ClinVar Miner

Submissions for variant NM_177402.5(SYT2):c.71T>C (p.Ile24Thr)

gnomAD frequency: 0.00033  dbSNP: rs199582045
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
CeGaT Center for Human Genetics Tuebingen RCV000761691 SCV000891870 likely benign not provided 2018-06-01 criteria provided, single submitter clinical testing
GeneDx RCV000761691 SCV001996666 uncertain significance not provided 2019-11-12 criteria provided, single submitter clinical testing Has not been previously published as pathogenic or benign to our knowledge; In silico analysis, which includes protein predictors and evolutionary conservation, supports that this variant does not alter protein structure/function
Labcorp Genetics (formerly Invitae), Labcorp RCV000761691 SCV002195754 uncertain significance not provided 2025-01-28 criteria provided, single submitter clinical testing This sequence change replaces isoleucine, which is neutral and non-polar, with threonine, which is neutral and polar, at codon 24 of the SYT2 protein (p.Ile24Thr). This variant is present in population databases (rs199582045, gnomAD 0.06%). This variant has not been reported in the literature in individuals affected with SYT2-related conditions. ClinVar contains an entry for this variant (Variation ID: 623712). An algorithm developed to predict the effect of missense changes on protein structure and function outputs the following: PolyPhen-2: "Benign". The threonine 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.
Ambry Genetics RCV002533877 SCV003677845 uncertain significance Inborn genetic diseases 2021-10-20 criteria provided, single submitter clinical testing The c.71T>C (p.I24T) alteration is located in exon 2 (coding exon 1) of the SYT2 gene. This alteration results from a T to C substitution at nucleotide position 71, causing the isoleucine (I) at amino acid position 24 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.

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