ClinVar Miner

Submissions for variant NM_006772.3(SYNGAP1):c.2362T>A (p.Ser788Thr)

gnomAD frequency: 0.00003  dbSNP: rs201062426
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000437108 SCV000536044 uncertain significance not provided 2017-02-03 criteria provided, single submitter clinical testing The S788T variant in the SYNGAP1 gene has not been reported previously as a pathogenic variant, nor as a benign variant, to our knowledge. The S788T variant was not observed in approximately 6,500 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations. The S788T variant is a conservative amino acid substitution, which occurs at a position that is conserved across species. However, in silico analysis is inconsistent in its predictions as to whether or not the variant is damaging to the protein structure/function. We interpret S788T as a variant of uncertain significance.
Labcorp Genetics (formerly Invitae), Labcorp RCV003615838 SCV004531839 uncertain significance Intellectual disability, autosomal dominant 5 2024-01-12 criteria provided, single submitter clinical testing This sequence change replaces serine, which is neutral and polar, with threonine, which is neutral and polar, at codon 788 of the SYNGAP1 protein (p.Ser788Thr). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with SYNGAP1-related conditions. ClinVar contains an entry for this variant (Variation ID: 392728). 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 SYNGAP1 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.

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