ClinVar Miner

Submissions for variant NM_006772.3(SYNGAP1):c.1499T>C (p.Leu500Pro)

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Total submissions: 1
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV003508144 SCV004262118 pathogenic Intellectual disability, autosomal dominant 5 2024-08-05 criteria provided, single submitter clinical testing This sequence change replaces leucine, which is neutral and non-polar, with proline, which is neutral and non-polar, at codon 500 of the SYNGAP1 protein (p.Leu500Pro). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individual(s) with clinical features of developmental and epileptic encephalopathy (Invitae). In at least one individual the variant was observed to be de novo. 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 SYNGAP1 protein function with a positive predictive value of 95%. For these reasons, this variant has been classified as Pathogenic.

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