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

Gene ID: 8314, updated on 7-Apr-2024

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; AllianceGenome:HGNC:950
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
UBM2; UVM2; KURIS; TPDS1; 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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Location:
3p21.1
Exon count:
17
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (52401008..52410008, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (52433990..52442989, complement)
105.20220307 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 H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:52332967-52333837 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:52333838-52334707 Neighboring gene glycerate kinase Neighboring gene microRNA 135a-1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:52344635-52345552 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19940 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:52350849-52351787 Neighboring gene dynein axonemal heavy chain 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:52377569-52378070 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:52385639-52386434 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:52396307-52396860 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14440 Neighboring gene protein phosphatase 2 regulatory subunit B'gamma pseudogene Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:52443144-52443692 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:52443693-52444241 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14443 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19941 Neighboring gene VISTA enhancer hs2179 Neighboring gene PHD finger protein 7 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:52471583-52472088 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:52478216-52479092 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:52479093-52479969 Neighboring gene semaphorin 3G

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. DNA methylation of GITR, OX40, 4-1BB, CD27 , and CD40 correlates with BAP1 aberrancy and prognosis in uveal melanoma. Hoffmann F, et al. Melanoma Res, 2023 Apr 1. PMID 36735464
  2. Two unique BAP1 pathogenic variants identified in the same family by panel cascade testing. Byrne L, et al. Fam Cancer, 2023 Jul. PMID 36513904,
  3. BAP1 depletion in human B-lymphoblast cells affects the production of innate immune cytokines and chemokines. Takagi-Kimura M, et al. Genes Cells, 2022 Dec. PMID 36300836
  4. Intrinsic Disorder in BAP1 and Its Association with Uveal Melanoma. Djulbegovic MB, et al. Genes (Basel), 2022 Sep 22. PMID 36292588, Free PMC Article
  5. Histopathologic and molecular characterization of BAP-1-inactivated melanoma. Miller EM, et al. J Cutan Pathol, 2023 Apr. PMID 36285428

See all (380) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Functional assay for assessment of pathogenicity of BAP1 variants.
    Title: Functional assay for assessment of pathogenicity of BAP1 variants.
  2. Morphological characteristics of SETD2-mutated locally advanced clear cell renal cell carcinoma: Comparison with BAP1-mutated clear cell renal cell carcinoma.
    Title: Morphological characteristics of SETD2-mutated locally advanced clear cell renal cell carcinoma: Comparison with BAP1-mutated clear cell renal cell carcinoma.
  3. Balanced Epigenetic Regulation of MHC Class I Expression in Tumor Cells by the Histone Ubiquitin Modifiers BAP1 and PCGF1.
    Title: Balanced Epigenetic Regulation of MHC Class I Expression in Tumor Cells by the Histone Ubiquitin Modifiers BAP1 and PCGF1.
  4. Methylthioadenosine Phosphorylase and Breast Cancer 1 Protein-Associated Protein 1 as Biomarkers for the Peritoneal Mesothelioma.
    Title: Methylthioadenosine Phosphorylase and Breast Cancer 1 Protein-Associated Protein 1 as Biomarkers for the Peritoneal Mesothelioma.
  5. Contribution of BAP1 loss and p16 (CDKN2A) deletion analysis to the definitive diagnosis of mesothelioma in effusion cytology.
    Title: Contribution of BAP1 loss and p16 (CDKN2A) deletion analysis to the definitive diagnosis of mesothelioma in effusion cytology.
  6. BAP1 promotes osteoclast function by metabolic reprogramming.
    Title: BAP1 promotes osteoclast function by metabolic reprogramming.
  7. BAP1 mutations inhibit the NF-kappaB signaling pathway to induce an immunosuppressive microenvironment in uveal melanoma.
    Title: BAP1 mutations inhibit the NF-κB signaling pathway to induce an immunosuppressive microenvironment in uveal melanoma.
  8. BAP1 as a guardian of genome stability: implications in human cancer.
    Title: BAP1 as a guardian of genome stability: implications in human cancer.
  9. Investigating the Role of FoxP3 in Renal Cell Carcinoma Metastasis with BAP1 or SEDT2 Mutation.
    Title: Investigating the Role of FoxP3 in Renal Cell Carcinoma Metastasis with BAP1 or SEDT2 Mutation.
  10. Structural basis of histone H2A lysine 119 deubiquitination by Polycomb repressive deubiquitinase BAP1/ASXL1.
    Title: Structural basis of histone H2A lysine 119 deubiquitination by Polycomb repressive deubiquitinase BAP1/ASXL1.
Submit: New GeneRIF Correction See all GeneRIFs (314)

