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

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Summary
Information
Links
Disease area statistics
MGeND
ClinVar
CIViC
DisGeNET
Annotation
Genome browser

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

SCN5A

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
	NM_001160160.1:c.6010T>G	NP_001153632.1:p.Phe2004Val
Ensemble	ENST00000333535.9:c.6010T>G	ENST00000333535.9:p.Phe2004Val
	ENST00000413689.6:c.6010T>G	ENST00000413689.6:p.Phe2004Val
	ENST00000414099.6:c.5956T>G	ENST00000414099.6:p.Phe1986Val
	ENST00000423572.7:c.6007T>G	ENST00000423572.7:p.Phe2003Val
	ENST00000449557.6:c.5848T>G	ENST00000449557.6:p.Phe1950Val
	ENST00000450102.6:c.5848T>G	ENST00000450102.6:p.Phe1950Val
	ENST00000455624.6:c.5911T>G	ENST00000455624.6:p.Phe1971Val

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

SCN5A

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

Descrption	Source	Links
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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