BRCA2-related cancer predisposition

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Summary

BRCA2-related cancer predisposition (MONDO:0700269) is a cancer caused by BRCA2 (GenCC Definitive), with 4 cohort genes (1 CIViC-evidence somatic driver; 1,000 ClinVar predisposition records).

At a glance

  • Classification: Cancer
  • Causal gene: BRCA2 (GenCC Definitive)
  • Cohort genes: 4
  • ClinVar variants: 1,000

Clinical features

No curated clinical features (Orphanet) for this disease.

Identifiers

Disease identifiers

FieldValue
Canonical nameBRCA2-related cancer predisposition
Mondo IDMONDO:0700269
GARD0026409
Is cancer (heuristic)yes

Data availability: 1,000 ClinVar variants · 68 ClinGen variant curations · 1 GenCC gene-disease record.

Disease family

An umbrella term covering 3 Mondo subtypes.

Classification path: disease › human disease › disease by etiologic mechanism › disease of genetic or genomic mechanism › hereditary diseasehereditary neoplastic syndromeBRCA2-related cancer predisposition

Related subtypes (116): mosaic variegated aneuploidy syndrome, tuberous sclerosis, hereditary breast ovarian cancer syndrome, hereditary multiple osteochondromas, nevoid basal cell carcinoma syndrome, leukemia, chronic lymphocytic, susceptibility to, 2, blue rubber bleb nevus, cherubism, Beckwith-Wiedemann syndrome, multiple self-healing squamous epithelioma, erythroleukemia, familial, susceptibility to, goiter, multinodular 1, with or without Sertoli-Leydig cell tumors, hyperparathyroidism 2 with jaw tumors, Kaposi sarcoma, susceptibility to, hereditary leiomyomatosis and renal cell cancer, susceptibility to uveal melanoma, melanoma and neural system tumor syndrome, nasopharyngeal carcinoma, susceptibility to, 2, WAGR syndrome, neuroblastoma, susceptibility to, 1, Rothmund-Thomson syndrome, mismatch repair cancer syndrome 1, Wiskott-Aldrich syndrome, N syndrome, hereditary thrombocytopenia and hematologic cancer predisposition syndrome, prostate cancer/brain cancer susceptibility, Brooke-Spiegler syndrome, pancreatic cancer, susceptibility to, 1, Carney-Stratakis syndrome, nasopharyngeal carcinoma, susceptibility to, 1, ovarian cancer, susceptibility to, 1, colorectal cancer, susceptibility to, 1, lung cancer susceptibility 1, leukemia, chronic lymphocytic, susceptibility to, 1, Kostmann syndrome, colorectal cancer, susceptibility to, 2, colorectal cancer, susceptibility to, 3, colorectal cancer, susceptibility to, 5, colorectal cancer, susceptibility to, 6, colorectal cancer, susceptibility to, 7, leukemia, chronic lymphocytic, susceptibility to, 3, leukemia, chronic lymphocytic, susceptibility to, 4, leukemia, chronic lymphocytic, susceptibility to, 5, lung cancer susceptibility 3, colorectal cancer, susceptibility to, 8, colorectal cancer, susceptibility to, 9, colorectal cancer, susceptibility to, 10, colorectal cancer, susceptibility