ClinVar Miner

Submissions for variant NM_001365999.1(SZT2):c.8930C>T (p.Pro2977Leu)

gnomAD frequency: 0.00003  dbSNP: rs761830930
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV002313510 SCV000848531 uncertain significance Inborn genetic diseases 2016-12-19 criteria provided, single submitter clinical testing The p.P2920L variant (also known as c.8759C>T), located in coding exon 63 of the SZT2 gene, results from a C to T substitution at nucleotide position 8759. The proline at codon 2920 is replaced by leucine, an amino acid with similar 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.
Invitae RCV001325832 SCV001516839 uncertain significance not provided 2022-08-13 criteria provided, single submitter clinical testing This sequence change replaces proline, which is neutral and non-polar, with leucine, which is neutral and non-polar, at codon 2920 of the SZT2 protein (p.Pro2920Leu). This variant is present in population databases (no rsID available, gnomAD 0.003%). 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: 588569). Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Tolerated"; PolyPhen-2: "Benign"; Align-GVGD: "Class C15". The leucine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. 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 RCV001325832 SCV001998523 uncertain significance not provided 2019-11-21 criteria provided, single submitter clinical testing Not observed at a significant frequency in large population cohorts (Lek et al., 2016); In silico analysis, which includes protein predictors and evolutionary conservation, supports that this variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge
Genome-Nilou Lab RCV003457763 SCV004178048 uncertain significance Developmental and epileptic encephalopathy, 18 2023-04-11 criteria provided, single submitter clinical testing

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