BRCC3

gene
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Also known as C6.1ABRCC36

Summary

BRCC3 (BRCA1/BRCA2-containing complex subunit 3, HGNC:24185) is a protein-coding gene on chromosome Xq28, encoding Lys-63-specific deubiquitinase BRCC36 (P46736). Metalloprotease that specifically cleaves ‘Lys-63’-linked polyubiquitin chains.

This gene encodes a subunit of the BRCA1-BRCA2-containing complex (BRCC), which is an E3 ubiquitin ligase. This complex plays a role in the DNA damage response, where it is responsible for the stable accumulation of BRCA1 at DNA break sites. The component encoded by this gene can specifically cleave Lys 63-linked polyubiquitin chains, and it regulates the abundance of these polyubiquitin chains in chromatin. The loss of this gene results in abnormal angiogenesis and is associated with syndromic moyamoya, a cerebrovascular angiopathy. Alternative splicing results in multiple transcript variants. A related pseudogene has been identified on chromosome 5.

Source: NCBI Gene 79184 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): Moyamoya disease (Limited, GenCC)
  • GWAS associations: 1
  • Clinical variants (ClinVar): 126 total — 21 pathogenic, 6 likely-pathogenic
  • Phenotypes (HPO): 27
  • Druggable target: yes
  • MANE Select transcript: NM_001018055

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:24185
Approved symbolBRCC3
NameBRCA1/BRCA2-containing complex subunit 3
LocationXq28
Locus typegene with protein product
StatusApproved
AliasesC6.1A, BRCC36
Ensembl geneENSG00000185515
Ensembl biotypeprotein_coding
OMIM300617
Entrez79184

Gene structure

Transcript identifiers

Ensembl transcripts: 7 — 6 protein_coding, 1 nonsense_mediated_decay

ENST00000330045, ENST00000340647, ENST00000369459, ENST00000369462, ENST00000399026, ENST00000411985, ENST00000453705

RefSeq mRNA: 3 — MANE Select: NM_001018055 NM_001018055, NM_001242640, NM_024332

CCDS: CCDS56610, CCDS56611, CCDS56612

Canonical transcript exons

ENST00000330045 — 11 exons

ExonStartEnd
ENSE00001450104155073377155073431
ENSE00001761409155072327155072343
ENSE00001856280155071508155071650
ENSE00001950263155121223155123077
ENSE00003465734155089263155089351
ENSE00003549592155116711155116754
ENSE00003584139155119999155120168
ENSE00003590279155090784155090839
ENSE00003596470155078616155078703
ENSE00003627027155116057155116188
ENSE00003650453155077170155077289

Expression profiles

Bgee: expression breadth ubiquitous, 281 present calls, max score 95.36.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 10.2588 / max 199.4382, expressed in 1741 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter IDTPM avgSamples expressed
1982158.99651716
1982141.2623825

Top tissues by expression

287 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
parotid glandUBERON:000183195.36gold quality
oral cavityUBERON:000016793.57gold quality
buccal mucosa cellCL:000233693.19gold quality
mucosa of sigmoid colonUBERON:000499390.89gold quality
colonic mucosaUBERON:000031790.86gold quality
corpus epididymisUBERON:000435990.51gold quality
biceps brachiiUBERON:000150790.06gold quality
rectumUBERON:000105289.96gold quality
skeletal muscle tissue of biceps brachiiUBERON:000450289.81gold quality
esophagus squamous epitheliumUBERON:000692089.40gold quality
bronchial epithelial cellCL:000232888.74gold quality
islet of LangerhansUBERON:000000688.68gold quality
nasal cavity epitheliumUBERON:000538488.64gold quality
heart right ventricleUBERON:000208088.39gold quality
skeletal muscle tissue of rectus abdominisUBERON:000451188.05gold quality
upper arm skinUBERON:000426387.93gold quality
mucosa of paranasal sinusUBERON:000503087.82gold quality
cortical plateUBERON:000534387.82gold quality
nasal cavity mucosaUBERON:000182687.72gold quality
cauda epididymisUBERON:000436087.65gold quality
caput epididymisUBERON:000435887.29gold quality
epithelium of esophagusUBERON:000197687.11gold quality
jejunumUBERON:000211586.78gold quality
jejunal mucosaUBERON:000039986.76gold quality
vastus lateralisUBERON:000137986.74gold quality
duodenumUBERON:000211486.74gold quality
mammalian vulvaUBERON:000099786.65gold quality
endometriumUBERON:000129586.59gold quality
trabecular bone tissueUBERON:000248386.57gold quality
monocyteCL:000057686.56gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-ANND-3yes6.33

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

89 targeting BRCC3, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-1193100.0065.93529
HSA-MIR-6867-5P100.0082.213464
HSA-MIR-190A-3P100.0080.355520
HSA-MIR-477599.9875.006394
HSA-MIR-569699.9872.364487
HSA-MIR-806899.9873.852376
HSA-MIR-6778-3P99.9667.292693
HSA-MIR-335-3P99.9373.364958
HSA-MIR-218-5P99.9372.222103
HSA-MIR-4760-3P99.9370.502385
HSA-MIR-145-5P99.9271.131836
HSA-MIR-5195-3P99.9270.921877
HSA-MIR-6768-5P99.9267.361942
HSA-MIR-338-5P99.9272.342951
HSA-MIR-311999.9271.342390
HSA-MIR-806399.9169.763146
HSA-MIR-579-3P99.8671.663628
HSA-MIR-664B-3P99.8471.653590
HSA-MIR-6875-3P99.8270.262983
HSA-MIR-4659A-3P99.8072.624248
HSA-MIR-4659B-3P99.8072.624248
HSA-MIR-63699.8069.581500
HSA-MIR-204-5P99.7971.622439
HSA-MIR-211-5P99.7971.652440
HSA-MIR-5002-5P99.7670.841763
HSA-MIR-3059-5P99.7069.932491
HSA-MIR-670-5P99.6769.941565
HSA-MIR-6757-3P99.6366.881089
HSA-MIR-466399.6265.33957
HSA-MIR-6832-5P99.5864.821132

