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BAP1 BRCA1 associated protein 1 [ Homo sapiens (human) ]

Gene ID: 8314, updated on 12-Mar-2019

Summary

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Official Symbol
BAP1provided by HGNC
Official Full Name
BRCA1 associated protein 1provided by HGNC
Primary source
HGNC:HGNC:950
See related
Ensembl:ENSG00000163930 MIM:603089
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
UCHL2; hucep-6; HUCEP-13
Summary
This gene belongs to the ubiquitin C-terminal hydrolase subfamily of deubiquitinating enzymes that are involved in the removal of ubiquitin from proteins. The encoded enzyme binds to the breast cancer type 1 susceptibility protein (BRCA1) via the RING finger domain of the latter and acts as a tumor suppressor. In addition, the enzyme may be involved in regulation of transcription, regulation of cell cycle and growth, response to DNA damage and chromatin dynamics. Germline mutations in this gene may be associated with tumor predisposition syndrome (TPDS), which involves increased risk of cancers including malignant mesothelioma, uveal melanoma and cutaneous melanoma. [provided by RefSeq, May 2013]
Expression
Ubiquitous expression in testis (RPKM 47.8), skin (RPKM 26.6) and 25 other tissues See more
Orthologs
mouse all

Genomic context

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See BAP1 in Genome Data Viewer
Location:
3p21.1
Exon count:
17
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 3 NC_000003.12 (52401004..52410105, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (52435020..52444121, complement)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene glycerate kinase Neighboring gene microRNA 135a-1 Neighboring gene dynein axonemal heavy chain 1 Neighboring gene protein phosphatase 2 regulatory subunit B'gamma pseudogene Neighboring gene PHD finger protein 7 Neighboring gene VISTA enhancer hs2179

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Comparison of Germline versus Somatic BAP1 Mutations for Risk of Metastasis in Uveal Melanoma. Ewens KG, et al. BMC Cancer, 2018 Nov 26. PMID 30477459, Free PMC Article
  2. Loss of BAP1 expression in metastatic tumor tissue is an event of poor prognosis in patients with metastatic clear cell renal cell carcinoma. da Costa WH, et al. Urol Oncol, 2019 Jan. PMID 30446457
  3. Sensitivity to asbestos is increased in patients with mesothelioma and pathogenic germline variants in BAP1 or other DNA repair genes. Betti M, et al. Genes Chromosomes Cancer, 2018 Nov. PMID 30338612
  4. Nuclear BAP1 loss is common in intrahepatic cholangiocarcinoma and a subtype of hepatocellular carcinoma but rare in pancreatic ductal adenocarcinoma. Mosbeh A, et al. Cancer Genet, 2018 Aug. PMID 29778232,
  5. Analysis of the exome aggregation consortium (ExAC) database suggests that the BAP1-tumor predisposition syndrome is underreported in cancer patients. Massengill JB, et al. Genes Chromosomes Cancer, 2018 Sep. PMID 29761599,

See all (231) citations in PubMed

See citations in PubMed for homologs of this gene provided by HomoloGene

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

  1. Patients with metastatic ccRCC that present loss of BAP1 expression in metastatic tissue demonstrated poor survival rates and represent a relevant risk group for tumor recurrence and death.
    Title: Loss of BAP1 expression in metastatic tumor tissue is an event of poor prognosis in patients with metastatic clear cell renal cell carcinoma.
  2. Defining germline vs. somatic nature of BAP1 mutations in UM can inform the individual about both the risk of metastasis, and the time to metastasis, which are critically important outcomes for the individual. This information can also change the cascade screening and surveillance of family members.
    Title: Comparison of Germline versus Somatic BAP1 Mutations for Risk of Metastasis in Uveal Melanoma.
  3. Loss of BAP1 expression in atypical mesothelial proliferation helps to predict malignant mesothelioma.
    Title: Loss of BAP1 Expression in Atypical Mesothelial Proliferations Helps to Predict Malignant Mesothelioma.
  4. we show a strong relationship between the expression profiles of PBRM1, BAP1 and SETD2 in ccRCC suggesting reciprocal synergy effects in the context of tumor suppression.
    Title: Expression and Mutation Patterns of PBRM1, BAP1 and SETD2 Mirror Specific Evolutionary Subtypes in Clear Cell Renal Cell Carcinoma.
  5. Letter: BAP1 expression is not lost in trichoblastomas, whether solitary sporadic or those occurring in the setting of multiple familial trichoepithelioma (MFT)/Brooke-Spiegler syndrome.
    Title: Sporadic Trichoblastomas and Those Occurring in the Setting of Multiple Familial Trichoepithelioma/Brooke-Spiegler Syndrome Show No BAP1 Loss.
  6. BAP1 complex promotes transcription by opposing PRC1-mediated H2A ubiquitylation.
    Title: BAP1 complex promotes transcription by opposing PRC1-mediated H2A ubiquitylation.
  7. In intrahepatic cholangiocarcinoma retained expression of BAP-1 and PBRM-1, and an overexpression of S100P are related to a poor prognosis.
    Title: Prognostic role of BAP-1 and PBRM-1 expression in intrahepatic cholangiocarcinoma.
  8. Loss of BAP1 expression due to BAP1 Mutation is associated with tumorigenesis.
    Title: Familial and Somatic <i>BAP1</i> Mutations Inactivate ASXL1/2-Mediated Allosteric Regulation of BAP1 Deubiquitinase by Targeting Multiple Independent Domains.
  9. Results confirm the high frequency of BAP1 alterations in ICC and low frequency in pancreatic cancers. It also suggests that BAP1 is commonly altered in a subtype of HCC with both hepatocytic and biliary differentiation.
    Title: Nuclear BAP1 loss is common in intrahepatic cholangiocarcinoma and a subtype of hepatocellular carcinoma but rare in pancreatic ductal adenocarcinoma.
  10. Mutant ASXL1 cooperates with BAP1 to promote myeloid leukemogenesis.
    Title: Mutant ASXL1 cooperates with BAP1 to promote myeloid leukaemogenesis.
Submit: New GeneRIF Correction See all GeneRIFs (187)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

