rs199473161

Positions:

• chr3-38586038-G-A
• chr3-38586038-G-T

Variant summary

Our verdict is Pathogenic. Variant got 17 ACMG points: 17P and 0B. PM1 PM2 PP2 PP3_Strong PP5_Very_Strong

The NM_000335.5(SCN5A):​c.2440C>T​(p.Arg814Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,458,640 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★★).

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0000014 (0 hom.)
• Consequence: SCN5A NM_000335.5 missense
• Clinical Significance: Pathogenic/Likely pathogenic criteria provided, multiple submitters, no conflicts P:8 O:1
• Conservation: PhyloP100: 0.905

Genes affected

SCN5A (HGNC:10593): (sodium voltage-gated channel alpha subunit 5) The protein encoded by this gene is an integral membrane protein and tetrodotoxin-resistant voltage-gated sodium channel subunit. This protein is found primarily in cardiac muscle and is responsible for the initial upstroke of the action potential in an electrocardiogram. Defects in this gene have been associated with long QT syndrome type 3 (LQT3), atrial fibrillation, cardiomyopathy, and Brugada syndrome 1, all autosomal dominant cardiac diseases. Alternative splicing results in several transcript variants encoding different isoforms. [provided by RefSeq, May 2022]

SCN5A (HGNC:):

ACMG classification

Verdict is Pathogenic. Variant got 17 ACMG points.

• PM1: In a transmembrane_region Helical; Name=S4 of repeat II (size 17) in uniprot entity SCN5A_HUMAN there are 7 pathogenic changes around while only 0 benign (100%) in NM_000335.5
• PM2: Very rare variant in population databases, with high coverage
• PP2: Missense variant in gene, where missense usually causes diseases (based on misZ statistic), SCN5A. . Gene score misZ 2.7504 (greater than the threshold 3.09). Trascript score misZ 4.8279 (greater than threshold 3.09). GenCC has associacion of gene with progressive familial heart block, type 1A, Brugada syndrome, familial sick sinus syndrome, short QT syndrome, paroxysmal familial ventricular fibrillation, progressive familial heart block, long QT syndrome 3, familial atrial fibrillation, catecholaminergic polymorphic ventricular tachycardia, dilated cardiomyopathy, dilated cardiomyopathy 1E, arrhythmogenic right ventricular cardiomyopathy, Brugada syndrome 1, atrial standstill, familial isolated dilated cardiomyopathy, familial long QT syndrome, sick sinus syndrome 1.
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.992
• PP5: Variant 3-38586038-G-A is Pathogenic according to our data. Variant chr3-38586038-G-A is described in ClinVar as [Likely_pathogenic]. Clinvar id is 67731.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-38586038-G-A is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SCN5A	NM_001099404.2	c.2440C>T	p.Arg814Trp	missense_variant	16/28	ENST00000413689.6	NP_001092874.1
SCN5A	NM_000335.5	c.2440C>T	p.Arg814Trp	missense_variant	16/28	ENST00000423572.7	NP_000326.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SCN5A	ENST00000413689.6	c.2440C>T	p.Arg814Trp	missense_variant	16/28	5	NM_001099404.2	ENSP00000410257.1
SCN5A	ENST00000423572.7	c.2440C>T	p.Arg814Trp	missense_variant	16/28	1	NM_000335.5	ENSP00000398266.2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000137 AC: 2 AN: 1458640 Hom.: 0 Cov.: 35 AF XY: 0.00000138 AC XY: 1 AN XY: 725026

