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NM_001037.5(SCN1B):c.448+88G>A AND Brugada syndrome 5

Germline classification:
Likely pathogenic (2 submissions)
Last evaluated:
Sep 17, 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:
RCV000009836.17

Allele description [Variation Report for NM_001037.5(SCN1B):c.448+88G>A]

NM_001037.5(SCN1B):c.448+88G>A

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.448+88G>A
Other names:
SCN1B, 536G-A, TRP179TER; p.W179*:TGG>TAG
HGVS:
  • NC_000019.10:g.35033827G>A
  • NG_013359.1:g.8140G>A
  • NM_001037.5:c.448+88G>AMANE SELECT
  • NM_001321605.2:c.349+88G>A
  • NM_199037.5:c.536G>A
  • NP_950238.1:p.Trp179Ter
  • NP_950238.1:p.Trp179Ter
  • LRG_420t1:c.448+88G>A
  • LRG_420:g.8140G>A
  • NC_000019.9:g.35524731G>A
  • NM_001037.3:c.448+88G>A
  • NM_001037.4:c.448+88G>A
  • NM_199037.2:c.536G>A
  • NM_199037.3:c.536G>A
Protein change:
W179*; TRP179TER
Links:
OMIM: 600235.0003; dbSNP: rs267607028
NCBI 1000 Genomes Browser:
rs267607028
Molecular consequence:
  • NM_001037.5:c.448+88G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001321605.2:c.349+88G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_199037.5:c.536G>A - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

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

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000030057OMIM
no assertion criteria provided
Pathogenic
(Jun 1, 2008)
germlineliterature only

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

SCV000959398Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Likely pathogenic
(Sep 17, 2023)
germlineclinical testing

PubMed (5)
[See all records that cite these PMIDs]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlinenot providednot providednot providednot providednot providednot providedliterature only
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Sodium channel β1 subunit mutations associated with Brugada syndrome and cardiac conduction disease in humans.

Watanabe H, Koopmann TT, Le Scouarnec S, Yang T, Ingram CR, Schott JJ, Demolombe S, Probst V, Anselme F, Escande D, Wiesfeld AC, Pfeufer A, Kääb S, Wichmann HE, Hasdemir C, Aizawa Y, Wilde AA, Roden DM, Bezzina CR.

J Clin Invest. 2008 Jun;118(6):2260-8. doi: 10.1172/JCI33891.

PubMed [citation]
PMID:
18464934
PMCID:
PMC2373423

A connexin40 mutation associated with a malignant variant of progressive familial heart block type I.

Makita N, Seki A, Sumitomo N, Chkourko H, Fukuhara S, Watanabe H, Shimizu W, Bezzina CR, Hasdemir C, Mugishima H, Makiyama T, Baruteau A, Baron E, Horie M, Hagiwara N, Wilde AA, Probst V, Le Marec H, Roden DM, Mochizuki N, Schott JJ, Delmar M.

Circ Arrhythm Electrophysiol. 2012 Feb;5(1):163-72. doi: 10.1161/CIRCEP.111.967604. Epub 2012 Jan 13.

PubMed [citation]
PMID:
22247482
PMCID:
PMC4274644
See all PubMed Citations (5)

Details of each submission

From OMIM, SCV000030057.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (1)

Description

In a 53-year-old French man who presented with chest pain but had normal coronary angiography and echocardiography, in whom electrocardiogram (ECG) revealed ST segment elevation typical of Brugada syndrome (BRGDA5; 612838), Watanabe et al. (2008) identified heterozygosity for a 536G-A transition in exon 3A of the SCN1B gene, resulting in a trp179-to-ter (W179X) substitution predicted to generate a truncated protein lacking the membrane-spanning segment and intracellular portion. The proband also had conduction abnormalities, including a prolonged PR interval of 220 ms and left anterior hemiblock, and ventricular fibrillation was induced by programmed electrical stimulation in the absence of drugs. The mutation was also found in the proband's brother, who had no history of palpitations or syncope, but on baseline ECG had left anterior hemiblock and minor ST segment elevation suggestive of Brugada syndrome (type II saddleback abnormalities); on flecainide challenge, the ST segment elevation was exacerbated but did not meet the criteria for a diagnostic (type I) pattern. Their sister, who also carried the mutation, had a normal ECG and a negative flecainide test, but her mutation-positive son was found to have right bundle branch block and type II Brugada syndrome after flecainide challenge. There was no family history of tachyarrhythmias, syncope, sudden cardiac death, or epilepsy. The mutation was not found in 1,404 population controls. Functional studies of the W179X mutation, which occurs only in the beta-1B transcript, showed that coexpression of wildtype beta-1B with Na(v)1.5 increased sodium current density by 69%, whereas coexpression with mutant beta-1B did not increase the sodium current compared to Na(v)1.5 alone; there was no evidence of a dominant-negative effect by the mutant. In addition, wildtype beta-1B produced negative shifts in the voltage dependence of Na(v)1.5 activation and inactivation, whereas mutant beta-1B did not modulate Na(v)1.5 gating.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenot providednot providednot providednot providednot providednot providednot providednot provided

From Labcorp Genetics (formerly Invitae), Labcorp, SCV000959398.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (5)

Description

In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic. This variant disrupts a region of the SCN1B protein in which other variant(s) (p.Pro184Leu) have been observed in individuals with SCN1B-related conditions (Invitae). This suggests that this is a clinically significant region of the protein, and that variants that disrupt it are likely to be disease-causing. Experimental studies have shown that this premature translational stop signal affects SCN1B function (PMID: 18464934). Algorithms developed to predict the effect of variants on protein structure and function are not available or were not evaluated for this variant. ClinVar contains an entry for this variant (Variation ID: 9254). This premature translational stop signal has been observed in individual(s) with Brugada syndrome, sudden arrythmic death syndrome and progressive familial heart block type 1 (PMID: 18464934, 22247482, 28449774, 29758173). This variant is present in population databases (rs267607028, gnomAD 0.002%). This sequence change creates a premature translational stop signal (p.Trp179*) in the SCN1B gene. While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 90 amino acid(s) of the SCN1B protein.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Nov 10, 2024