NM_000059.4(BRCA2):c.6491_6494del (p.Gln2164fs) AND Hereditary breast ovarian cancer syndrome

Germline classification:: Pathogenic (2 submissions)
Last evaluated:: Apr 22, 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:: RCV000496413.16

Allele description [Variation Report for NM_000059.4(BRCA2):c.6491_6494del (p.Gln2164fs)]

NM_000059.4(BRCA2):c.6491_6494del (p.Gln2164fs)

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.6491_6494del (p.Gln2164fs)

Other names:

6719del4

HGVS:

NC_000013.11:g.32340846_32340849del
NG_012772.3:g.30367_30370del
NM_000059.4:c.6491_6494delMANE SELECT
NP_000050.3:p.Gln2164fs
LRG_293:g.30367_30370del
NC_000013.10:g.32914983_32914986del
NC_000013.10:g.32914983_32914986delAGTT
NM_000059.3:c.6491_6494delAGTT
p.Gln2164fs

Links:

dbSNP: rs397507862

NCBI 1000 Genomes Browser:

rs397507862

Molecular consequence:

NM_000059.4:c.6491_6494del - frameshift variant - [Sequence Ontology: SO:0001589]

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

Recent activity

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Mus musculus mitochondrial ribosomal protein S5 (Mrps5), mRNA
Mus musculus mitochondrial ribosomal protein S5 (Mrps5), mRNA
gi|21914844|ref|NM_029963.2|

Nucleotide
Mus musculus proline-rich coiled-coil 2C (Prrc2c), mRNA
Mus musculus proline-rich coiled-coil 2C (Prrc2c), mRNA
gi|124486834|ref|NM_001081290.1|

Nucleotide
N-terminal EF-hand calcium-binding protein 3 isoform 3 [Mus musculus]
N-terminal EF-hand calcium-binding protein 3 isoform 3 [Mus musculus]
gi|148922939|ref|NP_067521.2|

Protein
Mus musculus lysine (K)-specific demethylase 4A (Kdm4a), transcript variant 6, m...
Mus musculus lysine (K)-specific demethylase 4A (Kdm4a), transcript variant 6, mRNA
gi|2630406352|ref|NM_001426258.1|

Nucleotide
Mus musculus R1-type mRNA for choline acetyltransferase, N-terminal
Mus musculus R1-type mRNA for choline acetyltransferase, N-terminal
gi|220372|dbj|D12490.1|MUSCATR1

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000587853	Research Molecular Genetics Laboratory, Women's College Hospital, University of Toronto - The Canadian Open Genetics Repository (COGR)	no assertion criteria provided	Pathogenic (Jan 31, 2014)	germline	research
SCV001578506	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Apr 22, 2023)	germline	clinical testing	PubMed (6) [See all records that cite these PMIDs] 21232165, 22366370, 28477318, 30606148, 20104584, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000587853

Research Molecular Genetics Laboratory, Women's College Hospital, University of Toronto - The Canadian Open Genetics Repository (COGR)

no assertion criteria provided

Pathogenic
(Jan 31, 2014)

germline

research

SCV001578506

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Apr 22, 2023)

germline

clinical testing

PubMed (6)
[See all records that cite these PMIDs]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	research
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

The occurrence of germline BRCA1 and BRCA2 sequence alterations in Slovenian population.

Stegel V, Krajc M, Zgajnar J, Teugels E, De Grève J, Hočevar M, Novaković S.

BMC Med Genet. 2011 Jan 14;12:9. doi: 10.1186/1471-2350-12-9.

PubMed [citation]

PMID:: 21232165
PMCID:: PMC3025939

Three novel BRCA1/BRCA2 mutations in breast/ovarian cancer families in Croatia.

Levanat S, Musani V, Cvok ML, Susac I, Sabol M, Ozretic P, Car D, Eljuga D, Eljuga L, Eljuga D.

Gene. 2012 May 1;498(2):169-76. doi: 10.1016/j.gene.2012.02.010. Epub 2012 Feb 17.

PubMed [citation]

PMID:: 22366370

See all PubMed Citations (6)

Details of each submission

From Research Molecular Genetics Laboratory, Women's College Hospital, University of Toronto - The Canadian Open Genetics Repository (COGR), SCV000587853.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	research	not provided

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001578506.4

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (6)

Description

For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 52116). This variant is also known as 6719del4. This premature translational stop signal has been observed in individual(s) with breast and/or ovarian cancer (PMID: 21232165, 22366370, 28477318, 30606148). This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Gln2164Argfs*3) in the BRCA2 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in BRCA2 are known to be pathogenic (PMID: 20104584).

#	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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