ClinVar Miner

Submissions for variant NM_001365999.1(SZT2):c.7802G>A (p.Arg2601His)

gnomAD frequency: 0.00006  dbSNP: rs757425191
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000799049 SCV000938696 uncertain significance not provided 2022-10-13 criteria provided, single submitter clinical testing This sequence change replaces arginine, which is basic and polar, with histidine, which is basic and polar, at codon 2544 of the SZT2 protein (p.Arg2544His). This variant is present in population databases (rs757425191, gnomAD 0.006%). 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: 645034). 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 SZT2 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.
CeGaT Center for Human Genetics Tuebingen RCV000799049 SCV001247450 uncertain significance not provided 2019-07-01 criteria provided, single submitter clinical testing
GeneDx RCV000799049 SCV002012553 uncertain significance not provided 2021-10-27 criteria provided, single submitter clinical testing Not observed at 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
Ambry Genetics RCV002388465 SCV002672801 uncertain significance Inborn genetic diseases 2017-07-18 criteria provided, single submitter clinical testing The p.R2544H variant (also known as c.7631G>A), located in coding exon 55 of the SZT2 gene, results from a G to A substitution at nucleotide position 7631. The arginine at codon 2544 is replaced by histidine, an amino acid with highly 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. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.
Genome-Nilou Lab RCV003457806 SCV004181518 uncertain significance Developmental and epileptic encephalopathy, 18 2023-04-11 criteria provided, single submitter clinical testing

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