to, 11, lung cancer susceptibility 4, neuroblastoma, susceptibility to, 3, neuroblastoma, susceptibility to, 4, neuroblastoma, susceptibility to, 5, neuroblastoma, susceptibility to, 6, leukemia, acute lymphocytic, susceptibility to, 1, leukemia, acute lymphocytic, susceptibility to, 2, lung cancer susceptibility 5, BAP1-related tumor predisposition syndrome, familial cutaneous telangiectasia and oropharyngeal predisposition cancer syndrome, Maffucci syndrome, basal cell carcinoma, susceptibility to, 7, colorectal cancer, susceptibility to, 12, leukemia, acute lymphoblastic, susceptibility to, 3, cholangiocarcinoma, susceptibility to, progeroid features-hepatocellular carcinoma predisposition syndrome, neuroblastoma, susceptibility to, 7, DDX41-related hematologic malignancy predisposition syndrome, nasopharyngeal carcinoma, susceptibility to, 3, familial isolated hyperparathyroidism, intestinal polyposis syndrome, dyskeratosis congenita, familial rhabdoid tumor, multiple endocrine neoplasia, hereditary pheochromocytoma-paraganglioma, PTEN hamartoma tumor syndrome, familial multiple fibrofolliculoma, hereditary retinoblastoma, familial atypical multiple mole melanoma syndrome, hereditary nonpolyposis colon cancer, Li-Fraumeni syndrome, Cobb syndrome, neurofibromatosis, susceptibility to familial cutaneous melanoma, pancreatic cancer, susceptibility to, 5, leukemia, acute myeloid, susceptibility to, diffuse gastric and lobular breast cancer syndrome with or without cleft lip and/or palate, glioma susceptibility, hemangioma, capillary infantile, susceptibility to, CDH1-related diffuse gastric and lobular breast cancer syndrome, NTHL1-deficiency tumor predisposition syndrome, SAMD9-related spectrum and myeloid neoplasm risk, neuroblastoma, susceptibility to, 2, BARD1-related cancer predisposition, BRCA1-related cancer predisposition, ATM-related cancer predisposition, CHEK2-related cancer predisposition, PALB2-related cancer predisposition, RAD51C-related cancer predisposition, RAD51D-related cancer predisposition, Li-fraumeni-like syndrome, breast cancer, familial, susceptibility to, 1, breast cancer, familial, susceptibility to, 2, breast cancer, familial, susceptibility to, 3, colorectal cancer, susceptibility to, 4, colorectal cancer, susceptibility to, on chromosome 15, ovarian cancer, familial, susceptibility to, 1, ovarian cancer, familial, susceptibility to, 2, ovarian cancer, familial, susceptibility to, 3, inherited hematologic cancer-predisposing syndrome, mosaic neurofibromatosis/schwannomatosis, tumor predisposition syndrome 2, prostate cancer, hereditary, X-linked 3, follicular lymphoma, susceptibility to, GPR161-related medulloblastoma predisposition, SAMD9L-related spectrum and myeloid neoplasm risk, HAVCR2-related cancer predisposition, EGLN1-related erythrocytosis and pheochromocytoma/paraganglioma predisposition

