3-38585926-A-AAC

Position:

• chr3-38585926-A-AAC

Variant summary

Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PVS1 PM2 PP5_Very_Strong

The NM_000335.5(SCN5A):​c.2550_2551dupGT​(p.Phe851fs) variant causes a frameshift change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,894 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Pathogenic (★★). Synonymous variant affecting the same amino acid position (i.e. F851F) has been classified as Likely benign. Variant results in nonsense mediated mRNA decay.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 6.8e-7 (0 hom.)
• Consequence: SCN5A NM_000335.5 frameshift
• Clinical Significance: Pathogenic criteria provided, multiple submitters, no conflicts P:9
• Conservation: PhyloP100: 9.32

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 18 ACMG points.

• PVS1: Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 3-38585926-A-AAC is Pathogenic according to our data. Variant chr3-38585926-A-AAC is described in ClinVar as [Pathogenic]. Clinvar id is 201560.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SCN5A	NM_001099404.2	c.2550_2551dupGT	p.Phe851fs	frameshift_variant	16/28	ENST00000413689.6	NP_001092874.1
SCN5A	NM_000335.5	c.2550_2551dupGT	p.Phe851fs	frameshift_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.2550_2551dupGT	p.Phe851fs	frameshift_variant	16/28	5	NM_001099404.2	ENSP00000410257.1
SCN5A	ENST00000423572.7	c.2550_2551dupGT	p.Phe851fs	frameshift_variant	16/28	1	NM_000335.5	ENSP00000398266.2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 6.84e-7 AC: 1 AN: 1461894 Hom.: 0 Cov.: 36 AF XY: 0.00000138 AC XY: 1 AN XY: 727248

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: 8.99e-7

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:9

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Pathogenic:4

Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Apr 22, 2024	Identified in individuals with DCM, Brugada syndrome, and/or unexplained cardiac arrest referred for genetic testing at GeneDx and in published literature (Olson et al., 2005; Kapplinger et al., 2010; Mellor et al., 2017); Not observed at significant frequency in large population cohorts (gnomAD); Frameshift variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss of function is a known mechanism of disease; This variant is associated with the following publications: (PMID: 34949099, 20129283, 15671429, 19716085, 35352813, 28600387) -
Pathogenic, criteria provided, single submitter	clinical testing	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	Sep 25, 2023	The SCN5A c.2550_2551dupGT; p.Phe851CysfsTer19variant (rs397514450), also reported as 2552_2553dupGTA, is reported in the literature in individuals affected with various cardiac defects, including dilated cardiomyopathy, long QT syndrome, or unexplained cardiac arrest (Kapplinger 2009, Mellor 2017, Olson 2005). This variant is also reported in ClinVar (Variation ID: 201560), but is absent from the Genome Aggregation Database, indicating it is not a common polymorphism. This variant causes a frameshift by inserting 2 nucleotides, so it is predicted to result in a truncated protein or mRNA subject to nonsense-mediated decay. Based on available information, this variant is considered to be pathogenic. References: Kapplinger JD et al. Spectrum and prevalence of mutations from the first 2,500 consecutive unrelated patients referred for the FAMILION long QT syndrome genetic test. Heart Rhythm. 2009 Sep;6(9):1297-303. PMID: 19716085 Mellor G et al. Genetic Testing in the Evaluation of Unexplained Cardiac Arrest: From the CASPER (Cardiac Arrest Survivors With Preserved Ejection Fraction Registry). Circ Cardiovasc Genet. 2017 Jun;10(3):e001686. PMID: 28600387 Olson TM et al. Sodium channel mutations and susceptibility to heart failure and atrial fibrillation. JAMA. 2005 Jan 26;293(4):447-54. PMID: 15671429 -
Pathogenic, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 11, 2024	This sequence change creates a premature translational stop signal (p.Phe851Cysfs*19) in the SCN5A gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in SCN5A are known to be pathogenic (PMID: 20129283, 22789973). This variant is not present in population databases (gnomAD no frequency). This premature translational stop signal has been observed in individuals with cardiac arrest, dilated cardiomyopathy, and ventricular tachycardia (PMID: 15671429, 19716085, 20129283, 28600387). ClinVar contains an entry for this variant (Variation ID: 201560). For these reasons, this variant has been classified as Pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	AiLife Diagnostics, AiLife Diagnostics	Jun 29, 2021	- -