NHGRI GWAS Catalog

Description
Genome-wide association analysis identifies 13 new risk loci for schizophrenia.
NHGRI GWA Catalog
Large-scale genome-wide association analysis of bipolar disorder identifies a new susceptibility locus near ODZ4.
NHGRI GWA Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from BioSystems

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  • DNA Double Strand Break Response, organism-specific biosystem (from REACTOME)
    DNA Double Strand Break Response, organism-specific biosystemDNA double strand break (DSB) response involves sensing of DNA DSBs by the MRN complex which triggers ATM activation. ATM phosphorylates a number of proteins involved in DNA damage checkpoint signali...
  • DNA Double-Strand Break Repair, organism-specific biosystem (from REACTOME)
    DNA Double-Strand Break Repair, organism-specific biosystemNumerous types of DNA damage can occur within a cell due to the endogenous production of oxygen free radicals, normal alkylation reactions, or exposure to exogenous radiations and chemicals. Double-s...
  • DNA Repair, organism-specific biosystem (from REACTOME)
    DNA Repair, organism-specific biosystemDNA repair is a phenomenal multi-enzyme, multi-pathway system required to ensure the integrity of the cellular genome. Living organisms are constantly exposed to harmful metabolic by-products, enviro...
  • Deubiquitination, organism-specific biosystem (from REACTOME)
    Deubiquitination, organism-specific biosystemUbiquitination, the modification of proteins by the covalent attachment of ubiquitin (Ub), is a key regulatory mechanism for many many cellular processes, including protein degradation by the 26S pro...
  • Metabolism of proteins, organism-specific biosystem (from REACTOME)
    Metabolism of proteins, organism-specific biosystemProtein metabolism comprises the pathways of translation, post-translational modification and protein folding.
  • Post-translational protein modification, organism-specific biosystem (from REACTOME)
    Post-translational protein modification, organism-specific biosystemAfter translation, many newly formed proteins undergo further covalent modifications that alter their functional properties and that are essentially irreversible under physiological conditions in the...
  • Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks, organism-specific biosystem (from REACTOME)
    Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks, organism-specific biosystemActivated ATM phosphorylates a number of proteins involved in the DNA damage checkpoint and DNA repair (Thompson and Schild 2002, Ciccia and Elledge 2010), thereby triggering and coordinating accumul...
  • UCH proteinases, organism-specific biosystem (from REACTOME)
    UCH proteinases, organism-specific biosystemDUBs of the Ub C-terminal Hydrolase (UCH) family are thiol proteases that have an N-terminal catalytic domain sometimes followed by C-terminal extensions that mediate protein-protein interactions. Hu...

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ35406, FLJ37180, KIAA0272, DKFZp686N04275

Gene Ontology Provided by GOA

Function Evidence Code Pubs
chromatin binding IDA
Inferred from Direct Assay
more info
 PubMed 
peptidase activity NAS
Non-traceable Author Statement
more info
 PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
thiol-dependent ubiquitin-specific protease activity IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
thiol-dependent ubiquitin-specific protease activity IDA
Inferred from Direct Assay
more info
 PubMed 
thiol-dependent ubiquitinyl hydrolase activity IDA
Inferred from Direct Assay
more info
 PubMed 
thiol-dependent ubiquitinyl hydrolase activity IMP
Inferred from Mutant Phenotype
more info
 PubMed 
thiol-dependent ubiquitinyl hydrolase activity TAS
Traceable Author Statement
more info
  