Subtypes (3): breast-ovarian cancer, familial, susceptibility to, 2, glioma susceptibility 3, pancreatic cancer, susceptibility to, 2

Genetics & variants

GWAS landscape

No GWAS associations recorded — common-variant (GWAS) studies don’t cover this disease (typical for Mendelian / rare diseases). See the curated gene cohort and Mendelian overlap below.

Variant details and genetic-evidence tiers

ClinVar germline variants

600 retrieved; paginated sample, class counts are floors:

240 conflicting classifications of pathogenicity, 122 likely benign, 96 pathogenic, 87 uncertain significance, 30 benign, 15 likely pathogenic, 8 pathogenic/likely pathogenic, 2 benign/likely benign

ClinVarVariant (HGVS)GeneClassificationReview
1069017NM_000059.4(BRCA2):c.156_157insGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCGGGCGGATCACGAGGTCAGGAGATCGACACCATCCTGGCTAGCACGGTGAAACCCCATCTCTACTAAAAATACAACAAATTAGCCGGGCGTGGTGGCGGGTGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGTGTGAACCTGGGAGACGGAGCTTGCAGTGAGCCGAGATCGCGCCACTGCACTCCAGCCTGGGCGACAGAGTGAGACTCCATCTCAAAAAAAAAAAAAAAAAAAAAAAAAAAAGAATCTGAACAT (p.Lys53delinsAlaGlyArgGlyGlySerArgLeuTer)BRCA2Pathogeniccriteria provided, multiple submitters, no conflicts
1076700NM_000059.4(BRCA2):c.9699T>A (p.Cys3233Ter)BRCA2Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
126203NM_000059.4(BRCA2):c.9227G>T (p.Gly3076Val)BRCA2Pathogenicreviewed by expert panel
126217NM_000059.4(BRCA2):c.9672dup (p.Tyr3225fs)BRCA2Pathogenicreviewed by expert panel
141509NM_000059.4(BRCA2):c.6816_6820del (p.Gly2274fs)BRCA2Pathogenicreviewed by expert panel
142095NM_000059.4(BRCA2):c.8954-1_8955delinsAABRCA2Pathogenicreviewed by expert panel
142868NM_000059.4(BRCA2):c.2059_2063del (p.Leu686_Asp687insTer)BRCA2Pathogenicreviewed by expert panel
142998NM_000059.4(BRCA2):c.476-4_476-1delinsTBRCA2Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
1454980NM_000059.4(BRCA2):c.3125dup (p.Leu1042fs)BRCA2Pathogeniccriteria provided, multiple submitters, no conflicts
186927NM_000059.4(BRCA2):c.3353_3355del (p.Leu1118_Glu1119delinsTer)BRCA2Pathogenicreviewed by expert panel
187740NM_000059.4(BRCA2):c.2612C>G (p.Ser871Ter)BRCA2Pathogenicreviewed by expert panel
220844NM_000059.4(BRCA2):c.3201del (p.Val1068fs)BRCA2Pathogenicreviewed by expert panel
225754NM_000059.4(BRCA2):c.8566_8567delinsC (p.Glu2856fs)BRCA2Pathogenicreviewed by expert panel
230582NM_000059.4(BRCA2):c.2641G>T (p.Glu881Ter)BRCA2Pathogenicreviewed by expert panel
230991NM_000059.4(BRCA2):c.5334_5340del (p.Asn1778fs)BRCA2Pathogenicreviewed by expert panel
234524NM_000059.4(BRCA2):c.4651C>T (p.Gln1551Ter)BRCA2Pathogenicreviewed by expert panel
236835NM_000059.4(BRCA2):c.2095C>T (p.Gln699Ter)BRCA2Pathogenicreviewed by expert panel
254556NM_000059.4(BRCA2):c.5281G>T (p.Gly1761Ter)BRCA2Pathogenicreviewed by expert panel
266609NM_000059.4(BRCA2):c.1097T>G (p.Leu366Ter)BRCA2Pathogenicreviewed by expert panel
266703NM_000059.4(BRCA2):c.2490_2491insT (p.Val831fs)BRCA2Pathogenicreviewed by expert panel
266918NM_000059.4(BRCA2):c.6052_6053del (p.Lys2017_Ser2018insTer)BRCA2Pathogenicreviewed by expert panel
266953NM_000059.4(BRCA2):c.6502G>T (p.Gly2168Ter)BRCA2Pathogenicreviewed by expert panel
266960NM_000059.4(BRCA2):c.6536_6537insA (p.Leu2180fs)BRCA2Pathogenicreviewed by expert panel
266970NM_000059.4(BRCA2):c.6676G>T (p.Glu2226Ter)BRCA2Pathogenicreviewed by expert panel
267094NM_000059.4(BRCA2):c.8517C>A (p.Tyr2839Ter)BRCA2Pathogenicreviewed by expert panel
267157NM_000059.4(BRCA2):c.9357_9360del (p.Ile3120fs)BRCA2Pathogenicreviewed by expert panel
267172NM_000059.4(BRCA2):c.9789_9790del (p.Asn3264fs)BRCA2Pathogenicreviewed by expert panel
3236852NM_000059.4(BRCA2):c.8085del (p.Ser2695_Leu2696insTer)BRCA2Pathogeniccriteria provided, multiple submitters, no conflicts
3386239NM_000059.4(BRCA2):c.3090del (p.Phe1031fs)BRCA2Pathogeniccriteria provided, single submitter
3386251NM_000059.4(BRCA2):c.6052del (p.Ser2018fs)BRCA2Pathogeniccriteria provided, multiple submitters, no conflicts

