ClinVar Miner

Submissions for variant NM_006772.3(SYNGAP1):c.121C>T (p.Arg41Cys)

gnomAD frequency: 0.00001  dbSNP: rs762142487
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV000691962 SCV000819764 uncertain significance Intellectual disability, autosomal dominant 5 2020-01-22 criteria provided, single submitter clinical testing Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Possibly Damaging"; Align-GVGD: "Class C0"). 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. This sequence change replaces arginine with cysteine at codon 41 of the SYNGAP1 protein (p.Arg41Cys). The arginine residue is moderately conserved and there is a large physicochemical difference between arginine and cysteine. This variant is present in population databases (rs762142487, ExAC 0.01%). This variant has been observed in individual(s) with clinical features of SYNGAP1-related conditions (PMID: 30541864, Invitae).
Diagnostic Laboratory, Strasbourg University Hospital RCV001260775 SCV001437867 uncertain significance Intellectual disability 2020-09-10 criteria provided, single submitter clinical testing
GeneDx RCV001771955 SCV001992496 likely benign not provided 2021-12-08 criteria provided, single submitter clinical testing Reported as a variant of uncertain significance in an individual with myoclonic astatic epilepsy and intellectual disability (Vlaskamp et al., 2019); In silico analysis supports that this missense variant does not alter protein structure/function; This variant is associated with the following publications: (PMID: 30685520, 30541864)

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