Literature-anchored findings (GeneRIF, showing 31)

  • These findings demonstrate that BRCC3 is a novel effector of Raf-1, and implicate a role of BRCC3 in modulation of p-ERK, cell survival and proliferation. (PMID:17143545)
  • the human Ubc13/Rnf8 ubiquitin ligases control foci formation of the Rap80/Abraxas/Brca1/Brcc36 complex in response to DNA damage (PMID:18077395)
  • Specificity for K63-linked polyubiquitin is a common property of the JAMM/MPN+ family of deubiquitinating enzymes. (PMID:19214193)
  • scaffold proteins not only participate in the regulation of BRCC36 activity but also determine its subcellular localization and cellular functions. (PMID:20656690)
  • NBA1/MERIT40 and BRE interaction is required for the integrity of two distinct deubiquitinating enzyme BRCC36-containing complexes (PMID:21282113)
  • these data strongly suggest that BRCC3, a deubiquitinating enzyme that is part of the cellular BRCA1 and BRISC complexes, is an important player in angiogenesis and that BRCC3 loss-of-function mutations are associated with moyamoya angiopathy. (PMID:21596366)
  • upregulation of BRCC3 expression is associated with glioma. (PMID:25337721)
  • BRCC3 likely plays a role as tumor-associated gene in myelodysplastic syndromes and myelodysplastic/myeloproliferative neoplasms. (PMID:26001790)
  • BRCC3 inversely correlated with NPC overall and relapse-free survival. Its expression was higher in radioresistant NPC cells, where BRCC3 knockdown increased the cell survival fraction, attenuated DNA damage repair and resulted in G2/M cell cycle arrest. (PMID:26024915)
  • KIAA0157 allosterically activates a cognate deubiquitinating enzyme (DUB) partner and implicates super dimerization as a new regulatory mechanism underlying BRCC36 DUB activity. (PMID:26344097)
  • BRCC3 may play a role in B7-H3-induced 5-Fu resistance. (PMID:27175567)
  • findings uncover a pivotal role of BRCC36 DUB in limiting DSB processing and repair and illustrate how cells may physically couple ubiquitin recognition and metabolizing activities for fine tuning of DNA repair processes. (PMID:27288411)
  • In late S/G2 phase, the DNA damage-responsive E3 ligase RNF8 conjugates K63-linked ubiquitin chains to tankyrase 1, while in G1 phase such ubiquitin chains are removed by BRISC, an ABRO1/BRCC36-containing deubiquitinase complex. (PMID:27993934)
  • this study shows that mitochondrial DNA oxidation induces imbalanced activity of NLRP3/NLRP6 inflammasomes by activation of caspase-8 and BRCC36 in dry eye (PMID:28238526)
  • Knockdown of BRCC3 in HeLa and SiHa cervical cancer cells revealed that BRCC3 interference inhibited the viability, in addition to the invasion and migration abilities, of cervical cancer cells via regulation of Snai family members and MMPs, which subsequently inhibit the progress of EMT. (PMID:30272359)
  • Luciferase reporter assay and in vitro rescue experiment confirmed that ANRIL promoted NLRP3 inflammasome activation by up-regulating BRCC3 expression via sponging miR-122-5p. (PMID:30347231)
  • a LNK-associated lysine-63 (K63)-deubiquitinating enzyme complex, Brcc36 isopeptidase complex (BRISC), attenuates HSC expansion through control of JAK2 signaling. (PMID:30755420)
  • BRCC3 expressed in oligodendrocyte precursor cells in vitro is required for the oligodendrocyte lineage progression toward the mature stage. Lack of BRCC3 function could deteriorate demyelination at the lesion site. An increase in Lys63-linked ubiquitination levels induced by the deregulation of BRCC3 expression promotes the endosomal/lysosomal processing of myelin proteins. (PMID:31184779)
  • Here we show that in the BRCA1-A complex structure, ABRAXAS integrates the DNA repair protein RAP80 and provides a high-affinity binding site that sequesters the tumor suppressor BRCA1 away from the break site. In the BRISC structure, ABRO1 binds SHMT2alpha, a metabolic enzyme enabling cancer growth in hypoxic environments, which we find prevents BRCC36 from binding and cleaving ubiquitin chains (PMID:31253574)
  • Cell lines and primary mouse cells with inactivation of BRCC3 had a higher sensitivity to doxorubicin. (PMID:31576005)
  • Vitamin D Receptor Inhibits NLRP3 Activation by Impeding Its BRCC3-Mediated Deubiquitination. (PMID:31866999)
  • BRCC36 functions noncatalytically to promote antiviral response by maintaining STAT1 protein stability. (PMID:32673428)
  • ABRO1 stabilizes the deubiquitinase BRCC3 through inhibiting its degradation mediated by the E3 ubiquitin ligase WWP2. (PMID:33107021)
  • BRCA1-A and BRISC: Multifunctional Molecular Machines for Ubiquitin Signaling. (PMID:33142801)
  • Identification and Verification of the Ability of Cdk5 to Phosphorylate Deubiquitinating Enzyme BRCC3 In Vitro. (PMID:35503584)
  • Identification of BRCC3 and BRCA1 as Regulators of TAZ Stability and Activity. (PMID:37887275)
  • The deubiquitinase BRCC3 increases the stability of ZEB1 and promotes the proliferation and metastasis of triple-negative breast cancer cells. (PMID:38449391)
  • Deubiquitinase BRCC3 promotes the migration, invasion and EMT progression of colon adenocarcinoma by stabilizing MET expression. (PMID:38470543)
  • BRCC3 mediates inflammation and pyroptosis in cerebral ischemia/reperfusion injury by activating the NLRP6 inflammasome. (PMID:38544474)
  • BRCC3 Regulation of ALK2 in Vascular Smooth Muscle Cells: Implication in Pulmonary Hypertension. (PMID:38557054)
  • BRCC36 regulates beta-catenin ubiquitination to alleviate vascular calcification in chronic kidney disease. (PMID:39227917)

