NM_000059.4(BRCA2):c.2589del (p.Gln864fs) AND Hereditary cancer-predisposing syndrome

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Feb 17, 2021
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:: RCV002426593.9

Allele description [Variation Report for NM_000059.4(BRCA2):c.2589del (p.Gln864fs)]

NM_000059.4(BRCA2):c.2589del (p.Gln864fs)

Gene:

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

Variant type:

Deletion

Cytogenetic location:

13q13.1

Genomic location:

Preferred name:

NM_000059.4(BRCA2):c.2589del (p.Gln864fs)

HGVS:

NC_000013.11:g.32336944del
NG_012772.3:g.26465del
NM_000059.4:c.2589delMANE SELECT
NM_000059.4:c.2589delT
NP_000050.3:p.Gln864fs
LRG_293:g.26465del
NC_000013.10:g.32911081del
NM_000059.3:c.2589delT

Protein change:

Q864fs

Links:

dbSNP: rs397507632

NCBI 1000 Genomes Browser:

rs397507632

Molecular consequence:

NM_000059.4:c.2589del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:: Hereditary cancer-predisposing syndrome
Synonyms:: Neoplastic Syndromes, Hereditary; Tumor predisposition; Cancer predisposition; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0015356; MeSH: D009386; MedGen: C0027672

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002742174	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Pathogenic (Feb 17, 2021)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 17257844, 29215753, 31209999 Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002742174

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Pathogenic
(Feb 17, 2021)

germline

clinical testing

PubMed (3)
[See all records that cite these PMIDs]

Citation Link

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

BRCA mutations, molecular markers, and clinical variables in early-onset breast cancer: a population-based study.

Musolino A, Bella MA, Bortesi B, Michiara M, Naldi N, Zanelli P, Capelletti M, Pezzuolo D, Camisa R, Savi M, Neri TM, Ardizzoni A.

Breast. 2007 Jun;16(3):280-92. Epub 2007 Jan 25.

PubMed [citation]

PMID:: 17257844

Combined annotation-dependent depletion score for BRCA1/2 variants in patients with breast and/or ovarian cancer.

Nakagomi H, Mochizuki H, Inoue M, Hirotsu Y, Amemiya K, Sakamoto I, Nakagomi S, Kubota T, Omata M.

Cancer Sci. 2018 Feb;109(2):453-461. doi: 10.1111/cas.13464. Epub 2018 Jan 17.

PubMed [citation]

PMID:: 29215753
PMCID:: PMC5797818

See all PubMed Citations (3)

Details of each submission

From Ambry Genetics, SCV002742174.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

The c.2589delT pathogenic mutation, located in coding exon 10 of the BRCA2 gene, results from a deletion of one nucleotide at nucleotide position 2589, causing a translational frameshift with a predicted alternate stop codon (p.Q864Kfs*10). This mutation has been reported in multiple individuals with breast and/or ovarian cancer (Musolino A et al. Breast, 2007 Jun;16:280-92; Nakagomi H et al. Cancer Sci, 2018 Feb;109:453-461; Laitman Y et al. Hum Mutat, 2019 11;40:e1-e23). Of note, this alteration is also designated as 2817delT in published literature. In addition to the clinical data presented in the literature, this alteration is expected to result in loss of function by premature protein truncation or nonsense-mediated mRNA decay. As such, this alteration is interpreted as a disease-causing mutation.

#	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: Nov 3, 2024

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