NM_000335.5(SCN5A):c.3873del (p.Phe1292fs) AND not provided

This record was updated by the submitter. Please see the current version.

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jun 2, 2017
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV003654432.1

Allele description

NM_000335.5(SCN5A):c.3873del (p.Phe1292fs)

Gene:

SCN5A:sodium voltage-gated channel alpha subunit 5 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

3p22.2

Genomic location:

Preferred name:

NM_000335.5(SCN5A):c.3873del (p.Phe1292fs)

HGVS:

NC_000003.12:g.38562502del
NG_008934.1:g.92171del
NM_000335.5:c.3873delMANE SELECT
NM_001099404.2:c.3876del
NM_001099405.2:c.3876del
NM_001160160.2:c.3873del
NM_001160161.2:c.3714del
NM_001354701.2:c.3873del
NM_198056.3:c.3876del
NP_000326.2:p.Phe1292fs
NP_001092874.1:p.Phe1293fs
NP_001092875.1:p.Phe1293fs
NP_001153632.1:p.Phe1292fs
NP_001153633.1:p.Phe1239fs
NP_001341630.1:p.Phe1292fs
NP_932173.1:p.Phe1293fs
LRG_289:g.92171del
NC_000003.11:g.38603993del
NM_198056.2:c.3876delC

Protein change:

F1239fs

Links:

dbSNP: rs1553695847

NCBI 1000 Genomes Browser:

rs1553695847

Molecular consequence:

NM_000335.5:c.3873del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001099404.2:c.3876del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001099405.2:c.3876del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001160160.2:c.3873del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001160161.2:c.3714del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001354701.2:c.3873del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_198056.3:c.3876del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

Clear Turn Off Turn On

Particle Size
Particle Size
Relating to the size of solids.<br/>Year introduced: 1973

MeSH
Chromosome neighbors for GEO Profiles (Select 76503798) (19)
GEO Profiles
Homo sapiens nuclear receptor coactivator 4 (NCOA4), transcript variant 2, mRNA
Homo sapiens nuclear receptor coactivator 4 (NCOA4), transcript variant 2, mRNA
gi|1890265737|ref|NM_001145261.2|

Nucleotide

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000637144	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Jun 2, 2017)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 20129283, 22789973, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000637144

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Jun 2, 2017)

germline

clinical testing

PubMed (3)
[See all records that cite these PMIDs]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

An international compendium of mutations in the SCN5A-encoded cardiac sodium channel in patients referred for Brugada syndrome genetic testing.

Kapplinger JD, Tester DJ, Alders M, Benito B, Berthet M, Brugada J, Brugada P, Fressart V, Guerchicoff A, Harris-Kerr C, Kamakura S, Kyndt F, Koopmann TT, Miyamoto Y, Pfeiffer R, Pollevick GD, Probst V, Zumhagen S, Vatta M, Towbin JA, Shimizu W, Schulze-Bahr E, et al.

Heart Rhythm. 2010 Jan;7(1):33-46. doi: 10.1016/j.hrthm.2009.09.069. Epub 2009 Oct 8.

PubMed [citation]

PMID:: 20129283
PMCID:: PMC2822446

Brugada syndrome 2012.

Berne P, Brugada J.

Circ J. 2012;76(7):1563-71. Epub 2012 Jun 13. Review.

PubMed [citation]

PMID:: 22789973

See all PubMed Citations (3)

Details of each submission

From Invitae, SCV000637144.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

This sequence change creates a premature translational stop signal (p.Phe1293Leufs*19) in the SCN5A gene. It is expected to result in an absent or disrupted protein product. This variant is not present in population databases (ExAC no frequency). For these reasons, this variant has been classified as Pathogenic. Loss-of-function variants in SCN5A are known to be pathogenic (PMID: 20129283, 22789973). This variant has not been reported in the literature in individuals with a SCN5A-related disease.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 16, 2024

ClinVar

Relating variation to medicine