chr3:38591853:A>T Detail (hg19) (SCN5A)

Information

Genome

Assembly Position
hg19 chr3:38,591,853-38,591,853
hg38 chr3:38,550,362-38,550,362 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_000335.4:c.6010T>A NP_000326.2:p.Phe2004Ile
NM_198056.2:c.6010T>A NP_932173.1:p.Phe2004Ile
NM_001099404.1:c.6010T>A NP_001092874.1:p.Phe2004Ile
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 Uncertain significance
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 tgv12111253 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Uncertain significance 2023-10-02 criteria provided, multiple submitters, no conflicts Cardiac arrhythmia germline Detail
Uncertain significance 2022-07-13 criteria provided, single submitter germline Detail
Uncertain significance 2021-10-12 criteria provided, single submitter dilated cardiomyopathy 1E,Progressive familial heart block, type 1A,Atrial fibrillation, familial, 10,Brugada syndrome 1,long QT syndrome 3,sudden infant death syndrome,Ventricular fibrillation, paroxysmal familial, type 1,Sick sinus syndrome 1 unknown Detail
Uncertain significance 2021-10-12 criteria provided, single submitter dilated cardiomyopathy 1E,Progressive familial heart block, type 1A,Atrial fibrillation, familial, 10,Brugada syndrome 1,long QT syndrome 3,sudden infant death syndrome,Ventricular fibrillation, paroxysmal familial, type 1,Sick sinus syndrome 1 unknown Detail
Uncertain significance 2021-10-12 criteria provided, single submitter dilated cardiomyopathy 1E,Progressive familial heart block, type 1A,Atrial fibrillation, familial, 10,Brugada syndrome 1,long QT syndrome 3,sudden infant death syndrome,Ventricular fibrillation, paroxysmal familial, type 1,Sick sinus syndrome 1 unknown Detail
Uncertain significance 2021-10-12 criteria provided, single submitter dilated cardiomyopathy 1E,Progressive familial heart block, type 1A,Atrial fibrillation, familial, 10,Brugada syndrome 1,long QT syndrome 3,sudden infant death syndrome,Ventricular fibrillation, paroxysmal familial, type 1,Sick sinus syndrome 1 unknown Detail
Uncertain significance 2021-10-12 criteria provided, single submitter dilated cardiomyopathy 1E,Progressive familial heart block, type 1A,Atrial fibrillation, familial, 10,Brugada syndrome 1,long QT syndrome 3,sudden infant death syndrome,Ventricular fibrillation, paroxysmal familial, type 1,Sick sinus syndrome 1 unknown Detail
Uncertain significance 2021-10-12 criteria provided, single submitter dilated cardiomyopathy 1E,Progressive familial heart block, type 1A,Atrial fibrillation, familial, 10,Brugada syndrome 1,long QT syndrome 3,sudden infant death syndrome,Ventricular fibrillation, paroxysmal familial, type 1,Sick sinus syndrome 1 unknown Detail
Uncertain significance 2021-10-12 criteria provided, single submitter dilated cardiomyopathy 1E,Progressive familial heart block, type 1A,Atrial fibrillation, familial, 10,Brugada syndrome 1,long QT syndrome 3,sudden infant death syndrome,Ventricular fibrillation, paroxysmal familial, type 1,Sick sinus syndrome 1 unknown Detail
Uncertain significance 2021-10-12 criteria provided, single submitter dilated cardiomyopathy 1E,Progressive familial heart block, type 1A,Atrial fibrillation, familial, 10,Brugada syndrome 1,long QT syndrome 3,sudden infant death syndrome,Ventricular fibrillation, paroxysmal familial, type 1,Sick sinus syndrome 1 unknown Detail
Uncertain significance 2023-12-03 criteria provided, single submitter not provided germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.335 long QT syndrome In contrast, in 6 of 60 women (10%), we identified 5 rare missense variants in S... BeFree 18071069 Detail
0.130 Congenital long QT syndrome NA CLINVAR Detail
0.335 long QT syndrome Five variants (S216L, T1304M, F1486L, F2004L, and P2006A) exhibited significantl... BeFree 17210841 Detail
0.440 long QT syndrome 3 Cardiac sodium channel (SCN5A) variants associated with atrial fibrillation. UNIPROT 18378609 Detail
0.837 Brugada Syndrome (disorder) Cardiac sodium channel (SCN5A) variants associated with atrial fibrillation. UNIPROT 18378609 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_000335.5(SCN5A):c.6007T>A (p.Phe2003Ile) AND Cardiac arrhythmia ClinVar Detail
NM_000335.5(SCN5A):c.6007T>A (p.Phe2003Ile) AND Cardiovascular phenotype ClinVar Detail
NM_000335.5(SCN5A):c.6007T>A (p.Phe2003Ile) AND multiple conditions ClinVar Detail
NM_000335.5(SCN5A):c.6007T>A (p.Phe2003Ile) AND multiple conditions ClinVar Detail
NM_000335.5(SCN5A):c.6007T>A (p.Phe2003Ile) AND multiple conditions ClinVar Detail
NM_000335.5(SCN5A):c.6007T>A (p.Phe2003Ile) AND multiple conditions ClinVar Detail
NM_000335.5(SCN5A):c.6007T>A (p.Phe2003Ile) AND multiple conditions ClinVar Detail
NM_000335.5(SCN5A):c.6007T>A (p.Phe2003Ile) AND multiple conditions ClinVar Detail
NM_000335.5(SCN5A):c.6007T>A (p.Phe2003Ile) AND multiple conditions ClinVar Detail
NM_000335.5(SCN5A):c.6007T>A (p.Phe2003Ile) AND multiple conditions ClinVar Detail
NM_000335.5(SCN5A):c.6007T>A (p.Phe2003Ile) AND not provided ClinVar Detail
In contrast, in 6 of 60 women (10%), we identified 5 rare missense variants in SCN5A that either had... DisGeNET Detail
NA DisGeNET Detail
Five variants (S216L, T1304M, F1486L, F2004L, and P2006A) exhibited significantly increased persiste... DisGeNET Detail
Cardiac sodium channel (SCN5A) variants associated with atrial fibrillation. DisGeNET Detail
Cardiac sodium channel (SCN5A) variants associated with atrial fibrillation. 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
rs41311117 dbSNP
Genome
hg19
Position
chr3:38,591,853-38,591,853
Variant Type
snv
Reference Allele
A
Alternative Allele
T
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))
rs41311117
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)
8476
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)
109036
Allele Counts in All Race (ExAC)
2
Heterozygous Counts in All Race (ExAC)
2
Homozygous Counts in All Race (ExAC)
0
Allele Frequency in All Race (ExAC)
1.8342565758098242E-5
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