ClinVar Miner

Submissions for variant NM_003098.3(SNTA1):c.1204C>T (p.Arg402Trp)

gnomAD frequency: 0.00002  dbSNP: rs373387978
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV002345666 SCV002650027 uncertain significance Cardiovascular phenotype 2023-02-16 criteria provided, single submitter clinical testing The p.R402W variant (also known as c.1204C>T), located in coding exon 6 of the SNTA1 gene, results from a C to T substitution at nucleotide position 1204. The arginine at codon 402 is replaced by tryptophan, an amino acid with dissimilar 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. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.
Fulgent Genetics, Fulgent Genetics RCV000185534 SCV002785375 uncertain significance Long QT syndrome 12 2022-05-12 criteria provided, single submitter clinical testing
Invitae RCV003532046 SCV004291919 uncertain significance Long QT syndrome 2023-06-06 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 not expected to disrupt SNTA1 protein function. ClinVar contains an entry for this variant (Variation ID: 203366). This variant has not been reported in the literature in individuals affected with SNTA1-related conditions. This variant is present in population databases (rs373387978, gnomAD 0.006%). This sequence change replaces arginine, which is basic and polar, with tryptophan, which is neutral and slightly polar, at codon 402 of the SNTA1 protein (p.Arg402Trp).
Division of Human Genetics, Children's Hospital of Philadelphia RCV000185534 SCV000238409 uncertain significance Long QT syndrome 12 2014-07-17 no assertion criteria provided research This test identified a missense variant (c.1204G>A; p.Arg402Trp) in the SNTA1 gene, which is implicated in Long QT syndrome 12. This variant is considered a variant of unknown significance because it has not been reported in patients with Long QT syndrome and has properties that are suggestive of it being both a pathogenic and benign variant. This variant was maternally inherited and also observed in the maternal grandmother with Long QT syndrome, but not in the similarly affected siblings. In this family, the variant did not segregate with disease, making it less likely to be associated with the cardiac findings.

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