uncertain significance not provided 2020-01-21 criteria provided, single submitter clinical testing Has not been previously published as pathogenic or benign to our knowledge; Not observed at a significant frequency in large population cohorts (Lek et al., 2016); In silico analysis, which includes protein predictors and evolutionary conservation, supports that this variant does not alter protein structure/function
Ambry Genetics RCV002348091 SCV002649217 uncertain significance Cardiovascular phenotype 2022-01-12 criteria provided, single submitter clinical testing The p.R402Q variant (also known as c.1205G>A), located in coding exon 6 of the SNTA1 gene, results from a G to A substitution at nucleotide position 1205. The arginine at codon 402 is replaced by glutamine, an amino acid with highly similar properties. This amino acid position is not well conserved in available vertebrate species. In addition, this alteration is predicted to be tolerated by in silico analysis. The evidence for this gene-disease relationship is limited; therefore, the clinical significance of this alteration is unclear.
Fulgent Genetics, Fulgent Genetics RCV000317445 SCV002812758 uncertain significance Long QT syndrome 12 2021-08-31 criteria provided, single submitter clinical testing

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