ClinVar Miner

Submissions for variant NM_001040142.2(SCN2A):c.5924A>G (p.Tyr1975Cys) (rs1574754722)

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Total submissions: 1
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000820518 SCV000961234 uncertain significance Benign familial neonatal-infantile seizures; Early infantile epileptic encephalopathy 11 2019-11-11 criteria provided, single submitter clinical testing This sequence change replaces tyrosine with cysteine at codon 1975 of the SCN2A protein (p.Tyr1975Cys). The tyrosine residue is highly conserved and there is a large physicochemical difference between tyrosine and cysteine. This variant is not present in population databases (ExAC no frequency) and has not been reported in the literature in individuals with a SCN2A-related disease. This variant identified in the SCN2A gene is located in the cytoplasmic C-terminal region of the resulting protein (PMID: 25348405, 23935176, 22029951), but it is unclear how this variant impacts the function of this protein. 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 disruptive, but these predictions have not been confirmed by published functional studies. In summary, this variant is a novel missense change with uncertain impact on protein function. It has been classified as a Variant of Uncertain Significance.

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