chr3:38616876:C>T Detail (hg19) (SCN5A)

Information

Genome

Assembly Position
hg19 chr3:38,616,876-38,616,876
hg38 chr3:38,575,385-38,575,385 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_001099404.1:c.3578G>A NP_001092874.1:p.Arg1193Gln
NM_001160160.1:c.3578G>A NP_001153632.1:p.Arg1193Gln
NM_000335.4:c.3578G>A NP_000326.2:p.Arg1193Gln
Summary

MGeND

Clinical significance Pathogenic
Variant entry 2
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.060
ToMMo:0.063
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.071

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 tgv12112572 TogoVar
COSMIC
MONDO
Disease area statistics
MGeND
Clinical significance Last evaluated Condition Origin Submission ID Submitter Institute Citation Comment Image
Pathogenic other germline MGS000001
(TMGS000154) 		Kenjiro Kosaki Keio University
Pathogenic other germline MGS000001
(TMGS000174) 		Kenjiro Kosaki Keio University
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2018-03-06 criteria provided, single submitter Brugada syndrome 1 germline Detail
risk factor 2006-10-01 no assertion criteria provided Long QT syndrome 3, acquired, susceptibility to germline Detail
Benign Likely benign 2024-02-01 criteria provided, multiple submitters, no conflicts not provided germline Detail
Benign Likely benign 2016-12-28 criteria provided, multiple submitters, no conflicts not specified germline Detail
Uncertain significance 2014-04-17 no assertion criteria provided Primary familial hypertrophic cardiomyopathy germline Detail
Benign 2013-06-24 criteria provided, single submitter Brugada syndrome unknown Detail
Benign 2016-02-01 criteria provided, single submitter germline Detail
Benign 2018-11-21 criteria provided, multiple submitters, no conflicts long QT syndrome 3 germline unknown Detail
Likely benign 2018-03-06 criteria provided, single submitter Progressive familial heart block, type 1A germline Detail
Benign 2018-03-06 criteria provided, single submitter Sick sinus syndrome 1 germline Detail
Benign 2018-03-06 criteria provided, single submitter Ventricular fibrillation, paroxysmal familial, type 1 germline Detail
Likely benign 2018-03-06 criteria provided, single submitter dilated cardiomyopathy 1E germline Detail
Benign 2018-03-15 criteria provided, single submitter Cardiac arrhythmia germline Detail
Benign 2021-10-21 criteria provided, single submitter long QT syndrome 3,sudden infant death syndrome,Brugada syndrome 1,dilated cardiomyopathy 1E,Progressive familial heart block, type 1A,Atrial fibrillation, familial, 10,Sick sinus syndrome 1,Ventricular fibrillation, paroxysmal familial, type 1 unknown Detail
Benign 2021-10-21 criteria provided, single submitter long QT syndrome 3,sudden infant death syndrome,Brugada syndrome 1,dilated cardiomyopathy 1E,Progressive familial heart block, type 1A,Atrial fibrillation, familial, 10,Sick sinus syndrome 1,Ventricular fibrillation, paroxysmal familial, type 1 unknown Detail
Benign 2021-10-21 criteria provided, single submitter long QT syndrome 3,sudden infant death syndrome,Brugada syndrome 1,dilated cardiomyopathy 1E,Progressive familial heart block, type 1A,Atrial fibrillation, familial, 10,Sick sinus syndrome 1,Ventricular fibrillation, paroxysmal familial, type 1 unknown Detail
Benign 2021-10-21 criteria provided, single submitter long QT syndrome 3,sudden infant death syndrome,Brugada syndrome 1,dilated cardiomyopathy 1E,Progressive familial heart block, type 1A,Atrial fibrillation, familial, 10,Sick sinus syndrome 1,Ventricular fibrillation, paroxysmal familial, type 1 unknown Detail
