chr3:38550362:A>C Detail (hg38) (SCN5A)

Information

Genome

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

HGVS

Type Transcript Protein
RefSeq NM_000335.4:c.6010T>G NP_000326.2:p.Phe2004Val
NM_198056.2:c.6010T>G NP_932173.1:p.Phe2004Val
NM_001099404.1:c.6010T>G NP_001092874.1:p.Phe2004Val
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

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

Prediction

ClinVar

Clinical Significance Conflicting classifications of pathogenicity
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
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
not provided no assertion provided Congenital long QT syndrome germline Detail
Benign 2017-09-15 criteria provided, single submitter dilated cardiomyopathy 1E germline Detail
Uncertain significance 2017-09-15 criteria provided, single submitter Progressive familial heart block, type 1A germline Detail
Uncertain significance 2017-09-15 criteria provided, single submitter Ventricular fibrillation, paroxysmal familial, type 1 germline Detail
Benign 2017-09-15 criteria provided, single submitter Brugada syndrome 1 germline Detail
Uncertain significance 2017-09-15 criteria provided, single submitter Sick sinus syndrome 1 germline Detail
Benign 2017-09-15 criteria provided, single submitter long QT syndrome 3 germline Detail
Uncertain significance 2024-02-05 criteria provided, multiple submitters, no conflicts Cardiac arrhythmia germline Detail
Likely benign 2023-12-22 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>G (p.Phe2003Val) AND Congenital long QT syndrome ClinVar Detail
NM_000335.5(SCN5A):c.6007T>G (p.Phe2003Val) AND Dilated cardiomyopathy 1E ClinVar Detail
NM_000335.5(SCN5A):c.6007T>G (p.Phe2003Val) AND Progressive familial heart block, type 1A ClinVar Detail
NM_000335.5(SCN5A):c.6007T>G (p.Phe2003Val) AND Ventricular fibrillation, paroxysmal familial, type ... ClinVar Detail
NM_000335.5(SCN5A):c.6007T>G (p.Phe2003Val) AND Brugada syndrome 1 ClinVar Detail
NM_000335.5(SCN5A):c.6007T>G (p.Phe2003Val) AND Sick sinus syndrome 1 ClinVar Detail
NM_000335.5(SCN5A):c.6007T>G (p.Phe2003Val) AND Long QT syndrome 3 ClinVar Detail
NM_000335.5(SCN5A):c.6007T>G (p.Phe2003Val) AND Cardiac arrhythmia ClinVar Detail
NM_000335.5(SCN5A):c.6007T>G (p.Phe2003Val) 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
hg38
Position
chr3:38,550,362-38,550,362
Variant Type
snv
Reference Allele
A
Alternative Allele
C
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)
3
Heterozygous Counts in All Race (ExAC)
3
Homozygous Counts in All Race (ExAC)
0
Allele Frequency in All Race (ExAC)
2.7513848637147363E-5
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