ClinVar Miner

Submissions for variant NM_003098.3(SNTA1):c.776C>T (p.Ser259Leu)

gnomAD frequency: 0.00003  dbSNP: rs774643587
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000462505 SCV000553687 uncertain significance Long QT syndrome 2023-05-23 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: 412218). This missense change has been observed in individual(s) with Brugada syndrome (PMID: 24981977). This variant is present in population databases (rs774643587, gnomAD 0.006%). This sequence change replaces serine, which is neutral and polar, with leucine, which is neutral and non-polar, at codon 259 of the SNTA1 protein (p.Ser259Leu).
Ambry Genetics RCV000620167 SCV000735859 uncertain significance Cardiovascular phenotype 2022-12-11 criteria provided, single submitter clinical testing The p.S259L variant (also known as c.776C>T), located in coding exon 4 of the SNTA1 gene, results from a C to T substitution at nucleotide position 776. The serine at codon 259 is replaced by leucine, an amino acid with dissimilar properties. This alteration has been reported in one case of Brugada syndrome; however, clinical details were limited (Brion M et al. Electrophoresis, 2014 Nov;35:3111-6). This amino acid position is 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.
GeneDx RCV003325485 SCV004031801 uncertain significance not provided 2023-08-29 criteria provided, single submitter clinical testing Has been reported in association with Brugada syndrome (Brion et al., 2014); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 24981977)

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