chr3:38613787:G>A Detail (hg38) (SCN5A)

Information

Genome

Assembly Position
hg19 chr3:38,655,278-38,655,278 View the variant detail on this assembly version.
hg38 chr3:38,613,787-38,613,787

HGVS

Type Transcript Protein
RefSeq NM_000335.4:c.659C>T NP_000326.2:p.Thr220Ile
NM_198056.2:c.659C>T NP_932173.1:p.Thr220Ile
NM_001099404.1:c.703+188C>T
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 tgv317584133 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Pathogenic 2005-01-26 no assertion criteria provided Sick sinus syndrome 1 germline Detail
not provided criteria provided, single submitter Brugada syndrome germline Detail
Uncertain significance 2014-06-01 no assertion criteria provided AV junctional rhythm germline Detail
Likely benign 2024-01-30 criteria provided, multiple submitters, no conflicts not specified germline Detail
Likely benign 2021-05-18 criteria provided, single submitter germline Detail
Pathogenic 2005-01-26 no assertion criteria provided dilated cardiomyopathy 1E germline Detail
Conflicting interpretations of pathogenicity 2024-01-27 criteria provided, conflicting interpretations not provided germline Detail
Uncertain significance 2017-04-21 criteria provided, single submitter Primary familial dilated cardiomyopathy germline Detail
Uncertain significance 2018-02-17 criteria provided, single submitter long QT syndrome 3 unknown Detail
Likely benign 2018-08-31 criteria provided, single submitter Cardiac arrhythmia germline Detail
Uncertain significance 2017-04-27 criteria provided, single submitter SCN5A-related disorder germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.837 Brugada Syndrome (disorder) NA CLINVAR Detail
0.360 CARDIOMYOPATHY, DILATED, 1E NA CLINVAR Detail
0.010 Heart Diseases In the DCM cohort, additional missense (T220I, R814W, D1595H) and truncation (25... BeFree 15671429 Detail
0.360 SICK SINUS SYNDROME 1, AUTOSOMAL RECESSIVE NA CLINVAR Detail
0.360 SICK SINUS SYNDROME 1, AUTOSOMAL RECESSIVE Congenital sick sinus syndrome caused by recessive mutations in the cardiac sodi... UNIPROT 14523039 Detail
0.837 Brugada Syndrome (disorder) Congenital sick sinus syndrome caused by recessive mutations in the cardiac sodi... UNIPROT 14523039 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_000335.5(SCN5A):c.659C>T (p.Thr220Ile) AND Sick sinus syndrome 1 ClinVar Detail
NM_000335.5(SCN5A):c.659C>T (p.Thr220Ile) AND Brugada syndrome ClinVar Detail
NM_000335.5(SCN5A):c.659C>T (p.Thr220Ile) AND AV junctional rhythm ClinVar Detail
NM_000335.5(SCN5A):c.659C>T (p.Thr220Ile) AND not specified ClinVar Detail
NM_000335.5(SCN5A):c.659C>T (p.Thr220Ile) AND Cardiovascular phenotype ClinVar Detail
NM_000335.5(SCN5A):c.659C>T (p.Thr220Ile) AND Dilated cardiomyopathy 1E ClinVar Detail
NM_000335.5(SCN5A):c.659C>T (p.Thr220Ile) AND not provided ClinVar Detail
NM_000335.5(SCN5A):c.659C>T (p.Thr220Ile) AND Primary familial dilated cardiomyopathy ClinVar Detail
NM_000335.5(SCN5A):c.659C>T (p.Thr220Ile) AND Long QT syndrome 3 ClinVar Detail
NM_000335.5(SCN5A):c.659C>T (p.Thr220Ile) AND Cardiac arrhythmia ClinVar Detail
NM_000335.5(SCN5A):c.659C>T (p.Thr220Ile) AND SCN5A-related disorder ClinVar Detail
NA DisGeNET Detail
NA DisGeNET Detail
In the DCM cohort, additional missense (T220I, R814W, D1595H) and truncation (2550-2551insTG) SCN5A ... DisGeNET Detail
NA DisGeNET Detail
Congenital sick sinus syndrome caused by recessive mutations in the cardiac sodium channel gene (SCN... DisGeNET Detail
Congenital sick sinus syndrome caused by recessive mutations in the cardiac sodium channel gene (SCN... 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
rs45620037 dbSNP
Genome
hg38
Position
chr3:38,613,787-38,613,787
Variant Type
snv
Reference Allele
G
Alternative Allele
A
Homozygous Counts in All Race (ExAC)
0
East Asian Chromosome Counts (ExAC)
5706
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)
77106
Allele Counts in All Race (ExAC)
78
Heterozygous Counts in All Race (ExAC)
78
Allele Frequency in All Race (ExAC)
0.001011594428449148
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