ClinVar Genomic variation as it relates to human health
NM_000335.5(SCN5A):c.665G>A (p.Arg222Gln)
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.665G>A (p.Arg222Gln)
Variation ID: 39444 Accession: VCV000039444.19
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 3p22.2 3: 38613781 (GRCh38) [ NCBI UCSC ] 3: 38655272 (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 1, 2016 Aug 25, 2024 Dec 30, 2023 - HGVS
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Nucleotide Protein Molecular
consequenceNM_000335.5:c.665G>A MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_000326.2:p.Arg222Gln missense NM_001099404.2:c.703+194G>A MANE Plus Clinical Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
intron variant NM_001099405.2:c.703+194G>A intron variant NM_001160160.2:c.703+194G>A intron variant NM_001160161.2:c.703+194G>A intron variant NM_001354701.2:c.703+194G>A intron variant NM_198056.3:c.665G>A NP_932173.1:p.Arg222Gln missense NC_000003.12:g.38613781C>T NC_000003.11:g.38655272C>T NG_008934.1:g.40892G>A LRG_289:g.40892G>A LRG_289t1:c.665G>A LRG_289p1:p.Arg222Gln LRG_289t2:c.665G>A LRG_289p2:p.Arg222Gln Q14524:p.Arg222Gln - Protein change
- R222Q
- Other names
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SCN5A, ARG222GLN (rs45546039)
p.R222Q:CGA>CAA
- Canonical SPDI
- NC_000003.12:38613780: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.
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The Genome Aggregation Database (gnomAD) 0.00001
- Links
Genes
Gene | OMIM | ClinGen Gene Dosage Sensitivity Curation |
Variation Viewer
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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 |
3783 | 4224 |
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
Help
The most recent date that a submitter evaluated this variant for the condition. |
Variation/condition record
Help
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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Pathogenic (2) |
criteria provided, single submitter
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Nov 9, 2021 | RCV000032639.11 | |
not provided (1) |
no classification provided
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- | RCV000058833.4 | |
Pathogenic (1) |
no assertion criteria provided
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Mar 6, 2013 | RCV000211852.5 | |
Pathogenic (4) |
criteria provided, multiple submitters, no conflicts
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Dec 30, 2023 | RCV000182941.12 | |
Pathogenic (1) |
criteria provided, single submitter
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May 22, 2018 | RCV000678965.3 | |
Pathogenic (1) |
criteria provided, single submitter
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Oct 31, 2018 | RCV000763109.3 |
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
Help
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
(Oct 19, 2018)
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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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Blueprint Genetics
Accession: SCV000928005.1
First in ClinVar: Jul 24, 2019 Last updated: Jul 24, 2019
Comment:
Patient analyzed with Dilated Cardiomyopathy (DCM) Panel
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Pathogenic
(Dec 16, 2021)
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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: SCV000235337.15
First in ClinVar: Jul 05, 2015 Last updated: Mar 04, 2023 |
Comment:
Not observed at significant frequency in large population cohorts (gnomAD); Published functional studies demonstrate a damaging effect as the p.(R222Q) variant results in abnormal sodium … (more)
Not observed at significant frequency in large population cohorts (gnomAD); Published functional studies demonstrate a damaging effect as the p.(R222Q) variant results in abnormal sodium channel current (Cheng et al., 2010; Laurent et al., 2012; Mann et al., 2012; Nair et el., 2012; Daniel et al., 2019); 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: 27532257, 25624448, 24815523, 22999724, 24136861, 19412328, 19716085, 21167004, 28779003, 22766342, 29506689, 31317183, 31125670, 31514951, 25741286, 29871609, 27535533, 33131149, 20458009, 22710484, 21596231) (less)
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Pathogenic
(Dec 30, 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: SCV000545097.7
First in ClinVar: Apr 17, 2017 Last updated: Feb 20, 2024 |
Comment:
This sequence change replaces arginine, which is basic and polar, with glutamine, which is neutral and polar, at codon 222 of the SCN5A protein (p.Arg222Gln). … (more)
This sequence change replaces arginine, which is basic and polar, with glutamine, which is neutral and polar, at codon 222 of the SCN5A protein (p.Arg222Gln). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individuals with autosomal dominant dilated cardiomyopathy, arrhythmias and long QT syndrome (PMID: 19716085, 21483645, 22766342, 22999724, 25210054). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 39444). 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: 22710484, 24815523, 25624448). For these reasons, this variant has been classified as Pathogenic. (less)
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Pathogenic
(Oct 31, 2018)
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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: SCV000893651.1
First in ClinVar: Mar 31, 2019 Last updated: Mar 31, 2019 |
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Pathogenic
(Nov 09, 2021)
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criteria provided, single submitter
Method: clinical testing
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Dilated cardiomyopathy 1E
Affected status: yes
Allele origin:
germline
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Genetics and Molecular Pathology, SA Pathology
Additional submitter:
Shariant Australia, Australian Genomics
Accession: SCV004175210.1
First in ClinVar: Dec 17, 2023 Last updated: Dec 17, 2023 |
Comment:
The SCN5A c.665G>A variant is a single nucleotide change in exon 6/28 of the SCN5A gene, which is predicted to change the amino acid arginine … (more)
The SCN5A c.665G>A variant is a single nucleotide change in exon 6/28 of the SCN5A gene, which is predicted to change the amino acid arginine at position 222 in the protein, to glutamine. Well-established functional studies show this variant has a deleterious effect on the resultant protein, with gain of function of the sodium channel due to proton leakage reported (PMID#22710484, 24815523, 25624448) (PS3). The variant has been identified in >15 probands with a clinical presentation of (or similar to) Dilated Cardiomyopathy 1E/Arrhythmia. This represents a significant increase in the prevalence of the variant in affected individuals compared with the prevalence in control subjects (PS4). This variant has been reported to co-segregate with disease (>20 segregants over 4 families PMID#19716085. 22766342) (PP1_strong) and is rare in population databases (gnomAD allele frequency = 0.00065%; 1 het) (PM2). The variant has been reported in dbSNP, is reported as Pathogenic (2 star) by other diagnostic laboratories (ClinVar Variation ID: 39444) and is reported in HGMD as disease causing with a dilated cardiomyopathy phenotype (CM087605). Computational predictions support a deleterious effect on the gene or gene product (PP3). (less)
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Pathogenic
(May 22, 2018)
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criteria provided, single submitter
Method: clinical testing
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Long QT syndrome 3
Affected status: yes
Allele origin:
unknown
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Center For Human Genetics And Laboratory Diagnostics, Dr. Klein, Dr. Rost And Colleagues
Accession: SCV000805181.1
First in ClinVar: Sep 14, 2018 Last updated: Sep 14, 2018 |
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Pathogenic
(Jul 13, 2022)
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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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Clinical Genetics Laboratory, Skane University Hospital Lund
Accession: SCV005198178.1
First in ClinVar: Aug 25, 2024 Last updated: Aug 25, 2024 |
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Pathogenic
(Oct 16, 2012)
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no assertion criteria provided
Method: literature only
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CARDIOMYOPATHY, DILATED, 1E
Affected status: not provided
Allele origin:
germline
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OMIM
Accession: SCV000056402.5
First in ClinVar: Apr 04, 2013 Last updated: Jun 09, 2024 |
Comment on evidence:
In 6 affected members over 3 generations of a non-Hispanic white family with cardiomyopathy and conduction system disease (CMD1E; 601154), Hershberger et al. (2008) identified … (more)
In 6 affected members over 3 generations of a non-Hispanic white family with cardiomyopathy and conduction system disease (CMD1E; 601154), Hershberger et al. (2008) identified heterozygosity for a 36683G-A (numbering per SeattleSNP) transition in exon 6 of the SCN5A gene, resulting in an arg222-to-gln (R222Q) substitution at a conserved residue. The mutation was not found in unaffected family members or in 253 controls. In 19 affected individuals from 3 unrelated 3-generation families with multifocal ectopic Purkinje-related premature contractions and dilated cardiomyopathy, Laurent et al. (2012) identified heterozygosity for the 665G-A (R222Q) mutation in the SCN5A gene, located in the voltage-sensing S4 segment of domain I. The mutation, which was fully penetrant and strictly segregated with the cardiac phenotype in each family, was not found in 600 control chromosomes; haplotype analysis showed that a founder effect for these 3 families was very unlikely. In vitro studies recapitulated the normalization of the ventricular action potentials in the presence of quinidine. Because only 6 of the 19 patients carrying the R222Q mutation had CMD, and the cardiomyopathy recovered at least partially with antiarrhythmia treatment and a reduction in the number of premature ventricular contractions, Laurent et al. (2012) suggested that CMD might be a consequence of the arrhythmia and not directly linked to the mutation. In affected members of a 3-generation Canadian family with CMD and junctional escape ventricular capture bigeminy, Nair et al. (2012) identified the R222Q mutation in the SCN5A gene. Heterologous expression studies in Chinese hamster ovary K1 cells revealed a unique biophysical phenotype of R222Q channels in which an approximately 10-mV leftward shift in the sodium current steady-state activation curve occurs without corresponding shifts in steady-state inactivation at cardiomyocyte resting membrane-potential voltages. The activation and inactivation of cells expressing equimolar combinations of wildtype and R222Q channels showed properties intermediate between those seen in cells expressing either wildtype or mutant channels alone. The changes in mutant channel properties were predicted to produce hyperexcitability of R222Q sodium channels. In 16 affected members over 3 generations of a large kindred with CMD and multiple arrhythmias, including premature ventricular complexes (PVCs) of variable morphology, Mann et al. (2012) identified heterozygosity for the R222Q mutation in the SCN5A gene. The mutation was also identified in 1 clinically unaffected family member, a 56-year-old man with a normal EKG and echocardiogram, but was not found in 200 control chromosomes. Patch-clamp studies showed that the R222Q mutation did not alter sodium channel current density, but did shift steady-state parameters of activation and inactivation to the left. Using a voltage ramp protocol, normalized current responses of mutant channels were of earlier onset and greater magnitude than wildtype. Action potential modeling using Purkinje fiber and ventricular cell models suggested that rate-dependent ectopy of Purkinje fiber origin is the predominant ventricular effect of the R222Q variant; this was supported by the clinical observation that PVC frequency increased during periods of low heart rate at rest and at night, and was reduced by high heart rates during exercise. Patients responded to sodium-channel blocking drugs with early and substantial reductions in PVCs followed by normalization of CMD over time. (less)
