chr3:38551513:G>A Detail (hg38) (SCN5A)

Information

Genome

Assembly Position
hg19 chr3:38,593,004-38,593,004 View the variant detail on this assembly version.
hg38 chr3:38,551,513-38,551,513

HGVS

Type Transcript Protein
RefSeq NM_000335.4:c.4859C>T NP_000326.2:p.Thr1620Met
NM_198056.2:c.4859C>T NP_932173.1:p.Thr1620Met
NM_001099404.1:c.4859C>T NP_001092874.1:p.Thr1620Met
Summary

MGeND

Clinical significance
Variant entry
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 tgv12111606 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Pathogenic 2000-01-04 no assertion criteria provided Brugada syndrome 1 germline Detail
not provided criteria provided, single submitter Brugada syndrome germline Detail
Likely pathogenic 2022-06-15 criteria provided, single submitter Brugada syndrome 1 germline Detail
Pathogenic Likely pathogenic 2024-01-08 criteria provided, multiple submitters, no conflicts not provided germline Detail
Likely pathogenic 2021-09-28 criteria provided, single submitter Cardiac arrhythmia germline Detail
Likely pathogenic 2021-07-01 criteria provided, single submitter Brugada syndrome 1,Atrial fibrillation, familial, 10,sudden infant death syndrome,Sick sinus syndrome 1,Ventricular fibrillation, paroxysmal familial, type 1,dilated cardiomyopathy 1E,long QT syndrome 3,Progressive familial heart block, type 1A unknown Detail
Likely pathogenic 2021-07-01 criteria provided, single submitter Brugada syndrome 1,Atrial fibrillation, familial, 10,sudden infant death syndrome,Sick sinus syndrome 1,Ventricular fibrillation, paroxysmal familial, type 1,dilated cardiomyopathy 1E,long QT syndrome 3,Progressive familial heart block, type 1A unknown Detail
Likely pathogenic 2021-07-01 criteria provided, single submitter Brugada syndrome 1,Atrial fibrillation, familial, 10,sudden infant death syndrome,Sick sinus syndrome 1,Ventricular fibrillation, paroxysmal familial, type 1,dilated cardiomyopathy 1E,long QT syndrome 3,Progressive familial heart block, type 1A unknown Detail
Likely pathogenic 2021-07-01 criteria provided, single submitter Brugada syndrome 1,Atrial fibrillation, familial, 10,sudden infant death syndrome,Sick sinus syndrome 1,Ventricular fibrillation, paroxysmal familial, type 1,dilated cardiomyopathy 1E,long QT syndrome 3,Progressive familial heart block, type 1A unknown Detail
Likely pathogenic 2021-07-01 criteria provided, single submitter Brugada syndrome 1,Atrial fibrillation, familial, 10,sudden infant death syndrome,Sick sinus syndrome 1,Ventricular fibrillation, paroxysmal familial, type 1,dilated cardiomyopathy 1E,long QT syndrome 3,Progressive familial heart block, type 1A unknown Detail
Likely pathogenic 2021-07-01 criteria provided, single submitter Brugada syndrome 1,Atrial fibrillation, familial, 10,sudden infant death syndrome,Sick sinus syndrome 1,Ventricular fibrillation, paroxysmal familial, type 1,dilated cardiomyopathy 1E,long QT syndrome 3,Progressive familial heart block, type 1A unknown Detail
Likely pathogenic 2021-07-01 criteria provided, single submitter Brugada syndrome 1,Atrial fibrillation, familial, 10,sudden infant death syndrome,Sick sinus syndrome 1,Ventricular fibrillation, paroxysmal familial, type 1,dilated cardiomyopathy 1E,long QT syndrome 3,Progressive familial heart block, type 1A unknown Detail
Likely pathogenic 2021-07-01 criteria provided, single submitter Brugada syndrome 1,Atrial fibrillation, familial, 10,sudden infant death syndrome,Sick sinus syndrome 1,Ventricular fibrillation, paroxysmal familial, type 1,dilated cardiomyopathy 1E,long QT syndrome 3,Progressive familial heart block, type 1A unknown Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.837 Brugada Syndrome (disorder) NA CLINVAR Detail
0.120 CARDIAC CONDUCTION DEFECT, NONSPECIFIC (disorder) NA CLINVAR Detail
0.837 Brugada Syndrome (disorder) Absence of a trafficking defect in R1232W/T1620M, a double SCN5A mutant responsi... BeFree 18503232 Detail
0.837 Brugada Syndrome (disorder) Expression and intracellular localization of an SCN5A double mutant R1232W/T1620... BeFree 11786529 Detail
0.837 Brugada Syndrome (disorder) SCN5A mutation (T1620M) causing Brugada syndrome exhibits different phenotypes w... BeFree 10664447 Detail
0.837 Brugada Syndrome (disorder) The biophysical properties of the SCN5A mutation T1620M associated with Brugada ... BeFree 11029409 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_198056.2(SCN5A):c.[3694C>T;4859C>T] AND Brugada syndrome 1 ClinVar Detail
NM_000335.5(SCN5A):c.4856C>T (p.Thr1619Met) AND Brugada syndrome ClinVar Detail
NM_000335.5(SCN5A):c.4856C>T (p.Thr1619Met) AND Brugada syndrome 1 ClinVar Detail
NM_000335.5(SCN5A):c.4856C>T (p.Thr1619Met) AND not provided ClinVar Detail
NM_000335.5(SCN5A):c.4856C>T (p.Thr1619Met) AND Cardiac arrhythmia ClinVar Detail
NM_000335.5(SCN5A):c.4856C>T (p.Thr1619Met) AND multiple conditions ClinVar Detail
NM_000335.5(SCN5A):c.4856C>T (p.Thr1619Met) AND multiple conditions ClinVar Detail
NM_000335.5(SCN5A):c.4856C>T (p.Thr1619Met) AND multiple conditions ClinVar Detail
NM_000335.5(SCN5A):c.4856C>T (p.Thr1619Met) AND multiple conditions ClinVar Detail
NM_000335.5(SCN5A):c.4856C>T (p.Thr1619Met) AND multiple conditions ClinVar Detail
NM_000335.5(SCN5A):c.4856C>T (p.Thr1619Met) AND multiple conditions ClinVar Detail
NM_000335.5(SCN5A):c.4856C>T (p.Thr1619Met) AND multiple conditions ClinVar Detail
NM_000335.5(SCN5A):c.4856C>T (p.Thr1619Met) AND multiple conditions ClinVar Detail
NA DisGeNET Detail
NA DisGeNET Detail
Absence of a trafficking defect in R1232W/T1620M, a double SCN5A mutant responsible for Brugada synd... DisGeNET Detail
Expression and intracellular localization of an SCN5A double mutant R1232W/T1620M implicated in Brug... DisGeNET Detail
SCN5A mutation (T1620M) causing Brugada syndrome exhibits different phenotypes when expressed in Xen... DisGeNET Detail
The biophysical properties of the SCN5A mutation T1620M associated with Brugada syndrome were examin... 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
rs199473282 dbSNP
Genome
hg38
Position
chr3:38,551,513-38,551,513
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))
rs199473282
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))
2
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16758
East Asian Chromosome Counts (ExAC)
8638
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)
120994
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)
8.264872638312644E-6
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