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

Gene ID: 8314, updated on 26-Jul-2021

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
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Genomic context

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See BAP1 in Genome Data Viewer
Location:
3p21.1
Exon count:
17
Annotation release Status Assembly Chr Location
109.20210514 current GRCh38.p13 (GCF_000001405.39) 3 NC_000003.12 (52401004..52410030, complement)
105.20201022 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (52435024..52444024, 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. Bioinformatic Analysis of Differentially Expressed Genes and Screening of Hub Genes in Uveal Melanoma Cells with BRCA1-Associated Protein 1 Related Protein 1 Depletion. Li W, et al. J Biomed Nanotechnol, 2020 Aug 1. PMID 33397551
  2. Uveal Melanoma in BAP1 Tumor Predisposition Syndrome: Estimation of Risk. Singh N, et al. Am J Ophthalmol, 2021 Apr. PMID 33316260,
  3. BAP1-Mutated Clear Cell Renal Cell Carcinoma. Gallan AJ, et al. Am J Clin Pathol, 2021 Apr 26. PMID 33210135
  4. Ameloblastoma shows nuclear BAP1 immunoexpression, independently of the BRAF V600E status. Santana LADM, et al. Oral Dis, 2021 Jul. PMID 32945606
  5. Large-scale analysis of BAP1 expression reveals novel associations with clinical and molecular features of malignant pleural mesothelioma. De Rienzo A, et al. J Pathol, 2021 Jan. PMID 32944962, Free PMC Article

See all (297) citations in PubMed

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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Whole exome sequencing reveals BAP1 somatic abnormalities in mesothelioma in situ.
    Title: Whole exome sequencing reveals BAP1 somatic abnormalities in mesothelioma in situ.
  2. Ameloblastoma shows nuclear BAP1 immunoexpression, independently of the BRAF V600E status.
    Title: Ameloblastoma shows nuclear BAP1 immunoexpression, independently of the BRAF V600E status.
  3. Intraocular Metastasis in Unilateral Multifocal Uveal Melanoma Without Melanocytosis or Germline BAP1 Mutations.
    Title: Intraocular Metastasis in Unilateral Multifocal Uveal Melanoma Without Melanocytosis or Germline BAP1 Mutations.
  4. BAP1-Mutated Clear Cell Renal Cell Carcinoma.
    Title: BAP1-Mutated Clear Cell Renal Cell Carcinoma.
  5. Large-scale analysis of BAP1 expression reveals novel associations with clinical and molecular features of malignant pleural mesothelioma.
    Title: Large-scale analysis of BAP1 expression reveals novel associations with clinical and molecular features of malignant pleural mesothelioma.
  6. Uveal Melanoma in BAP1 Tumor Predisposition Syndrome: Estimation of Risk.
    Title: Uveal Melanoma in BAP1 Tumor Predisposition Syndrome: Estimation of Risk.
  7. circASXL1-1 regulates BAP1 deubiquitinase activity in leukemia.
    Title: circASXL1-1 regulates BAP1 deubiquitinase activity in leukemia.
  8. Ubiquitin Carboxyl-Terminal Hydrolases (UCHs): Potential Mediators for Cancer and Neurodegeneration.
    Title: Ubiquitin Carboxyl-Terminal Hydrolases (UCHs): Potential Mediators for Cancer and Neurodegeneration.
  9. Testing for BAP1 loss and CDKN2A/p16 homozygous deletion improves the accurate diagnosis of mesothelial proliferations in effusion cytology.
    Title: Testing for BAP1 loss and CDKN2A/p16 homozygous deletion improves the accurate diagnosis of mesothelial proliferations in effusion cytology.
  10. BAP1 regulates AMPK-mTOR signalling pathway through deubiquitinating and stabilizing tumour-suppressor LKB1.
    Title: BAP1 regulates AMPK-mTOR signalling pathway through deubiquitinating and stabilizing tumour-suppressor LKB1.
Submit: New GeneRIF Correction See all GeneRIFs (242)

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

Associated conditions

Description Tests
Genome-wide association analysis identifies 13 new risk loci for schizophrenia.
GeneReviews: Not available
Large-scale genome-wide association analysis of bipolar disorder identifies a new susceptibility locus near ODZ4.
GeneReviews: Not available
Tumor susceptibility linked to germline BAP1 mutations
MedGen: C3280492 OMIM: 614327 GeneReviews: BAP1 Tumor Predisposition Syndrome
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Copy number response

Description
Copy number response
Triplosensitivity

No evidence available (Last evaluated 2019-12-27)

ClinGen Genome Curation Page
Haploinsufficency

Sufficient evidence for dosage pathogenicity (Last evaluated 2019-12-27)

ClinGen Genome Curation PagePubMed

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 PubChem

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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
enables chromatin binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables peptidase activity NAS
Non-traceable Author Statement
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables thiol-dependent deubiquitinase IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
enables thiol-dependent deubiquitinase IDA
Inferred from Direct Assay
more info
 PubMed 
enables thiol-dependent deubiquitinase TAS
Traceable Author Statement
more info
  
Process Evidence Code Pubs
involved_in cellular protein modification process NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in macrophage homeostasis IEA
Inferred from Electronic Annotation
more info
  
involved_in monoubiquitinated histone H2A deubiquitination IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in monoubiquitinated protein deubiquitination IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in negative regulation of cell population proliferation TAS
Traceable Author Statement
more info
 PubMed 
involved_in negative regulation of transcription, DNA-templated IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in positive regulation of protein targeting to mitochondrion HMP PubMed 
involved_in protein K48-linked deubiquitination IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in protein deubiquitination IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
involved_in protein deubiquitination IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in protein deubiquitination TAS
Traceable Author Statement
more info
  
involved_in regulation of cell cycle IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in regulation of cell growth IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in regulation of cytokine production involved in inflammatory response IEA
Inferred from Electronic Annotation
more info
  
involved_in regulation of inflammatory response IEA
Inferred from Electronic Annotation
more info
  
involved_in response to inorganic substance IEA
Inferred from Electronic Annotation
more info
  
involved_in ubiquitin-dependent protein catabolic process IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
part_of PR-DUB complex IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
located_in cytoplasm IDA
Inferred from Direct Assay
more info
 PubMed 
located_in cytosol IDA
Inferred from Direct Assay
more info
  
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  
located_in nucleoplasm TAS
Traceable Author Statement
more info
  
located_in 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, ENST00000460680.6
    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 Updated Annotation Release 109.20210514

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000003.12 Reference GRCh38.p13 Primary Assembly

    Range
    52401004..52410030 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

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