Dilated cardiomyopathy 1E Pathogenic:1

Pathogenic, no assertion criteria provided

literature only

OMIM

Jan 26, 2005

- -

SUDDEN INFANT DEATH SYNDROME;C1832680:Dilated cardiomyopathy 1E;C1837845:Sick sinus syndrome 1;C1859062:Long QT syndrome 3;C1879286:Progressive familial heart block, type 1A;C2751898:Ventricular fibrillation, paroxysmal familial, type 1;C3151464:Atrial fibrillation, familial, 10;C4551804:Brugada syndrome 1 Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Fulgent Genetics, Fulgent Genetics

Sep 07, 2021

- -

Brugada syndrome Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

All of Us Research Program, National Institutes of Health

Sep 27, 2024

This variant inserts 2 nucleotides in exon 16 of the SCN5A gene, creating a frameshift and premature translation stop signal. This variant is expected to result in an absent or non-functional protein product. This variant has been reported in a few individuals affected with or suspected of having Brugada syndrome (PMID: 20129283, 32268277), in an individual suspected of having long QT syndrome (PMID: 19716085), in a few related individuals affected with arrhythmia and/or cardiomyopathy-related phenotypes (PMID: 15671429), and in an unexplained cardiac arrest survivor affected with idiopathic ventricular tachycardia (PMID: 28600387). This variant has not been identified in the general population by the Genome Aggregation Database (gnomAD). Loss of SCN5A function is a known mechanism of disease (clinicalgenome.org). Based on the available evidence, this variant is classified as Pathogenic. -

Cardiovascular phenotype Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Ambry Genetics

Feb 16, 2024

The c.2550_2551dupGT (p.F851Cfs*19) alteration, located in exon 16 (coding exon 15) of the SCN5A gene, consists of a duplication of GT at position 2550, causing a translational frameshift with a predicted alternate stop codon after 19 amino acids. This alteration is expected to result in loss of function by premature protein truncation or nonsense-mediated mRNA decay. This variant was not reported in population-based cohorts in the Genome Aggregation Database (gnomAD). This alteration has been reported in a subject with dilated cardiomyopathy (DCM) and was also observed in affected family members (Olson, 2005). This alteration was also identified in subjects who had genetic testing for long QT syndrome (LQTS), Brugada syndrome, and unexplained cardiac arrest (Kapplinger, 2009; Kapplinger, 2010; Mellor, 2017). Based on the available evidence, this alteration is classified as pathogenic. -

Cardiac arrhythmia Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Color Diagnostics, LLC DBA Color Health

Feb 15, 2023

This variant inserts 2 nucleotides in exon 16 of the SCN5A gene, creating a frameshift and premature translation stop signal. This variant is expected to result in an absent or non-functional protein product. This variant has been reported in a few individuals affected with or suspected of having Brugada syndrome (PMID: 20129283, 32268277), in an individual suspected of having long QT syndrome (PMID: 19716085), in a few related individuals affected with arrhythmia and/or cardiomyopathy-related phenotypes (PMID: 15671429), and in an unexplained cardiac arrest survivor affected with idiopathic ventricular tachycardia (PMID: 28600387). This variant has not been identified in the general population by the Genome Aggregation Database (gnomAD). Loss of SCN5A function is a known mechanism of disease (clinicalgenome.org). Based on the available evidence, this variant is classified as Pathogenic. -

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs397514450; hg19: chr3-38627417;