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Pathogenic
(Mar 06, 2013)
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no assertion criteria provided
Method: clinical testing
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Primary dilated cardiomyopathy
Affected status: not provided
Allele origin:
germline
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Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine
Accession: SCV000065333.6
First in ClinVar: May 03, 2013 Last updated: Jun 01, 2016 |
Comment:
The Arg222Gln variant in SCN5A has been reported in at least 8 families with DCM , LQTS and/or arrhythmias and segregated with disease in at … (more)
The Arg222Gln variant in SCN5A has been reported in at least 8 families with DCM , LQTS and/or arrhythmias and segregated with disease in at least 38 relatives a cross (Hershberger 2008, Kapplinger 2009, Morales 2010, Mann 2012, Laurent 2012, Nair 2012, McNair 2012). Electrophysiological studies have shown that the Arg22 2Gln variant impacts protein function (Mann 2012, Laurent 2012, Nair 2012, Cheng 2012). This variant has not been identified in large and broad European America n and African American populations by the NHLBI Exome Sequencing Project (http:/ /evs.gs.washington.edu/EVS; dbSNP rs45546039), which is consistent with a pathog enic role. In summary, this variant meets our criteria to be classified as patho genic (http://pcpgm.partners.org/LMM) based upon segregation studies and absence from controls. (less)
Number of individuals with the variant: 1
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not provided
(-)
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no classification provided
Method: literature only
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Congenital long QT syndrome
Affected status: unknown
Allele origin:
germline
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Cardiovascular Biomedical Research Unit, Royal Brompton & Harefield NHS Foundation Trust
Accession: SCV000090353.3
First in ClinVar: Oct 22, 2013 Last updated: Oct 09, 2016 |
Comment:
This variant has been reported as associated with Long QT syndrome in the following publications (PMID:19716085). This is a literature report, and does not necessarily … (more)
This variant has been reported as associated with Long QT syndrome in the following publications (PMID:19716085). 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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Gating pore currents are defects in common with two Nav1.5 mutations in patients with mixed arrhythmias and dilated cardiomyopathy. | Moreau A | The Journal of general physiology | 2015 | PMID: 25624448 |
Gain-of-function mutation of the SCN5A gene causes exercise-induced polymorphic ventricular arrhythmias. | Swan H | Circulation. Cardiovascular genetics | 2014 | PMID: 25210054 |
Novel SCN5A mutation in amiodarone-responsive multifocal ventricular ectopy-associated cardiomyopathy. | Beckermann TM | Heart rhythm | 2014 | PMID: 24815523 |
R222Q SCN5A mutation is associated with reversible ventricular ectopy and dilated cardiomyopathy. | Mann SA | Journal of the American College of Cardiology | 2012 | PMID: 22999724 |
Multifocal ectopic Purkinje-related premature contractions: a new SCN5A-related cardiac channelopathy. | Laurent G | Journal of the American College of Cardiology | 2012 | PMID: 22766342 |
Escape capture bigeminy: phenotypic marker of cardiac sodium channel voltage sensor mutation R222Q. | Nair K | Heart rhythm | 2012 | PMID: 22710484 |
Criteria to predict carriers of a novel SCN5A mutation in a large Portuguese family affected by the Brugada syndrome. | Santos LF | Europace : European pacing, arrhythmias, and cardiac electrophysiology : journal of the working groups on cardiac pacing, arrhythmias, and cardiac cellular electrophysiology of the European Society of Cardiology | 2012 | PMID: 22277643 |
SCN5A mutations associate with arrhythmic dilated cardiomyopathy and commonly localize to the voltage-sensing mechanism. | McNair WP | Journal of the American College of Cardiology | 2011 | PMID: 21596231 |
Rare variant mutations identified in pediatric patients with dilated cardiomyopathy. | Rampersaud E | Progress in pediatric cardiology | 2011 | PMID: 21483645 |
SCN5A rare variants in familial dilated cardiomyopathy decrease peak sodium current depending on the common polymorphism H558R and common splice variant Q1077del. | Cheng J | Clinical and translational science | 2010 | PMID: 21167004 |
Rare variant mutations in pregnancy-associated or peripartum cardiomyopathy. | Morales A | Circulation | 2010 | PMID: 20458009 |
Spectrum and prevalence of mutations from the first 2,500 consecutive unrelated patients referred for the FAMILION long QT syndrome genetic test. | Kapplinger JD | Heart rhythm | 2009 | PMID: 19716085 |
Coding sequence mutations identified in MYH7, TNNT2, SCN5A, CSRP3, LBD3, and TCAP from 313 patients with familial or idiopathic dilated cardiomyopathy. | Hershberger RE | Clinical and translational science | 2008 | PMID: 19412328 |
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Text-mined citations for rs45546039 ...
HelpRecord last updated Nov 03, 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.