ClinVar Miner

Submissions for variant NM_006772.3(SYNGAP1):c.1286G>A (p.Arg429Gln)

gnomAD frequency: 0.00002  dbSNP: rs772336493
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV001070170 SCV001235386 uncertain significance Intellectual disability, autosomal dominant 5 2020-03-06 criteria provided, single submitter clinical testing This sequence change replaces arginine with glutamine at codon 429 of the SYNGAP1 protein (p.Arg429Gln). The arginine residue is moderately conserved and there is a small physicochemical difference between arginine and glutamine. This variant is present in population databases (rs772336493, ExAC 0.002%). This variant has not been reported in the literature in individuals with SYNGAP1-related conditions. 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: "Tolerated"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site, but this prediction has not been confirmed by published transcriptional studies. 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.
New York Genome Center RCV001070170 SCV001622954 uncertain significance Intellectual disability, autosomal dominant 5 2020-05-12 criteria provided, single submitter clinical testing

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