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00000180

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

Bravo AF: 0.00000378

ClinVar

Significance: Pathogenic/Likely pathogenic

Submissions summary: Pathogenic:8 Other:1

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Pathogenic:3

Likely pathogenic, no assertion criteria provided	clinical testing	Stanford Center for Inherited Cardiovascular Disease, Stanford University	Apr 27, 2012	Note this variant was found in clinical genetic testing performed by one or more labs who may also submit to ClinVar. Thus any internal case data may overlap with the internal case data of other labs. The interpretation reviewed below is that of the Stanford Center for Inherited Cardiovascular Disease. p.Arg814Trp (R814W) c.2440 C>T in exon 16 of the SCN5A gene (NM_198056.2) It has been estimated that SCN5A variants may explain 2-3% of cases of familial DCM (Hershberger et al 2008, 2013). In a kindred with DCM, sinus node dysfunction, supraventricular tachyarrhythmias, stroke and conduction delay Olsen et al (1996) found linkage to a locus containing SCN5A, with a LOD score of 6.09. McNair et al (2004) later found a specific SCN5A variant segregating with the disease in this family. Since then, several other cases have been reported (Olson et al 2005, McNair et al 2011, Ge et al 2008, Shi et al 2008, Bezzina et al 2003, Mann et al 2012), Laurent et al 2012, Nguyen et al 2 008, Watanabe et al 2011, Beckerman et al 2014). Given the strong case data (albeit mostly unpublished), the genotype-phenotype match in our patient, and the absence in unselected populations, we consider this variant likely disease and we do feel it is suitable for assessing risk in healthy relatives ("predictive genetic testing"). The variant has been seen in at least four unrelated cases of arrhythmia and/or cardiomyopathy (not including this patient's family). Note that most of these cases are unpublished. Olson et al 2005) reported the variant with disease: "identified in a 23-year-old woman (DC-96) with sporadic DCM (EF,30%), atrial flutter, and short runs of nonsustained ventricular tachycardia on 1 of 2 Holter monitor recordings. Cardiac biopsy revealed mild to moderate myocellular hypertrophy and mild interstitial fibrosis. Her parents and 7 siblings (aged from 19–36 years) had normal echocardiogram and electrocardiogram results. A heterozygous point mutation, C2440T, was identified in exon 16 resulting in an R814W substitution. The mutation arose de novo, because it was absent in the patient’s parents and siblings and biological paternity and maternity were verified (Figure 3)." The genetic testing lab shared that they have seen this variant in three other individuals with personal and family history cardiomyopathy and/or arrhythmias, including sudden cardiac death. There is one entry in ClinVar, from "Cardiovascular Biomedical Research Unit Royal Brompton & Harefield NHS Foundation Trust" who classify it as pathogenic (as of June 11th, 2015). It is unclear if this is based solely on literature or if they observed it in affected individuals within their lab. The variant is included in a few reviews, but without new data (ex. Norton et al 2012). Some in vitro work has been done on the variant: " R814W channels exhibited prominent and novel defects in the kinetics and voltage dependence of activation characterized by slower rise times and a hyperpolarized conductance-voltage relationship resulting in an increased “window current.” This mutant also displayed enhanced slow inactivation and greater use-dependent reduction in peak current at fast pulsing frequencies" (Nguyen et al 2008). Though it is important to note that there are common variants in ion channels that have an in vitro phenotype but do not cause severe genetic disease. The variant was not observed in the following published control samples: 500 individuals with normal ECGs and echocardiograms (Olson et al 2005). This variant is not listed in the Exome Aggregation Consortium dataset (http://exac.broadinstitute.org/), which currently includes variant calls on ~64,000 individuals of European, African, Latino and Asian descent (as of June 11th, 2015). Another variant at this codon, p.Arg814Gln is present in 2/56766 individuals in this dataset. -
Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Mar 10, 2022	Published functional studies demonstrate that p.(R814W) alters sodium channel properties (Nguyen et al., 2008; Beckermann et al., 2014; Moreau et al., 2015); Not observed at a significant frequency in large population cohorts (gnomAD); 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: 17442746, 18048769, 26733869, 26916278, 28363160, 27532257, 22581653, 31737537, 15671429, 24815523, 25179549) -
Pathogenic, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 25, 2024	This sequence change replaces arginine, which is basic and polar, with tryptophan, which is neutral and slightly polar, at codon 814 of the SCN5A protein (p.Arg814Trp). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individual(s) with cardiomyopathy and dilated cardiomyopathy (PMID: 15671429, 25179549). In at least one individual the variant was observed to be de novo. It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 67731). 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. Experimental studies have shown that this missense change affects SCN5A function (PMID: 18048769, 24815523, 26733869). For these reasons, this variant has been classified as Pathogenic. -

Cardiovascular phenotype Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Jul 18, 2016	Variant summary: The SCN5A c.2440C>T (p.Arg814Trp) variant involves the alteration of a non-conserved nucleotide. 5/5 in silico tools predict a damaging outcome for this variant. The SCN5A encoded protein has 24 TM segments organized into 4 domains (DI-DIV), each containing 6 TM. Arg814 is highly conserved across species and is located in the second voltage-dependent channel, four helix bundle domain and the second iron transport domain (segment 4 of DII; Moreau_Front Pharmacol_2015 and InterPro). Several related SCN5A variants classified as Pathogenic/Likely Pathogenic in ClinVar (p.R814W, p.R222Q, p.R219H, etc) neutralize arginine residues that are localized in the S4 segment of domain I and II (Olson etal., 2005; Laurentetal.,2012; Mannetal.,2012; Nairetal.,2012; Beckermannetal.,2014). When compared to the WT condition, the R814W mutant was shown to negatively shift the voltage dependence of activation, slow activation kinetics, and increase the sodium window current (Nguyen_2008). However, it is unclear if these functional alterations would cause DCM since a consensus on disease mechanism has not yet been established.This variant was absent in 113532 control chromosomes, but has been cited in at least 6 DCM patients in the literature, and show to co-segregate with the DCM phenotype in a large family. In addition, multiple clinical diagnostic laboratories/reputable databases classified this variant as Pathogenic/Likely Pathogenic. Taken together, this variant is classified as Pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	Ambry Genetics	Jul 13, 2021	The p.R814W pathogenic mutation (also known as c.2440C>T), located in coding exon 15 of the SCN5A gene, results from a C to T substitution at nucleotide position 2440. The arginine at codon 814 is replaced by tryptophan, an amino acid with dissimilar properties, and is located in the transmembrane DII-S4 region. This mutation was first reported as de novo in a sporadic dilated cardiomyopathy (DCM) case (Olson TM et al. JAMA, 2005 Jan;293:447-54). In addition, this variant was found to co-segregate with disease in two unrelated families with cardiomyopathy and arrhythmia findings in multiple relatives (Golbus JR et al. Circ Cardiovasc Genet, 2014 Dec;7:751-759; Zakrzewska-Koperska J et al. ESC Heart Fail, 2020 Oct;doi: 10.1002/ehf2.12993). This variant was also detected in a DCM genetic testing case and a suspected Brugada syndrome case; however, clinical details were limited (Walsh R et al. Genet Med, 2017 02;19:192-203; Marschall C et al. Cardiovasc Diagn Ther, 2019 Oct;9:S292-S298). Functional studies with this variant demonstrated hyperpolarized activation and slowed inactivation in sodium channels (Nguyen TP et al. Circ Res, 2008 Feb;102:364-71; Beckermann TM et al. Heart Rhythm, 2014 Aug;11:1446-53; Moreau A et al. Front Pharmacol, 2015 Dec;6:301). Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation. -

