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BAP1 Gene

protein-coding   GIFtS: 65
GCID: GC03M052410

BRCA1 Associated Protein-1 (Ubiquitin Carboxy-Terminal Hydrolase)

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(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
BRCA1 Associated Protein-1 (Ubiquitin Carboxy-Terminal Hydrolase)1 2     Ubiquitin Carboxyl-Terminal Hydrolase BAP12
Cerebral Protein 62 3     EC 3.4.19.123
HUCEP-132     KIAA02723
UCHL22     BRCA1-Associated Protein 13
Cerebral Protein-132     TPDS5

External Ids:    HGNC: 9501   Entrez Gene: 83142   Ensembl: ENSG000001639307   OMIM: 6030895   UniProtKB: Q925603   

Export aliases for BAP1 gene to outside databases

Previous GC identifers: GC03M051527 GC03M051687 GC03M052290 GC03M052393


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Entrez Gene summary for BAP1 Gene:
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)

GeneCards Summary for BAP1 Gene:
BAP1 (BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase)) is a protein-coding gene. Diseases associated with BAP1 include tumor predisposition syndrome, and familial cylindromatosis. GO annotations related to this gene include peptidase activity and chromatin binding. An important paralog of this gene is UCHL5.

UniProtKB/Swiss-Prot: BAP1_HUMAN, Q92560
Function: Deubiquitinating enzyme that plays a key role in chromatin by mediating deubiquitination of histone H2A
and HCFC1. Catalytic component of the PR-DUB complex, a complex that specifically mediates deubiquitination of
histone H2A monoubiquitinated at 'Lys-119' (H2AK119ub1). Does not deubiquitinate monoubiquitinated histone H2B.
Acts as a regulator of cell growth by mediating deubiquitination of HCFC1 N-terminal and C-terminal chains, with
some specificity toward 'Lys-48'-linked polyubiquitin chains compared to 'Lys-63'-linked polyubiquitin chains.
Deubiquitination of HCFC1 does not lead to increase stability of HCFC1. Interferes with the BRCA1 and BARD1
heterodimer activity by inhibiting their ability to mediate ubiquitination and autoubiquitination. It however
does not mediate deubiquitination of BRCA1 and BARD1. Acts as a tumor suppressor

Gene Wiki entry for BAP1 Gene


(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence:
NC_000003.12  NC_018914.2  NT_022517.19  
Regulatory elements:
   Regulatory transcription factor binding sites in the BAP1 gene promoter:
         Sp1   SRF (504 AA)   Nkx2-5   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidBAP1 promoter sequence
   Search Chromatin IP Primers for BAP1

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat BAP1


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 3p21.31-p21.2   Ensembl cytogenetic band:  3p21.1   HGNC cytogenetic band: 3p21.31-p21.2

BAP1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
BAP1 gene location

GeneLoc information about chromosome 3         GeneLoc Exon Structure

GeneLoc location for GC03M052410:  view genomic region     (about GC identifiers)

Start:
52,435,024 bp from pter      End:
52,444,366 bp from pter
Size:
9,343 bases      Orientation:
minus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
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UniProtKB/Swiss-Prot: BAP1_HUMAN, Q92560 (See protein sequence)
Recommended Name: Ubiquitin carboxyl-terminal hydrolase BAP1  
Size: 729 amino acids; 80362 Da
Subunit: Component of the PR-DUB complex, at least composed of BAP1 and ASXL1. Interacts with BRCA1 (via the RING
finger). Interacts (via HBM-like motif) with HCFC1
Sequence caution: Sequence=BAA13401.2; Type=Erroneous initiation; Note=Translation N-terminally shortened;
Secondary accessions: A8K993 Q6LEM0 Q7Z5E8

Explore the universe of human proteins at neXtProt for BAP1: NX_Q92560

Explore proteomics data for BAP1 at MOPED

Post-translational modifications: 

  • Ubiquitination2 at Lys139, Lys155, Lys630
  • Modification sites at PhosphoSitePlus

  • See BAP1 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_004647.1  
    ENSEMBL proteins: 
     ENSP00000417132   ENSP00000418320   ENSP00000296288   ENSP00000420647   ENSP00000419709  
     ENSP00000417776  