Cross-species orthologs

4 orthologs

OrganismSymbolGene ID
danio_reriobrcc3ENSDARG00000098242
mus_musculusBrcc3ENSMUSG00000031201
mus_musculusBrcc3dcENSMUSG00000112039
rattus_norvegicusBrcc3dcENSRNOG00000070196

Paralogs (3): PSMD14 (ENSG00000115233), COPS5 (ENSG00000121022), EIF3H (ENSG00000147677)

Protein

Protein identifiers

Lys-63-specific deubiquitinase BRCC36P46736 (reviewed: P46736)

Alternative names: BRCA1-A complex subunit BRCC36, BRCA1/BRCA2-containing complex subunit 3, BRCA1/BRCA2-containing complex subunit 36, BRISC complex subunit BRCC36

All UniProt accessions (4): P46736, A0A0A0MS96, H7C413, X6RJS7

UniProt curated annotations — full annotation on UniProt →

Function. Metalloprotease that specifically cleaves ‘Lys-63’-linked polyubiquitin chains. Does not have activity toward ‘Lys-48’-linked polyubiquitin chains. Component of the BRCA1-A complex, a complex that specifically recognizes ‘Lys-63’-linked ubiquitinated histones H2A and H2AX at DNA lesions sites, leading to target the BRCA1-BARD1 heterodimer to sites of DNA damage at double-strand breaks (DSBs). In the BRCA1-A complex, it specifically removes ‘Lys-63’-linked ubiquitin on histones H2A and H2AX, antagonizing the RNF8-dependent ubiquitination at double-strand breaks (DSBs). Catalytic subunit of the BRISC complex, a multiprotein complex that specifically cleaves ‘Lys-63’-linked ubiquitin in various substrates. Mediates the specific ‘Lys-63’-specific deubiquitination associated with the COP9 signalosome complex (CSN), via the interaction of the BRISC complex with the CSN complex. The BRISC complex is required for normal mitotic spindle assembly and microtubule attachment to kinetochores via its role in deubiquitinating NUMA1. Plays a role in interferon signaling via its role in the deubiquitination of the interferon receptor IFNAR1; deubiquitination increases IFNAR1 activity by enhancing its stability and cell surface expression. Acts as a regulator of the NLRP3 inflammasome by mediating deubiquitination of NLRP3, leading to NLRP3 inflammasome assembly. Down-regulates the response to bacterial lipopolysaccharide (LPS) via its role in IFNAR1 deubiquitination. Deubiquitinates HDAC1 and PWWP2B leading to their stabilization.

Subunit / interactions. Component of the ARISC complex, at least composed of UIMC1/RAP80, ABRAXAS1, BRCC3/BRCC36, BABAM2 and BABAM1/NBA1. Component of the BRCA1-A complex, at least composed of BRCA1, BARD1, UIMC1/RAP80, ABRAXAS1, BRCC3/BRCC36, babam2 and BABAM1/NBA1. In the BRCA1-A complex, interacts directly with ABRAXAS1 and babam2. Component of the BRISC complex, at least composed of ABRAXAS2, BRCC3/BRCC36, BABAM2 and BABAM1/NBA1. Identified in a complex with SHMT2 and the other subunits of the BRISC complex. In the BRISC complex, interacts directly with ABRAXAS2. Identified in a complex with ABRAXAS2 and NUMA1. The BRISC complex interacts with the CSN complex. Component of the BRCA1/BRCA2 containing complex (BRCC), which also contains BRCA1, BRCA2, BARD1, BABAM2 and RAD51. BRCC is a ubiquitin E3 ligase complex that enhances cellular survival following DNA damage. Interacts with BRCA1. Binds polyubiquitin. Interacts with PWWP2B. Interacts with HDAC1; this interaction is enhanced in the presence of PWWP2B.

Subcellular location. Nucleus. Cytoplasm. Cytoskeleton. Spindle pole.

Tissue specificity. Heart, brain, placenta, lung, liver, skeletal muscle, kidney and pancreas. Aberrantly expressed in the vast majority of breast tumors.

Disease relevance. A chromosomal aberration involving BRCC3 is a cause of pro-lymphocytic T-cell leukemia (T-PLL). Translocation t(X;14)(q28;q11) with TCRA.

Cofactor. Binds 1 zinc ion per subunit.

Similarity. Belongs to the peptidase M67A family. BRCC36 subfamily.

Isoforms (5)

UniProt IDNamesCanonical?
P46736-12yes
P46736-21
P46736-33
P46736-44
P46736-55

RefSeq proteins (3): NP_001018065, NP_001229569, NP_077308 (=MANE)

Domains & families (InterPro)

IDNameType
IPR000555JAMM/MPN+_domDomain
IPR033860MPN_BRCC36Family
IPR037518MPNDomain
IPR040749BRCC36_CDomain
IPR050242JAMM_MPN+_peptidase_M67AFamily

Pfam: PF01398, PF18110

UniProt features (36 total): strand 8, helix 7, mutagenesis site 5, splice variant 4, binding site 3, modified residue 2, initiator methionine 1, chain 1, sequence variant 1, sequence conflict 1, domain 1, turn 1, short sequence motif 1

Structure

Experimental structures (PDB)

4 structures.

PDBMethodResolution (Å)
8PVYELECTRON MICROSCOPY3.02
8PY2ELECTRON MICROSCOPY3.32
6R8FELECTRON MICROSCOPY3.8
6H3CELECTRON MICROSCOPY3.9

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-P46736-F184.680.73

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Ligand- & substrate-binding residues (3): 122; 124; 135

Post-translational modifications (2): 2, 258

Mutagenesis-validated functional residues (5):

PositionPhenotype
23abolishes localization to sites of dna damage and interaction with abraxas2; uimc1; shmt2; baram2 and babam1; when assoc
27abolishes localization to sites of dna damage and interaction with abraxas2; uimc1; shmt2; babam2 and babam1; when assoc
122–124abolishes metalloprotease activity and function in dna repair.
122loss of deubiquitinase activity.
278abolishes interaction with uimc1 and shmt2.

