rs794728940

Positions:

chr3-38550542-G-A

Variant summary

Our verdict is Likely pathogenic. Variant got 7 ACMG points: 7P and 0B. PVS1_StrongPM2PP5

The NM_000335.5(SCN5A):c.5827C>T(p.Arg1943*) variant causes a stop gained change. The variant allele was found at a frequency of 0.00000992 in 1,613,312 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 Conflicting classifications of pathogenicity (no stars).

Frequency

Genomes: 𝑓 0.000026 ( 0 hom., cov: 33)

Exomes 𝑓: 0.0000082 ( 0 hom. )

Consequence

SCN5A
NM_000335.5 stop_gained

Scores

Clinical Significance

Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:4U:7O:1

Conservation

PhyloP100: 4.91

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]

SCN5A links:

SCN5A (HGNC:):

SCN5A links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_pathogenic. Variant got 7 ACMG points.

PVS1

Loss of function variant, product does not undergo nonsense mediated mRNA decay. Variant is located in the 3'-most exon, not predicted to undergo nonsense mediated mRNA decay. There are 6 pathogenic variants in the truncated region.

PM2

Very rare variant in population databases, with high coverage;

PP5

Variant 3-38550542-G-A is Pathogenic according to our data. Variant chr3-38550542-G-A is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 201596.We mark this variant Likely_pathogenic, oryginal submissions are: {Uncertain_significance=6, not_provided=1, Likely_pathogenic=3}.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SCN5A	NM_001099404.2 linkuse as main transcript	c.5830C>T	p.Arg1944*	stop_gained	28/28	ENST00000413689.6	NP_001092874.1	Q14524H9KVD2
SCN5A	NM_000335.5 linkuse as main transcript	c.5827C>T	p.Arg1943*	stop_gained	28/28	ENST00000423572.7	NP_000326.2	Q14524-2Q86V90

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SCN5A	ENST00000413689.6 linkuse as main transcript	c.5830C>T	p.Arg1944*	stop_gained	28/28	5	NM_001099404.2	ENSP00000410257.1		H9KVD2
SCN5A	ENST00000423572.7 linkuse as main transcript	c.5827C>T	p.Arg1943*	stop_gained	28/28	1	NM_000335.5	ENSP00000398266.2		Q14524-2

Frequencies

GnomAD3 genomes

AF:

0.0000263

AC:

AN:

152254

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000262

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00

Gnomad OTH

AF:

0.00

GnomAD3 exomes

AF:

0.0000121

AC:

AN:

248022

Hom.:

AF XY:

0.0000149

AC XY:

AN XY:

134634

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.0000178

Gnomad OTH exome

AF:

0.000166

GnomAD4 exome

AF:

0.00000821

AC:

AN:

1461058

Hom.:

Cov.:

AF XY:

0.00000688

AC XY:

AN XY:

726716

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.0000672

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.0000252

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.00000180

Gnomad4 OTH exome

AF:

0.0000994

GnomAD4 genome

AF:

0.0000263

AC:

AN:

152254

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

74386

show subpopulations

Gnomad4 AFR

AF:

0.00

Gnomad4 AMR

AF:

0.000262

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.00

Gnomad4 OTH

AF:

0.00

Alfa

AF:

0.0000282

Hom.:

Bravo

AF:

0.0000907

Asia WGS

AF:

0.000289

AC:

AN:

3478

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Pathogenic:4Uncertain:7Other:1

