chr3-38630342-G-A

Variant summary

Our verdict is Pathogenic. Variant got 19 ACMG points: 19P and 0B. PM1PM2PM5PP2PP3_StrongPP5_Very_Strong

The NM_000335.5(SCN5A):​c.361C>T​(p.Arg121Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000205 in 1,461,190 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. R121Q) has been classified as Pathogenic.

Frequency

Genomes: not found (cov: 32)
Exomes 𝑓: 0.0000021 ( 0 hom. )

Consequence

SCN5A
NM_000335.5 missense

Scores

15
4
1

Clinical Significance

Pathogenic/Likely pathogenic criteria provided, multiple submitters, no conflicts P:6O:1

Conservation

PhyloP100: 0.970
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Pathogenic. Variant got 19 ACMG points.

PM1
In a helix (size 7) in uniprot entity SCN5A_HUMAN there are 5 pathogenic changes around while only 0 benign (100%) in NM_000335.5
PM2
Very rare variant in population databases, with high coverage;
PM5
Other missense variant is known to change same aminoacid residue: Variant chr3-38630341-C-T is described in Lovd as [Pathogenic].
PP2
Missense variant in the SCN5A gene, where missense mutations are typically associated with disease (based on misZ statistic). The gene has 99 curated pathogenic missense variants (we use a threshold of 10). The gene has 60 curated benign missense variants. Gene score misZ: 2.7504 (below the threshold of 3.09). Trascript score misZ: 4.8279 (above the threshold of 3.09). GenCC associations: The gene is linked to 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, 0.991
PP5
Variant 3-38630342-G-A is Pathogenic according to our data. Variant chr3-38630342-G-A is described in ClinVar as [Likely_pathogenic]. Clinvar id is 67807.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-38630342-G-A is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
SCN5ANM_001099404.2 linkc.361C>T p.Arg121Trp missense_variant Exon 3 of 28 ENST00000413689.6 NP_001092874.1 Q14524H9KVD2
SCN5ANM_000335.5 linkc.361C>T p.Arg121Trp missense_variant Exon 3 of 28 ENST00000423572.7 NP_000326.2 Q14524-2Q86V90

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
SCN5AENST00000413689.6 linkc.361C>T p.Arg121Trp missense_variant Exon 3 of 28 5 NM_001099404.2 ENSP00000410257.1 H9KVD2
SCN5AENST00000423572.7 linkc.361C>T p.Arg121Trp missense_variant Exon 3 of 28 1 NM_000335.5 ENSP00000398266.2 Q14524-2

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
AF:
0.00000205
AC:
3
AN:
1461190
Hom.:
0
Cov.:
30
AF XY:
0.00000138
AC XY:
1
AN XY:
726930
show subpopulations
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:
0.00000270
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
32

ClinVar

Significance: Pathogenic/Likely pathogenic
Submissions summary: Pathogenic:6Other:1
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