Function

Pathways and Gene Ontology

Reactome pathways

16 pathways

IDPathway
R-HSA-5689901Metalloprotease DUBs
R-HSA-5693565Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks
R-HSA-5693571Nonhomologous End-Joining (NHEJ)
R-HSA-5693607Processing of DNA double-strand break ends
R-HSA-69473G2/M DNA damage checkpoint
R-HSA-1640170Cell Cycle
R-HSA-392499Metabolism of proteins
R-HSA-5688426Deubiquitination
R-HSA-5693532DNA Double-Strand Break Repair
R-HSA-5693538Homology Directed Repair
R-HSA-5693567HDR through Homologous Recombination (HRR) or Single Strand Annealing (SSA)
R-HSA-5693606DNA Double Strand Break Response
R-HSA-597592Post-translational protein modification
R-HSA-69481G2/M Checkpoints
R-HSA-69620Cell Cycle Checkpoints
R-HSA-73894DNA Repair

MSigDB gene sets: 306 (showing top): GOBP_RESPONSE_TO_NITROGEN_COMPOUND, GOBP_REGULATION_OF_CELL_CYCLE_CHECKPOINT, RODRIGUES_THYROID_CARCINOMA_ANAPLASTIC_UP, GOBP_RESPONSE_TO_IONIZING_RADIATION, BUYTAERT_PHOTODYNAMIC_THERAPY_STRESS_DN, GOMF_METALLOPEPTIDASE_ACTIVITY, GOBP_INFLAMMATORY_RESPONSE, REACTOME_G2_M_DNA_DAMAGE_CHECKPOINT, GOBP_CELL_CYCLE_PHASE_TRANSITION, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, GOBP_REGULATION_OF_CELLULAR_COMPONENT_BIOGENESIS, GOBP_PROTEIN_MODIFICATION_BY_SMALL_PROTEIN_REMOVAL, GOBP_REGULATION_OF_DNA_REPAIR, GOBP_MITOTIC_G2_M_TRANSITION_CHECKPOINT, GOBP_REGULATION_OF_CELL_CYCLE_G2_M_PHASE_TRANSITION

GO Biological Process (19): regulation of DNA repair (GO:0006282), double-strand break repair (GO:0006302), proteolysis (GO:0006508), mitotic G2 DNA damage checkpoint signaling (GO:0007095), response to X-ray (GO:0010165), response to ionizing radiation (GO:0010212), protein deubiquitination (GO:0016579), mitotic G2/M transition checkpoint (GO:0044818), positive regulation of DNA repair (GO:0045739), cell division (GO:0051301), protein K63-linked deubiquitination (GO:0070536), cellular response to ionizing radiation (GO:0071479), DNA repair-dependent chromatin remodeling (GO:0140861), positive regulation of NLRP3 inflammasome complex assembly (GO:1900227), regulation of DNA damage checkpoint (GO:2000001), DNA repair (GO:0006281), chromatin organization (GO:0006325), DNA damage response (GO:0006974), NLRP3 inflammasome complex assembly (GO:0044546)

GO Molecular Function (10): cysteine-type deubiquitinase activity (GO:0004843), metallopeptidase activity (GO:0008237), enzyme regulator activity (GO:0030234), polyubiquitin modification-dependent protein binding (GO:0031593), metal ion binding (GO:0046872), K63-linked deubiquitinase activity (GO:0061578), metal-dependent deubiquitinase activity (GO:0140492), protein binding (GO:0005515), peptidase activity (GO:0008233), hydrolase activity (GO:0016787)

GO Cellular Component (10): ubiquitin ligase complex (GO:0000151), nuclear ubiquitin ligase complex (GO:0000152), spindle pole (GO:0000922), nucleus (GO:0005634), nucleoplasm (GO:0005654), cytoplasm (GO:0005737), cytosol (GO:0005829), BRCA1-A complex (GO:0070531), BRISC complex (GO:0070552), cytoskeleton (GO:0005856)

Reactome top-level categories

Rollup of top-11 pathways:

CategoryPathways
DNA Double-Strand Break Repair3
Deubiquitination1
DNA Double Strand Break Response1
HDR through Homologous Recombination (HRR) or Single Strand Annealing (SSA)1
G2/M Checkpoints1
Post-translational protein modification1
DNA Repair1
Homology Directed Repair1
Metabolism of proteins1
Cell Cycle Checkpoints1
Cell Cycle1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure4
DNA repair3
deubiquitinase activity3
nuclear protein-containing complex3
regulation of cellular response to stress2
response to ionizing radiation2
DNA damage response2
catalytic activity2
regulation of DNA metabolic process1
protein metabolic process1
mitotic G2 phase1
mitotic DNA damage checkpoint signaling1
mitotic G2/M transition checkpoint1
response to radiation1
cysteine-type deubiquitinase activity1
protein modification by small protein removal1
mitotic cell cycle checkpoint signaling1
negative regulation of G2/M transition of mitotic cell cycle1
regulation of DNA repair1
positive regulation of response to stimulus1
positive regulation of DNA metabolic process1
cellular process1
protein deubiquitination1
cellular response to radiation1
chromatin remodeling1
positive regulation of protein-containing complex assembly1
NLRP3 inflammasome complex assembly1
positive regulation of inflammasome-mediated signaling pathway1
regulation of NLRP3 inflammasome complex assembly1
DNA damage checkpoint signaling1
regulation of cell cycle checkpoint1
DNA metabolic process1
cellular component organization1
cellular response to stress1
canonical inflammasome complex assembly1
cysteine-type peptidase activity1
peptidase activity1
molecular function regulator activity1
modification-dependent protein binding1
cation binding1

