ClinVar Miner

Submissions for variant NM_001040142.2(SCN2A):c.4877G>A (p.Arg1626Gln) (rs796053155)

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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000189169 SCV000242801 pathogenic not provided 2017-11-17 criteria provided, single submitter clinical testing The R1626Q pathogenic variant in the SCN2A gene has been reported previously as a de novo change in association with seizures in infancy (Soden et al., 2014; Willig et al., 2015). The R1626Q variant was not observed in approximately 6500 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations. The R1626Q variant is a semi-conservative amino acid substitution, which may impact secondary protein structure as these residues differ in some properties. This substitution occurs at a position within the S4 of repeat IV domain that is conserved across species. In silico analysis predicts this variant is probably damaging to the protein structure/function. Missense variants in nearby residues (T1623N, R1629L) have been reported in the Human Gene Mutation Database in association with SCN2A-related disorders (Stenson et al., 2014), supporting the functional importance of this region of the protein. We interpret R1626Q as a pathogenic variant.
Center for Pediatric Genomic Medicine,Children's Mercy Hospital and Clinics RCV000189169 SCV000280873 pathogenic not provided 2014-05-19 criteria provided, single submitter clinical testing
Baylor Genetics RCV000679890 SCV000807294 uncertain significance Early infantile epileptic encephalopathy 11 2017-09-01 criteria provided, single submitter clinical testing Likely pathogenicity based on finding it once in our laboratory de novo in a 2-month-old male with early-onset intractable epilepsy, hydrocephalus

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