    BAP1 Human Recombinant Protein Products:

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    Novus Biologicals BAP1 Proteins
    Novus Biologicals BAP1 Lysates
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    Browse Sino Biological Cell Lysates
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    Cloud-Clone Corp. Proteins for BAP1

    BAP1 Antibody Products:

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    LSBio Antibodies in human, mouse, rat for BAP1

    BAP1 Assay Products:

    Browse Kits and Assays available from EMD Millipore
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    Cloud-Clone Corp. ELISAs for BAP1
    Cloud-Clone Corp. CLIAs for BAP1


    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    1 InterPro protein domain:
     IPR001578 Peptidase_C12_UCH

    Graphical View of Domain Structure for InterPro Entry Q92560

    ProtoNet protein and cluster: Q92560

    1 Blocks protein domain: IPB001578 Ubiquitin carboxyl-terminal hydrolase

    UniProtKB/Swiss-Prot: BAP1_HUMAN, Q92560
    Similarity: Belongs to the peptidase C12 family. BAP1 subfamily


    BAP1 for domains           About GeneDecksing


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: BAP1_HUMAN, Q92560
    Function: Deubiquitinating enzyme that plays a key role in chromatin by mediating deubiquitination of histone H2A
    and HCFC1. Catalytic component of the PR-DUB complex, a complex that specifically mediates deubiquitination of
    histone H2A monoubiquitinated at 'Lys-119' (H2AK119ub1). Does not deubiquitinate monoubiquitinated histone H2B.
    Acts as a regulator of cell growth by mediating deubiquitination of HCFC1 N-terminal and C-terminal chains, with
    some specificity toward 'Lys-48'-linked polyubiquitin chains compared to 'Lys-63'-linked polyubiquitin chains.
    Deubiquitination of HCFC1 does not lead to increase stability of HCFC1. Interferes with the BRCA1 and BARD1
    heterodimer activity by inhibiting their ability to mediate ubiquitination and autoubiquitination. It however
    does not mediate deubiquitination of BRCA1 and BARD1. Acts as a tumor suppressor
    Catalytic activity: Thiol-dependent hydrolysis of ester, thioester, amide, peptide and isopeptide bonds formed by
    the C-terminal Gly of ubiquitin (a 76-residue protein attached to proteins as an intracellular targeting signal)

         Genatlas biochemistry entry for BAP1:
    BRCA1 associated protein 1,widely expressed,binding to the BRCA1 RING finger domain and enhancing BRCA1-mediated
    cell growth suppression

         Enzyme Number (IUBMB): EC 3.4.19.121

         Gene Ontology (GO): 5 molecular function terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003682chromatin binding IDA19815555
    GO:0004221ubiquitin thiolesterase activity IMP18757409
    GO:0004843ubiquitin-specific protease activity IDA18757409
    GO:0005515protein binding IPI19117993
    GO:0008233peptidase activity NAS9528852
         
    BAP1 for ontologies           About GeneDecksing


    Phenotypes:
         3 GenomeRNAi human phenotypes for BAP1:
     Cell division defect  Increased S DNA content  Increased cell death HMECs cel 

         10 MGI mutant phenotypes (inferred from 4 alleles(MGI details for Bap1):
     cardiovascular system  embryogenesis  growth/size/body  hematopoietic system  homeostasis/metabolism 
     immune system  mortality/aging  muscle  no phenotypic analysis  tumorigenesis 

    BAP1 for phenotypes           About GeneDecksing

    Animal Models:
         MGI mouse knock-out Bap1tm1.2Geno for BAP1

       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for BAP1
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       genOway customized KO model: permanent, tissue-specific or time-controlled inactivation for BAP1
       genOway customized Knockin model: humanization, point mutation, expression monitoring, etc. for BAP1

    miRNA
    Products:
        
    miRTarBase miRNAs that target BAP1:
    hsa-mir-877-3p (MIRT037201), hsa-mir-141-3p (MIRT000727), hsa-mir-200c-3p (MIRT000726), hsa-mir-93-3p (MIRT038727), hsa-mir-200b-3p (MIRT000724), hsa-mir-1229-3p (MIRT036361), hsa-mir-429 (MIRT016637), hsa-mir-200a-3p (MIRT000730)

