ClinVar Miner

Submissions for variant NM_001040142.2(SCN2A):c.599C>G (p.Thr200Ser)

gnomAD frequency: 0.00001  dbSNP: rs202234412
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Total submissions: 1
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000688609 SCV000816229 uncertain significance Seizures, benign familial infantile, 3; Developmental and epileptic encephalopathy, 11 2020-03-06 criteria provided, single submitter clinical testing 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. Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated, but these predictions have not been confirmed by published functional studies and their clinical significance is uncertain. This variant has not been reported in the literature in individuals with SCN2A-related disease. This variant is present in population databases (rs202234412, ExAC 0.002%). This sequence change replaces threonine with serine at codon 200 of the SCN2A protein (p.Thr200Ser). The threonine residue is highly conserved and there is a small physicochemical difference between threonine and serine.

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