NM_000059.4(BRCA2):c.7675T>A (p.Ser2559Thr) AND Hereditary breast ovarian cancer syndrome

This record was updated by the submitter. Please see the current version.

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Oct 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:: RCV003530803.1

Allele description

NM_000059.4(BRCA2):c.7675T>A (p.Ser2559Thr)

Gene:

BRCA2:BRCA2 DNA repair associated [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

13q13.1

Genomic location:

Preferred name:

NM_000059.4(BRCA2):c.7675T>A (p.Ser2559Thr)

HGVS:

NC_000013.11:g.32357799T>A
NG_012772.3:g.47320T>A
NM_000059.4:c.7675T>AMANE SELECT
NM_001406719.1:c.7579T>A
NM_001406720.1:c.7675T>A
NM_001406721.1:c.2743T>A
NM_001406722.1:c.1258T>A
NP_000050.2:p.Ser2559Thr
NP_000050.3:p.Ser2559Thr
NP_001393648.1:p.Ser2527Thr
NP_001393649.1:p.Ser2559Thr
NP_001393650.1:p.Ser915Thr
NP_001393651.1:p.Ser420Thr
LRG_293t1:c.7675T>A
LRG_293:g.47320T>A
LRG_293p1:p.Ser2559Thr
NC_000013.10:g.32931936T>A
NM_000059.3:c.7675T>A
NR_176251.1:n.7874T>A

Protein change:

S2527T

Molecular consequence:

NM_000059.4:c.7675T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406719.1:c.7579T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406720.1:c.7675T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406721.1:c.2743T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001406722.1:c.1258T>A - missense variant - [Sequence Ontology: SO:0001583]
NR_176251.1:n.7874T>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:: Hereditary breast ovarian cancer syndrome
Synonyms:: Hereditary breast and ovarian cancer syndrome; Hereditary breast and ovarian cancer; Hereditary breast and ovarian cancer syndrome (HBOC); See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0003582; MeSH: D061325; MedGen: C0677776; Orphanet: 145

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004281774	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Oct 6, 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

SCV004281774

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Oct 6, 2023)

germline

clinical testing

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

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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 Invitae, SCV004281774.1

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

Description

This sequence change replaces serine, which is neutral and polar, with threonine, which is neutral and polar, at codon 2559 of the BRCA2 protein (p.Ser2559Thr). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with BRCA2-related conditions. Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt BRCA2 protein function. 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.

#	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 1, 2024

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