Submissions for variant NM_000335.5(SCN5A):c.5689C>T (p.Arg1897Cys)

gnomAD frequency: 0.00006  dbSNP: rs373118001

Total submissions: 15

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
Ambry Genetics	RCV000619017	SCV000736116	uncertain significance	Cardiovascular phenotype	2023-03-23	criteria provided, single submitter	clinical testing	The p.R1898C variant (also known as c.5692C>T), located in coding exon 27 of the SCN5A gene, results from a C to T substitution at nucleotide position 5692. The arginine at codon 1898 is replaced by cysteine, an amino acid with highly dissimilar properties. This alteration has been reported in Brugada syndrome and sudden unexplained nocturnal death cohorts; however, clinical details were limited and the sudden death case also had a second SCN5A variant detected (Selga E et al. PLoS ONE, 2015 Jul;10:e0132888; Zhang L et al. Mayo Clin. Proc., 2016 Nov;91:1503-1514). This variant has also been detected in individuals reported to have dilated cardiomyopathy or noncompaction cardiomyopathy; however, clinical details were limited and some reports may overlap (van Waning JI et al. J Am Coll Cardiol. 2018 Feb;71(7):711-722; van Lint FHM et al. Neth Heart J. 2019 Jun;27(6):304-309; Verdonschot JAJ et al. Circ Genom Precis Med. 2020 Oct;13(5):476-487). In addition, this variant has been detected in cohorts not selected for the presence of cardiovascular disease; however, details were limited (Chetruengchai W et al. J Hum Genet. 2022 Mar;67(3):137-142; Kars ME et al. Proc Natl Acad Sci U S A. 2021 Sep;118(36)). Functional studies suggest this variant may result in reduced ion channel current; however, additional evidence is needed to confirm this finding (Glazer AM et al. Am J Hum Genet. 2020 Jul;107(1):111-123).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.
Labcorp Genetics (formerly Invitae), Labcorp	RCV000801579	SCV000941360	uncertain significance	Brugada syndrome	2022-11-01	criteria provided, single submitter	clinical testing	This sequence change replaces arginine, which is basic and polar, with cysteine, which is neutral and slightly polar, at codon 1898 of the SCN5A protein (p.Arg1898Cys). This variant is present in population databases (rs373118001, gnomAD 0.006%). This missense change has been observed in individual(s) with Brugada syndrome and/or dilated cardiomyopathy (PMID: 26173111, 29306897, 30847666, 32880476). ClinVar contains an entry for this variant (Variation ID: 518750). Advanced modeling performed at Invitae incorporating data from internal and/or published experimental studies (PMID: 32533946) indicates that this missense variant is expected to disrupt SCN5A function. 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.
Mendelics	RCV000987196	SCV001136445	uncertain significance	Brugada syndrome 1	2019-05-28	criteria provided, single submitter	clinical testing
Illumina Laboratory Services, Illumina	RCV001148679	SCV001309587	uncertain significance	Sick sinus syndrome 1	2017-04-27	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). No publications were found based on this search. Allele frequency data from public databases did not allow this variant to be ruled in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance.
Illumina Laboratory Services, Illumina	RCV001148680	SCV001309588	uncertain significance	Dilated cardiomyopathy 1E	2017-04-27	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). No publications were found based on this search. Allele frequency data from public databases did not allow this variant to be ruled in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance.
Illumina Laboratory Services, Illumina	RCV001148681	SCV001309589	uncertain significance	Progressive familial heart block, type 1A	2017-04-27	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). No publications were found based on this search. Allele frequency data from public databases did not allow this variant to be ruled in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance.
Illumina Laboratory Services, Illumina	RCV001148682	SCV001309590	uncertain significance	Long QT syndrome 3	2017-04-27	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). No publications were found based on this search. Allele frequency data from public databases did not allow this variant to be ruled in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance.
Illumina Laboratory Services, Illumina	RCV001148683	SCV001309591	uncertain significance	Ventricular fibrillation, paroxysmal familial, type 1	2017-04-27	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). No publications were found based on this search. Allele frequency data from public databases did not allow this variant to be ruled in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance.
Illumina Laboratory Services, Illumina	RCV000987196	SCV001311262	uncertain significance	Brugada syndrome 1	2017-04-27	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. However, the evidence from the literature, in combination with allele frequency data from public databases where available, was not sufficient to rule this variant in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance.