Protein interactions and networks

STRING

3074 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
BRCC3UIMC1Q96RL1999
BRCC3BABAM2Q9NXR7998
BRCC3BABAM1Q9NWV8998
BRCC3ABRAXAS1Q6UWZ7998
BRCC3BRCA1P38398995
BRCC3BARD1Q99728994
BRCC3ABRAXAS2Q15018992
BRCC3BRCA2P51587858
BRCC3RNF8O76064780
BRCC3MDC1Q14676775
BRCC3RAD51Q06609752
BRCC3RBBP8Q99708733
BRCC3ZUP1Q96AP4711
BRCC3RNF168Q8IYW5659
BRCC3STAMBPL1Q96FJ0654

IntAct

78 interactions, top by confidence:

ABTypeScore
JUNBFOSpsi-mi:“MI:0914”(association)0.950
SHMT2BRCC3psi-mi:“MI:0915”(physical association)0.720
CFTRESYT2psi-mi:“MI:2364”(proximity)0.710
UIMC1BRCC3psi-mi:“MI:0915”(physical association)0.690
BRCC3UIMC1psi-mi:“MI:0915”(physical association)0.690
ABRAXAS2BRCC3psi-mi:“MI:2364”(proximity)0.690
BRCC3ABRAXAS2psi-mi:“MI:2364”(proximity)0.690
BRCC3ABRAXAS2psi-mi:“MI:0915”(physical association)0.690
ABRAXAS2BRCC3psi-mi:“MI:0915”(physical association)0.690
BABAM2BRCC3psi-mi:“MI:0914”(association)0.670
ABRAXAS1BRCC3psi-mi:“MI:0915”(physical association)0.640
BABAM1TNKSpsi-mi:“MI:0914”(association)0.640
BRCC3BRCA1psi-mi:“MI:0914”(association)0.610
BRCA1BRCC3psi-mi:“MI:0914”(association)0.610
ANKRD11BRCC3psi-mi:“MI:0915”(physical association)0.560
BRCC3ANKRD11psi-mi:“MI:0915”(physical association)0.560
YWHAGSHTN1psi-mi:“MI:0914”(association)0.560
KSR2POLR3Apsi-mi:“MI:0914”(association)0.530
TNS1SORBS3psi-mi:“MI:0914”(association)0.530
DEF6ARHGAP42psi-mi:“MI:0914”(association)0.530
TFDP3E2F3psi-mi:“MI:0914”(association)0.530

BioGRID (276): BRCC3 (Affinity Capture-Western), FANCG (Biochemical Activity), BRCC3 (Affinity Capture-Western), BRCC3 (Affinity Capture-MS), BRCC3 (Affinity Capture-MS), BRCC3 (Affinity Capture-MS), BRCC3 (Affinity Capture-MS), BRCC3 (Affinity Capture-MS), BRCC3 (Affinity Capture-MS), BRCC3 (Two-hybrid), BRCC3 (Affinity Capture-MS), BRCC3 (Affinity Capture-MS), BRCC3 (Affinity Capture-MS), BRCC3 (Affinity Capture-MS), BRCC3 (Affinity Capture-MS)

ESM2 similar proteins: A0A8M3B525, A2AHJ4, A5PJP6, B0KWU8, B2RYM5, B5X8M4, E1C3P4, E9Q4Z2, O00763, O42611, O94967, O95630, P46736, P46737, P48553, Q15386, Q15542, Q3TLI0, Q4VA72, Q5KSL6, Q5R558, Q5R9L6, Q5RAQ5, Q5VVJ2, Q641K1, Q66GV6, Q66H62, Q69Z66, Q6RI45, Q6WKZ8, Q76N33, Q7M757, Q80U95, Q8BPM2, Q8CGF6, Q8IVH8, Q8QFR2, Q8TAT6, Q8VDD9, Q8W206

Diamond homologs: A0A8M3B525, A5PJP6, B0KWU8, B2RYM5, B5X8M4, E2AXC7, O35864, P46736, P46737, Q3TV65, Q4VA72, Q5R9L6, Q66GV6, Q6GLM9, Q6P635, Q6PC30, Q7M757, Q8H936, Q8N594, Q92905, Q9LT08, A6ZXB7, B3LH96, O94454, P91001, Q12468, Q4IJM4, Q4P804, Q6BMQ3, Q6C703, Q7RXX8, Q9FVU9, O00487, O35593, O76577, P0CQ24, P0CQ25, P41878, P41883, P43588

SIGNOR signaling

4 interactions.

AEffectBMechanism
BRCC3down-regulatesH2AC11deubiquitination
BRCC3“form complex”“BRCC ubiquitin ligase complex”binding
BRCC3“form complex”“BRCA1-A complex”binding
BRCC3down-regulates“Histone H2A”deubiquitination

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 80 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

PathwayPartnersFoldFDR
Metalloprotease DUBs840.1×3e-09
DNA Double Strand Break Response539.6×1e-05
Homology Directed Repair525.7×7e-05
HDR through Homologous Recombination (HRR) or Single Strand Annealing (SSA)525.7×7e-05
G2/M Checkpoints1124.6×3e-10
G2/M DNA damage checkpoint1122.0×5e-10
Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks922.0×3e-08
DNA Double-Strand Break Repair520.7×2e-04

GO biological processes:

GO termPartnersFoldFDR
mitotic G2/M transition checkpoint557.3×4e-06
protein K63-linked deubiquitination544.6×1e-05
positive regulation of DNA repair735.9×5e-07
mitotic G2 DNA damage checkpoint signaling531.7×5e-05
response to ionizing radiation529.4×6e-05
regulation of DNA repair623.7×2e-05
double-strand break repair823.2×6e-07

Disease & clinical

Clinical variants and AI predictions

ClinVar

126 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic21
Likely pathogenic6
Uncertain significance27
Likely benign12
Benign1

Top pathogenic / likely-pathogenic (27)

