ClinVar Genomic variation as it relates to human health
NM_000335.5(SCN5A):c.1127G>A (p.Arg376His)
The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.
Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.
No data submitted for somatic clinical impact
No data submitted for oncogenicity
Variant Details
- Identifiers
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NM_000335.5(SCN5A):c.1127G>A (p.Arg376His)
Variation ID: 67639 Accession: VCV000067639.24
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 3p22.2 3: 38606682 (GRCh38) [ NCBI UCSC ] 3: 38648173 (GRCh37) [ NCBI UCSC ]
- Timeline in ClinVar
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First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.
Last submission Help The date of the most recent submission for each type of classification for this variant.
Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline Jun 9, 2014 Sep 16, 2024 Apr 24, 2024 - HGVS
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Nucleotide Protein Molecular
consequenceNM_000335.5:c.1127G>A MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_000326.2:p.Arg376His missense NM_001099404.2:c.1127G>A MANE Plus Clinical Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_001092874.1:p.Arg376His missense NM_001099405.2:c.1127G>A NP_001092875.1:p.Arg376His missense NM_001160160.2:c.1127G>A NP_001153632.1:p.Arg376His missense NM_001160161.2:c.1127G>A NP_001153633.1:p.Arg376His missense NM_001354701.2:c.1127G>A NP_001341630.1:p.Arg376His missense NM_198056.3:c.1127G>A NP_932173.1:p.Arg376His missense NC_000003.12:g.38606682C>T NC_000003.11:g.38648173C>T NG_008934.1:g.47991G>A LRG_289:g.47991G>A LRG_289t1:c.1127G>A LRG_289p1:p.Arg376His Q14524:p.Arg376His - Protein change
- R376H
- Other names
- p.R376H:CGC>CAC
- Canonical SPDI
- NC_000003.12:38606681:C:T
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Functional
consequence HelpThe effect of the variant on RNA or protein function, based on experimental evidence from submitters.
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Global minor allele
frequency (GMAF) HelpThe global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.
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Allele frequency
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The frequency of the allele represented by this VCV record.
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00008
Exome Aggregation Consortium (ExAC) 0.00000
The Genome Aggregation Database (gnomAD), exomes 0.00001
The Genome Aggregation Database (gnomAD) 0.00003
Trans-Omics for Precision Medicine (TOPMed) 0.00003
Genes
Gene | OMIM | ClinGen Gene Dosage Sensitivity Curation |
Variation Viewer
Help
Links to Variation Viewer, a genome browser to view variation data from NCBI databases. |
Related variants | ||
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HI score
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The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
TS score
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The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
Within gene
Help
The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants. |
All
Help
The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene. |
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SCN5A | Sufficient evidence for dosage pathogenicity | No evidence available |
GRCh38 GRCh37 |
3773 | 4212 |
Conditions - Germline
Condition
Help
The condition for this variant-condition (RCV) record in ClinVar. |
Classification
Help
The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions) |
Review status
Help
The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. |
Last evaluated
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The most recent date that a submitter evaluated this variant for the condition. |
Variation/condition record
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The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page. |
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not provided (1) |
criteria provided, single submitter
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- | RCV000058396.15 | |
Pathogenic (3) |
criteria provided, multiple submitters, no conflicts
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Apr 24, 2024 | RCV000182960.18 | |
Likely pathogenic (1) |
criteria provided, single submitter
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Jan 10, 2024 | RCV000617435.11 | |
Pathogenic (1) |
criteria provided, single submitter
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Aug 8, 2023 | RCV001842271.11 | |
Pathogenic (1) |
criteria provided, single submitter
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Nov 12, 2021 | RCV002498339.8 | |
Likely pathogenic (1) |
criteria provided, single submitter
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Nov 11, 2021 | RCV003457639.1 |
Submissions - Germline
Classification
Help
The submitted germline classification for each SCV record. (Last evaluated) |
Review status
Help
Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria) |
Condition
Help
