NM_201596.3(CACNB2):c.1793G>C (p.Ser598Thr) AND Brugada syndrome 4

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: May 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:: RCV003623104.3

Allele description [Variation Report for NM_201596.3(CACNB2):c.1793G>C (p.Ser598Thr)]

NM_201596.3(CACNB2):c.1793G>C (p.Ser598Thr)

Gene:

CACNB2:calcium voltage-gated channel auxiliary subunit beta 2 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

10p12.31

Genomic location:

Preferred name:

NM_201596.3(CACNB2):c.1793G>C (p.Ser598Thr)

HGVS:

NC_000010.11:g.18539534G>C
NG_016195.1:g.403858G>C
NM_000724.4:c.1628G>C
NM_001167945.2:c.1595G>C
NM_001330060.2:c.1514G>C
NM_001410882.1:c.1535G>C
NM_201570.3:c.1649G>C
NM_201571.4:c.1709G>C
NM_201572.4:c.1637G>C
NM_201590.3:c.1631G>C
NM_201593.3:c.1679G>C
NM_201596.3:c.1793G>CMANE SELECT
NM_201597.3:c.1721G>C
NP_000715.2:p.Ser543Thr
NP_001161417.1:p.Ser532Thr
NP_001316989.1:p.Ser505Thr
NP_001397811.1:p.Ser512Thr
NP_963864.1:p.Ser550Thr
NP_963865.2:p.Ser570Thr
NP_963866.2:p.Ser546Thr
NP_963884.2:p.Ser544Thr
NP_963887.2:p.Ser560Thr
NP_963890.2:p.Ser598Thr
NP_963891.1:p.Ser574Thr
LRG_381t1:c.1793G>C
LRG_381t2:c.1631G>C
LRG_381:g.403858G>C
LRG_381p1:p.Ser598Thr
LRG_381p2:p.Ser544Thr
NC_000010.10:g.18828463G>C

Protein change:

S505T

Molecular consequence:

NM_000724.4:c.1628G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001167945.2:c.1595G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001330060.2:c.1514G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001410882.1:c.1535G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_201570.3:c.1649G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_201571.4:c.1709G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_201572.4:c.1637G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_201590.3:c.1631G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_201593.3:c.1679G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_201596.3:c.1793G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_201597.3:c.1721G>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Brugada syndrome 4 (BRGDA4)
Identifiers:: MONDO: MONDO:0012743; MedGen: C2678477; Orphanet: 130; OMIM: 611876

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004505775	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (May 17, 2023)	germline	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

SCV004505775

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(May 17, 2023)

germline

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

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, SCV004505775.1

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

Description

This variant is not present in population databases (gnomAD no frequency). 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. An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant¬† is likely to be tolerated. This variant has not been reported in the literature in individuals affected with CACNB2-related conditions. This sequence change replaces serine, which is neutral and polar, with threonine, which is neutral and polar, at codon 544 of the CACNB2 protein (p.Ser544Thr).

#	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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