    Block miRNA regulation of human, mouse, rat BAP1 using miScript Target Protectors
    Selected qRT-PCR Assays for microRNAs that regulate BAP1 (see all 21):
    hsa-miR-3678-3p hsa-miR-125a-5p hsa-miR-429 hsa-miR-1914* hsa-miR-200a hsa-let-7a-2* hsa-miR-141 hsa-miR-125b
    SwitchGear 3'UTR luciferase reporter plasmidBAP1 3' UTR sequence
    Inhib. RNA
    Products:
        
    OriGene RNAi products in human, mouse, rat for BAP1
    Predesigned siRNA for gene silencing in human, mouse, rat BAP1

    Gene Editing
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    Browse Sino Biological Human cDNA Clones
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    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat BAP1

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    In Situ Assay
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for BAP1


    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from UniProtKB/Swiss-Prot
    BAP1_HUMAN, Q92560: Cytoplasm. Nucleus. Note=Mainly nuclear. Binds to chromatin
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    nucleus5
    cytosol2

    Gene Ontology (GO): Selected cellular component terms (see all 6):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005622intracellular ----
    GO:0005634nucleus IDA--
    GO:0005730NOT nucleolus IDA--
    GO:0005737cytoplasm IDA--
    GO:0035517PR-DUB complex IDA--

    BAP1 for ontologies           About GeneDecksing


    (SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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    SuperPaths for BAP1 About                                                                                                See pathways by source

    SuperPathContained pathways About
    1Inactivation of APC/C via direct inhibition of the APC/C complex
    Common schema of ubiquitination0.33
    2Selected targets of ESR1
    Selected targets of ESR1
    3Protein Stability
    Protein Stability
    4Cytoskeletal Signaling
    Cytoskeletal Signaling

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways


    2 Cell Signaling Technology (CST) Pathways for BAP1
        Cytoskeletal Signaling
    Protein Stability



    BAP1 for pathways           About GeneDecksing

        Pathway & Disease-focused RT2 Profiler PCR Array including BAP1: 
              Polycomb & Trithorax Complexes in human mouse rat

    Interactions:

        GeneGlobe Interaction Network for BAP1

    STRING Interaction Network Preview (showing 5 interactants - click image to see 25)

    Selected Interacting proteins for BAP1 (Q925601, 3 ENSP000004171324) via UniProtKB, MINT, STRING, and/or I2D (see all 91)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    BRCA1P383981, 3, ENSP000003502834EBI-1791447,EBI-349905 I2D: score=3 STRING: ENSP00000350283
    ASXL1Q8IXJ91, 3, ENSP000003648394EBI-1791447,EBI-1646500 I2D: score=2 STRING: ENSP00000364839
    HCFC1P516101, 3, ENSP000003095554EBI-1791447,EBI-396176 I2D: score=3 STRING: ENSP00000309555
    AHCYL2Q96HN23, ENSP000003159314I2D: score=2 STRING: ENSP00000315931
    ANAPC7Q9UJX33, ENSP000003943944I2D: score=2 STRING: ENSP00000394394
    About this table

    Gene Ontology (GO): Selected biological process terms (see all 8):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0001558regulation of cell growth IMP19815555
    GO:0006464cellular protein modification process NAS9528852
    GO:0006511ubiquitin-dependent protein catabolic process IEA--
    GO:0008285negative regulation of cell proliferation TAS9528852
    GO:0016579protein deubiquitination IDA18757409

    BAP1 for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for BAP1



    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    Conferences by KenesGroup, exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, and/or QIAGEN )
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    REFSEQ mRNAs for BAP1 gene: 
    NM_004656.3  

    Unigene Cluster for BAP1:

    BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase)
    Hs.106674  [show with all ESTs]
    Unigene Representative Sequence: NM_004656
    10 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000460680(uc003ddw.3 uc010hmg.3 uc010hmh.3 uc003ddx.3)
    ENST00000469613 ENST00000296288 ENST00000478368 ENST00000466093 ENST00000490804
    ENST00000471532 ENST00000483984 ENST00000490917 ENST00000470173

    miRNA
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    Block miRNA regulation of human, mouse, rat BAP1 using miScript Target Protectors
    Selected qRT-PCR Assays for microRNAs that regulate BAP1 (see all 21):
    hsa-miR-3678-3p hsa-miR-125a-5p hsa-miR-429 hsa-miR-1914* hsa-miR-200a hsa-let-7a-2* hsa-miR-141 hsa-miR-125b
    SwitchGear 3'UTR luciferase reporter plasmidBAP1 3' UTR sequence
    Inhib. RNA
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    Primer
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    Pre-validated RT2 qPCR Primer Assay in human, mouse, rat BAP1
      QuantiTect SYBR Green Assays in human, mouse, rat BAP1
      QuantiFast Probe-based Assays in human, mouse, rat BAP1

    Additional mRNA sequence: 

    AB002534.1 AF045581.1 AK092725.1 AK094499.1 AK225494.1 AK292608.1 AK295395.1 AK307274.1 
    AY130008.1 BC001596.1 BX647318.1 D87462.2 D88812.1 

    18 DOTS entries:

    DT.217303  DT.91763316  DT.102820838  DT.100795050  DT.100795049  DT.120914317  DT.120914340  DT.120914236 
    DT.100032503  DT.120914364  DT.86854177  DT.97791879  DT.100029516  DT.100795048  DT.102820839  DT.120914363 
    DT.120914282  DT.80100384 

    Selected AceView cDNA sequences (see all 369):

    BQ955178 CK430805 CF125903 BM820350 BQ417342 CA748699 BM451889 Z45707 
    BI088030 BE464104 D87462 BE671970 BU846231 BQ058097 BM833483 BQ717541 
    BM665639 AA515069 AI962244 BU729539 BQ421640 AY130008 Z41371 AL039264 

    GeneLoc Exon Structure

    Selected Alternative Splicing Database (ASD) splice patterns (SP) for BAP1 (see all 13)    About this scheme

    ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6a · 6b ^ 7a · 7b · 7c ^ 8a · 8b ^ 9 ^ 10a · 10b ^ 11a · 11b · 11c ^ 12 ^ 13 ^ 14a · 14b ^ 15 ^ 16 ^ 17 ^ 18a ·
    SP1:                                                  -     -     -                 -           -                                                     -         
    SP2:                                -     -                                                                                                                     
    SP3:                                                                                                                                                  -         
    SP4:                          -                                                                                                                                 
    SP5:              -                                                                                                                                             

    ExUns: 18b · 18c ^ 19 ^ 20a · 20b · 20c · 20d · 20e
    SP1:                                                
    SP2:                                                
    SP3:                                                
    SP4:                                                
    SP5:                                                


    ECgene alternative splicing isoforms for BAP1

    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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    BAP1 expression in normal human tissues (normalized intensities)      BAP1 embryonic expression: see
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: GCCTCTGCCA
    BAP1 Expression
    About this image


    BAP1 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 2) fully expand
     
     Bone (Muscoskeletal System)
             Bone Marrow
     
     Testis (Reproductive System)
    BAP1 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    BAP1 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.106674

    UniProtKB/Swiss-Prot: BAP1_HUMAN, Q92560
    Tissue specificity: Highly expressed in testis, placenta and ovary. Expressed in breast

        Pathway & Disease-focused RT2 Profiler PCR Array including BAP1: 
              Polycomb & Trithorax Complexes in human mouse rat

    Primer
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    OriGene qPCR primer pairs and template standards for BAP1
    OriGene qSTAR qPCR primer pairs in human, mouse for BAP1
    Pre-validated RT2 qPCR Primer Assay in human, mouse, rat BAP1
    QuantiTect SYBR Green Assays in human, mouse, rat BAP1
    QuantiFast Probe-based Assays in human, mouse, rat BAP1
    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for BAP1

    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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    This gene was present in the common ancestor of animals.