Variant IDHGVSClassification
1340345GRCh37/hg19 Xq28(chrX:154120629-154565718)x0Pathogenic
1342389NC_000023.11:g.(154612552_154656872)_(156005236_156038495)delPathogenic
146792GRCh38/hg38 Xq28(chrX:154679854-156003229)x1Pathogenic
1808575GRCh37/hg19 Xq28(chrX:154110981-154565718)x2Pathogenic
253454GRCh37/hg19 Xq28(chrX:154115785-154528181)x1Pathogenic
2583089GRCh37/hg19 Xq28(chrX:154124352-154563736)x2Pathogenic
3062537GRCh37/hg19 Xq28(chrX:154260005-154739500)Pathogenic
441839GRCh37/hg19 Xq28(chrX:154120620-154565718)x1Pathogenic
442510GRCh37/hg19 Xq28(chrX:154250433-154317840)x0Pathogenic
443466GRCh37/hg19 Xq28(chrX:154117578-154553189)x2Pathogenic
4796313GRCh38/hg38 Xq28(chrX:154881139-155396181)x2Pathogenic
564944GRCh37/hg19 Xq28(chrX:154120640-154565718)x1Pathogenic
58019GRCh38/hg38 Xq28(chrX:154897608-155335682)x1Pathogenic
58020GRCh38/hg38 Xq28(chrX:154984506-155098444)x0Pathogenic
625645GRCh37/hg19 Xq28(chrX:154305031-154307464)Pathogenic
684993GRCh37/hg19 Xq28(chrX:154117563-154617602)x2Pathogenic
687057GRCh37/hg19 Xq28(chrX:154117563-154633634)x3Pathogenic
687523GRCh37/hg19 Xq28(chrX:154306330-154680053)x2Pathogenic
929335GRCh37/hg19 Xq28(chrX:154130223-154563104)x3Pathogenic
929354GRCh37/hg19 Xq28(chrX:154051891-155236747)x3Pathogenic
980881GRCh37/hg19 Xq28(chrX:154078238-154563469)x3Pathogenic
144350GRCh38/hg38 Xq28(chrX:154931352-155331063)x1Likely pathogenic
150981GRCh38/hg38 Xq28(chrX:154890313-155331062)x1Likely pathogenic
1808711GRCh37/hg19 Xq28(chrX:154120621-154565718)x1Likely pathogenic
3906917GRCh37/hg19 Xq28(chrX:154285587-154310562)x0Likely pathogenic
560116Single alleleLikely pathogenic
625803GRCh37/hg19 Xq28(chrX:153761240-155227607)Likely pathogenic

SpliceAI

1851 predictions. Top by Δscore:

VariantEffectΔscore
X:155071624:G:GTdonor_gain1.0000
X:155071624:G:Tdonor_gain1.0000
X:155073361:A:AGacceptor_gain1.0000
X:155077284:G:GTdonor_gain1.0000
X:155077285:C:Tdonor_gain1.0000
X:155089338:A:Gdonor_gain1.0000
X:155090782:A:AGacceptor_gain1.0000
X:155090783:G:GGacceptor_gain1.0000
X:155090838:GA:Gdonor_gain1.0000
X:155116709:A:AGacceptor_gain1.0000
X:155116710:G:GGacceptor_gain1.0000
X:155119997:A:AGacceptor_gain1.0000
X:155119998:G:GGacceptor_gain1.0000
X:155120115:G:GTdonor_gain1.0000
X:155120630:G:Tdonor_gain1.0000
X:155071621:G:GTdonor_gain0.9900
X:155071627:G:GGdonor_gain0.9900
X:155071651:GTGA:Gdonor_loss0.9900
X:155072325:A:AGacceptor_gain0.9900
X:155072326:G:GAacceptor_gain0.9900
X:155073362:A:Gacceptor_gain0.9900
X:155073366:A:AGacceptor_gain0.9900
X:155077164:CTTTA:Cacceptor_loss0.9900
X:155077165:TTTA:Tacceptor_loss0.9900
X:155077166:TTA:Tacceptor_loss0.9900
X:155077167:TAGGT:Tacceptor_loss0.9900
X:155077168:A:Cacceptor_loss0.9900
X:155077232:G:GTdonor_gain0.9900
X:155089347:CAAAG:Cdonor_loss0.9900
X:155089348:AAAGG:Adonor_loss0.9900

AlphaMissense

1918 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
X:155071568:T:CL14P1.000
X:155071591:T:CC22R1.000
X:155071593:T:GC22W1.000
X:155071600:C:GH25D1.000
X:155071602:C:AH25Q1.000
X:155071602:C:GH25Q1.000
X:155071604:C:AA26D1.000
X:155071607:T:CL27P1.000
X:155071609:A:CS28R1.000
X:155071611:C:AS28R1.000
X:155071611:C:GS28R1.000
X:155071624:G:AE33K1.000
X:155071624:G:CE33Q1.000
X:155071625:A:CE33A1.000
X:155071625:A:GE33G1.000
X:155071625:A:TE33V1.000
X:155071626:A:CE33D1.000
X:155071626:A:TE33D1.000
X:155071633:G:AG36R1.000
X:155071633:G:CG36R1.000
X:155071633:G:TG36W1.000
X:155071634:G:AG36E1.000
X:155071634:G:TG36V1.000
X:155071637:T:CL37P1.000
X:155071639:T:CC38R1.000
X:155071645:G:TG40W1.000
X:155071646:G:AG40E1.000
X:155077218:C:AR82S1.000
X:155077218:C:GR82G1.000
X:155077229:G:CK85N1.000

dbSNP variants (sampled 300 via entrez): RS1000285506 (X:155070923 A>G), RS1000521820 (X:155087068 G>A,C), RS1000547692 (X:155105985 C>T), RS1000653258 (X:155098723 A>G), RS1000662050 (X:155078642 C>T), RS1000892706 (X:155119625 C>T), RS1000956402 (X:155086703 C>A,T), RS1001297703 (X:155075670 T>C), RS1001456016 (X:155114537 T>A), RS1001520543 (X:155107803 G>A), RS1001591818 (X:155114071 A>G), RS1001712295 (X:155093202 G>A), RS1001825476 (X:155104989 T>A), RS1001893280 (X:155084598 C>G,T), RS1002300198 (X:155076829 G>A)

