NM_001037.5(SCN1B):c.3G>C (p.Met1Ile) AND Brugada syndrome 5

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Apr 6, 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:: RCV001343823.5

Allele description [Variation Report for NM_001037.5(SCN1B):c.3G>C (p.Met1Ile)]

NM_001037.5(SCN1B):c.3G>C (p.Met1Ile)

Gene:

SCN1B:sodium voltage-gated channel beta subunit 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

19q13.11

Genomic location:

Preferred name:

NM_001037.5(SCN1B):c.3G>C (p.Met1Ile)

HGVS:

NC_000019.10:g.35030823G>C
NG_013359.1:g.5136G>C
NM_001037.4:c.3G>C
NM_001037.5:c.3G>CMANE SELECT
NM_199037.5:c.3G>C
NP_001028.1:p.Met1Ile
NP_950238.1:p.Met1Ile
LRG_420t1:c.3G>C
LRG_420:g.5136G>C
LRG_420p1:p.Met1Ile
NC_000019.9:g.35521727G>C

Protein change:

M1I

Links:

dbSNP: rs2064208424

NCBI 1000 Genomes Browser:

rs2064208424

Molecular consequence:

NM_001037.5:c.3G>C - initiator_codon_variant - [Sequence Ontology: SO:0001582]
NM_199037.5:c.3G>C - initiator_codon_variant - [Sequence Ontology: SO:0001582]
NM_001037.5:c.3G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_199037.5:c.3G>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Brugada syndrome 5 (BRGDA5)
Identifiers:: MONDO: MONDO:0013015; MedGen: C2748541; Orphanet: 130; Orphanet: 871; OMIM: 612838

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001537832	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Apr 6, 2023)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 30660056, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001537832

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Apr 6, 2023)

germline

clinical testing

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	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Sudden unexpected death in GEFS+ families with sodium channel pathogenic variants.

Myers KA, Shevell MI, Sébire G.

Epilepsy Res. 2019 Feb;150:66-69. doi: 10.1016/j.eplepsyres.2019.01.009. Epub 2019 Jan 14.

PubMed [citation]

PMID:: 30660056

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001537832.5

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

Description

ClinVar contains an entry for this variant (Variation ID: 1040220). For these reasons, this variant has been classified as Pathogenic. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. Disruption of the initiator codon has been observed in individuals with clinical features of autosomal dominant SCN1B-related conditions (PMID: 30660056; Invitae). It has also been observed to segregate with disease in related individuals. This variant is not present in population databases (gnomAD no frequency). This sequence change affects the initiator methionine of the SCN1B mRNA. The next in-frame methionine is located at codon 34.

#	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 29, 2024

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