Genes & proteins

Mendelian disease overlap and somatic drivers

GenCC: 13 · Orphanet: 13 · OMIM-shared: 0 · Dual-evidence (GWAS+Mendelian): 0

Somatic driver evidence (intOGen + CIViC, cohort fanout)

GeneintOGen roleCancer typesCIViC
BRCA2LoFBLCA,BRCA,CESC,CHOL,HCC,HNSC,LUSC,MBL,OVT,PAAD,PRAD,PROSTATE,RCC,VULVACIViC #7

GenCC gene–disease validity (cohort genes)

the Disease column is the GenCC-asserted condition — a cohort gene’s strongest validity may be for a related predisposition syndrome.

GeneClassificationInheritanceDiseaseRecords
BRCA2DefinitiveAutosomal dominantBRCA2-related cancer predisposition13

Orphanet rare-disease linkage (cohort genes)

GeneOrphanet IDRare disease
BRCA2Orphanet:1331Familial prostate cancer
BRCA2Orphanet:1333Familial pancreatic carcinoma
BRCA2Orphanet:145Hereditary breast and/or ovarian cancer syndrome
BRCA2Orphanet:178Chordoma
BRCA2Orphanet:227535Hereditary breast cancer
BRCA2Orphanet:319462Inherited cancer-predisposing syndrome due to biallelic BRCA2 mutations
BRCA2Orphanet:440437Familial colorectal cancer Type X
BRCA2Orphanet:654Nephroblastoma
BRCA2Orphanet:667662Breast implant-associated anaplastic large cell lymphoma
BRCA2Orphanet:694963Inflammatory breast cancer
BRCA2Orphanet:70567Cholangiocarcinoma
BRCA2Orphanet:84Fanconi anemia
TMEM132EOrphanet:90636Rare autosomal recessive non-syndromic sensorineural deafness type DFNB

Cohort genes → proteins

4 cohort genes, 3 distinct canonical proteins.

Evidence partition

SubsetGenes
multi_evidence4

Cohort genes (full)

SymbolHGNCEnsemblUniProtNameEvidence
BRCA2HGNC:1101ENSG00000139618P51587Breast cancer type 2 susceptibility proteingencc,clinvar
TMEM132EHGNC:26991ENSG00000181291Q6IEE7Transmembrane protein 132Eclinvar
NALF1HGNC:33877ENSG00000204442B1AL88NALCN channel auxiliary factor 1clinvar
LINC00373HGNC:42695ENSG00000231019long intergenic non-protein coding RNA 373clinvar

Cohort function summary

Lead sentence per gene, UniProt-curated.

SymbolProtein nameFunction (lead sentence)
BRCA2Breast cancer type 2 susceptibility proteinInvolved in double-strand break repair and/or homologous recombination.
TMEM132ETransmembrane protein 132ERequired for normal inner ear hair cell function and hearing.
NALF1NALCN channel auxiliary factor 1Auxillary component of the NALCN sodium channel complex, a channel that regulates the resting membrane potential and controls neuronal excitability.

Protein-family classification

Druggable: 0 · Difficult: 0 · Unknown: 4 · Druggable fraction: 0.0

Family distribution

Cohort families vs a genome-wide background (hypergeometric, BH-FDR; fold = observed/expected). Counts kept; sorted by enrichment, so the catch-all Other/Unknown bucket no longer leads.

FamilyGenesFoldFDR
Other/Unknown41.8×0.097

Per-gene assignment

SymbolFamilyDruggable?ECInterPro (top 3)
BRCA2Other/UnknownnoBRCA2_repeat, NA-bd_OB-fold, BRCA2_OB_1
TMEM132EOther/UnknownnoTMEM132, TMEM132_N, TMEM132_C
NALF1Other/UnknownnoNALCN_aux_factor_1/2
LINC00373Other/Unknownno

Expression context

Cohort genes with no expression data: 0.

