ClinVar Miner

Submissions for variant NM_001040142.2(SCN2A):c.1747C>T (p.Arg583Ter)

dbSNP: rs1553571901
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000760475 SCV000890364 pathogenic not provided 2018-10-12 criteria provided, single submitter clinical testing The R583X nonsense variant in the SCN2A gene has been reported previously as a de novo change in an individual with autism (Codina-Solà et al., 2015). This pathogenic variant is predicted to cause loss of normal protein function either through protein truncation or nonsense-mediated mRNA decay. The R583X variant is not observed in large population cohorts (Lek et al., 2016). Therefore, this variant is classified as pathogenic.
Labcorp Genetics (formerly Invitae), Labcorp RCV002533837 SCV003524689 pathogenic Seizures, benign familial infantile, 3; Developmental and epileptic encephalopathy, 11 2023-02-03 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Arg583*) in the SCN2A gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in SCN2A are known to be pathogenic (PMID: 28379373). This variant is not present in population databases (gnomAD no frequency). This premature translational stop signal has been observed in individual(s) with clinical features of SCN2A-related conditions (PMID: 25969726, 33000761). ClinVar contains an entry for this variant (Variation ID: 620152). For these reasons, this variant has been classified as Pathogenic.

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