Primary dilated cardiomyopathy Pathogenic:1 Other:1

not provided, no classification provided	literature only	Cardiovascular Biomedical Research Unit, Royal Brompton & Harefield NHS Foundation Trust	-	This variant has been reported as associated with Dilated cardiomyopathy in the following publications (PMID:15671429;PMID:18048769). This is a literature report, and does not necessarily reflect the clinical interpretation of the Imperial College / Royal Brompton Cardiovascular Genetics laboratory. -
Likely pathogenic, criteria provided, single submitter	clinical testing	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	Oct 31, 2015	The p.Arg814Trp variant in SCN5A has been reported de novo in 1 individual with DCM and cardiac biopsy findings showing myocellular hypertrophy and interstitial fibrosis (paternity confirmed; Olson 2005). The variant was absent from large p opulation studies. In vitro functional studies showed that the p.Arg814Trp varia nt affected protein function (leading to altered sodium channel function; Nguyen 2008, Beckermann 2014). However, these types of assays may not accurately repre sent biological function. Computational prediction tools and conservation analys is also support pathogenicity. In summary, although additional studies are requi red to fully establish its clinical significance, the p.Arg814Trp variant is lik ely pathogenic based on absence in the general population and de novo occurrence -

Dilated cardiomyopathy 1E Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

Institute of Human Genetics, University of Leipzig Medical Center

Jan 01, 2019

- -

Sick sinus syndrome 1 Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Centre for Mendelian Genomics, University Medical Centre Ljubljana

Nov 22, 2019

This variant was classified as: Pathogenic. The following ACMG criteria were applied in classifying this variant: PS1,PS3,PM2,PM5,PP3. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.97
CardioboostCm	Pathogenic	1.0
BayesDel_addAF	Pathogenic	0.52	D
BayesDel_noAF	Pathogenic	0.52
CADD	Pathogenic	32
DANN	Pathogenic	1.0
DEOGEN2	Pathogenic	0.99	.;.;.;.;.;D;.;.;.
Eigen	Uncertain	0.60
Eigen_PC	Uncertain	0.43
FATHMM_MKL	Benign	0.57	D
LIST_S2	Uncertain	0.96	.;D;D;D;D;D;D;.;D
M_CAP	Pathogenic	0.94	D
MetaRNN	Pathogenic	0.99	D;D;D;D;D;D;D;D;D
MetaSVM	Pathogenic	0.97	D
MutationAssessor	Pathogenic	4.8	.;H;.;.;.;H;.;.;.
PrimateAI	Pathogenic	0.94	D
PROVEAN	Pathogenic	-7.9	D;D;D;D;D;D;D;D;D
REVEL	Pathogenic	0.93
Sift	Pathogenic	0.0	D;D;D;D;D;D;D;D;D
Sift4G	Pathogenic	0.0	D;D;D;D;D;D;D;D;D
Polyphen		1.0	D;D;.;D;.;D;D;.;.
Vest4		0.98
MutPred		0.95		Gain of catalytic residue at L812 (P = 0.0115);Gain of catalytic residue at L812 (P = 0.0115);Gain of catalytic residue at L812 (P = 0.0115);Gain of catalytic residue at L812 (P = 0.0115);Gain of catalytic residue at L812 (P = 0.0115);Gain of catalytic residue at L812 (P = 0.0115);Gain of catalytic residue at L812 (P = 0.0115);Gain of catalytic residue at L812 (P = 0.0115);Gain of catalytic residue at L812 (P = 0.0115);
MVP		1.0
MPC		1.1
ClinPred		1.0	D
GERP RS		3.5
Varity_R		0.97
gMVP		0.99

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs199473161; hg19: chr3-38627529; COSMIC: COSV61129337;