    Orthologs for BAP1 gene from Selected species (see all 14)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Bap11 , 5 Brca1 associated protein 11, 5 88.37(n)1
    92.86(a)1
      14 (19.09 cM)5
    1044161  NM_027088.21  NP_081364.11 
     312514895 
    chicken
    (Gallus gallus)
    Aves BAP11 BRCA1 associated protein-1 (ubiquitin carboxy-terminal more 80.83(n)
    85.55(a)
      415944  NM_001030590.1  NP_001025761.1 
    lizard
    (Anolis carolinensis)
    Reptilia BAP16
    BRCA1 associated protein-1 (ubiquitin carboxy-term...
    79(a)
    1 ↔ 1
    GL343474.1(136799-155466)
    African clawed frog
    (Xenopus laevis)
    Amphibia Xl.114452 Xenopus laevis transcribed sequence with strong similarity more 78.64(n)    CA793749.1 
    zebrafish
    (Danio rerio)
    Actinopterygii bap11 BRCA1 associated protein-1 (ubiquitin carboxy-terminal more 67(n)
    72.07(a)
      558885  NM_001163837.1  NP_001157309.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta CG84453
    calypso1
    NOT ubiquitin C-terminal hydrolase3
    calypso1
    58(a)3
    61.34(n)1
    59.76(a)1
      52F73
    367941  NM_176194.11  NP_788374.11 


    ENSEMBL Gene Tree for BAP1 (if available)
    TreeFam Gene Tree for BAP1 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for BAP1 gene
    UCHL52  
    1 SIMAP similar gene for BAP1 using alignment to 6 protein entries:     BAP1_HUMAN (see all proteins):
    UCHL5

    BAP1 for paralogs           About GeneDecksing



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    Selected SNPs for BAP1 (see all 347)    About this table    
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 3 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    VAR_0634984
    A lung cancer sample4--see VAR_0634982 A D mis40--------
    VAR_0634994
    A lung cancer sample4--see VAR_0634992 G V mis40--------
    rs710841821,2
    C--52439509(-) TTTTT-/T/TTT 
            
    CTTCC
    2 -- int1 cds11NA 2
    rs287588601,2
    C,F,H--52497181(+) CCCCTA/C/TTGCAG 1 -- ds50017NS NA WA 1010
    rs1449563091,2
    --52497230(+) CTCAGC/TAGACG 1 -- ds50010--------
    rs1489738071,2
    --52497298(+) CCAAAA/CGCAAC 1 -- ds50010--------
    rs1877970121,2
    --52497437(+) CCATGC/GCCCTC 1 -- ds50010--------
    rs1932849201,2
    --52497582(+) TTCTGA/GTCCCA 1 -- ds50010--------
    rs4989461,2
    C,F,A,H--52497602(+) GCCCAT/CGAGGT 1 -- ds500126Minor allele frequency- C:0.32MN NS EA NA WA CSA 2645
    rs1843012921,2
    --52497629(+) TCCATA/TTCTCA 1 -- ds50010--------

    HapMap Linkage Disequilibrium report for BAP1 (52435024 - 52444366 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 4 variations for BAP1:    About this table    
    Variant IDTypeSubtypePubMed ID
    dgv5137n71CNV Loss21882294
    nsv834697CNV Loss17160897
    nsv834696CNV Loss17160897
    nsv876789CNV Loss21882294

    Human Gene Mutation Database (HGMD): BAP1
    1 Site Specific Mutation Identification with PCR Assay for BAP1:
    Cosmic IdAA Change
    51976p.H169Q
    SeqTarget long-range PCR primers for resequencing BAP1
    DNA2.0 Custom Variant and Variant Library Synthesis for BAP1

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    OMIM gene information: 603089   
    OMIM disorders: 614327  
    UniProtKB/Swiss-Prot: BAP1_HUMAN, Q92560
  • Mesothelioma, malignant (MESOM) [MIM:156240]: An aggressive neoplasm of the serosal lining of the chest.
    It appears as broad sheets of cells, with some regions containing spindle-shaped, sarcoma-like cells and other
    regions showing adenomatous patterns. Pleural mesotheliomas have been linked to exposure to asbestos. Note=The
    gene represented in this entry is involved in disease pathogenesis
  • Tumor predisposition syndrome (TPDS) [MIM:614327]: A condition characterized by predisposition to develop
    a variety of tumors, including benign melanocytic tumors as well as several malignant tumors, including uveal
    melanoma, cutaneous melanoma, malignant mesothelioma on exposure to asbestos, lung adenocarcinoma and meningioma.
    Note=The disease is caused by mutations affecting the gene represented in this entry

