ClinVar Miner

Submissions for variant NM_001040142.2(SCN2A):c.2638G>T (p.Ala880Ser)

dbSNP: rs1574641522
Minimum review status: Collection method:
Minimum conflict level:
ClinVar version:
Total submissions: 5
Download table as spreadsheet
Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
CeGaT Center for Human Genetics Tuebingen RCV000997258 SCV001152480 likely pathogenic not provided 2019-01-01 criteria provided, single submitter clinical testing
Pediatrics, MediClubGeorgia RCV001263485 SCV001441531 likely pathogenic Developmental and epileptic encephalopathy, 11 criteria provided, single submitter clinical testing This variant is absent in population databases. This variant has not been described in the literature, but is submitted in ClinVar as a likely pathogenic. Parents were also tested and this variant was not detected. Algorithms developed to predict the effect of missense variants showed: Sift- Deleterious, PolyPhen2-HDIV- Probably damaging, MutationTaster- Damaging, Provean - Damaging. This alanine residue is highly conserved.
Labcorp Genetics (formerly Invitae), Labcorp RCV001324429 SCV001515381 likely pathogenic Seizures, benign familial infantile, 3; Developmental and epileptic encephalopathy, 11 2021-01-05 criteria provided, single submitter clinical testing In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic. This sequence change replaces alanine with serine at codon 880 of the SCN2A protein (p.Ala880Ser). The alanine residue is highly conserved and there is a moderate physicochemical difference between alanine and serine. This variant is not present in population databases (ExAC no frequency). This variant has been observed in individual(s) with clinical features of SCN2A-related conditions (Invitae). In at least one individual the variant was observed to be de novo. ClinVar contains an entry for this variant (Variation ID: 808846). 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").
GenomeConnect - Simons Searchlight RCV001265497 SCV001443641 pathogenic Complex neurodevelopmental disorder 2016-09-15 no assertion criteria provided provider interpretation Submission from Simons Searchlight facilitated by GenomeConnect. Variant interpreted by the Simons Searchlight team most recently on 2016-09-15 and interpreted as Pathogenic. Variant was initially reported on 2015-04-10 by GTR ID of laboratory name North East Thames Genetic Service. The reporting laboratory might also submit to ClinVar.
Channelopathy-Associated Epilepsy Research Center RCV001265497 SCV004232420 not provided Complex neurodevelopmental disorder no assertion provided literature only

The information on this website is not intended for direct diagnostic use or medical decision-making without review by a genetics professional. Individuals should not change their health behavior solely on the basis of information contained on this website. Neither the University of Utah nor the National Institutes of Health independently verfies the submitted information. If you have questions about the information contained on this website, please see a health care professional.