chr3:38620907:G>T Detail (hg19) (SCN5A, LOC110121269)

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

Information

Genome

Assembly	Position
hg19	chr3:38,620,907-38,620,907
hg38	chr3:38,579,416-38,579,416 View the variant detail on this assembly version.

HGVS

SCN5A

Type	Transcript	Protein
RefSeq	NM_000335.4:c.3308C>A	NP_000326.2:p.Ser1103Tyr
	NM_198056.2:c.3308C>A	NP_932173.1:p.Ser1103Tyr
	NM_001099404.1:c.3308C>A	NP_001092874.1:p.Ser1103Tyr
	NM_001160160.1:c.3308C>A	NP_001153632.1:p.Ser1103Tyr
Ensemble	ENST00000333535.9:c.3308C>A	ENST00000333535.9:p.Ser1103Tyr
	ENST00000413689.6:c.3308C>A	ENST00000413689.6:p.Ser1103Tyr
	ENST00000414099.6:c.3308C>A	ENST00000414099.6:p.Ser1103Tyr
	ENST00000423572.7:c.3305C>A	ENST00000423572.7:p.Ser1102Tyr
	ENST00000449557.6:c.3228+1515C>A
	ENST00000450102.6:c.3228+1515C>A
	ENST00000455624.6:c.3305C>A	ENST00000455624.6:p.Ser1102Tyr

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
risk factor	2008-04-15	no assertion criteria provided	Long QT syndrome 3, acquired, susceptibility to	germline	Detail
Pathogenic	2008-04-15	no assertion criteria provided	sudden infant death syndrome	germline	Detail
Benign	2020-08-10	criteria provided, multiple submitters, no conflicts	not specified	germline	Detail
Benign Likely benign	2024-02-01	criteria provided, multiple submitters, no conflicts	not provided	germline	Detail
Conflicting interpretations of pathogenicity	2023-01-26	criteria provided, conflicting interpretations	Brugada syndrome	germline	Detail
Likely benign	2018-02-02	criteria provided, single submitter	dilated cardiomyopathy 1E	germline	Detail
Likely benign	2018-02-02	criteria provided, single submitter	Progressive familial heart block, type 1A	germline	Detail
Likely benign	2016-06-14	criteria provided, single submitter	Congenital long QT syndrome	germline	Detail
Likely benign	2018-02-02	criteria provided, single submitter	Ventricular fibrillation, paroxysmal familial, type 1	germline	Detail
Likely benign	2018-02-02	criteria provided, single submitter	Sick sinus syndrome 1	germline	Detail
Benign	2017-07-12	criteria provided, single submitter		germline	Detail
Benign Likely benign	2018-11-21	criteria provided, multiple submitters, no conflicts	long QT syndrome 3	germline unknown	Detail
Likely benign	2018-02-02	criteria provided, single submitter	Brugada syndrome 1	germline	Detail
Benign	2018-03-19	criteria provided, multiple submitters, no conflicts	Cardiac arrhythmia	germline unknown	Detail
Benign	2021-08-02	criteria provided, single submitter	Sick sinus syndrome 1,Atrial fibrillation, familial, 10,Brugada syndrome 1,dilated cardiomyopathy 1E,long QT syndrome 3,sudden infant death syndrome,Progressive familial heart block, type 1A,Ventricular fibrillation, paroxysmal familial, type 1	unknown	Detail
Benign	2021-08-02	criteria provided, single submitter	Sick sinus syndrome 1,Atrial fibrillation, familial, 10,Brugada syndrome 1,dilated cardiomyopathy 1E,long QT syndrome 3,sudden infant death syndrome,Progressive familial heart block, type 1A,Ventricular fibrillation, paroxysmal familial, type 1	unknown	Detail
Benign	2021-08-02	criteria provided, single submitter	Sick sinus syndrome 1,Atrial fibrillation, familial, 10,Brugada syndrome 1,dilated cardiomyopathy 1E,long QT syndrome 3,sudden infant death syndrome,Progressive familial heart block, type 1A,Ventricular fibrillation, paroxysmal familial, type 1	unknown	Detail
Benign	2021-08-02	criteria provided, single submitter	Sick sinus syndrome 1,Atrial fibrillation, familial, 10,Brugada syndrome 1,dilated cardiomyopathy 1E,long QT syndrome 3,sudden infant death syndrome,Progressive familial heart block, type 1A,Ventricular fibrillation, paroxysmal familial, type 1	unknown	Detail
Benign	2021-08-02	criteria provided, single submitter	Sick sinus syndrome 1,Atrial fibrillation, familial, 10,Brugada syndrome 1,dilated cardiomyopathy 1E,long QT syndrome 3,sudden infant death syndrome,Progressive familial heart block, type 1A,Ventricular fibrillation, paroxysmal familial, type 1	unknown	Detail
Benign	2021-08-02	criteria provided, single submitter	Sick sinus syndrome 1,Atrial fibrillation, familial, 10,Brugada syndrome 1,dilated cardiomyopathy 1E,long QT syndrome 3,sudden infant death syndrome,Progressive familial heart block, type 1A,Ventricular fibrillation, paroxysmal familial, type 1	unknown	Detail
Benign	2021-08-02	criteria provided, single submitter	Sick sinus syndrome 1,Atrial fibrillation, familial, 10,Brugada syndrome 1,dilated cardiomyopathy 1E,long QT syndrome 3,sudden infant death syndrome,Progressive familial heart block, type 1A,Ventricular fibrillation, paroxysmal familial, type 1	unknown	Detail
Benign	2021-08-02	criteria provided, single submitter	Sick sinus syndrome 1,Atrial fibrillation, familial, 10,Brugada syndrome 1,dilated cardiomyopathy 1E,long QT syndrome 3,sudden infant death syndrome,Progressive familial heart block, type 1A,Ventricular fibrillation, paroxysmal familial, type 1	unknown	Detail
Benign	2022-09-27	criteria provided, single submitter	Primary dilated cardiomyopathy	germline	Detail
Benign	2021-09-22	criteria provided, single submitter	cardiomyopathy	germline	Detail

