chr3:38613773:G>A Detail (hg38) (SCN5A)

Information

Genome

Assembly Position
hg19 chr3:38,655,264-38,655,264 View the variant detail on this assembly version.
hg38 chr3:38,613,773-38,613,773

HGVS

Type Transcript Protein
RefSeq NM_000335.4:c.673C>T NP_000326.2:p.Arg225Trp
NM_198056.2:c.673C>T NP_932173.1:p.Arg225Trp
NM_001099404.1:c.703+202C>T
Summary

MGeND

Clinical significance Pathogenic
Variant entry 1
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:[No Data.]
ToMMo:<0.001
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:<0.001

Prediction

ClinVar

Clinical Significance Pathogenic Likely pathogenic
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 tgv12114365 TogoVar
COSMIC COSM2986834 COSMIC
MONDO
Disease area statistics
MGeND
Clinical significance Last evaluated Condition Origin Submission ID Submitter Institute Citation Comment Image
Pathogenic sick sinus syndrome germline MGS000001
(TMGS000174) 		Kenjiro Kosaki Keio University
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
not provided no assertion provided Congenital long QT syndrome germline Detail
Uncertain significance 2014-06-01 no assertion criteria provided Conduction system disorder germline Detail
Pathogenic 2024-01-19 criteria provided, multiple submitters, no conflicts not provided germline Detail
Pathogenic 2017-07-05 criteria provided, multiple submitters, no conflicts long QT syndrome 3 germline unknown Detail
Pathogenic 2023-07-18 criteria provided, single submitter germline Detail
Pathogenic 2023-05-11 criteria provided, single submitter Cardiac arrhythmia germline Detail
Pathogenic 2021-08-17 criteria provided, single submitter long QT syndrome 3,sudden infant death syndrome,Brugada syndrome 1,dilated cardiomyopathy 1E,Sick sinus syndrome 1,Atrial fibrillation, familial, 10,Progressive familial heart block, type 1A,Ventricular fibrillation, paroxysmal familial, type 1 unknown Detail
Pathogenic 2021-08-17 criteria provided, single submitter long QT syndrome 3,sudden infant death syndrome,Brugada syndrome 1,dilated cardiomyopathy 1E,Sick sinus syndrome 1,Atrial fibrillation, familial, 10,Progressive familial heart block, type 1A,Ventricular fibrillation, paroxysmal familial, type 1 unknown Detail
Pathogenic 2021-08-17 criteria provided, single submitter long QT syndrome 3,sudden infant death syndrome,Brugada syndrome 1,dilated cardiomyopathy 1E,Sick sinus syndrome 1,Atrial fibrillation, familial, 10,Progressive familial heart block, type 1A,Ventricular fibrillation, paroxysmal familial, type 1 unknown Detail
Pathogenic 2021-08-17 criteria provided, single submitter long QT syndrome 3,sudden infant death syndrome,Brugada syndrome 1,dilated cardiomyopathy 1E,Sick sinus syndrome 1,Atrial fibrillation, familial, 10,Progressive familial heart block, type 1A,Ventricular fibrillation, paroxysmal familial, type 1 unknown Detail
Pathogenic 2021-08-17 criteria provided, single submitter long QT syndrome 3,sudden infant death syndrome,Brugada syndrome 1,dilated cardiomyopathy 1E,Sick sinus syndrome 1,Atrial fibrillation, familial, 10,Progressive familial heart block, type 1A,Ventricular fibrillation, paroxysmal familial, type 1 unknown Detail
Pathogenic 2021-08-17 criteria provided, single submitter long QT syndrome 3,sudden infant death syndrome,Brugada syndrome 1,dilated cardiomyopathy 1E,Sick sinus syndrome 1,Atrial fibrillation, familial, 10,Progressive familial heart block, type 1A,Ventricular fibrillation, paroxysmal familial, type 1 unknown Detail
Pathogenic 2021-08-17 criteria provided, single submitter long QT syndrome 3,sudden infant death syndrome,Brugada syndrome 1,dilated cardiomyopathy 1E,Sick sinus syndrome 1,Atrial fibrillation, familial, 10,Progressive familial heart block, type 1A,Ventricular fibrillation, paroxysmal familial, type 1 unknown Detail
Pathogenic 2021-08-17 criteria provided, single submitter long QT syndrome 3,sudden infant death syndrome,Brugada syndrome 1,dilated cardiomyopathy 1E,Sick sinus syndrome 1,Atrial fibrillation, familial, 10,Progressive familial heart block, type 1A,Ventricular fibrillation, paroxysmal familial, type 1 unknown Detail
Likely pathogenic 2019-08-16 criteria provided, single submitter SCN5A-related disorder germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.130 Congenital long QT syndrome NA CLINVAR Detail
0.120 CARDIAC CONDUCTION DEFECT, NONSPECIFIC (disorder) NA CLINVAR Detail
Annotation

Annotations

DescrptionSourceLinks
NM_000335.5(SCN5A):c.673C>T (p.Arg225Trp) AND Congenital long QT syndrome ClinVar Detail
NM_000335.5(SCN5A):c.673C>T (p.Arg225Trp) AND Conduction system disorder ClinVar Detail
NM_000335.5(SCN5A):c.673C>T (p.Arg225Trp) AND not provided ClinVar Detail
NM_000335.5(SCN5A):c.673C>T (p.Arg225Trp) AND Long QT syndrome 3 ClinVar Detail
NM_000335.5(SCN5A):c.673C>T (p.Arg225Trp) AND Cardiovascular phenotype ClinVar Detail
NM_000335.5(SCN5A):c.673C>T (p.Arg225Trp) AND Cardiac arrhythmia ClinVar Detail
NM_000335.5(SCN5A):c.673C>T (p.Arg225Trp) AND multiple conditions ClinVar Detail
NM_000335.5(SCN5A):c.673C>T (p.Arg225Trp) AND multiple conditions ClinVar Detail
NM_000335.5(SCN5A):c.673C>T (p.Arg225Trp) AND multiple conditions ClinVar Detail
NM_000335.5(SCN5A):c.673C>T (p.Arg225Trp) AND multiple conditions ClinVar Detail
NM_000335.5(SCN5A):c.673C>T (p.Arg225Trp) AND multiple conditions ClinVar Detail
NM_000335.5(SCN5A):c.673C>T (p.Arg225Trp) AND multiple conditions ClinVar Detail
NM_000335.5(SCN5A):c.673C>T (p.Arg225Trp) AND multiple conditions ClinVar Detail
NM_000335.5(SCN5A):c.673C>T (p.Arg225Trp) AND multiple conditions ClinVar Detail
NM_000335.5(SCN5A):c.673C>T (p.Arg225Trp) AND SCN5A-related disorder ClinVar Detail
NA DisGeNET Detail
NA 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
rs199473072 dbSNP
Genome
hg38
Position
chr3:38,613,773-38,613,773
Variant Type
snv
Reference Allele
G
Alternative Allele
A
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))
rs199473072
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.0001
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
1
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
5134
East Asian Allele Counts (ExAC)
0
East Asian Heterozygous Counts (ExAC)
0
East Asian Homozygous Counts (ExAC)
0
East Asian Allele Frequency (ExAC)
0.0
Chromosome Counts in All Race (ExAC)
70176
Allele Counts in All Race (ExAC)
1
Heterozygous Counts in All Race (ExAC)
1
Homozygous Counts in All Race (ExAC)
0
Allele Frequency in All Race (ExAC)
1.4249886000911993E-5
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