chr3:38603929:T>C Detail (hg38) (SCN5A)

Information

Genome

Assembly Position
hg19 chr3:38,645,420-38,645,420 View the variant detail on this assembly version.
hg38 chr3:38,603,929-38,603,929

HGVS

Type Transcript Protein
RefSeq NM_000335.4:c.1673A>G NP_000326.2:p.His558Arg
NM_198056.2:c.1673A>G NP_932173.1:p.His558Arg
NM_001099404.1:c.1673A>G NP_001092874.1:p.His558Arg
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.094
ToMMo:0.097
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.099

Prediction

ClinVar

Clinical Significance Benign Likely benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 600163 OMIM
HGNC 10593 HGNC
Ensembl ENSG00000183873 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv12113802 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Pathogenic 2008-04-15 no assertion criteria provided Progressive familial heart block, type 1A germline Detail
Benign 2020-03-05 criteria provided, multiple submitters, no conflicts not specified germline unknown Detail
Benign 2024-02-01 criteria provided, multiple submitters, no conflicts not provided germline Detail
Benign 2015-03-16 criteria provided, single submitter germline Detail
Likely benign 2017-04-27 criteria provided, single submitter long QT syndrome 3 germline Detail
Likely benign 2017-04-27 criteria provided, single submitter Sick sinus syndrome 1 germline Detail
Likely benign 2016-06-14 criteria provided, single submitter Congenital long QT syndrome germline Detail
Likely benign 2017-04-27 criteria provided, single submitter dilated cardiomyopathy 1E germline Detail
Likely benign 2017-04-27 criteria provided, single submitter Ventricular fibrillation, paroxysmal familial, type 1 germline Detail
Likely benign 2017-04-27 criteria provided, single submitter Progressive familial heart block, type 1A germline Detail
Benign Likely benign 2019-05-28 criteria provided, multiple submitters, no conflicts Brugada syndrome 1 germline unknown Detail
Benign 2018-03-15 criteria provided, single submitter Cardiac arrhythmia germline Detail
Benign 2022-04-28 criteria provided, single submitter Progressive familial heart block, type 1A,sudden infant death syndrome,dilated cardiomyopathy 1E,Brugada syndrome 1,long QT syndrome 3,Ventricular fibrillation, paroxysmal familial, type 1,Sick sinus syndrome 1,Atrial fibrillation, familial, 10 unknown Detail
Benign 2022-04-28 criteria provided, single submitter Progressive familial heart block, type 1A,sudden infant death syndrome,dilated cardiomyopathy 1E,Brugada syndrome 1,long QT syndrome 3,Ventricular fibrillation, paroxysmal familial, type 1,Sick sinus syndrome 1,Atrial fibrillation, familial, 10 unknown Detail
Benign 2022-04-28 criteria provided, single submitter Progressive familial heart block, type 1A,sudden infant death syndrome,dilated cardiomyopathy 1E,Brugada syndrome 1,long QT syndrome 3,Ventricular fibrillation, paroxysmal familial, type 1,Sick sinus syndrome 1,Atrial fibrillation, familial, 10 unknown Detail
Benign 2022-04-28 criteria provided, single submitter Progressive familial heart block, type 1A,sudden infant death syndrome,dilated cardiomyopathy 1E,Brugada syndrome 1,long QT syndrome 3,Ventricular fibrillation, paroxysmal familial, type 1,Sick sinus syndrome 1,Atrial fibrillation, familial, 10 unknown Detail
Benign 2022-04-28 criteria provided, single submitter Progressive familial heart block, type 1A,sudden infant death syndrome,dilated cardiomyopathy 1E,Brugada syndrome 1,long QT syndrome 3,Ventricular fibrillation, paroxysmal familial, type 1,Sick sinus syndrome 1,Atrial fibrillation, familial, 10 unknown Detail
Benign 2022-04-28 criteria provided, single submitter Progressive familial heart block, type 1A,sudden infant death syndrome,dilated cardiomyopathy 1E,Brugada syndrome 1,long QT syndrome 3,Ventricular fibrillation, paroxysmal familial, type 1,Sick sinus syndrome 1,Atrial fibrillation, familial, 10 unknown Detail
Benign 2022-04-28 criteria provided, single submitter Progressive familial heart block, type 1A,sudden infant death syndrome,dilated cardiomyopathy 1E,Brugada syndrome 1,long QT syndrome 3,Ventricular fibrillation, paroxysmal familial, type 1,Sick sinus syndrome 1,Atrial fibrillation, familial, 10 unknown Detail
Benign 2022-04-28 criteria provided, single submitter Progressive familial heart block, type 1A,sudden infant death syndrome,dilated cardiomyopathy 1E,Brugada syndrome 1,long QT syndrome 3,Ventricular fibrillation, paroxysmal familial, type 1,Sick sinus syndrome 1,Atrial fibrillation, familial, 10 unknown Detail
Benign 2022-09-27 criteria provided, single submitter Primary dilated cardiomyopathy germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.442 Hereditary bundle branch system defect NA CLINVAR Detail
0.247 sick sinus syndrome Mutation-specific effects of polymorphism H558R in SCN5A-related sick sinus synd... BeFree 20384651 Detail
0.005 Fibrillation Polymorphism H558R in the human cardiac sodium channel SCN5A gene is associated ... BeFree 22117993 Detail
<0.001 Keshan disease H558R polymorphism in SCN5A is associated with Keshan disease and QRS prolongati... BeFree 25177937 Detail
<0.001 Familial sick sinus syndrome To clarify the effects of a common polymorphism in SCN5A gene, H558R, on SCN5A-r... BeFree 20384651 Detail
<0.001 Familial dilated cardiomyopathy SCN5A rare variants in familial dilated cardiomyopathy decrease peak sodium curr... BeFree 21167004 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_198056.2(SCN5A):c.[1535C>T;1673A>G] AND Progressive familial heart block, type 1A ClinVar Detail
NM_000335.5(SCN5A):c.1673A>G (p.His558Arg) AND not specified ClinVar Detail
NM_000335.5(SCN5A):c.1673A>G (p.His558Arg) AND not provided ClinVar Detail
NM_000335.5(SCN5A):c.1673A>G (p.His558Arg) AND Cardiovascular phenotype ClinVar Detail
NM_000335.5(SCN5A):c.1673A>G (p.His558Arg) AND Long QT syndrome 3 ClinVar Detail
NM_000335.5(SCN5A):c.1673A>G (p.His558Arg) AND Sick sinus syndrome 1 ClinVar Detail
NM_000335.5(SCN5A):c.1673A>G (p.His558Arg) AND Congenital long QT syndrome ClinVar Detail
NM_000335.5(SCN5A):c.1673A>G (p.His558Arg) AND Dilated cardiomyopathy 1E ClinVar Detail
NM_000335.5(SCN5A):c.1673A>G (p.His558Arg) AND Ventricular fibrillation, paroxysmal familial, type 1 ClinVar Detail
NM_000335.5(SCN5A):c.1673A>G (p.His558Arg) AND Progressive familial heart block, type 1A ClinVar Detail
NM_000335.5(SCN5A):c.1673A>G (p.His558Arg) AND Brugada syndrome 1 ClinVar Detail
NM_000335.5(SCN5A):c.1673A>G (p.His558Arg) AND Cardiac arrhythmia ClinVar Detail
NM_000335.5(SCN5A):c.1673A>G (p.His558Arg) AND multiple conditions ClinVar Detail
NM_000335.5(SCN5A):c.1673A>G (p.His558Arg) AND multiple conditions ClinVar Detail
NM_000335.5(SCN5A):c.1673A>G (p.His558Arg) AND multiple conditions ClinVar Detail
NM_000335.5(SCN5A):c.1673A>G (p.His558Arg) AND multiple conditions ClinVar Detail
NM_000335.5(SCN5A):c.1673A>G (p.His558Arg) AND multiple conditions ClinVar Detail
NM_000335.5(SCN5A):c.1673A>G (p.His558Arg) AND multiple conditions ClinVar Detail
NM_000335.5(SCN5A):c.1673A>G (p.His558Arg) AND multiple conditions ClinVar Detail
NM_000335.5(SCN5A):c.1673A>G (p.His558Arg) AND multiple conditions ClinVar Detail
NM_000335.5(SCN5A):c.1673A>G (p.His558Arg) AND Primary dilated cardiomyopathy ClinVar Detail
NA DisGeNET Detail
Mutation-specific effects of polymorphism H558R in SCN5A-related sick sinus syndrome. DisGeNET Detail
Polymorphism H558R in the human cardiac sodium channel SCN5A gene is associated with atrial fibrilla... DisGeNET Detail
H558R polymorphism in SCN5A is associated with Keshan disease and QRS prolongation in Keshan disease... DisGeNET Detail
To clarify the effects of a common polymorphism in SCN5A gene, H558R, on SCN5A-related SSS phenotype... DisGeNET Detail
SCN5A rare variants in familial dilated cardiomyopathy decrease peak sodium current depending on the... DisGeNET Detail