Benign 2021-10-21 criteria provided, single submitter long QT syndrome 3,sudden infant death syndrome,Brugada syndrome 1,dilated cardiomyopathy 1E,Progressive familial heart block, type 1A,Atrial fibrillation, familial, 10,Sick sinus syndrome 1,Ventricular fibrillation, paroxysmal familial, type 1 unknown Detail
Benign 2021-10-21 criteria provided, single submitter long QT syndrome 3,sudden infant death syndrome,Brugada syndrome 1,dilated cardiomyopathy 1E,Progressive familial heart block, type 1A,Atrial fibrillation, familial, 10,Sick sinus syndrome 1,Ventricular fibrillation, paroxysmal familial, type 1 unknown Detail
Benign 2021-10-21 criteria provided, single submitter long QT syndrome 3,sudden infant death syndrome,Brugada syndrome 1,dilated cardiomyopathy 1E,Progressive familial heart block, type 1A,Atrial fibrillation, familial, 10,Sick sinus syndrome 1,Ventricular fibrillation, paroxysmal familial, type 1 unknown Detail
Benign 2021-10-21 criteria provided, single submitter long QT syndrome 3,sudden infant death syndrome,Brugada syndrome 1,dilated cardiomyopathy 1E,Progressive familial heart block, type 1A,Atrial fibrillation, familial, 10,Sick sinus syndrome 1,Ventricular fibrillation, paroxysmal familial, type 1 unknown Detail
Benign 2021-09-15 criteria provided, single submitter cardiomyopathy germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.837 Brugada Syndrome (disorder) NA CLINVAR Detail
0.120 Cardiomyopathy, Hypertrophic, Familial NA CLINVAR Detail
0.837 Brugada Syndrome (disorder) We screened patients with SUNDS for mutations in SCN5A, the gene known to cause ... UNIPROT 11823453 Detail
0.008 Channelopathies We report a Korean case of an overlap syndrome of cardiac sodium channelopathy w... BeFree 22519808 Detail
0.837 Brugada Syndrome (disorder) DNA analysis revealed a missense mutation (R1193Q) in the SCN5A gene, previously... BeFree 15851440 Detail
0.133 Cardiomyopathy, Dilated Long QT syndrome and dilated cardiomyopathy with SCN5A p.R1193Q polymorphism: ca... BeFree 22519808 Detail
0.335 long QT syndrome It was reported that the R1193Q polymorphism in the SCN5A gene destabilizes chan... BeFree 22682427 Detail
<0.001 Sudden unexpected nocturnal death syndrome An autopsy case of sudden unexpected nocturnal death syndrome with R1193Q polymo... BeFree 22682427 Detail
0.440 long QT syndrome 3 Genetic and biophysical basis of sudden unexplained nocturnal death syndrome (SU... UNIPROT 11823453 Detail
0.120 LONG QT SYNDROME 3, ACQUIRED, SUSCEPTIBILITY TO (finding) NA CLINVAR Detail
<0.001 Sudden unexpected nocturnal death syndrome DNA analysis revealed a missense mutation (R1193Q) in the SCN5A gene, previously... BeFree 15851440 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_000335.5(SCN5A):c.3575G>A (p.Arg1192Gln) AND Brugada syndrome 1 ClinVar Detail
NM_000335.5(SCN5A):c.3575G>A (p.Arg1192Gln) AND Long QT syndrome 3, acquired, susceptibility to ClinVar Detail
NM_000335.5(SCN5A):c.3575G>A (p.Arg1192Gln) AND not provided ClinVar Detail
NM_000335.5(SCN5A):c.3575G>A (p.Arg1192Gln) AND not specified ClinVar Detail
NM_000335.5(SCN5A):c.3575G>A (p.Arg1192Gln) AND Primary familial hypertrophic cardiomyopathy ClinVar Detail
NM_000335.5(SCN5A):c.3575G>A (p.Arg1192Gln) AND Brugada syndrome ClinVar Detail
NM_000335.5(SCN5A):c.3575G>A (p.Arg1192Gln) AND Cardiovascular phenotype ClinVar Detail
