NM_000335.5(SCN5A):c.1673A>G (p.His558Arg) AND Brugada syndrome 1

Germline classification:: Benign/Likely benign (3 submissions)
Last evaluated:: May 28, 2019
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000987225.14

Allele description [Variation Report for NM_000335.5(SCN5A):c.1673A>G (p.His558Arg)]

NM_000335.5(SCN5A):c.1673A>G (p.His558Arg)

Gene:

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

Variant type:

single nucleotide variant

Cytogenetic location:

3p22.2

Genomic location:

Preferred name:

NM_000335.5(SCN5A):c.1673A>G (p.His558Arg)

HGVS:

NC_000003.12:g.38603929T>C
NG_008934.1:g.50744A>G
NM_000335.5:c.1673A>GMANE SELECT
NM_001099404.2:c.1673A>G
NM_001099405.2:c.1673A>G
NM_001160160.2:c.1673A>G
NM_001160161.2:c.1673A>G
NM_001354701.2:c.1673A>G
NM_198056.3:c.1673A>G
NP_000326.2:p.His558Arg
NP_001092874.1:p.His558Arg
NP_001092874.1:p.His558Arg
NP_001092875.1:p.His558Arg
NP_001153632.1:p.His558Arg
NP_001153633.1:p.His558Arg
NP_001341630.1:p.His558Arg
NP_932173.1:p.His558Arg
NP_932173.1:p.His558Arg
LRG_289t1:c.1673A>G
LRG_289t3:c.1673A>G
LRG_289:g.50744A>G
LRG_289p1:p.His558Arg
LRG_289p3:p.His558Arg
NC_000003.11:g.38645420T>C
NM_001099404.1:c.1673A>G
NM_198056.2:c.1673A>G
Q14524:p.His558Arg
c.1673A>G

Protein change:

H558R; HIS558ARG

Links:

UniProtKB: Q14524#VAR_008955; OMIM: 600163.0031; dbSNP: rs1805124

NCBI 1000 Genomes Browser:

rs1805124

Molecular consequence:

NM_000335.5:c.1673A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001099404.2:c.1673A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001099405.2:c.1673A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001160160.2:c.1673A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001160161.2:c.1673A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001354701.2:c.1673A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_198056.3:c.1673A>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Brugada syndrome 1 (BRGDA1)
Synonyms:: Right bundle branch block, ST segment elevation, and sudden death syndrome
Identifiers:: MONDO: MONDO:0011001; MedGen: C4551804; Orphanet: 130; OMIM: 601144

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000444132	Illumina Laboratory Services, Illumina	criteria provided, single submitter (ICSL Variant Classification Criteria 13 December 2019)	Likely benign (Apr 27, 2017)	germline	clinical testing	Citation Link,
SCV001136474	Mendelics	criteria provided, single submitter (Mendelics Assertion Criteria 2017)	Benign (May 28, 2019)	unknown	clinical testing	Citation Link,
SCV001440390	Institute of Human Genetics, University of Leipzig Medical Center	criteria provided, single submitter (ACMG Guidelines, 2015)	Benign (Jan 1, 2019)	unknown	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000444132

Illumina Laboratory Services, Illumina

criteria provided, single submitter

(ICSL Variant Classification Criteria 13 December 2019)

Likely benign
(Apr 27, 2017)

germline

clinical testing

Citation Link,

SCV001136474

Mendelics

criteria provided, single submitter

(Mendelics Assertion Criteria 2017)

Benign
(May 28, 2019)

unknown

clinical testing

Citation Link,

SCV001440390

Institute of Human Genetics, University of Leipzig Medical Center

criteria provided, single submitter

(ACMG Guidelines, 2015)

Benign
(Jan 1, 2019)

unknown

clinical testing

PubMed (1)
[See all records that cite this PMID]

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
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	unknown	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Illumina Laboratory Services, Illumina, SCV000444132.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

Description

This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases allowed determination this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign.

#	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

From Mendelics, SCV001136474.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

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

From Institute of Human Genetics, University of Leipzig Medical Center, SCV001440390.1

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

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

Last Updated: Oct 13, 2024

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