ClinVar Miner

Submissions for variant NM_003098.3(SNTA1):c.1169C>T (p.Ala390Val)

gnomAD frequency: 0.00002  dbSNP: rs121434500
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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000414434 SCV000490823 uncertain significance not provided 2024-09-18 criteria provided, single submitter clinical testing 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: 22378279, 19862833, 29661707, 20009079, 23376825, 27028743, 31589614, Postrigan2022[Review], 18591664)
Center for Advanced Laboratory Medicine, UC San Diego Health, University of California San Diego RCV000852541 SCV000995239 likely pathogenic Atrial fibrillation; Long QT syndrome 2019-04-17 criteria provided, single submitter clinical testing
AiLife Diagnostics, AiLife Diagnostics RCV000414434 SCV002502836 likely pathogenic not provided 2022-01-03 criteria provided, single submitter clinical testing
Ambry Genetics RCV002326671 SCV002628618 uncertain significance Cardiovascular phenotype 2022-02-10 criteria provided, single submitter clinical testing The p.A390V variant (also known as c.1169C>T), located in coding exon 6 of the SNTA1 gene, results from a C to T substitution at nucleotide position 1169. The alanine at codon 390 is replaced by valine, an amino acid with similar properties. This amino acid position is not well 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.
Labcorp Genetics (formerly Invitae), Labcorp RCV002512925 SCV002932939 uncertain significance Long QT syndrome 2024-10-21 criteria provided, single submitter clinical testing This sequence change replaces alanine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 390 of the SNTA1 protein (p.Ala390Val). This variant is present in population databases (rs121434500, gnomAD 0.006%). This missense change has been observed in individual(s) with long QT syndrome (PMID: 18591664). ClinVar contains an entry for this variant (Variation ID: 8476). Invitae Evidence Modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) indicates that this missense variant is not expected to disrupt SNTA1 protein function with a negative predictive value of 80%. Experimental studies have shown that this missense change affects SNTA1 function (PMID: 18591664, 27028743). 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.
OMIM RCV000008997 SCV000029211 pathogenic Long QT syndrome 12 2008-07-08 no assertion criteria provided literature only

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