Color Diagnostics, LLC DBA Color Health	RCV001841789	SCV001343957	uncertain significance	Cardiac arrhythmia	2023-01-27	criteria provided, single submitter	clinical testing	This missense variant replaces arginine with cysteine at codon 1898 of the SCN5A protein. Computational prediction suggests that this variant may have deleterious impact on protein structure and function (internally defined REVEL score threshold >= 0.7, PMID: 27666373). A functional study has shown that this variant had 28% of the peak current density compared to wild type (PMID: 32533946). This variant has been reported in two individuals affected with Brugada syndrome (PMID: 26173111, 29306897). One of these individuals carried a pathogenic truncation variant in the same gene that could explain the observed phenotype. This variant has also been reported in an individual affected with noncompaction cardiomyopathy (PMID: 29447731). This variant has been identified in 10/280692 chromosomes in the general population by the Genome Aggregation Database (gnomAD). The available evidence is insufficient to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance.
GeneDx	RCV001701400	SCV001987706	uncertain significance	not provided	2024-03-19	criteria provided, single submitter	clinical testing	Reported in patients with clinically diagnosed Brugada syndrome, some of whom harbored additional cardiogenetic variants (PMID: 26173111, 27707468, 29306897, 25904541); Published functional studies suggest a damaging effect (PMID: 32533946); 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: 25904541, 27707468, 30662450, 34426522, 32880476, 30847666, 26746457, 30203441, 34621001, 26173111, 29306897, 29447731, 32533946)
Women's Health and Genetics/Laboratory Corporation of America, LabCorp	RCV003330832	SCV004038529	uncertain significance	not specified	2023-08-09	criteria provided, single submitter	clinical testing	Variant summary: SCN5A c.5692C>T (p.Arg1898Cys) results in a non-conservative amino acid change in the encoded protein sequence. Four of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 3.2e-05 in 249288 control chromosomes (gnomAD). The variant, c.5692C>T, has been reported in the literature in at least two individuals affected with Brugada syndrome, however one of these patient also carried a potentially pathogenic SCN5A variant (Selga_2015, Zhang_2016, Huang_2018). In addition, the variant has been reported in at least two patients affected with noncompaction cardiomyopathy and dilated cardiomyopathy, however without strong evidence for causality (van Waning_2018, van Lint_2019, Verdonschot_2020). These data do not allow any conclusion about variant significance. At least one publication reports experimental evidence evaluating an impact on protein function, and demonstrated a reduced ion channel current, indicating a partial loss of function for the variant protein (Glazer_2020). The following publications have been ascertained in the context of this evaluation (PMID: 32533946, 26173111, 25904541, 27707468, 29306897, 29447731, 30847666, 32880476). Six submitters have cited clinical-significance assessments for this variant to ClinVar after 2014. All submitters classified the variant as uncertain significance. Based on the evidence outlined above, the variant was classified as VUS-possibly pathogenic.
All of Us Research Program, National Institutes of Health	RCV001841789	SCV004823248	uncertain significance	Cardiac arrhythmia	2023-12-01	criteria provided, single submitter	clinical testing	This missense variant replaces arginine with cysteine at codon 1898 of the SCN5A protein. Computational prediction suggests that this variant may have deleterious impact on protein structure and function (internally defined REVEL score threshold >= 0.7, PMID: 27666373). A functional study has shown that the variant protein exhibit 28% of the peak current density compared to wild type protein (PMID: 32533946). This variant has been reported in two individuals affected with Brugada syndrome (PMID: 26173111, 29306897). One of these individuals carried a pathogenic truncation variant in the same gene that could explain the observed phenotype. This variant has also been reported in an individual affected with noncompaction cardiomyopathy (PMID: 29447731). This variant has been identified in 10/280692 chromosomes in the general population by the Genome Aggregation Database (gnomAD). The available evidence is insufficient to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance.
Clinical Genetics, Academic Medical Center	RCV001701400	SCV001922210	uncertain significance	not provided		no assertion criteria provided	clinical testing
Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+	RCV001701400	SCV001954604	uncertain significance	not provided		no assertion criteria provided	clinical testing