NM_000335.5(SCN5A):c.3575G>A (p.Arg1192Gln) AND Long QT syndrome 3 ClinVar Detail
NM_000335.5(SCN5A):c.3575G>A (p.Arg1192Gln) AND Progressive familial heart block, type 1A ClinVar Detail
NM_000335.5(SCN5A):c.3575G>A (p.Arg1192Gln) AND Sick sinus syndrome 1 ClinVar Detail
NM_000335.5(SCN5A):c.3575G>A (p.Arg1192Gln) AND Ventricular fibrillation, paroxysmal familial, type ... ClinVar Detail
NM_000335.5(SCN5A):c.3575G>A (p.Arg1192Gln) AND Dilated cardiomyopathy 1E ClinVar Detail
NM_000335.5(SCN5A):c.3575G>A (p.Arg1192Gln) AND Cardiac arrhythmia ClinVar Detail
NM_000335.5(SCN5A):c.3575G>A (p.Arg1192Gln) AND multiple conditions ClinVar Detail
NM_000335.5(SCN5A):c.3575G>A (p.Arg1192Gln) AND multiple conditions ClinVar Detail
NM_000335.5(SCN5A):c.3575G>A (p.Arg1192Gln) AND multiple conditions ClinVar Detail
NM_000335.5(SCN5A):c.3575G>A (p.Arg1192Gln) AND multiple conditions ClinVar Detail
NM_000335.5(SCN5A):c.3575G>A (p.Arg1192Gln) AND multiple conditions ClinVar Detail
NM_000335.5(SCN5A):c.3575G>A (p.Arg1192Gln) AND multiple conditions ClinVar Detail
NM_000335.5(SCN5A):c.3575G>A (p.Arg1192Gln) AND multiple conditions ClinVar Detail
NM_000335.5(SCN5A):c.3575G>A (p.Arg1192Gln) AND multiple conditions ClinVar Detail
NM_000335.5(SCN5A):c.3575G>A (p.Arg1192Gln) AND Cardiomyopathy ClinVar Detail
NA DisGeNET Detail
NA DisGeNET Detail
We screened patients with SUNDS for mutations in SCN5A, the gene known to cause Brugada syndrome, as... DisGeNET Detail
We report a Korean case of an overlap syndrome of cardiac sodium channelopathy with SCN5A p.R1193Q p... DisGeNET Detail
DNA analysis revealed a missense mutation (R1193Q) in the SCN5A gene, previously linked with familia... DisGeNET Detail
Long QT syndrome and dilated cardiomyopathy with SCN5A p.R1193Q polymorphism: cardioverter-defibrill... DisGeNET Detail
It was reported that the R1193Q polymorphism in the SCN5A gene destabilizes channel inactivation and... DisGeNET Detail
An autopsy case of sudden unexpected nocturnal death syndrome with R1193Q polymorphism in the SCN5A ... DisGeNET Detail
Genetic and biophysical basis of sudden unexplained nocturnal death syndrome (SUNDS), a disease alle... DisGeNET Detail
NA DisGeNET Detail
DNA analysis revealed a missense mutation (R1193Q) in the SCN5A gene, previously linked with familia... 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
rs41261344 dbSNP
Genome
hg19
Position
chr3:38,616,876-38,616,876
Variant Type
snv
Reference Allele
C
Alternative Allele
T
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1207
Mean of sample read depth (HGVD)
65.58
Standard deviation of sample read depth (HGVD)
32.06
Number of reference allele (HGVD)
2269
Number of alternative allele (HGVD)
145
Allele Frequency (HGVD)
0.06006628003314002
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))
rs41261344
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.0629
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
1054
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
6498
East Asian Allele Counts (ExAC)
461
East Asian Heterozygous Counts (ExAC)
427
East Asian Homozygous Counts (ExAC)
17
East Asian Allele Frequency (ExAC)
0.07094490612496153
Chromosome Counts in All Race (ExAC)
87204
Allele Counts in All Race (ExAC)
542
Heterozygous Counts in All Race (ExAC)
508
Homozygous Counts in All Race (ExAC)
17
Allele Frequency in All Race (ExAC)
0.006215311224255768
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