NM_000335.5(SCN5A):c.1890G>A (p.Thr630=) AND Brugada syndrome 1

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Oct 5, 2022
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:: RCV002298705.8

Allele description [Variation Report for NM_000335.5(SCN5A):c.1890G>A (p.Thr630=)]

NM_000335.5(SCN5A):c.1890G>A (p.Thr630=)

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.1890G>A (p.Thr630=)

HGVS:

NC_000003.12:g.38603712C>T
NG_008934.1:g.50961G>A
NM_000335.5:c.1890G>AMANE SELECT
NM_001099404.2:c.1890G>A
NM_001099405.2:c.1890G>A
NM_001160160.2:c.1890G>A
NM_001160161.2:c.1890G>A
NM_001354701.2:c.1890G>A
NM_198056.3:c.1890G>A
NP_000326.2:p.Thr630=
NP_001092874.1:p.Thr630=
NP_001092875.1:p.Thr630=
NP_001153632.1:p.Thr630=
NP_001153633.1:p.Thr630=
NP_001341630.1:p.Thr630=
NP_932173.1:p.Thr630=
NP_932173.1:p.Thr630=
LRG_289t1:c.1890G>A
LRG_289:g.50961G>A
LRG_289p1:p.Thr630=
NC_000003.11:g.38645203C>T
NM_198056.2:c.1890G>A
p.Thr630Thr

Links:

dbSNP: rs1204915217

NCBI 1000 Genomes Browser:

rs1204915217

Molecular consequence:

NM_000335.5:c.1890G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001099404.2:c.1890G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001099405.2:c.1890G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001160160.2:c.1890G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001160161.2:c.1890G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001354701.2:c.1890G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_198056.3:c.1890G>A - synonymous variant - [Sequence Ontology: SO:0001819]

Functional consequence:

sequence_variant_affecting_splicing [Sequence Ontology: SO:1000071]

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
SCV002588734	Roden Lab, Vanderbilt University Medical Center	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Oct 5, 2022)	unknown, not applicable	research, in vitro	PubMed (2) [See all records that cite these PMIDs] 25741868, 36197721

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002588734

Roden Lab, Vanderbilt University Medical Center

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Oct 5, 2022)

unknown, not applicable

research, in vitro

PubMed (2)
[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	not applicable	not applicable	not provided	not provided	not provided	not provided	not provided	in vitro
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	research

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

Functional Assays Reclassify Suspected Splice-Altering Variants of Uncertain Significance in Mendelian Channelopathies.

O'Neill MJ, Wada Y, Hall LD, Mitchell DW, Glazer AM, Roden DM.

Circ Genom Precis Med. 2022 Dec;15(6):e003782. doi: 10.1161/CIRCGEN.122.003782. Epub 2022 Oct 5.

PubMed [citation]

PMID:: 36197721
PMCID:: PMC9772980

Details of each submission

From Roden Lab, Vanderbilt University Medical Center, SCV002588734.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	research	PubMed (2)
2	not provided	not provided	not provided	not provided	in vitro	PubMed (2)

Description

The synonymous SCN5A variant c.1890G>A was observed in 1 case of Brugada Syndrome and is absent from large population databases (PMID: 32893267). The variant is predicted to alter RNA splicing. A minigene functional assay showed aberrant splicing induced by the variant. These findings support the classification of this variant as Likely Pathogenic

#	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
2	not applicable	not applicable	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Oct 8, 2024

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