CIViC

[No Data.]

DisGeNET

Score	Disease name	Description	Source	Pubmed	Links
0.386	sudden infant death syndrome	NA	CLINVAR		Detail
0.120	LONG QT SYNDROME 3, ACQUIRED, SUSCEPTIBILITY TO (finding)	NA	CLINVAR		Detail
0.386	sudden infant death syndrome	Our data provide evidence that SCN5A allelic expression imbalance occurs in Afri...	BeFree	20470418	Detail
0.003	congestive heart failure	We hypothesized that the S1103Y cardiac sodium channel SCN5A variant influences ...	BeFree	21498565	Detail
0.386	sudden infant death syndrome	The common polymorphism SCN5A-S1103Y (∼13% allelic frequency in African American...	BeFree	21385947	Detail
0.004	Syncope	In this study, we define an SCN5A mutation, S1103Y, in a white family associated...	BeFree	12471205	Detail
0.091	Heart failure	We hypothesized that the S1103Y cardiac sodium channel SCN5A variant influences ...	BeFree	21498565	Detail
<0.001	Acidosis, Respiratory	Wild-type and mutant SCN5A channels both functioned typically under normal condi...	BeFree	16453014	Detail
0.386	sudden infant death syndrome	Targeted mutational analysis of exon 18 in SCN5A of the African-American SIDS co...	BeFree	18452875	Detail
0.386	sudden infant death syndrome	Wild-type and mutant SCN5A channels both functioned typically under normal condi...	BeFree	16453014	Detail

