ClinVar Miner

Submissions for variant NM_001365999.1(SZT2):c.8939C>T (p.Thr2980Ile)

gnomAD frequency: 0.00001  dbSNP: rs766294629
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV001343243 SCV001537211 uncertain significance not provided 2022-01-07 criteria provided, single submitter clinical testing This sequence change replaces threonine, which is neutral and polar, with isoleucine, which is neutral and non-polar, at codon 2923 of the SZT2 protein (p.Thr2923Ile). This variant is present in population databases (rs766294629, gnomAD 0.003%). This missense change has been observed in individual(s) with clinical features of Rolandic epilepsy (PMID: 29358611). ClinVar contains an entry for this variant (Variation ID: 433096). 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: "Tolerated"; PolyPhen-2: "Possibly Damaging"; Align-GVGD: "Class C25"). 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 RCV001343243 SCV002003041 uncertain significance not provided 2023-09-28 criteria provided, single submitter clinical testing Reported homozygous in an individual with persistent elevations of urine L-3-hydroxyisobutyric acid in published literature; however, a homozygous variant in another gene was identified that was more likely to explain phenotype (Sasarman et al., 2022); 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: 35174513)
Genome-Nilou Lab RCV003457711 SCV004178049 uncertain significance Developmental and epileptic encephalopathy, 18 2023-04-11 criteria provided, single submitter clinical testing
Bioinformatics Core, Luxembourg Center for Systems Biomedicine RCV000655979 SCV000588255 pathogenic Self-limited epilepsy with centrotemporal spikes 2017-01-01 no assertion criteria provided case-control CAADphred>15

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