Overlapped Transcript Coordinates

Gene Transcript ID Exon Number Chromosome Start Stop Type Amino Mutation Transcript Position Links

Overlapped Transcript

Gene Transcript ID Chromosome Start Stop Links
Gene
-
dbSNP
rs1805124 dbSNP
Genome
hg38
Position
chr3:38,603,929-38,603,929
Variant Type
snv
Reference Allele
T
Alternative Allele
C
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1210
Mean of sample read depth (HGVD)
130.09
Standard deviation of sample read depth (HGVD)
60.26
Number of reference allele (HGVD)
2193
Number of alternative allele (HGVD)
227
Allele Frequency (HGVD)
0.09380165289256198
Gene Symbol (HGVD)
SCN5A
ToMMo VCF FILTER column value (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
PASS
Total VCF ID column value (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
rs1805124
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.0972
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
1629
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8604
East Asian Allele Counts (ExAC)
854
East Asian Heterozygous Counts (ExAC)
778
East Asian Homozygous Counts (ExAC)
38
East Asian Allele Frequency (ExAC)
0.099256159925616
Chromosome Counts in All Race (ExAC)
120472
Allele Counts in All Race (ExAC)
26713
Heterozygous Counts in All Race (ExAC)
20427
Homozygous Counts in All Race (ExAC)
3143
Allele Frequency in All Race (ExAC)
0.2217361710604954
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