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
BAP1-related tumor predisposition syndrome
MedGen: C3280492 OMIM: 614327 GeneReviews: BAP1 Tumor Predisposition Syndrome
Compare labs
Kury-Isidor syndrome
MedGen: C5676925 OMIM: 619762 GeneReviews: Not available
Compare labs
Melanoma, uveal, susceptibility to, 2
MedGen: C1847723 OMIM: 606661 GeneReviews: Not available
Compare labs

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

EBI GWAS Catalog

Description
Genome-wide association analysis identifies 13 new risk loci for schizophrenia.
EBI GWAS Catalog
Large-scale genome-wide association analysis of bipolar disorder identifies a new susceptibility locus near ODZ4.
EBI GWAS 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 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 DNA binding IEA
Inferred from Electronic Annotation
more info
  
enables chromatin binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables cysteine-type deubiquitinase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables cysteine-type deubiquitinase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables cysteine-type deubiquitinase activity TAS
Traceable Author Statement
more info
  
enables histone H2A deubiquitinase activity IMP
Inferred from Mutant Phenotype
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 
Process Evidence Code Pubs
involved_in chromatin remodeling IEA
Inferred from Electronic Annotation
more info
  
involved_in common myeloid progenitor cell proliferation IEA
Inferred from Electronic Annotation
more info
  
involved_in erythrocyte maturation IEA
Inferred from Electronic Annotation
more info
  
involved_in gene expression IEA
Inferred from Electronic Annotation
more info
  
involved_in hematopoietic stem cell homeostasis IEA
Inferred from Electronic Annotation
more info
  
involved_in in utero embryonic development IEA
Inferred from Electronic Annotation
more info
  
involved_in leukocyte proliferation IEA
Inferred from Electronic Annotation
more info
  
involved_in macrophage homeostasis IEA
Inferred from Electronic Annotation
more info
  
involved_in mitotic cell cycle IEA
Inferred from Electronic Annotation
more info
  
involved_in monoubiquitinated protein deubiquitination IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in myeloid cell apoptotic process IEA
Inferred from Electronic Annotation
more info
  
involved_in negative regulation of DNA-templated transcription 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 neuron cellular homeostasis IEA
Inferred from Electronic Annotation
more info
  
involved_in neutrophil differentiation IEA
Inferred from Electronic Annotation
more info
  
involved_in nucleate erythrocyte differentiation IEA
Inferred from Electronic Annotation
more info
  
involved_in platelet morphogenesis IEA
Inferred from Electronic Annotation
more info
  
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
  
involved_in protein deubiquitination IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in protein modification process NAS
Non-traceable Author Statement
more info
 PubMed 
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 thrombocyte differentiation IEA
Inferred from Electronic Annotation
more info
  
involved_in tissue homeostasis 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 
part_of PR-DUB complex IPI
Inferred from Physical Interaction
more info
 PubMed 
is_active_in cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
  
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_001397701.1
NP_004647.1
XP_011532451.1
XP_011532452.1
XP_011532453.1
XP_011532454.1
XP_047305000.1
XP_054204030.1
XP_054204031.1
XP_054204032.1
XP_054204033.1
XP_054204034.1

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_001410772.1 → NP_001397701.1  ubiquitin carboxyl-terminal hydrolase BAP1 isoform 2

    Status: REVIEWED

    Source sequence(s)
    AC092045
    Consensus CDS
    CCDS93284.1
    UniProtKB/TrEMBL
    F8W6N3
    Related
    ENSP00000296288.5, ENST00000296288.9

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

    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
    A8K993, Q6LEM0, Q7Z5E8, Q92560
    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: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    52401008..52410008 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047449044.1 → XP_047305000.1  ubiquitin carboxyl-terminal hydrolase BAP1 isoform X5

  2. XM_011534151.4 → 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_011534152.3 → 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_011534150.4 → 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_011534149.4 → 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

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    52433990..52442989 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054348059.1 → XP_054204034.1  ubiquitin carboxyl-terminal hydrolase BAP1 isoform X5

  2. XM_054348057.1 → XP_054204032.1  ubiquitin carboxyl-terminal hydrolase BAP1 isoform X3

  3. XM_054348058.1 → XP_054204033.1  ubiquitin carboxyl-terminal hydrolase BAP1 isoform X4

  4. XM_054348056.1 → XP_054204031.1  ubiquitin carboxyl-terminal hydrolase BAP1 isoform X2

  5. XM_054348055.1 → XP_054204030.1  ubiquitin carboxyl-terminal hydrolase BAP1 isoform X1

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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