NM_000335.5(SCN5A):c.3127del (p.Glu1043fs) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Dec 31, 2023
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:: RCV003852547.1

Allele description [Variation Report for NM_000335.5(SCN5A):c.3127del (p.Glu1043fs)]

NM_000335.5(SCN5A):c.3127del (p.Glu1043fs)

Genes:

LOC110121269:VISTA enhancer hs2177 [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.3127del (p.Glu1043fs)

HGVS:

NC_000003.12:g.38581032del
NG_008934.1:g.73641del
NG_053884.1:g.2771del
NM_000335.5:c.3127delMANE SELECT
NM_001099404.2:c.3127del
NM_001099405.2:c.3127del
NM_001160160.2:c.3127del
NM_001160161.2:c.3127del
NM_001354701.2:c.3127del
NM_198056.3:c.3127del
NP_000326.2:p.Glu1043Serfs
NP_000326.2:p.Glu1043fs
NP_001092874.1:p.Glu1043Serfs
NP_001092874.1:p.Glu1043fs
NP_001092875.1:p.Glu1043fs
NP_001153632.1:p.Glu1043fs
NP_001153633.1:p.Glu1043fs
NP_001341630.1:p.Glu1043fs
NP_932173.1:p.Glu1043Serfs
NP_932173.1:p.Glu1043fs
LRG_289t1:c.3127del
LRG_289t2:c.3127del
LRG_289t3:c.3127del
LRG_289:g.73641del
LRG_289p1:p.Glu1043Serfs
LRG_289p2:p.Glu1043Serfs
LRG_289p3:p.Glu1043Serfs
NC_000003.11:g.38622523del
NM_000335.4:c.3127delG
NM_001099404.1:c.3127delG
NM_198056.2:c.3127delG
NR_176299.1:n.3873del

Protein change:

E1043fs

Molecular consequence:

NM_000335.5:c.3127del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001099404.2:c.3127del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001099405.2:c.3127del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001160160.2:c.3127del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001160161.2:c.3127del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001354701.2:c.3127del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_198056.3:c.3127del - frameshift variant - [Sequence Ontology: SO:0001589]
NR_176299.1:n.3873del - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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hypothetical protein E5Q_03378 [Mixia osmundae IAM 14324]
hypothetical protein E5Q_03378 [Mixia osmundae IAM 14324]
gi|358057359|dbj|GAA96708.1||gnl|WG T|GAA96708

Protein
Homo sapiens eukaryotic translation initiation factor 5A (EIF5A), transcript var...
Homo sapiens eukaryotic translation initiation factor 5A (EIF5A), transcript variant D, mRNA
gi|1890327853|ref|NM_001143762.2|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004662814	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Dec 31, 2023)	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

SCV004662814

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Dec 31, 2023)

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, SCV004662814.1

#	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.Glu1043Serfs*102) in the SCN5A gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in SCN5A are known to be pathogenic (PMID: 20129283, 22789973). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with SCN5A-related conditions. For these reasons, this variant has been classified as Pathogenic.

#	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: Mar 5, 2024

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