ClinVar Miner

Submissions for variant NM_001365999.1(SZT2):c.5831C>T (p.Pro1944Leu)

gnomAD frequency: 0.00001  dbSNP: rs754585816
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000811302 SCV000951562 uncertain significance not provided 2024-01-19 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 1887 of the SZT2 protein (p.Pro1887Leu). This variant is present in population databases (rs754585816, gnomAD 0.04%). 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: 655177). 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 expected to disrupt SZT2 protein function with a positive 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.
Ambry Genetics RCV002345839 SCV002653800 uncertain significance Inborn genetic diseases 2019-10-26 criteria provided, single submitter clinical testing The p.P1887L variant (also known as c.5660C>T), located in coding exon 40 of the SZT2 gene, results from a C to T substitution at nucleotide position 5660. The proline at codon 1887 is replaced by leucine, an amino acid with similar properties. This amino acid position is well conserved in available vertebrate species; however, leucine is the reference amino acid in other 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 RCV003457819 SCV004177792 uncertain significance Developmental and epileptic encephalopathy, 18 2023-04-11 criteria provided, single submitter clinical testing

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