ClinVar Miner

Submissions for variant NM_001040142.2(SCN2A):c.1861C>T (p.Arg621Cys)

dbSNP: rs796053205
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000189247 SCV000242879 uncertain significance not provided 2013-08-23 criteria provided, single submitter clinical testing The R621C variant has not been published as a mutation, nor has it been reported as a benign polymorphism to our knowledge. It was not observed in approximately 6,500 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 R621C 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 highly conserved position in the cytoplasmic loop between the first and second homologous domains of the SCN2A protein (Shi et al., 2012), and in silico analysis predicts this variant is probably damaging to the protein structure/function. The variant is found in SCN2A panel(s).
Fulgent Genetics, Fulgent Genetics RCV000764278 SCV000895295 uncertain significance Seizures, benign familial infantile, 3; Developmental and epileptic encephalopathy, 11 2018-10-31 criteria provided, single submitter clinical testing
Invitae RCV000764278 SCV001535701 uncertain significance Seizures, benign familial infantile, 3; Developmental and epileptic encephalopathy, 11 2022-10-18 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. Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt SCN2A protein function. ClinVar contains an entry for this variant (Variation ID: 207092). This missense change has been observed in individual(s) with Lennox-Gastaut syndrome (Invitae). The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This sequence change replaces arginine, which is basic and polar, with cysteine, which is neutral and slightly polar, at codon 621 of the SCN2A protein (p.Arg621Cys).

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