ClinVar Miner

Submissions for variant NM_001365999.1(SZT2):c.5515C>T (p.Arg1839Cys)

gnomAD frequency: 0.00010  dbSNP: rs147748994
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV002314859 SCV000848712 uncertain significance Inborn genetic diseases 2020-01-09 criteria provided, single submitter clinical testing The p.R1782C variant (also known as c.5344C>T), located in coding exon 37 of the SZT2 gene, results from a C to T substitution at nucleotide position 5344. The arginine at codon 1782 is replaced by cysteine, an amino acid with highly dissimilar properties. 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 variant remains unclear.
Invitae RCV001212620 SCV001384209 uncertain significance not provided 2022-08-10 criteria provided, single submitter clinical testing This sequence change replaces arginine, which is basic and polar, with cysteine, which is neutral and slightly polar, at codon 1782 of the SZT2 protein (p.Arg1782Cys). This variant is present in population databases (rs147748994, gnomAD 0.01%). This variant has not been reported in the literature in individuals affected with SZT2-related conditions. ClinVar contains an entry for this variant (Variation ID: 433091). 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"). 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.
GeneDx RCV001212620 SCV003936662 uncertain significance not provided 2022-12-29 criteria provided, single submitter clinical testing Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge
Genome-Nilou Lab RCV003457710 SCV004181141 uncertain significance Developmental and epileptic encephalopathy, 18 2023-04-11 criteria provided, single submitter clinical testing
Bioinformatics Core, Luxembourg Center for Systems Biomedicine RCV000655974 SCV000588250 pathogenic Childhood epilepsy with centrotemporal spikes 2017-01-01 no assertion criteria provided case-control CAADphred>15

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