Brugada syndrome 1 Pathogenic:2
Pathogenic, criteria provided, single submitterclinical testingPetrovsky National Research Centre of Surgery, The Federal Agency for Scientific OrganizationsSep 24, 2024Heterozygous variant NM_000335.5:c.361C>T (p.Arg121Trp) in the SCN5A gene was found on WES data in male proband (9 y.o., Caucasian) with Brugada syndrome. This genetic variant is in The Genome Aggregation Database (gnomAD) v4.1.0 with total MAF 0.000001859 (Date of access 23-09-2024). Clinvar contains an entry for this variant (Variation ID: 67807). This variant located in a mutational hot spot and/or critical and well-established functional domain (PM1_moderate according to Walsh R. et al. (PMID: 32893267). Most in silico predictors show pathogenic result of the protein change (varsome.com). Published functional studies demonstrate a significant reduction of sodium current and reduced amounts of sodium channels (Holst et al., 2010; Clatot et al., 2012). This variant is associated with the following publications: (PMID: 31737537, 26173111, 28449774, 20395683, 22739120, 23874304, 20129283, 25863800, 23123192, 19606473, 24136861, 25904541, 30662450). In accordance with ACMG (2015) criteria this variant is classified as Pathogenic with following criteria selected: PM2, PM5, PP3, PS3, PM1, PP5. -
Pathogenic, criteria provided, single submitterclinical testingCenter For Human Genetics And Laboratory Diagnostics, Dr. Klein, Dr. Rost And ColleaguesMay 24, 2017- -
not provided Pathogenic:2
Pathogenic, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpAug 02, 2023This variant disrupts the p.Arg121 amino acid residue in SCN5A. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 20129283, 24529773). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. Experimental studies have shown that this missense change affects SCN5A function (PMID: 20395683, 22739120). 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. ClinVar contains an entry for this variant (Variation ID: 67807). This missense change has been observed in individuals with Brugada syndrome (PMID: 19606473, 20129283, 20395683, 24136861, 26173111, 28449774). This variant is not present in population databases (gnomAD no frequency). This sequence change replaces arginine, which is basic and polar, with tryptophan, which is neutral and slightly polar, at codon 121 of the SCN5A protein (p.Arg121Trp). For these reasons, this variant has been classified as Pathogenic. -
Likely pathogenic, criteria provided, single submitterclinical testingGeneDxJun 16, 2020Identified in at least two unrelated individuals with Brugada syndrome in published literature (Kapplinger et al., 2010; Selga et al., 2015); Identified in a patient with arrhythmia and was also identified in his father who had a milder phenotype (Holst et al., 2010); Identified in a patient with sudden arrhythmic death syndrome (SADS) who had no cardiac symptoms prior to death and was also identified in his mother and brother who showed Brugada pattern on electrocardiogram (Lahrouchi et al., 2017); Not observed in large population cohorts (Lek et al., 2016); Reported as pathogenic/likely pathogenic in ClinVar but additional evidence is not available (ClinVar Variant ID#67807; Landrum et al., 2016); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Published functional studies demonstrate a significant reduction of sodium current and reduced amounts of sodium channels (Holst et al., 2010; Clatot et al., 2012); A different missense change at this residue (R121Q) has been reported as pathogenic in ClinVar (ClinVar SCV#67808; Landrum et al., 2016); This variant is associated with the following publications: (PMID: 31737537, 26173111, 28449774, 20395683, 22739120, 23874304, 20129283, 25863800, 23123192, 19606473, 24136861, 25904541, 30662450) -
Dilated cardiomyopathy 1E;C1859062:Long QT syndrome 3;C1879286:Progressive familial heart block, type 1A;C3151464:Atrial fibrillation, familial, 10;C4551804:Brugada syndrome 1 Pathogenic:1
Likely pathogenic, criteria provided, single submitterclinical testingFoundation for Research in Genetics and Endocrinology, FRIGE's Institute of Human Genetics-A heterozygous missense variant in exon 3 of the SCN5A gene that results in the amino acid substitution of Tryptophan for Arginine at codon 121 was detected. The observed variant c.361C>T (p.Arg121Trp) has not been reported in the 1000 genomes and gnomAD databases. The in silico prediction of the variant are damaging by SIFT, LRT and MutationTaster2. The reference codon is conserved across species. In summary, the variant meets our criteria to be classified as likely pathogenic. -
Cardiovascular phenotype Pathogenic:1
Likely pathogenic, criteria provided, single submitterclinical testingAmbry GeneticsOct 28, 2024The p.R121W variant (also known as c.361C>T), located in coding exon 2 of the SCN5A gene, results from a C to T substitution at nucleotide position 361. The arginine at codon 121 is replaced by tryptophan, an amino acid with dissimilar properties. This alteration has been reported in association with Brugada syndrome (Kapplinger JD et al. Heart Rhythm, 2010 Jan;7:33-46; Hertz CL et al. Int. J. Legal Med., 2015 Jul;129:793-800; Leong KM et al. HeartRhythm Case Rep, 2017 Mar;3:167-171). This alteration was also reported in a proband and his father who both had cardiac conduction disease (Holst AG et al. Cardiology, 2010 Apr;115:311-6). In addition, functional studies demonstrate a reduction of sodium current and are consistent with a dominant negative effect through retention in the endoplasmic reticulum (Holst AG et al. Cardiology, 2010 Apr;115:311-6; Clatot J et al. Cardiovasc. Res., 2012 Oct;96:53-63). This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. This variant is considered to be rare based on population cohorts in the Genome Aggregation Database (gnomAD). Based on the majority of available evidence to date, this variant is likely to be pathogenic. -
Brugada syndrome Other:1
not provided, no classification providedliterature onlyCardiovascular Biomedical Research Unit, Royal Brompton & Harefield NHS Foundation Trust-This variant has been reported as associated with Brugada syndrome in the following publications (PMID:19606473;PMID:20129283;PMID:20395683;PMID:22739120). 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
Pathogenic
0.92
CardioboostCm
Pathogenic
0.98
BayesDel_addAF
Pathogenic
0.53
D
BayesDel_noAF
Pathogenic
0.52
CADD
Pathogenic
27
DANN
Pathogenic
1.0
DEOGEN2
Pathogenic
0.95
.;.;.;.;.;D;.;.;.;D
Eigen
Uncertain
0.64
Eigen_PC
Uncertain
0.52
FATHMM_MKL
Uncertain
0.84
D
LIST_S2
Pathogenic
1.0
.;D;D;D;D;D;D;.;D;D
M_CAP
Pathogenic
0.60
D
MetaRNN
Pathogenic
0.99
D;D;D;D;D;D;D;D;D;D
MetaSVM
Pathogenic
1.1
D
MutationAssessor
Pathogenic
3.5
.;M;.;.;.;M;.;.;.;.
PrimateAI
Uncertain
0.69
T
PROVEAN
Pathogenic
-7.6
D;D;D;D;D;D;D;D;D;.
REVEL
Pathogenic
0.89
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;D
Polyphen
1.0
D;D;.;D;.;D;D;.;.;.
Vest4
0.99
MutPred
0.94
Loss of methylation at K126 (P = 0.046);Loss of methylation at K126 (P = 0.046);Loss of methylation at K126 (P = 0.046);Loss of methylation at K126 (P = 0.046);Loss of methylation at K126 (P = 0.046);Loss of methylation at K126 (P = 0.046);Loss of methylation at K126 (P = 0.046);Loss of methylation at K126 (P = 0.046);Loss of methylation at K126 (P = 0.046);Loss of methylation at K126 (P = 0.046);
MVP
0.98
MPC
1.1
ClinPred
0.99
D
GERP RS
4.2
Varity_R
0.92
gMVP
0.93

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.16
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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs199473556; hg19: chr3-38671833; COSMIC: COSV60067309; COSMIC: COSV60067309; API