Revision: criteria provided, conflicting classifications

LINK: link

Submissions by phenotype

not provided

Pathogenic:1Uncertain:3

Uncertain significance, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 02, 2024	This sequence change creates a premature translational stop signal (p.Arg1944*) in the SCN5A gene. While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 73 amino acid(s) of the SCN5A protein. This variant is present in population databases (rs794728940, gnomAD 0.005%). This premature translational stop signal has been observed in individual(s) with Brugada syndrome and/or sudden unexplained death (PMID: 24631775, 29247119, 33221895, 36007526). ClinVar contains an entry for this variant (Variation ID: 201596). Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. This variant disrupts a region of the SCN5A protein in which other variant(s) (p.Arg2012) have been observed in individuals with SCN5A-related conditions (PMID: 27287068). This suggests that this is a clinically significant region of the protein, and that variants that disrupt it are likely to be disease-causing. 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. -
Uncertain significance, criteria provided, single submitter	clinical testing	GeneDx	Nov 26, 2024	Identified in the literature in an infant with sudden unexplained death and in an individual with Brugada syndrome; however, both patients also harbored an additional variant in the SCN5A gene and no segregation data was reported (PMID: 24631775, 33221895); Identified by clinical exome sequencing in a patient with skeletal muscle involvement but no evidence of cardiac involvement in the literature (PMID: 31130284); Not observed at significant frequency in large population cohorts (gnomAD); Nonsense variant predicted to result in protein truncation as the last 73 amino acids are lost; This variant is associated with the following publications: (PMID: 29247119, 28316956, 28370132, 31698696, 33221895, 36007526, 24631775, 31130284, 36129056) -
Uncertain significance, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Nov 15, 2022	The SCN5A c.5830C>T (p.Arg1944Ter) nonsense variant results in the substitution of arginine at amino acid position 1944 with a stop codon. This variant occurs in the last exon of the gene and may escape nonsense-mediated mRNA decay. This variant has been reported in a heterozygous state in at least three individuals in the literature, including a proband with Brugada syndrome (PMID: 33221895), and two female infants with sudden infant death syndrome, one of whom carried a second missense variant in SCN5A (PMID: 28370132; PMID: 29247119; PMID: 24631775). This variant is reported in the Genome Aggregation Database in four alleles at a frequency of 0.000262 in the Latino/Admixed American population (version 3.1.2). This frequency is high but may be consistent with reduced penetrance. Patch clamp studies in HEK293 cells overexpressing the Arg1944Ter mutant protein demonstrated no significant alteration in Na(v)1.5 channel kinetics compared to the wild type protein (PMID: 28370132). Based on the available evidence, the c.5830C>T (p.Arg1944Ter) variant is classified as a variant of uncertain significance for SCN5A-related disorders. -
Likely pathogenic, criteria provided, single submitter	clinical testing	AiLife Diagnostics, AiLife Diagnostics	Sep 17, 2021	- -

SCN5A-related disorder

Pathogenic:2Other:1

not provided, no classification provided	phenotyping only	GenomeConnect, ClinGen	-	Variant interpretted as Likely pathogenic and reported on 03/29/2018 by GTR ID 26957. GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical significance of the variant. -
Likely pathogenic, criteria provided, single submitter	clinical testing	Rady Children's Institute for Genomic Medicine, Rady Children's Hospital San Diego	-	This nonsense variant is found in the last exon of SCN5A and is predicted to cause loss of normal protein function by protein truncation with loss of the last 73 amino acids of the protein. This variant has been previously reported as a heterozygous change in patients with cardiac arrhythmia (PMID: 29247119) and sudden unexplained death (SUD) (PMID: 24631775). However, the patient with SUD harbored an additional variant in the SCN5A gene, and segregation data was not available (PMID: 24631775). One other nonsense variant located downstream of this variant has been reported as disease-causing in the literature (PMID: 23538271, 28600387, 31447099, 27532257, 19862833), and loss of function is a known mechanism of disease in the SCN5A gene. It is present in the heterozygous state in the gnomAD population database at a frequency of 0.001% (4/279424) and thus is presumed to be rare. Based on the available evidence, the c.5830C>T (p.Arg1944Ter) variant is classified as Likely Pathogenic. -
Likely pathogenic, criteria provided, single submitter	clinical testing	Rady Children's Institute for Genomic Medicine, Rady Children's Hospital San Diego	-	This nonsense variant is found in the last exon of SCN5A and is predicted to cause loss of normal protein function by protein truncation with loss of the last 73 amino acids of the protein. Another nonsense variant located downstream of this variant has been reported in individuals with SCN5A-related disorders (PMID: 23538271, 28600387, 31447099, 27532257, 19862833). Loss of function variation in SCN5A is an established mechanism of disease (PMID: 14523039, 35305865, 20301690). This variant has been previously reported as a heterozygous change in individuals with cardiac arrhythmia and sudden unexplained death (PMID: 24631775, 28370132, 29247119). However, the individual with sudden unexplained death was reported to have an additional variant in the SCN5A gene and segregation data was not available (PMID: 24631775).The c.5830C>T (p.Arg1944Ter) variant is present in the heterozygous state in the gnomAD population database at a frequency of 0.001% (4/279424) and thus is presumed to be rare. Based on the available evidence, the c.5830C>T (p.Arg1944Ter) variant is classified as Likely Pathogenic. -

