ClinVar Miner

Submissions for variant NM_001365999.1(SZT2):c.10288C>T (p.Arg3430Cys)

gnomAD frequency: 0.00002  dbSNP: rs750291489
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV002312400 SCV000846733 uncertain significance Inborn genetic diseases 2016-05-17 criteria provided, single submitter clinical testing The p.R3373C variant (also known as c.10117C>T), located in coding exon 71 of the SZT2 gene, results from a C to T substitution at nucleotide position 10117. The arginine at codon 3373 is replaced by cysteine, an amino acid with highly dissimilar properties. This variant was not reported in population based cohorts in the following databases: Database of Single Nucleotide Polymorphisms (dbSNP), NHLBI Exome Sequencing Project (ESP), and 1000 Genomes Project. In the ESP, this variant was not observed in 6503 samples (13006 alleles) with coverage at this position. 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 variant remains unclear.
Invitae RCV001050900 SCV001215029 uncertain significance not provided 2023-11-27 criteria provided, single submitter clinical testing This sequence change replaces arginine, which is basic and polar, with cysteine, which is neutral and slightly polar, at codon 3373 of the SZT2 protein (p.Arg3373Cys). This variant is present in population databases (rs750291489, gnomAD 0.004%). 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: 587917). 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 with a negative predictive value of 80%. 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 RCV003457747 SCV004178121 uncertain significance Developmental and epileptic encephalopathy, 18 2023-04-11 criteria provided, single submitter clinical testing

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