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NM_000059.3(BRCA2):c.1796_1800del (p.Thr598_Ser599insTer) AND Breast-ovarian cancer, familial 2

Germline classification:
Pathogenic (7 submissions)
Last evaluated:
Apr 22, 2016
Review status:
3 stars out of maximum of 4 stars
reviewed by expert panel
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:
RCV000031337.8

Allele description

NM_000059.3(BRCA2):c.1796_1800del (p.Thr598_Ser599insTer)

Gene:
BRCA2:BRCA2 DNA repair associated [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
13q13.1
Genomic location:
Preferred name:
NM_000059.3(BRCA2):c.1796_1800del (p.Thr598_Ser599insTer)
Other names:
2022del5; 2024_2028delCTTAT
HGVS:
  • NC_000013.11:g.32333274_32333278del
  • NG_012772.3:g.22795_22799del
  • LRG_293t1:c.1796_1800del
  • LRG_293:g.22795_22799del
  • LRG_293p1:p.Thr598_Ser599insTer
  • NC_000013.10:g.32907409_32907413del
  • NC_000013.10:g.32907411_32907415del
  • NM_000059.3:c.1796_1800delCTTAT
  • U43746.1:c.1796_1800del
  • U43746.1:n.2022_2026delATTTT
  • U43746.1:n.2024_2028delTTTAT
  • p.S599*
  • p.S599X
  • p.Ser599*
Nucleotide change:
2024del5
Links:
Breast Cancer Information Core (BIC) (BRCA2): 2022&base_change=del ATTTT; Breast Cancer Information Core (BIC) (BRCA2): 2024&base_change=del TTTAT; dbSNP: rs276174813
NCBI 1000 Genomes Browser:
rs276174813
Observations:
37

Condition(s)

Name:
Breast-ovarian cancer, familial 2 (BROVCA2)
Synonyms:
BREAST-OVARIAN CANCER, FAMILIAL, SUSCEPTIBILITY TO, 2; BREAST CANCER, FAMILIAL, SUSCEPTIBILITY TO, 2; Breast cancer, familial 2
Identifiers:
MONDO: MONDO:0012933; MedGen: C2675520; Orphanet: 145; OMIM: 612555

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000053942Sharing Clinical Reports Project (SCRP)
no assertion criteria provided
Pathogenic
(May 2, 2011)
germlineclinical testing

SCV000145940Breast Cancer Information Core (BIC) (BRCA2)
no assertion criteria provided
Pathogenic
(May 29, 2002)
germlineclinical testing

SCV000282361Evidence-based Network for the Interpretation of Germline Mutant Alleles (ENIGMA)
reviewed by expert panel

(ENIGMA BRCA1/2 Classification Criteria (2015))
Pathogenic
(Apr 22, 2016)
germlinecuration

ENIGMA BRCA1/2 Classification Criteria (2015),

Citation Link,

SCV000296660Quest Diagnostics Nichols Institute San Juan Capistrano
criteria provided, single submitter

(Quest Diagnostics Criteria)
Pathogenic
(Nov 11, 2015)
germlineclinical testing

PubMed (5)
[See all records that cite these PMIDs]

SCV000326611Consortium of Investigators of Modifiers of BRCA1/2 (CIMBA), c/o University of Cambridge
criteria provided, single submitter

(CIMBA Mutation Classification guidelines May 2016)
Pathogenic
(Oct 2, 2015)
germlineclinical testing

CIMBA_Mutation_Classification_guidelines_May16.pdf,

Citation Link,

SCV000677720Counsyl
criteria provided, single submitter

(Counsyl Autosomal Dominant Disease Classification criteria (2015))
Pathogenic
(Mar 20, 2017)
unknownclinical testing

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

Citation Link,

SCV000839921Human Genome Sequencing Center Clinical Lab, Baylor College of Medicine
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(May 25, 2017)
germlineclinical testing

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlinenot provided10not providednot provided10not providedclinical testing
not providedgermlineyes12not providednot providednot providednot providedclinical testing
not providedgermlineunknownnot provided37not providednot providednot providedclinical testing, curation
not providedunknownunknownnot providednot providednot providednot providednot providedclinical testing
Caucasiangermlineyes1not providednot providednot providednot providedclinical testing
Western Europeangermlineyes3not providednot providednot providednot providedclinical testing
Western European, Italiangermlineyes1not providednot providednot providednot providedclinical testing

Citations

PubMed

Variation in breast cancer risk associated with factors related to pregnancies according to truncating mutation location, in the French National BRCA1 and BRCA2 mutations carrier cohort (GENEPSO).