The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant. |
Submitter
Help
The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar. |
More information
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This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter. |
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Pathogenic
(Apr 24, 2024)
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criteria provided, single submitter
Method: clinical testing
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Not Provided
Affected status: yes
Allele origin:
germline
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GeneDx
Accession: SCV000235357.17
First in ClinVar: Jul 05, 2015 Last updated: Sep 16, 2024 |
Comment:
Published functional studies demonstrate this variant results in a significant reduction of the inward sodium current (PMID: 15851228, 21840964, 24295898); Not observed at significant frequency … (more)
Published functional studies demonstrate this variant results in a significant reduction of the inward sodium current (PMID: 15851228, 21840964, 24295898); Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant does not alter protein structure/function; This variant is associated with the following publications: (PMID: 17512504, 20129283, 28341781, 34461752, 15851228, 23414114, 25194972, 18378609, 16344400, 23671135, 27930701, 21840964, 31737537, 30193851, 30662450, 29709101, 33164571, 33131149, 30203441, 34495297, 24295898) (less)
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Pathogenic
(Nov 12, 2021)
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criteria provided, single submitter
Method: clinical testing
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Progressive familial heart block, type 1A
SUDDEN INFANT DEATH SYNDROME Brugada syndrome 1 Dilated cardiomyopathy 1E Ventricular fibrillation, paroxysmal familial, type 1 Long QT syndrome 3 Sick sinus syndrome 1 Atrial fibrillation, familial, 10
Affected status: unknown
Allele origin:
unknown
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Fulgent Genetics, Fulgent Genetics
Accession: SCV002814864.1
First in ClinVar: Dec 31, 2022 Last updated: Dec 31, 2022 |
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Likely pathogenic
(Nov 11, 2021)
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criteria provided, single submitter
Method: clinical testing
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Atrial fibrillation, familial, 10
Brugada syndrome 1 Dilated cardiomyopathy 1E Progressive familial heart block, type 1A Long QT syndrome 3 Sick sinus syndrome 1 Ventricular fibrillation, paroxysmal familial, type 1
Explanation for multiple conditions: Uncertain.
The variant was classified for several related diseases, possibly a spectrum of disease; the variant may be associated with one or more the diseases. (Autosomal dominant inheritance)
Affected status: no
Allele origin:
germline
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Division Of Personalized Genomic Medicine, Columbia University Irving Medical Center
Accession: SCV004190147.1
First in ClinVar: Dec 24, 2023 Last updated: Dec 24, 2023 |
Comment:
The c.1127G>A variant in theSCN5A gene is a heterozygous missense variant, which results in the substitution of the highly conserved arginine residue at the 376 … (more)
The c.1127G>A variant in theSCN5A gene is a heterozygous missense variant, which results in the substitution of the highly conserved arginine residue at the 376 position to histidine p.(Arg376His). The following criteria was used in classifying this variant: This variant localizes to coding exon 9 of the SCN5A gene (27 exons in total;NM_001160161.2). Functional studies of the variant showed reduction of the inward sodium current in cells expressing the p.Arg376His variant compared with the wildtype, which is consistent with a Brugada syndrome pattern (PMID: 24295898). This variant has been observed in the Genome Aggregation Database (gnomAD) at a very low frequency (2/247,596, 0 homozygotes), indicating it is not a common benign variant in the populations represented in this database. This variant has been reported in the literature segregating with disease in one family affected with Brugada syndrome/conduction disease (PMID: 15851228), in several individuals affected with Brugada syndrome (PMID: 16344400, 28341781), in individuals referred for Brugada genetic testing (PMID: 20129283), atrial fibrillation (PMID: 18378609), hypertrophic cardiomyopathy (PMID: 27930701), in individuals referred for Brugada genetic testing (PMID: 20129283), and in individuals who suffered sudden unexplained death (PMID: 25194972, 23671135). (less)
Clinical Features:
Hemolytic-uremic syndrome (present) , Inflammation of the large intestine (present) , Renal insufficiency (present)
Age: 40-49 years
Sex: female
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Pathogenic
(Feb 26, 2020)
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criteria provided, single submitter
Method: clinical testing
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not provided
Affected status: unknown
Allele origin:
germline
