chr3:38592864:C>T Detail (hg19) (SCN5A)

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

Genome

Assembly	Position
hg19	chr3:38,592,864-38,592,864
hg38	chr3:38,551,373-38,551,373 View the variant detail on this assembly version.

HGVS

SCN5A

Type	Transcript	Protein
RefSeq	NM_001099404.1:c.4999G>A	NP_001092874.1:p.Val1667Ile
	NM_001160160.1:c.4999G>A	NP_001153632.1:p.Val1667Ile
	NM_000335.4:c.4999G>A	NP_000326.2:p.Val1667Ile
	NM_198056.2:c.4999G>A	NP_932173.1:p.Val1667Ile
Ensemble	ENST00000413689.6:c.4999G>A	ENST00000413689.6:p.Val1667Ile
	ENST00000450102.6:c.4837G>A	ENST00000450102.6:p.Val1613Ile
	ENST00000449557.6:c.4837G>A	ENST00000449557.6:p.Val1613Ile
	ENST00000423572.7:c.4996G>A	ENST00000423572.7:p.Val1666Ile
	ENST00000414099.6:c.4945G>A	ENST00000414099.6:p.Val1649Ile
	ENST00000455624.6:c.4900G>A	ENST00000455624.6:p.Val1634Ile
	ENST00000333535.9:c.4999G>A	ENST00000333535.9:p.Val1667Ile

Summary

MGeND

Clinical significance	Likely pathogenic Pathogenic
Variant entry	3
GWAS entry
Disease area statistics	Show details

Frequency

[No Data.]

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	COSM6887455	COSMIC
	MONDO

Disease area statistics

MGeND

Clinical significance	Last evaluated	Condition	Origin	Submission ID	Submitter	Institute	Citation	Comment	Image
Likely pathogenic	2017/03/30	long QT syndrome 3 (LQT3)	germline	MGS000001 (TMGS000137)	Kenjiro Kosaki	Keio University
Pathogenic		brugada syndrome	germline	MGS000001 (TMGS000137)	Kenjiro Kosaki	Keio University
Pathogenic		other	germline	MGS000001 (TMGS000154)	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
Likely pathogenic		no assertion criteria provided	long QT syndrome	germline	Detail
Conflicting interpretations of pathogenicity	2024-01-02	criteria provided, conflicting interpretations	not provided	germline	Detail
Conflicting interpretations of pathogenicity	2023-08-15	criteria provided, conflicting interpretations	Cardiac arrhythmia	germline	Detail
Likely pathogenic	2023-05-30	criteria provided, single submitter		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

Annotation

Annotations

Descrption	Source	Links
NM_000335.5(SCN5A):c.4996G>A (p.Val1666Ile) AND Congenital long QT syndrome	ClinVar	Detail
NM_000335.5(SCN5A):c.4996G>A (p.Val1666Ile) AND Long QT syndrome	ClinVar	Detail
NM_000335.5(SCN5A):c.4996G>A (p.Val1666Ile) AND not provided	ClinVar	Detail
NM_000335.5(SCN5A):c.4996G>A (p.Val1666Ile) AND Cardiac arrhythmia	ClinVar	Detail
NM_000335.5(SCN5A):c.4996G>A (p.Val1666Ile) AND Cardiovascular phenotype	ClinVar	Detail
NA	DisGeNET	Detail
NA	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: rs199473293 dbSNP
Genome: hg19
Position: chr3:38,592,864-38,592,864
Variant Type: snv
Reference Allele: C
Alternative Allele: T

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