Lecarpentier J, Noguès C, Mouret-Fourme E, Gauthier-Villars M, Lasset C, Fricker JP, Caron O, Stoppa-Lyonnet D, Berthet P, Faivre L, Bonadona V, Buecher B, Coupier I, Gladieff L, Gesta P, Eisinger F, Frénay M, Luporsi E, Lortholary A, Colas C, Dugast C, Longy M, et al.

Breast Cancer Res. 2012 Jul 3;14(4):R99. doi: 10.1186/bcr3218.

PubMed [citation]
PMID:
22762150
PMCID:
PMC3680948

Characteristics and spectrum of BRCA1 and BRCA2 mutations in 3,922 Korean patients with breast and ovarian cancer.

Kim H, Cho DY, Choi DH, Choi SY, Shin I, Park W, Huh SJ, Han SH, Lee MH, Ahn SH, Son BH, Kim SW; Korean Breast Cancer Study Group., Haffty BG.

Breast Cancer Res Treat. 2012 Aug;134(3):1315-26. doi: 10.1007/s10549-012-2159-5. Epub 2012 Jul 14.

PubMed [citation]
PMID:
22798144
See all PubMed Citations (8)

Details of each submission

From Sharing Clinical Reports Project (SCRP), SCV000053942.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenot provided10not providednot providednot providednot providednot provided See 1

Co-occurrences

#ZygosityAllelesNumber of Observations
1SingleHeterozygoteBRCA2:5864A>G (E1879G)1

From Breast Cancer Information Core (BIC) (BRCA2), SCV000145940.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided8not providednot providedclinical testingnot provided
2not provided2not providednot providedclinical testingnot provided
3not provided1not providednot providedclinical testingnot provided
4not provided1not providednot providedclinical testingnot provided
5Caucasian1not providednot providedclinical testingnot provided
6Western European3not providednot providedclinical testingnot provided
7Western European, Italian1not providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided8not providednot providednot provided
2germlineyesnot providednot providednot provided2not providednot providednot provided
3germlineyesnot providednot providednot provided1not providednot providednot provided
4germlineyesnot providednot providednot provided1not providednot providednot provided
5germlineyesnot providednot providednot provided1not providednot providednot provided
6germlineyesnot providednot providednot provided3not providednot providednot provided
7germlineyesnot providednot providednot provided1not providednot providednot provided

From Evidence-based Network for the Interpretation of Germline Mutant Alleles (ENIGMA), SCV000282361.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedcurationnot provided

Description

Variant allele predicted to encode a truncated non-functional protein.

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

From Quest Diagnostics Nichols Institute San Juan Capistrano, SCV000296660.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (5)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Consortium of Investigators of Modifiers of BRCA1/2 (CIMBA), c/o University of Cambridge, SCV000326611.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot provided37not provided

From Counsyl, SCV000677720.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (3)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownunknownnot providednot providednot providednot providednot providednot providednot provided

From Human Genome Sequencing Center Clinical Lab, Baylor College of Medicine, SCV000839921.1

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

Description

The c.1796_1800del (p.Ser599*) variant in the BRCA2 gene has been detected multiple patients with breast cancer [reported as 2022del5 in PMID 8988179]. This variant creates a premature stop codon at amino acid position 599 of the BRCA2 protein. This variant is thus predicted to result in a loss of function of the protein. This variant has not been observed in the ExAC population database. This variant thus classified as pathogenic.

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

Last Updated: Jun 26, 2021