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Revvity Omics, Revvity
Accession: SCV002020029.3
First in ClinVar: Nov 29, 2021 Last updated: Feb 04, 2024 |
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Pathogenic
(Dec 17, 2023)
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criteria provided, single submitter
Method: clinical testing
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not provided
Affected status: unknown
Allele origin:
germline
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Labcorp Genetics (formerly Invitae), Labcorp
Accession: SCV000760186.6
First in ClinVar: Jun 09, 2014 Last updated: Feb 14, 2024 |
Comment:
This sequence change replaces arginine, which is basic and polar, with histidine, which is basic and polar, at codon 376 of the SCN5A protein (p.Arg376His). … (more)
This sequence change replaces arginine, which is basic and polar, with histidine, which is basic and polar, at codon 376 of the SCN5A protein (p.Arg376His). This variant is present in population databases (rs199473101, gnomAD 0.004%). This missense change has been observed in individuals with Brugada syndrome (PMID: 15851228, 16344400, 18378609, 20129283, 23671135, 25194972, 27930701, 28341781). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 67639). 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: 15851228, 21840964, 24295898). For these reasons, this variant has been classified as Pathogenic. (less)
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Pathogenic
(Aug 08, 2023)
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criteria provided, single submitter
Method: clinical testing
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Cardiac arrhythmia
Affected status: unknown
Allele origin:
germline
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Color Diagnostics, LLC DBA Color Health
Accession: SCV001359848.3
First in ClinVar: Jun 22, 2020 Last updated: Feb 14, 2024 |
Comment:
This missense variant replaces arginine with histidine at codon 376 of the SCN5A protein. This variant is found within the highly conserved pore-forming region of … (more)
This missense variant replaces arginine with histidine at codon 376 of the SCN5A protein. This variant is found within the highly conserved pore-forming region of transmembrane domain DI (a.a. 277-389). Rare nontruncating variants in this region have been shown to be significantly overrepresented in individuals with Brugada syndrome (PMID: 32893267). Functional studies have shown that this variant significantly reduces sodium channel currents (PMID: 15851228, 21840964, 24295898, 26713557). This variant has shown a highly variable phenotypic presentation ranging from Brugada syndrome to conduction disease in 9 members from a single family (PMID: 15851228). This variant has been reported in multiple other individuals affected with Brugada syndrome or referred for Brugada syndrome genetic testing (PMID: 16344400, 20129283, 28341781, 29709101) in an individual affected with atrial fibrillation (PMID: 18378609) and in individuals affected with sudden death (PMID: 23671135, 25194972, 27930701). This variant has been identified in 2/247596 chromosomes in the general population by the Genome Aggregation Database (gnomAD). Based on the available evidence, this variant is classified as Pathogenic. (less)
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Likely pathogenic
(Jan 10, 2024)
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criteria provided, single submitter
Method: clinical testing
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Cardiovascular phenotype
Affected status: unknown
Allele origin:
germline
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Ambry Genetics
Accession: SCV000737601.5
First in ClinVar: Apr 14, 2018 Last updated: May 01, 2024 |
Comment:
The p.R376H variant (also known as c.1127G>A), located in coding exon 8 of the SCN5A gene, results from a G to A substitution at nucleotide … (more)
The p.R376H variant (also known as c.1127G>A), located in coding exon 8 of the SCN5A gene, results from a G to A substitution at nucleotide position 1127. The arginine at codon 376 is replaced by histidine, an amino acid with highly similar properties. This variant has been detected in multiple individuals with Brugada syndrome (BrS; Rossenbacker T et al. Heart Rhythm. 2004;1(5):610-5; Frustaci A et al. Circulation. 2005;112(24):3680-7; Kapplinger JD et al. Heart Rhythm. 2010;7(1):33-46). It has also been identified in an individual with atrial fibrillation (Darbar D et al. Circulation. 2008;117(15):1927-35) and in families with a history of sudden death (Papadakis M et al. Circ Arrhythm Electrophysiol. 2013;6(3):588-96; Wong LC et al. Circ Arrhythm Electrophysiol. 2014;7(5):800-6). Additionally, p.R376H has been shown to disrupt protein function, resulting in reduced sodium channel current (Rossenbacker T et al. Heart Rhythm 2004;1(5):610-5; Shinlapawittayatorn K et al. Heart Rhythm 2011; 8(3):455-62; Detta N et al. Int. J. Cardiol. 2014; 170(3):e63-5; Peters CH et al. Mol. Biol. 2016;120(1-3):77-88). This amino acid position is not well conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Based on the majority of available evidence to date, this variant is likely to be pathogenic. (less)
