ClinVar Miner

Submissions for variant NM_003098.3(SNTA1):c.1378G>A (p.Gly460Ser)

gnomAD frequency: 0.00001  dbSNP: rs368660364
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV002022102 SCV002257740 uncertain significance Long QT syndrome 2022-09-23 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. Experimental studies have shown that this missense change affects SNTA1 function (PMID: 20009079). 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: 1480612). This missense change has been observed in individual(s) with sudden infant death syndrome (PMID: 20009079). This variant is present in population databases (rs368660364, gnomAD 0.006%). This sequence change replaces glycine, which is neutral and non-polar, with serine, which is neutral and polar, at codon 460 of the SNTA1 protein (p.Gly460Ser).
GeneDx RCV004591679 SCV005080982 uncertain significance not provided 2023-04-03 criteria provided, single submitter clinical testing Identified in a case of sudden infant death syndrome (SIDS) in published literature (Cheng et al., 2009); Not observed at significant frequency in large population cohorts (gnomAD); A published functional study suggests a damaging effect via higher peak and late sodium currents compared to wild type alone (Cheng et al., 2009); 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: 20009079, 31043699, 23465283)

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