Disease associations

OMIM: gene MIM:300617 | disease phenotypes: MIM:300815, MIM:300845

GenCC curated gene-disease

DiseaseClassificationInheritance
Moyamoya diseaseLimitedAutosomal dominant

Mondo (4): chromosome Xq28 duplication syndrome (MONDO:0010436), hereditary neoplastic syndrome (MONDO:0015356), moyamoya angiopathy-short stature-facial dysmorphism-hypergonadotropic hypogonadism syndrome (MONDO:0010448), Moyamoya disease (MONDO:0016820)

Orphanet (3): Proximal Xq28 duplication syndrome (Orphanet:1762), Inherited cancer-predisposing syndrome (Orphanet:140162), Moyamoya angiopathy-short stature-facial dysmorphism-hypergonadotropic hypogonadism syndrome (Orphanet:280679)

HPO phenotypes

27 total (27 of 27 shown, HPO-id order):

HPOTerm
HP:0000027Azoospermia
HP:0000278Retrognathia
HP:0000316Hypertelorism
HP:0000343Long philtrum
HP:0000369Low-set ears
HP:0000445Wide nose
HP:0000454Flared nostrils
HP:0000490Deeply set eye
HP:0000518Cataract
HP:0000707Abnormality of the nervous system
HP:0000815Hypergonadotropic hypogonadism
HP:0000822Hypertension
HP:0000823Delayed puberty
HP:0000824Decreased response to growth hormone stimulation test
HP:0001263Global developmental delay
HP:0001324Muscle weakness
HP:0001342Cerebral hemorrhage
HP:0001644Dilated cardiomyopathy
HP:0001677Coronary artery atherosclerosis
HP:0001999Abnormal facial shape
HP:0002140Ischemic stroke
HP:0002216Premature graying of hair
HP:0004302Functional motor deficit
HP:0004322Short stature
HP:0007970Congenital ptosis
HP:0008734Decreased testicular size
HP:0011834Moyamoya phenomenon

GWAS associations

1 associations (top):

StudyTraitp-value
GCST009097_11Venous thromboembolism4.000000e-12

MeSH disease descriptors (3)

DescriptorNameTree numbers
D009072Moyamoya DiseaseC10.228.140.300.200.600; C10.228.140.300.510.200.737; C14.907.137.615; C14.907.253.123.620; C14.907.253.560.200.737
D009386Neoplastic Syndromes, HereditaryC04.700; C16.320.700
C567580Chromosome Xq28 Duplication Syndrome (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL4105965 (SINGLE PROTEIN)

PharmGKB: 1 entry (VIP=true, CPIC=false)

Binding affinities (BindingDB)

1 measured of 1 human assays (1 total across all organisms); most potent 1 below. Values come from heterogeneous assays and are not directly comparable.

LigandMeasureValuePatent
CapziminIC50340 nMUS-10005735: Inhibitors of RPN11

PubChem BioAssay actives

1 with measured affinity, of 2 total; 1 most potent distinct compounds. Largely complementary to BindingDB; screening values are coarse (µM, 4 dp), so sub-nM hits tie at the floor.

CompoundAssayTypeValueUnit
8-sulfanyl-N-[2-(1,3-thiazol-2-yl)ethyl]quinoline-3-carboxamide1802703: In Vitro BRCC36 Activity Assay from Article 10.1038/nchembio.2326: “Capzimin is a potent and specific inhibitor of proteasome isopeptidase Rpn11.”ic502.3000uM

CTD chemical–gene interactions

46 total (human), top 30 by PubMed support.

ChemicalActions (top 5)PubMed papers
bisphenol Adecreases expression, increases expression2
sodium arseniteaffects cotreatment, increases expression, decreases expression2
Plant Extractsaffects cotreatment, increases expression, decreases expression2
TAK-243decreases sumoylation1
2,4,6-tribromophenolincreases expression1
methylmercuric chloridedecreases expression1
triphenyl phosphateaffects expression1
4-biphenylaminedecreases expression, decreases reaction1
titanium dioxideincreases expression1
tris(1,3-dichloro-2-propyl)phosphatedecreases expression1
tetrabromobisphenol Adecreases expression1
potassium chromate(VI)decreases expression1
nickel sulfatedecreases expression1
CGP 52608affects binding, increases reaction1
K 7174decreases expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, increases expression1
torcetrapibincreases expression1
abrinedecreases expression1
2,2’,4,4’-tetrabromodiphenyl etherdecreases expression1
pentabrominated diphenyl ether 100decreases expression1
hexabrominated diphenyl ether 153decreases expression1
LDN 193189affects cotreatment, increases expression1
Bortezomibdecreases expression1
Resveratrolaffects cotreatment, increases expression1
Sunitinibdecreases expression1
Air Pollutantsdecreases expression, increases abundance1
Amiodaroneincreases expression1
Benzo(a)pyreneaffects methylation, increases methylation1
Cannabidioldecreases expression1
Catechindecreases expression1

ChEMBL screening assays

1 unique, capped per target: 1 binding

Representative assays (with source publication via chembl_document):

Assay IDTypeDescriptionSource paper
CHEMBL4049715BindingInhibition of BRCC36 (unknown origin) using DiUbK63TAMRA as substrate by fluorescence assayDiscovery of an Inhibitor of the Proteasome Subunit Rpn11. — J Med Chem

Cellosaurus cell lines

2 cell lines: 2 cancer cell line

First 10 cell lines (id-ordered, not curated):

CellosaurusNameCategorySex
CVCL_SF50HAP1 BRCC3 (-) 1Cancer cell lineMale
CVCL_SF51HAP1 BRCC3 (-) 2Cancer cell lineMale

Clinical trials (associated diseases)

74 trials via MONDO — disease-level, not drug-specific.