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not provided
(-)
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no classification provided
Method: literature only
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Brugada syndrome
Affected status: unknown
Allele origin:
germline
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Cardiovascular Biomedical Research Unit, Royal Brompton & Harefield NHS Foundation Trust
Accession: SCV000089916.3
First in ClinVar: Oct 22, 2013 Last updated: Jun 09, 2014 |
Comment:
This variant has been reported as associated with Brugada syndrome in the following publications (PMID:15851228;PMID:16344400;PMID:20129283;PMID:18378609). This is a literature report, and does not necessarily reflect … (more)
This variant has been reported as associated with Brugada syndrome in the following publications (PMID:15851228;PMID:16344400;PMID:20129283;PMID:18378609). This is a literature report, and does not necessarily reflect the clinical interpretation of the Imperial College / Royal Brompton Cardiovascular Genetics laboratory. (less)
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Germline Functional Evidence
There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar. |
Citations for germline classification of this variant
HelpTitle | Author | Journal | Year | Link |
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Genotype-Phenotype Correlation of SCN5A Genotype in Patients With Brugada Syndrome and Arrhythmic Events: Insights From the SABRUS in 392 Probands. | Milman A | Circulation. Genomic and precision medicine | 2021 | PMID: 34461752 |
Enhancing rare variant interpretation in inherited arrhythmias through quantitative analysis of consortium disease cohorts and population controls. | Walsh R | Genetics in medicine : official journal of the American College of Medical Genetics | 2021 | PMID: 32893267 |
SCN5A Mutation Type and a Genetic Risk Score Associate Variably With Brugada Syndrome Phenotype in SCN5A Families. | Wijeyeratne YD | Circulation. Genomic and precision medicine | 2020 | PMID: 33164571 |
Genotype-phenotype relationship and risk stratification in loss-of-function SCN5A mutation carriers. | Robyns T | Annals of noninvasive electrocardiology : the official journal of the International Society for Holter and Noninvasive Electrocardiology, Inc | 2018 | PMID: 29709101 |
Genotype-Phenotype Correlation of SCN5A Mutation for the Clinical and Electrocardiographic Characteristics of Probands With Brugada Syndrome: A Japanese Multicenter Registry. | Yamagata K | Circulation | 2017 | PMID: 28341781 |
Natural and Undetermined Sudden Death: Value of Post-Mortem Genetic Investigation. | Sanchez O | PloS one | 2016 | PMID: 27930701 |
Triggers for arrhythmogenesis in the Brugada and long QT 3 syndromes. | Peters CH | Progress in biophysics and molecular biology | 2016 | PMID: 26713557 |
Cardiac evaluation of pediatric relatives in sudden arrhythmic death syndrome: a 2-center experience. | Wong LC | Circulation. Arrhythmia and electrophysiology | 2014 | PMID: 25194972 |
Genetic analysis in a family affected by sick sinus syndrome may reduce the sudden death risk in a young aspiring competitive athlete. | Detta N | International journal of cardiology | 2014 | PMID: 24295898 |
Sudden cardiac death with autopsy findings of uncertain significance: potential for erroneous interpretation. | Papadakis M | Circulation. Arrhythmia and electrophysiology | 2013 | PMID: 23671135 |
A novel strategy using cardiac sodium channel polymorphic fragments to rescue trafficking-deficient SCN5A mutations. | Shinlapawittayatorn K | Circulation. Cardiovascular genetics | 2011 | PMID: 21840964 |
A common SCN5A polymorphism modulates the biophysical defects of SCN5A mutations. | Shinlapawittayatorn K | Heart rhythm | 2011 | PMID: 21109022 |
An international compendium of mutations in the SCN5A-encoded cardiac sodium channel in patients referred for Brugada syndrome genetic testing. | Kapplinger JD | Heart rhythm | 2010 | PMID: 20129283 |
Cardiac sodium channel (SCN5A) variants associated with atrial fibrillation. | Darbar D | Circulation | 2008 | PMID: 18378609 |
Cardiac histological substrate in patients with clinical phenotype of Brugada syndrome. | Frustaci A | Circulation | 2005 | PMID: 16344400 |
Novel pore mutation in SCN5A manifests as a spectrum of phenotypes ranging from atrial flutter, conduction disease, and Brugada syndrome to sudden cardiac death. | Rossenbacker T | Heart rhythm | 2004 | PMID: 15851228 |
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Text-mined citations for rs199473101 ...
HelpRecord last updated Sep 29, 2024
This date represents the last time this VCV record was updated. The update may be due to an update to one of the included submitted records (SCVs), or due to an update that ClinVar made to the variant such as adding HGVS expressions or a rs number. So this date may be different from the date of the “most recent submission” reported at the top of this page.