ClinVar Miner

Submissions for variant NM_003098.3(SNTA1):c.1015C>T (p.Arg339Cys)

gnomAD frequency: 0.00005  dbSNP: rs138164106
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000438313 SCV000536127 uncertain significance not provided 2021-06-30 criteria provided, single submitter clinical testing Has not been previously published as pathogenic or benign to our knowledge; In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Reported in ClinVar but additional evidence is not available (ClinVar Variant ID#392800; Landrum et al., 2016); This variant is associated with the following publications: (PMID: 26582918, 27535533)
Invitae RCV001244316 SCV001417527 uncertain significance Long QT syndrome 2022-05-27 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 missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0"). ClinVar contains an entry for this variant (Variation ID: 392800). This variant has not been reported in the literature in individuals affected with SNTA1-related conditions. This variant is present in population databases (rs138164106, gnomAD 0.02%). This sequence change replaces arginine, which is basic and polar, with cysteine, which is neutral and slightly polar, at codon 339 of the SNTA1 protein (p.Arg339Cys).
Ambry Genetics RCV002339102 SCV002637771 uncertain significance Cardiovascular phenotype 2019-07-18 criteria provided, single submitter clinical testing The p.R339C variant (also known as c.1015C>T), located in coding exon 5 of the SNTA1 gene, results from a C to T substitution at nucleotide position 1015. The arginine at codon 339 is replaced by cysteine, an amino acid with highly 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 RCV002480330 SCV002797170 uncertain significance Long QT syndrome 12 2022-02-24 criteria provided, single submitter clinical testing
Dept of Medical Biology, Uskudar University RCV001244316 SCV004022004 uncertain significance Long QT syndrome 2024-01-08 criteria provided, single submitter research Criteria: PM2

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