ClinVar Miner

Submissions for variant NM_001365999.1(SZT2):c.2950A>G (p.Thr984Ala)

gnomAD frequency: 0.00001  dbSNP: rs1057524780
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000419448 SCV000536446 uncertain significance not provided 2022-07-19 criteria provided, single submitter clinical testing Identified in a patient with sudden unexpected death in epilepsy who also harbored a second SZT2 variant, but it is not known whether the variants occurred on the same (in cis) or on different (in trans) chromosomes (Chahal et al., 2021); Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant does not alter protein structure/function; This variant is associated with the following publications: (PMID: 34816733)
Invitae RCV000419448 SCV000961536 uncertain significance not provided 2022-08-15 criteria provided, single submitter clinical testing This sequence change replaces threonine, which is neutral and polar, with alanine, which is neutral and non-polar, at codon 984 of the SZT2 protein (p.Thr984Ala). This variant is present in population databases (no rsID available, gnomAD 0.007%). 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: 393086). Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Deleterious"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0". The alanine 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.
Genome-Nilou Lab RCV003457682 SCV004180834 uncertain significance Developmental and epileptic encephalopathy, 18 2023-04-11 criteria provided, single submitter clinical testing

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