ClinVar Miner

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

dbSNP: rs796053155
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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000189169 SCV000242801 pathogenic not provided 2023-08-26 criteria provided, single submitter clinical testing Not observed at significant frequency in large population cohorts (gnomAD); Missense variants in this gene are often considered pathogenic (HGMD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 25473036, 25937001, 29655203)
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 pathogenic Developmental and epileptic encephalopathy, 11 2023-01-31 criteria provided, single submitter clinical testing
Invitae RCV001054289 SCV001218597 pathogenic Seizures, benign familial infantile, 3; Developmental and epileptic encephalopathy, 11 2019-12-04 criteria provided, single submitter clinical testing For these reasons, this variant has been classified as Pathogenic. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). This variant has been observed in individual(s) with early infantile epileptic encephalopathy (PMID: 25937001, Invitae). In at least one individual the variant was observed to be de novo. ClinVar contains an entry for this variant (Variation ID: 207017). This variant is not present in population databases (ExAC no frequency). This sequence change replaces arginine with glutamine at codon 1626 of the SCN2A protein (p.Arg1626Gln). The arginine residue is highly conserved and there is a small physicochemical difference between arginine and glutamine.
Institute Of Human Genetics Munich, Klinikum Rechts Der Isar, Tu München RCV000679890 SCV002764872 pathogenic Developmental and epileptic encephalopathy, 11 2020-12-15 criteria provided, single submitter clinical testing
GenomeConnect - Simons Searchlight RCV001265496 SCV001443640 likely pathogenic Complex neurodevelopmental disorder 2016-02-23 no assertion criteria provided provider interpretation Submission from Simons Searchlight facilitated by GenomeConnect. Variant interpreted by the Simons Searchlight team most recently on 2016-02-23 and interpreted as Likely Pathogenic. Variant was initially reported on 2014-03-26 by GTR ID of laboratory name 26957. The reporting laboratory might also submit to ClinVar.
Channelopathy-Associated Epilepsy Research Center RCV001265496 SCV004232407 not provided Complex neurodevelopmental disorder no assertion provided literature only

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