ClinVar Miner

Submissions for variant NM_003098.3(SNTA1):c.316C>T (p.Arg106Trp)

gnomAD frequency: 0.00001  dbSNP: rs552509775
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV001763514 SCV001990976 uncertain significance not provided 2019-04-05 criteria provided, single submitter clinical testing Identified in conjunction with several other variants via exome sequencing in a Chinese family with a history of atrial septal defect (ASD); the SNTA1 variant was not studied further, and the variant in LBX2 was found to be associated with ASD (Wang et al., 2018); Observed in 0.0028% (7/246242) of global alleles in large population cohorts (Lek et al., 2016); In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; This variant is associated with the following publications: (PMID: 29669692)
Ambry Genetics RCV002324182 SCV002610038 uncertain significance Cardiovascular phenotype 2024-01-29 criteria provided, single submitter clinical testing The p.R106W variant (also known as c.316C>T), located in coding exon 2 of the SNTA1 gene, results from a C to T substitution at nucleotide position 316. The arginine at codon 106 is replaced by tryptophan, an amino acid with dissimilar properties. This amino acid position is well conserved in available vertebrate species. In addition, this alteration is predicted to be tolerated by BayesDel in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.
Fulgent Genetics, Fulgent Genetics RCV002489767 SCV002784546 uncertain significance Long QT syndrome 12 2021-09-16 criteria provided, single submitter clinical testing
Invitae RCV003771977 SCV004678204 uncertain significance Long QT syndrome 2023-04-11 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 expected to disrupt SNTA1 protein function. ClinVar contains an entry for this variant (Variation ID: 1308602). This variant has not been reported in the literature in individuals affected with SNTA1-related conditions. This variant is present in population databases (rs552509775, gnomAD 0.01%). This sequence change replaces arginine, which is basic and polar, with tryptophan, which is neutral and slightly polar, at codon 106 of the SNTA1 protein (p.Arg106Trp).

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