TrialPhaseStatusTitle
NCT04205578PHASE3UNKNOWNNBP in Patients With Moyamoya Disease of High Risk for Ischemic Cerebrovascular Events
NCT07065409PHASE1RECRUITINGTreatment of Moyamoya Disease With iPSC-derived Exosomes
NCT07286110PHASE1NOT_YET_RECRUITINGChinese Herbal Therapy (Qiqi Shengmai Formula) for Moyamoya Vasculopathy: The CHIMES Trial
NCT03162588PHASE1/PHASE2COMPLETEDMultiple Burrhole Therapy With Erythropoietin for Unstable Moyamoya
NCT01419275Not specifiedCOMPLETEDQuantifying Collateral Perfusion in Cerebrovascular Disease-Moyamoya Disease and Stroke Patients
NCT01793168Not specifiedRECRUITINGRare Disease Patient Registry & Natural History Study - Coordination of Rare Diseases at Sanford
NCT02074111Not specifiedUNKNOWNMoyamoya Disease Biomarkers in Patients With Intracranial Atherosclerotic Stroke
NCT02305407Not specifiedUNKNOWNNeurocognitive and Radiological Assessments in Adult Moyamoya Undergoing Surgery
NCT02510586Not specifiedUNKNOWNSevoflurane and Hyperperfusion Syndrome
NCT02982135Not specifiedUNKNOWNDirect Bypass Versus Indirect Bypass in Treatment of Adults Hemorrhagic Moyamoya Disease
NCT03072914Not specifiedCOMPLETEDEffects of Remote Ischemic Preconditioning With Postconditioning on Neurologic Outcome
NCT03516851Not specifiedWITHDRAWNPrecision Bypass in Patients With Moyamoya Disease
NCT03543748Not specifiedUNKNOWNEfficacy and Safety of rTMS for Cognitive Rehabilitation in Moyamoya Disease
NCT03546309Not specifiedRECRUITINGSafety and Efficacy of RIC in Pediatric Moyamoya Disease Patients Treated With Revascularization Therapy
NCT03613701Not specifiedUNKNOWNRelationship Between Endothelial Progenitor Cells and Revascularization Effect of Moyamoya Disease
NCT03627975Not specifiedUNKNOWNEffect of Surgical Revascularization on Hemorrhagic Moyamoya Disease
NCT03785171Not specifiedUNKNOWNPredicative Value of Multimodal MRI in Moyamoya Disease
NCT03821181Not specifiedUNKNOWNThe Effect of RIC on TIA/Stroke in Children With Moyamoya Disease
NCT03882060Not specifiedUNKNOWNEffect of Recombinant Human EPO on the Postoperative Neurologic Outcome in Pediatric Moyamoya Patients
NCT04012268Not specifiedCOMPLETEDThe Safety and Efficacy of RIC on Adult Moyamoya Disease
NCT04064658Not specifiedSUSPENDEDEffects of Remote Ischemic Pre-Conditioning in Moyamoya Disease Patients
NCT04696094Not specifiedUNKNOWNThe Role of m6A RNA Modification in Moyamoya Disease
NCT04890782Not specifiedUNKNOWNGut Microbiota in Patients With Moyamoya Disease
NCT04906564Not specifiedCOMPLETEDRNF213 Variants and Collateral Vessels in Moyamoya Disease
NCT04917003Not specifiedUNKNOWNSafety and Efficacy of Remote Ischemic Conditioning Combined EDAS on Ischemic Moyamoya Disease
NCT05332756Not specifiedRECRUITINGLong-term Outcomes of Conservative Management in Patients with Moyamoya Disease and Their First-degree Relatives (LAMORA)
NCT05491980Not specifiedACTIVE_NOT_RECRUITINGFlorida Cerebrovascular Disease Biorepository and Genomics Center
NCT05619068Not specifiedRECRUITINGThe Evolution and Prognosis of Moyamoya Disease
NCT05772572Not specifiedCOMPLETEDFunctional Disorders Moya Moya Young Patients
NCT05860946Not specifiedUNKNOWNRemote Ischemic Conditioning in Adult Moyamoya Disease Patients
NCT05961748Not specifiedRECRUITINGRegistry of Multicenter Brain-Heart Comorbidity in China
NCT06041659Not specifiedRECRUITINGFunctional Magnetic Resonance-Based Observations of Brain Networks in Moyamoya Disease Patients Under Anesthesia
NCT06051552Not specifiedNOT_YET_RECRUITINGPrognostic Prediction Model in Patients With Moyamoya Disease Undergoing Revascularization Surgery
NCT06330818Not specifiedRECRUITINGImaging in Moyamoya Disease - Study to Investigate Different Imaging Technologies for a Better Understanding of Various Imaging Techniques to Evaluate Cerebral Hemodynamics, Disease-activity and Possibly the Etiology in Moyamoya Patients
NCT06477107Not specifiedENROLLING_BY_INVITATIONA Study of Cerebral Perfusion With tDCS in Chronic Hypoperfusion
NCT06634004Not specifiedENROLLING_BY_INVITATIONBiomarker-Led Optimization of Successful Surgical Outcomes in Moyamoya
NCT06714097Not specifiedRECRUITINGApplication of Digital Twins’ Technology in Patients Who Had a Stroke, With Moyamoya Disease and With Cerebral Amyloid Angiopathy (CAA) During the Secondary Prevention Phase: A Proof of Concept Using a Randomized Control Trial (Clinical Study 6, STRATIF-AI Project)
NCT06724029Not specifiedRECRUITINGNeurosurgical Outcome Network
NCT06817434Not specifiedRECRUITINGStudy on Evaluating the Effectiveness of Statins in the Treatment of Moyamoya Disease
NCT06832839Not specifiedRECRUITINGStudy on the Mechanism of Cognitive Impairment in Patients with Moyamoya Disease