ClinVar Miner

Submissions for variant NM_001165963.4(SCN1A):c.3481G>A (p.Ala1161Thr) (rs201079458)

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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Eurofins NTD, LLC RCV000724750 SCV000226591 uncertain significance not provided 2015-04-22 criteria provided, single submitter clinical testing
GeneDx RCV000188914 SCV000242544 uncertain significance not specified 2017-05-10 criteria provided, single submitter clinical testing The A1161T missense substitution was previously identified on the same chromosome (in cis) with the R604H variant in a patient with juvenile myoclonic epilepsy (JME); however, the variants did not segregate with JME in several affected family members, suggesting that they may be benign (Escayg et al., 2001). The A1161T variant was not observed with any significant frequency in approximately 6,500 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project. The A1161T 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 occurs at a position that is conserved in mammals and is predicted to be within the cytoplasmic loop between the second and third homologous domains of the SCN1A protein. However, in silico analysis predicts this variant likely does not alter the protein structure/function. Therefore, the currently available information suggests that A1161T may be a rare benign variant; however, the possibility that it is pathogenic cannot be completely excluded.
Invitae RCV000724750 SCV000559690 likely benign not provided 2019-01-28 criteria provided, single submitter clinical testing
Fulgent Genetics,Fulgent Genetics RCV000515245 SCV000611519 uncertain significance Familial hemiplegic migraine type 3; Severe myoclonic epilepsy in infancy; Generalized epilepsy with febrile seizures plus, type 2 2017-05-23 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV001132318 SCV001291977 benign SCN1A-Related Disorders 2017-04-28 criteria provided, single submitter clinical testing This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to rule this variant out of causing disease. Therefore, this variant is classified as benign.
Invitae RCV001444749 SCV001647760 likely benign Early infantile epileptic encephalopathy with suppression bursts 2020-11-20 criteria provided, single submitter clinical testing

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