ClinVar Miner

Submissions for variant NM_001365999.1(SZT2):c.9049A>G (p.Met3017Val)

gnomAD frequency: 0.00007  dbSNP: rs143624137
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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 RCV002318058 SCV000849697 uncertain significance Inborn genetic diseases 2017-05-26 criteria provided, single submitter clinical testing The p.M2960V variant (also known as c.8878A>G), located in coding exon 64 of the SZT2 gene, results from an A to G substitution at nucleotide position 8878. The methionine at codon 2960 is replaced by valine, an amino acid with highly similar properties. This amino acid position is highly conserved in available vertebrate species; however, valine is the reference amino acid in other 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.
Invitae RCV001068001 SCV001233088 uncertain significance not provided 2022-09-07 criteria provided, single submitter clinical testing This sequence change replaces methionine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 2960 of the SZT2 protein (p.Met2960Val). This variant is present in population databases (rs143624137, gnomAD 0.02%). 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: 589117). 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: "Probably Damaging"; Align-GVGD: "Class C0"). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site. 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 RCV001068001 SCV002765524 uncertain significance not provided 2022-12-15 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
Revvity Omics, Revvity Omics RCV003141722 SCV003818891 uncertain significance Developmental and epileptic encephalopathy, 18 2022-01-12 criteria provided, single submitter clinical testing
Genome-Nilou Lab RCV003141722 SCV004178054 uncertain significance Developmental and epileptic encephalopathy, 18 2023-04-11 criteria provided, single submitter clinical testing

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