Congenital long QT syndrome

Pathogenic:1

Likely pathogenic, no assertion criteria provided

research

Genetics and Genomics Program, Sidra Medicine

The c.5830C>T stop gained variant in SCN5A is absent in homozygous form in gnomAD, with a frequency of 0.0000318, indicating rarity (PM2). The variant results in a premature stop codon, likely leading to loss of function (PVS1). It was inherited from the affected mother, supporting its clinical relevance. Based on this evidence, the variant is classified as likely pathogenic (ACMG codes: PVS1, PM2, PP5). -

not specified

Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

Oct 12, 2023

Variant summary: SCN5A c.5830C>T (p.Arg1944X), located within the last exon, results in a premature termination codon and is predicted to cause a truncation of the encoded protein but is not expected to undergo nonsense mediated decay. The variant allele was found at a frequency of 1.2e-05 in 248022 control chromosomes (gnomAD). The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. c.5830C>T has been reported in the literature in a case of sudden unexplained death in an infant (Wang_2017, Lin_2017), and in an individual with Brugada syndrome, who also harbored a second putatively pathogenic variant in SCN5A (Ciconte_2021). The variant has also been reported in several individuals who underwent genetic testing, but whether they presented with a cardiac phenotype was not specified (e.g. Baruteau_2018, Yang_2022). These reports do not provide unequivocal conclusions about association of the variant with SCN5A-related cardiac conditions. At least one publication reported experimental evidence evaluating an impact on protein function and showed no damaging effect of this variant (Gando_2017). The following publications have been ascertained in the context of this evaluation (PMID: 30059973, 33221895, 28370132, 29247119, 24631775, 36129056). Seven submitters have cited clinical-significance assessments for this variant to ClinVar after 2014. Five classified the variant as uncertain significance and two classified it as likely pathogenic. Based on the evidence outlined above, the variant was classified as uncertain significance. -

Brugada syndrome

Uncertain:1

Uncertain significance, no assertion criteria provided

clinical testing

Molecular Genetics Laboratory, BC Children's and BC Women's Hospitals

Aug 27, 2024

- -

Cardiovascular phenotype

Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Ambry Genetics

Jan 02, 2024

The p.R1944* variant (also known as c.5830C>T), located in coding exon 27 of the SCN5A gene, results from a C to T substitution at nucleotide position 5830. This changes the amino acid from an arginine to a stop codon within coding exon 27. This alteration occurs at the 3' terminus of theSCN5A gene, is not expected to trigger nonsense-mediated mRNAdecay, and only impacts the last 3% of the protein. The exact functional effect of this alteration is unknown. This alteration has been previously reported in a sudden death case, but the infant victim was also heterozygous for a second alteration in SCN5A (p.Q1832E) (Wang D et al. Forensic Sci. Int. 2014;237:90-9). Functional studies indicate that this alteration does not have a significant effect on current density, gating kinetics, or trafficking (Gando I et al. Pacing Clin Electrophysiol. 2017;40:703-712). Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear. -

Cardiac arrhythmia

Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Color Diagnostics, LLC DBA Color Health

Mar 22, 2023

This variant changes 1 nucleotide in exon 28 of the SCN5A gene, creating a premature translation stop signal in the last exon. The mutant transcript is expected to escape nonsense-mediated decay and be expressed as a protein product containing a disrupted C-terminal region. The C-terminal region has been reported to be critical to sodium channel function (PMID: 16686678, 16798729). However, an experimental functional study has shown that this variant has negligible effects on the protein expression and function (PMID: 28370132). This variant has been reported in an individual affected with Brugada syndrome, who also carried another pathogenic variant in the same gene that could explain the observed phenotype (PMID: 33221895). This variant has also been reported in several young individuals affected with sudden unexplained death (PMID 24631775, 28370132, 29247119) or suspected of having a genetic disorder (PMID: 36007526, 36129056). This variant has been identified in 4/279424 chromosomes in the general population by the Genome Aggregation Database (gnomAD). Loss of SCN5A function is a known mechanism of disease (clinicalgenome.org). 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. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Pathogenic

0.55

BayesDel_noAF

Pathogenic

0.63

CADD

Pathogenic

DANN

Uncertain

1.0

Eigen

Pathogenic

0.85

Eigen_PC

Pathogenic

0.67

FATHMM_MKL

Pathogenic

0.97

Vest4

0.87

GERP RS

4.0

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

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

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over