Process Evidence Code Pubs
cellular protein modification process NAS
Non-traceable Author Statement
more info
 PubMed 
macrophage homeostasis IEA
Inferred from Electronic Annotation
more info
  
monoubiquitinated histone H2A deubiquitination IDA
Inferred from Direct Assay
more info
 PubMed 
monoubiquitinated protein deubiquitination IDA
Inferred from Direct Assay
more info
 PubMed 
negative regulation of cell proliferation TAS
Traceable Author Statement
more info
 PubMed 
positive regulation of protein targeting to mitochondrion HMP PubMed 
protein K48-linked deubiquitination IMP
Inferred from Mutant Phenotype
more info
 PubMed 
protein deubiquitination IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
protein deubiquitination IDA
Inferred from Direct Assay
more info
 PubMed 
protein deubiquitination TAS
Traceable Author Statement
more info
  
regulation of cell cycle IMP
Inferred from Mutant Phenotype
more info
 PubMed 
regulation of cell growth IMP
Inferred from Mutant Phenotype
more info
 PubMed 
regulation of cytokine production involved in inflammatory response IEA
Inferred from Electronic Annotation
more info
  
response to inorganic substance IEA
Inferred from Electronic Annotation
more info
  
ubiquitin-dependent protein catabolic process IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
PR-DUB complex IDA
Inferred from Direct Assay
more info
 PubMed 
cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
cytoplasm IDA
Inferred from Direct Assay
more info
 PubMed 
cytosol IDA
Inferred from Direct Assay
more info
  
nucleoplasm IDA
Inferred from Direct Assay
more info
  
nucleoplasm TAS
Traceable Author Statement
more info
  
nucleus IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
ubiquitin carboxyl-terminal hydrolase BAP1
Names
BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase)
cerebral protein 6
cerebral protein-13
NP_004647.1
XP_011532451.1
XP_011532452.1
XP_011532453.1
XP_011532454.1
XP_016862792.1

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_031859.1 RefSeqGene

    Range
    4889..13990
    Download
    GenBank, FASTA, Sequence Viewer (Graphics), LRG_529

mRNA and Protein(s)

  1. NM_004656.4 → NP_004647.1  ubiquitin carboxyl-terminal hydrolase BAP1

    See identical proteins and their annotated locations for NP_004647.1

    Status: REVIEWED

    Source sequence(s)
    AK292608, AY130008
    Consensus CDS
    CCDS2853.1
    UniProtKB/Swiss-Prot
    Q92560
    UniProtKB/TrEMBL
    A0A024R305
    Related
    ENSP00000417132.1, ENST00000460680.5
    Conserved Domains (1) summary
    cd09617
    Location:5 → 233
    Peptidase_C12_UCH37_BAP1; Cysteine peptidase C12 containing ubiquitin carboxyl-terminal hydrolase (UCH) families UCH37 (UCH-L5) and BAP1

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000003.12 Reference GRCh38.p12 Primary Assembly

    Range
    52401004..52410105 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017007303.2 → XP_016862792.1  ubiquitin carboxyl-terminal hydrolase BAP1 isoform X5

    UniProtKB/TrEMBL
    F8W6N3
    Related
    ENSP00000296288.5, ENST00000296288.9

  2. XM_011534151.3 → XP_011532453.1  ubiquitin carboxyl-terminal hydrolase BAP1 isoform X3

    Conserved Domains (1) summary
    cd09617
    Location:5 → 223
    Peptidase_C12_UCH37_BAP1; Cysteine peptidase C12 containing ubiquitin carboxyl-terminal hydrolase (UCH) families UCH37 (UCH-L5) and BAP1

  3. XM_011534152.2 → XP_011532454.1  ubiquitin carboxyl-terminal hydrolase BAP1 isoform X4

    Conserved Domains (1) summary
    cd09617
    Location:5 → 233
    Peptidase_C12_UCH37_BAP1; Cysteine peptidase C12 containing ubiquitin carboxyl-terminal hydrolase (UCH) families UCH37 (UCH-L5) and BAP1

  4. XM_011534150.3 → XP_011532452.1  ubiquitin carboxyl-terminal hydrolase BAP1 isoform X2

    Conserved Domains (1) summary
    cd09617
    Location:5 → 233
    Peptidase_C12_UCH37_BAP1; Cysteine peptidase C12 containing ubiquitin carboxyl-terminal hydrolase (UCH) families UCH37 (UCH-L5) and BAP1

  5. XM_011534149.3 → XP_011532451.1  ubiquitin carboxyl-terminal hydrolase BAP1 isoform X1

    Conserved Domains (1) summary
    cd09617
    Location:5 → 233
    Peptidase_C12_UCH37_BAP1; Cysteine peptidase C12 containing ubiquitin carboxyl-terminal hydrolase (UCH) families UCH37 (UCH-L5) and BAP1
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q92560.2 GenPept UniProtKB/Swiss-Prot:Q92560

Gene LinkOut

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