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NM_001037.5(SCN1B):c.542G>A (p.Cys181Tyr) AND Brugada syndrome 5

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Oct 30, 2018
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:
RCV000810034.3

Allele description [Variation Report for NM_001037.5(SCN1B):c.542G>A (p.Cys181Tyr)]

NM_001037.5(SCN1B):c.542G>A (p.Cys181Tyr)

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.542G>A (p.Cys181Tyr)
HGVS:
  • NC_000019.10:g.35039210G>A
  • NG_013359.1:g.13523G>A
  • NM_001037.5:c.542G>AMANE SELECT
  • NM_001321605.2:c.443G>A
  • NP_001028.1:p.Cys181Tyr
  • NP_001308534.1:p.Cys148Tyr
  • LRG_420t1:c.542G>A
  • LRG_420:g.13523G>A
  • LRG_420p1:p.Cys181Tyr
  • NC_000019.9:g.35530114G>A
  • NM_001037.4:c.542G>A
Protein change:
C148Y
Links:
dbSNP: rs1173931729
NCBI 1000 Genomes Browser:
rs1173931729
Molecular consequence:
  • NM_001037.5:c.542G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001321605.2:c.443G>A - 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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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000950220Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Oct 30, 2018) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

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, SCV000950220.1

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

Description

This sequence change replaces cysteine with tyrosine at codon 181 of the SCN1B protein (p.Cys181Tyr). The cysteine residue is highly conserved and there is a large physicochemical difference between cysteine and tyrosine. The SCN1B gene has multiple clinically relevant transcripts. The p.Cys181Tyr variant occurs in alternate transcript NM_001037.4, which corresponds to position c.*5112G>A in NM_199037.3, the primary transcript listed in the Methods. This variant is not present in population databases (ExAC no frequency). This variant has not been reported in the literature in individuals with SCN1B-related disease. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Not Available"; Align-GVGD: "Class C0"). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

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

Last Updated: Sep 29, 2024