chr3:38562467:G>A Detail (hg38) (SCN5A)

Information

Genome

Assembly Position
hg19 chr3:38,603,958-38,603,958 View the variant detail on this assembly version.
hg38 chr3:38,562,467-38,562,467

HGVS

Type Transcript Protein
RefSeq NM_000335.4:c.3911C>T NP_000326.2:p.Thr1304Met
NM_198056.2:c.3911C>T NP_932173.1:p.Thr1304Met
NM_001099404.1:c.3911C>T NP_001092874.1:p.Thr1304Met
Summary

MGeND

Clinical significance Pathogenic
Variant entry 1
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 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 tgv317582266 TogoVar
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
no classifications from unflagged records 2023-12-07 no classifications from unflagged records long QT syndrome germline Detail
no classifications from unflagged records 2023-12-07 no classifications from unflagged records Brugada syndrome germline Detail
Uncertain significance 2024-01-04 criteria provided, single submitter long QT syndrome 3 maternal unknown Detail
Uncertain significance 2024-01-04 criteria provided, single submitter germline Detail
Uncertain significance 2024-01-31 criteria provided, multiple submitters, no conflicts not provided germline Detail
Uncertain significance 2018-04-26 criteria provided, single submitter not specified germline Detail
Uncertain significance 2020-05-14 criteria provided, multiple submitters, no conflicts Brugada syndrome 1 germline maternal unknown Detail
Uncertain significance 2020-01-17 criteria provided, single submitter Conduction disorder of the heart maternal Detail
Uncertain significance 2023-12-04 criteria provided, single submitter Cardiac arrhythmia germline Detail
Uncertain significance 2024-01-12 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
0.335 long QT syndrome NA CLINVAR Detail
0.335 long QT syndrome Five variants (S216L, T1304M, F1486L, F2004L, and P2006A) exhibited significantl... BeFree 17210841 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_000335.5(SCN5A):c.3908C>T (p.Thr1303Met) AND Congenital long QT syndrome ClinVar Detail
NM_000335.5(SCN5A):c.3908C>T (p.Thr1303Met) AND Long QT syndrome ClinVar Detail
NM_000335.5(SCN5A):c.3908C>T (p.Thr1303Met) AND Brugada syndrome ClinVar Detail
NM_000335.5(SCN5A):c.3908C>T (p.Thr1303Met) AND Long QT syndrome 3 ClinVar Detail
NM_000335.5(SCN5A):c.3908C>T (p.Thr1303Met) AND Cardiovascular phenotype ClinVar Detail
NM_000335.5(SCN5A):c.3908C>T (p.Thr1303Met) AND not provided ClinVar Detail
NM_000335.5(SCN5A):c.3908C>T (p.Thr1303Met) AND not specified ClinVar Detail
NM_000335.5(SCN5A):c.3908C>T (p.Thr1303Met) AND Brugada syndrome 1 ClinVar Detail
NM_000335.5(SCN5A):c.3908C>T (p.Thr1303Met) AND Conduction disorder of the heart ClinVar Detail
NM_000335.5(SCN5A):c.3908C>T (p.Thr1303Met) AND Cardiac arrhythmia ClinVar Detail
NM_000335.5(SCN5A):c.3908C>T (p.Thr1303Met) AND SCN5A-related disorder ClinVar Detail
NA DisGeNET Detail
NA DisGeNET Detail
Five variants (S216L, T1304M, F1486L, F2004L, and P2006A) exhibited significantly increased persiste... 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
rs199473603 dbSNP
Genome
hg38
Position
chr3:38,562,467-38,562,467
Variant Type
snv
Reference Allele
G
Alternative Allele
A
East Asian Chromosome Counts (ExAC)
7802
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)
106676
Allele Counts in All Race (ExAC)
24
Heterozygous Counts in All Race (ExAC)
24
Homozygous Counts in All Race (ExAC)
0
Allele Frequency in All Race (ExAC)
2.2498031422250552E-4
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