2 cohort genes are a single-cell marker in ≥1 SCXA experiment.

Breadth distribution (Bgee present_calls)

BucketGenes
narrow (1-5 tissues)0
moderate (6-20)0
broad (>20)4
unknown0

Top tissues across cohort

TissueCohort genes
male germ line stem cell (sensu Vertebrata) in testis2
secondary oocyte1
ventricular zone1
cerebellar hemisphere1
kidney epithelium1
right hemisphere of cerebellum1
Brodmann (1909) area 231
buccal mucosa cell1
endothelial cell1
bone marrow1
lymph node1

Per-gene tissue summary (top 30)

SymbolBgee breadthFANTOM5 breadthSCXATop tissues
BRCA2184ubiquitousmarkermale germ line stem cell (sensu Vertebrata) in testis, secondary oocyte, ventricular zone
TMEM132E169tissue_specificyeskidney epithelium, right hemisphere of cerebellum, cerebellar hemisphere
NALF1187broadmarkerendothelial cell, Brodmann (1909) area 23, buccal mucosa cell
LINC0037332yesmale germ line stem cell (sensu Vertebrata) in testis, lymph node, bone marrow

Protein interactions among cohort

Intra-cohort edges: 0.

Hub genes (top 10 by interactor count)

SymbolInteractor count
BRCA24,839
NALF1662
TMEM132E653
LINC003730

Structural data

PDB: 2 · AlphaFold-only: 1 · No structure: 1

Cohort genes with PDB structures (top 30)

SymbolUniProtPDB entries
BRCA2P5158714
NALF1B1AL885

AlphaFold-only cohort genes (top 30 by pLDDT)

SymbolUniProtpLDDT
TMEM132EQ6IEE772.44

Function

Pathway analysis

Distinct Reactome pathways touched by cohort: 27. Enrichment computed across 4 evidence-associated genes (1 with Reactome annotation).

Pathways by enrichment

Over-representation of cohort genes vs the genome-wide background (hypergeometric test, Benjamini-Hochberg FDR; fold = observed/expected over 1 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.

PathwayCohort genesFoldFDRSample cohort genes
Impaired BRCA2 translocation to the nucleus13806.7×0.004BRCA2
Impaired BRCA2 binding to SEM1 (DSS1)13806.7×0.004BRCA2
Defective homologous recombination repair (HRR) due to PALB2 loss of function1951.7×0.005BRCA2
HDR through MMEJ (alt-NHEJ)1878.5×0.005BRCA2
Diseases of DNA Double-Strand Break Repair1815.7×0.005BRCA2
Defective homologous recombination repair (HRR) due to BRCA2 loss of function1815.7×0.005BRCA2
Resolution of D-Loop Structures1634.4×0.005BRCA2
Diseases of DNA repair1571.0×0.005BRCA2
Impaired BRCA2 binding to PALB21456.8×0.005BRCA2
Defective homologous recombination repair (HRR) due to BRCA1 loss of function1423.0×0.005BRCA2
Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA1 binding function1423.0×0.005BRCA2
Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA2/RAD51/RAD51C binding function1423.0×0.005BRCA2
Resolution of D-loop Structures through Synthesis-Dependent Strand Annealing (SDSA)1393.8×0.005BRCA2
Homologous DNA Pairing and Strand Exchange1380.7×0.005BRCA2
Homology Directed Repair1308.6×0.005BRCA2
HDR through Homologous Recombination (HRR) or Single Strand Annealing (SSA)1308.6×0.005BRCA2
Impaired BRCA2 binding to RAD511308.6×0.005BRCA2
Resolution of D-loop Structures through Holliday Junction Intermediates1300.5×0.005BRCA2
Meiosis1285.5×0.005BRCA2
Presynaptic phase of homologous DNA pairing and strand exchange1271.9×0.005BRCA2
DNA Double-Strand Break Repair1248.3×0.005BRCA2
Reproduction1190.3×0.006BRCA2
HDR through Homologous Recombination (HRR)1190.3×0.006BRCA2
Meiotic recombination1129.8×0.009BRCA2
DNA Repair198.5×0.011BRCA2
Cell Cycle136.0×0.029BRCA2
Disease113.1×0.076BRCA2

GO biological processes by enrichment

Over-representation of cohort genes vs the genome-wide background (hypergeometric test, Benjamini-Hochberg FDR; fold = observed/expected over 3 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.