Annotation

Annotations

Descrption	Source	Links
NM_000335.5(SCN5A):c.3305C>A (p.Ser1102Tyr) AND Long QT syndrome 3, acquired, susceptibility to	ClinVar	Detail
NM_000335.5(SCN5A):c.3305C>A (p.Ser1102Tyr) AND SUDDEN INFANT DEATH SYNDROME	ClinVar	Detail
NM_000335.5(SCN5A):c.3305C>A (p.Ser1102Tyr) AND not specified	ClinVar	Detail
NM_000335.5(SCN5A):c.3305C>A (p.Ser1102Tyr) AND not provided	ClinVar	Detail
NM_000335.5(SCN5A):c.3305C>A (p.Ser1102Tyr) AND Brugada syndrome	ClinVar	Detail
NM_000335.5(SCN5A):c.3305C>A (p.Ser1102Tyr) AND Dilated cardiomyopathy 1E	ClinVar	Detail
NM_000335.5(SCN5A):c.3305C>A (p.Ser1102Tyr) AND Progressive familial heart block, type 1A	ClinVar	Detail
NM_000335.5(SCN5A):c.3305C>A (p.Ser1102Tyr) AND Congenital long QT syndrome	ClinVar	Detail
NM_000335.5(SCN5A):c.3305C>A (p.Ser1102Tyr) AND Ventricular fibrillation, paroxysmal familial, type ...	ClinVar	Detail
NM_000335.5(SCN5A):c.3305C>A (p.Ser1102Tyr) AND Sick sinus syndrome 1	ClinVar	Detail
NM_000335.5(SCN5A):c.3305C>A (p.Ser1102Tyr) AND Cardiovascular phenotype	ClinVar	Detail
NM_000335.5(SCN5A):c.3305C>A (p.Ser1102Tyr) AND Long QT syndrome 3	ClinVar	Detail
NM_000335.5(SCN5A):c.3305C>A (p.Ser1102Tyr) AND Brugada syndrome 1	ClinVar	Detail
NM_000335.5(SCN5A):c.3305C>A (p.Ser1102Tyr) AND Cardiac arrhythmia	ClinVar	Detail
NM_000335.5(SCN5A):c.3305C>A (p.Ser1102Tyr) AND multiple conditions	ClinVar	Detail
NM_000335.5(SCN5A):c.3305C>A (p.Ser1102Tyr) AND multiple conditions	ClinVar	Detail
NM_000335.5(SCN5A):c.3305C>A (p.Ser1102Tyr) AND multiple conditions	ClinVar	Detail
NM_000335.5(SCN5A):c.3305C>A (p.Ser1102Tyr) AND multiple conditions	ClinVar	Detail
NM_000335.5(SCN5A):c.3305C>A (p.Ser1102Tyr) AND multiple conditions	ClinVar	Detail
NM_000335.5(SCN5A):c.3305C>A (p.Ser1102Tyr) AND multiple conditions	ClinVar	Detail
NM_000335.5(SCN5A):c.3305C>A (p.Ser1102Tyr) AND multiple conditions	ClinVar	Detail
NM_000335.5(SCN5A):c.3305C>A (p.Ser1102Tyr) AND multiple conditions	ClinVar	Detail
NM_000335.5(SCN5A):c.3305C>A (p.Ser1102Tyr) AND Primary dilated cardiomyopathy	ClinVar	Detail
NM_000335.5(SCN5A):c.3305C>A (p.Ser1102Tyr) AND Cardiomyopathy	ClinVar	Detail
NA	DisGeNET	Detail
NA	DisGeNET	Detail
Our data provide evidence that SCN5A allelic expression imbalance occurs in African-Americans hetero...	DisGeNET	Detail
We hypothesized that the S1103Y cardiac sodium channel SCN5A variant influences the propensity for v...	DisGeNET	Detail
The common polymorphism SCN5A-S1103Y (∼13% allelic frequency in African Americans) is a risk factor ...	DisGeNET	Detail
In this study, we define an SCN5A mutation, S1103Y, in a white family associated with syncope, ventr...	DisGeNET	Detail
We hypothesized that the S1103Y cardiac sodium channel SCN5A variant influences the propensity for v...	DisGeNET	Detail
Wild-type and mutant SCN5A channels both functioned typically under normal conditions in vitro, but ...	DisGeNET	Detail
Targeted mutational analysis of exon 18 in SCN5A of the African-American SIDS cohort (n = 71) reveal...	DisGeNET	Detail
Wild-type and mutant SCN5A channels both functioned typically under normal conditions in vitro, but ...	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: rs7626962 dbSNP
Genome: hg19
Position: chr3:38,620,907-38,620,907
Variant Type: snv
Reference Allele: G
Alternative Allele: T
East Asian Chromosome Counts (ExAC): 7580
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): 102000
Allele Counts in All Race (ExAC): 815
Heterozygous Counts in All Race (ExAC): 757
Homozygous Counts in All Race (ExAC): 29
Allele Frequency in All Race (ExAC): 0.007990196078431372

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