ClinVar Miner

Submissions for variant NM_001037.5(SCN1B):c.265C>T (p.Arg89Cys)

gnomAD frequency: 0.00004  dbSNP: rs766910280
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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Genomic Medicine Lab, University of California San Francisco RCV001007883 SCV001167587 uncertain significance Generalized epilepsy with febrile seizures plus, type 1 2018-08-16 criteria provided, single submitter clinical testing
Invitae RCV001050500 SCV001214610 pathogenic Brugada syndrome 5 2023-05-25 criteria provided, single submitter clinical testing This missense change has been observed in individuals with clinical features of autosomal recessive developmental and epileptic encephalopathy (PMID: 31465153; Invitae). It has also been observed to segregate with disease in related individuals. This variant is present in population databases (rs766910280, gnomAD 0.005%). This sequence change replaces arginine, which is basic and polar, with cysteine, which is neutral and slightly polar, at codon 89 of the SCN1B protein (p.Arg89Cys). ClinVar contains an entry for this variant (Variation ID: 816882). For these reasons, this variant has been classified as Pathogenic. An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive.
GeneDx RCV001766822 SCV001991643 uncertain significance not provided 2019-08-05 criteria provided, single submitter clinical testing In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; Has not been previously published as pathogenic or benign to our knowledge; This variant is associated with the following publications: (PMID: 31465153, 33084218)
Ambry Genetics RCV002454255 SCV002739472 uncertain significance Cardiovascular phenotype 2018-11-05 criteria provided, single submitter clinical testing The p.R89C variant (also known as c.265C>T), located in coding exon 3 of the SCN1B gene, results from a C to T substitution at nucleotide position 265. The arginine at codon 89 is replaced by cysteine, an amino acid with highly dissimilar properties. This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.
Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan RCV003483751 SCV004232391 likely pathogenic Epileptic encephalopathy 2024-01-11 criteria provided, single submitter clinical testing
Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center RCV003989622 SCV004807983 likely pathogenic Developmental and epileptic encephalopathy, 52 2024-03-29 criteria provided, single submitter clinical testing

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