ClinVar Miner

Submissions for variant NM_001040142.2(SCN2A):c.1976G>A (p.Gly659Asp) (rs368887417)

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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Athena Diagnostics Inc RCV000189224 SCV000615055 likely benign not specified 2017-07-03 criteria provided, single submitter clinical testing
GeneDx RCV000766774 SCV000242856 uncertain significance not provided 2017-01-31 criteria provided, single submitter clinical testing A variant of uncertain significance has been identified in the SCN2A gene. The G659D variant has not been published as a pathogenic variant, nor has it been reported as a benign variant to our knowledge. The G659D variant is observed in 16/61,030 (0.03%) alleles from individuals of Eurpoean background, in large population cohorts (Lek et al., 2016; 1000 Genomes Consortium et al., 2015; Exome Variant Server). The G659D variant is a non-conservative amino acid substitution, which is likely to impact secondary protein structure as these residues differ in polarity, charge, size and/or other properties. This substitution alters a conserved residue predicted to be in the cytoplasmic loop between the first and second homologous domains. Furthermore, in silico analysis predicts this variant is probably damaging to the protein structure/function. However, missense variants in nearby residues have not been reported in the Human Gene Mutation Database in association with SCN2A-related disorders (Stenson et al., 2014). Therefore, based on the currently available information, it is unclear whether this variant is a pathogenic variant or a rare benign variant.
Illumina Clinical Services Laboratory,Illumina RCV000391073 SCV000417412 uncertain significance Benign familial neonatal-infantile seizures 2016-06-14 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000310411 SCV000417413 uncertain significance Early Infantile Epileptic Encephalopathy, Autosomal Dominant 2016-06-14 criteria provided, single submitter clinical testing
Invitae RCV000477087 SCV000551880 likely benign Benign familial neonatal-infantile seizures; Early infantile epileptic encephalopathy 11 2017-06-23 criteria provided, single submitter clinical testing

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