GO termCohort genesFoldFDRSample cohort genes
posterior lateral line neuromast hair cell development15617.3×0.005TMEM132E
mitotic recombination-dependent replication fork processing12808.7×0.005BRCA2
negative regulation of mammary gland epithelial cell proliferation11123.5×0.009BRCA2
establishment of protein localization to telomere1702.2×0.009BRCA2
response to UV-C1561.7×0.009BRCA2
telomere maintenance via recombination1510.7×0.009BRCA2
regulation of DNA damage checkpoint1374.5×0.010BRCA2
inner cell mass cell proliferation1330.4×0.010BRCA2
centrosome duplication1312.1×0.010BRCA2
response to X-ray1295.6×0.010BRCA2
female gonad development1267.5×0.010BRCA2
hematopoietic stem cell proliferation1216.1×0.010BRCA2
oocyte maturation1200.6×0.010BRCA2
male meiosis I1193.7×0.010BRCA2
response to gamma radiation1193.7×0.010BRCA2
calcium ion import across plasma membrane1181.2×0.010NALF1
intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator1165.2×0.010BRCA2
positive regulation of mitotic cell cycle1156.0×0.010BRCA2
regulation of cytokinesis1140.4×0.011BRCA2
cellular response to ionizing radiation1137.0×0.011BRCA2
nucleotide-excision repair1127.7×0.011BRCA2
DNA damage response, signal transduction by p53 class mediator1119.5×0.011BRCA2
cellular senescence198.5×0.013BRCA2
double-strand break repair167.7×0.018BRCA2
double-strand break repair via homologous recombination152.0×0.022BRCA2
brain development126.5×0.042BRCA2
spermatogenesis111.7×0.089BRCA2
regulation of DNA-templated transcription110.5×0.095BRCA2
positive regulation of DNA-templated transcription19.3×0.104BRCA2

Therapeutics

Drug target analysis

Approved (phase 4): 0 · Phase ≥3: 0 · Phased (≥1): 0 · Undrugged: 4

Druggability breadth: 0 of 4 evidence-associated genes (0%) have a ChEMBL target (buckets above are over the deeply-mined display cohort).

Top cohort targets by molecule count

SymbolMoleculesMax phase
BRCA200
TMEM132E00
NALF100
LINC0037300

Bioactivity and enzyme data

Enzyme cohort genes (≥1 EC): 0.

Pharmacogenomics

Cohort genes with a PharmGKB record: 3; with CPIC/DPWG dosing guidelines: 0.

No cohort gene has a CPIC/DPWG genotype-guided dosing guideline (PharmGKB).

Drug repurposing candidates

0 approved/phased drugs hit cohort targets but don’t yet appear in disease-level clinical trials. Target-inhibition rationale is strongest for cancer driver genes; a bioactivity hit is a screening signal, not a treatment claim.

Druggability pyramid

Cohort genes binned by druggability tier (high → low):

TierDefinitionGenesSymbols
AApproved (phase 4 drug)0
BPhased (≥1) drug, not yet approved0
CDruggable family + PDB, no drug0
DDruggable family + AlphaFold only, no drug0
EDifficult family or no structure, no drug4BRCA2, TMEM132E, NALF1, LINC00373

Undrugged target profiles

4 cohort genes are undrugged. Ranked by ‘starting-point quality’ (assay depth + drugged-partner adjacency).

SymbolChEMBL assaysDrugged partners (top 3)
BRCA20
TMEM132E0
NALF10
LINC003730

Clinical trials & evidence

Clinical trials

Clinical trials: 0.