3-38560418-T-C

Position:

• chr3-38560418-T-C

Variant summary

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

The NM_001099404.2(SCN5A):​c.3974A>G​(p.Asn1325Ser) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000206 in 1,459,700 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 (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. N1325K) has been classified as Uncertain significance.

• Frequency:
  • Genomes: not found (cov: 33)
  • Exomes 𝑓: 0.0000021 (0 hom.)
• Consequence: SCN5A NM_001099404.2 missense
• Clinical Significance: Pathogenic/Likely pathogenic criteria provided, multiple submitters, no conflicts P:4 O:1
• Conservation: PhyloP100: 7.95

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]

ACMG classification

Verdict is Pathogenic. Variant got 17 ACMG points.

• PM1: In a hotspot region, there are 7 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 0 benign, 9 uncertain in NM_001099404.2
• 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 4.7729 (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, 0.988
• PP5: Variant 3-38560418-T-C is Pathogenic according to our data. Variant chr3-38560418-T-C is described in ClinVar as [Likely_pathogenic]. Clinvar id is 9370.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-38560418-T-C is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SCN5A	NM_001099404.2	c.3974A>G	p.Asn1325Ser	missense_variant	23/28	ENST00000413689.6
SCN5A	NM_000335.5	c.3971A>G	p.Asn1324Ser	missense_variant	23/28	ENST00000423572.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SCN5A	ENST00000413689.6	c.3974A>G	p.Asn1325Ser	missense_variant	23/28	5	NM_001099404.2	P4
SCN5A	ENST00000423572.7	c.3971A>G	p.Asn1324Ser	missense_variant	23/28	1	NM_000335.5	A1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome AF: 0.00000206 AC: 3 AN: 1459700 Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0 AN XY: 725988

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.0000386

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.: 33

Bravo AF: 0.00000378

ClinVar

Significance: Pathogenic/Likely pathogenic

Submissions summary: Pathogenic:4 Other:1

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Jun 13, 2023	Identified in patients with LQTS referred for genetic testing at GeneDx and in published literature (Wang et al., 1995; Splawski et al., 2000; Tester et al., 2005; Yong et al., 2007; Chung et al., 2007; Kapplinger et al., 2009; Anderson et al., 2017); Not observed at significant frequency in large population cohorts (gnomAD); Published functional studies demonstrate a damaging effect using patch clamp studies that showed that N1325S results in abnormal channel current, and N1325S mouse cardiomyocytes showed contractile dysfunction, possibly caused by aberrant cardiomyocyte apoptosis (Dumaine et al., 1996; Wang et al., 1996; Tian et al., 2004; Yong et al., 2007; Zhang et al., 2011); 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: 14736542, 8541846, 19762097, 8917568, 10973849, 19716085, 17118339, 17490620, 17157817, 21677263, 17905336, 8620612, 15840476, 28412158) -
Pathogenic, criteria provided, single submitter	clinical testing	Invitae	Sep 30, 2023	This sequence change replaces asparagine, which is neutral and polar, with serine, which is neutral and polar, at codon 1325 of the SCN5A protein (p.Asn1325Ser). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individuals with long QT syndrome (PMID: 8541846, 17905336, 28412158; Invitae). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 9370). 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: 8620612, 8917568, 19762097). For these reasons, this variant has been classified as Pathogenic. -

Cardiovascular phenotype Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

Ambry Genetics

Mar 16, 2023

The p.N1325S variant (also known as c.3974A>G), located in coding exon 22 of the SCN5A gene, results from an A to G substitution at nucleotide position 3974. The asparagine at codon 1325 is replaced by serine, an amino acid with highly similar properties. This alteration has been reported in multiple long QT syndrome (LQTS) cohorts and has been reported to segregate with disease in a large family (Wang Q, Hum. Mol. Genet. 1995 Sept;4(9):1603-7; Splawski I, Circulation 2000 Sep; 102(10):1178-85; Tester DJ, Heart Rhythm 2005 May; 2(5):507-17; Yong SL, Biochem. Biophys. Res. Commun. 2007 Jan; 352(2):378-83; Chung SK, Heart Rhythm 2007 Oct; 4(10):1306-14; Kapplinger JD, Heart Rhythm 2009 Sep; 6(9):1297-303). In addition, this alteration has been shown to have an impact on sodium channel current (Dumaine R, Circ. Res. 1996 May; 78(5):916-24; Tian XL, Cardiovasc. Res. 2004 Feb;61(2):256-67; Yong SL, Biochem. Biophys. Res. Commun. 2007 Jan; 352(2):378-83). This variant is considered to be rare based on population cohorts in the Genome Aggregation Database (gnomAD). This amino acid position is highly conserved in available vertebrate species. In addition, the in silico prediction for this alteration is inconclusive. Based on the majority of available evidence to date, this variant is likely to be pathogenic. -

Long QT syndrome 3 Pathogenic:1

Pathogenic, no assertion criteria provided

literature only

OMIM

Mar 10, 1995

- -

Congenital long QT syndrome 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 Long QT syndrome in the following publications (PMID:8541846;PMID:14736542;PMID:15840476;PMID:17905336;PMID:19716085;PMID:19841300;PMID:19762097;PMID:8620612;PMID:8917568). This is a literature report, and does not necessarily reflect the clinical interpretation of the Imperial College / Royal Brompton Cardiovascular Genetics laboratory. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.22
CardioboostCm	Uncertain	0.20
BayesDel_addAF	Pathogenic	0.24	D
BayesDel_noAF	Uncertain	0.10
CADD	Pathogenic	26
DANN	Uncertain	1.0
DEOGEN2	Pathogenic	0.96	.;.;.;.;.;D;.;.;.
Eigen	Uncertain	0.55
Eigen_PC	Uncertain	0.52
FATHMM_MKL	Uncertain	0.96	D
LIST_S2	Uncertain	0.91	.;D;D;D;D;D;D;.;D
M_CAP	Pathogenic	0.80	D
MetaRNN	Pathogenic	0.99	D;D;D;D;D;D;D;D;D
MetaSVM	Pathogenic	1.1	D
MutationAssessor	Uncertain	2.7	.;.;.;.;.;M;.;.;.
MutationTaster	Benign	1.0	A;A;A;A;A;A;A;A;A;A
PrimateAI	Pathogenic	0.81	D
PROVEAN	Uncertain	-4.2	D;D;D;D;D;D;D;D;D
REVEL	Pathogenic	0.92
Sift	Uncertain	0.0010	D;D;D;D;D;D;D;D;D
Sift4G	Uncertain	0.035	D;D;D;D;D;D;D;D;D
Polyphen		0.59	P;D;.;P;.;P;D;.;.
Vest4		0.86
MutPred		0.93		Loss of MoRF binding (P = 0.1367);.;Loss of MoRF binding (P = 0.1367);Loss of MoRF binding (P = 0.1367);.;Loss of MoRF binding (P = 0.1367);.;.;.;
MVP		0.97
MPC		1.3
ClinPred		0.99	D
GERP RS		4.1
Varity_R		0.61
gMVP		0.94

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.050		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: rs28937317; hg19: chr3-38601909;