  • Selected diseases for BAP1 (see all 30):    About MalaCards
    tumor predisposition syndrome    familial cylindromatosis    malignant mesothelioma    childhood medulloblastoma
    ocular melanoma    cerebritis    pandas    noma
    malignant pleural mesothelioma    sporadic breast cancer    melanoma    medulloblastoma
    breast cancer    parkinson's disease    paraganglioma    lung adenocarcinoma
    clear cell renal cell carcinoma    meningioma    renal cell carcinoma    bipolar disorder


    BAP1 for disorders           About GeneDecksing


    Congresses - knowledge worth sharing:
    Alzheimer's & Parkinson's Diseases Congress (ADPD) 18 - 22 March 2015

    3 Novoseek inferred disease relationships for BAP1 gene    About this table

    Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    parkinson disease 33.7 2 12775255 (1), 10203348 (1)
    breast cancer 17 4 9528852 (2), 19197335 (1)
    tumors 0 3 19815555 (1), 12800201 (1), 9528852 (1)

    Genetic Association Database (GAD): BAP1
    Human Genome Epidemiology (HuGE) Navigator: BAP1 (8 documents)

    Export disorders for BAP1 gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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    PubMed articles for BAP1 gene, integrated from 10 sources (see all 93):
    (articles sorted by number of sources associating them with BAP1)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. BAP1: a novel ubiquitin hydrolase which binds to the BRCA1 RING finger and enhances BRCA1-mediated cell growth suppression. (PubMed id 9528852)1, 2, 3, 9 Jensen D.E.... Rauscher F.J. III (Oncogene 1998)
    2. BRCA1-associated protein 1 interferes with BRCA1/BARD1 RING heterodimer activity. (PubMed id 19117993)1, 2, 9 Nishikawa H.... Ohta T. (Cancer Res. 2009)
    3. The deubiquitinating enzyme BAP1 regulates cell growth via interaction with HCF-1. (PubMed id 19815555)1, 2, 9 Machida Y.J.... Dutta A. (J. Biol. Chem. 2009)
    4. Genetic sequence variations of BRCA1-interacting genes AURKA, BAP1, BARD1 and DHX9 in French Canadian families with high risk of breast cancer. (PubMed id 19197335)1, 4, 9 GuAcnard F....Durocher F. (J. Hum. Genet. 2009)
    5. Novel tumor antigens identified by autologous antibody screening of childhood medulloblastoma cDNA libraries. (PubMed id 12800201)1, 2, 9 Behrends U.... Mautner J. (Int. J. Cancer 2003)
    6. Germline mutations in BAP1 predispose to melanocytic tumors. (PubMed id 21874003)1, 2 Wiesner T....Speicher M.R. (Nat. Genet. 2011)
    7. The nuclear deubiquitinase BAP1 is commonly inactivated by somatic mutations and 3p21.1 losses in malignant pleural mesothelioma. (PubMed id 21642991)1, 2 Bott M.... Ladanyi M. (Nat. Genet. 2011)
    8. Germline BAP1 mutations predispose to malignant mesothelioma. (PubMed id 21874000)1, 2 Testa J.R....Carbone M. (Nat. Genet. 2011)
    9. Single nucleotide polymorphisms in miRNA binding sites and miRNA genes as breast/ovarian cancer risk modifiers in Jewish high-risk women. (PubMed id 19950226)1, 4 Kontorovich T....Friedman E. (Int. J. Cancer 2010)
    10. Histone H2A deubiquitinase activity of the Polycomb repressive complex PR-DUB. (PubMed id 20436459)1, 2 Scheuermann J.C.... Muller J. (Nature 2010)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    Disorders
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 8314 HGNC: 950 AceView: BAP1 Ensembl:ENSG00000163930 euGenes: HUgn8314
    ECgene: BAP1 H-InvDB: BAP1

    (According to HUGE)
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    HUGE: KIAA0272

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
    About This Section

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    NameDescription
    PharmGKB entry for BAP1 Pharmacogenomics, SNPs, Pathways
    ATLAS Chromosomes in Cancer entry for BAP1 Genetics and Cytogenetics in Oncology and Haematology

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for BAP1 gene:
    Search GeneIP for patents involving BAP1

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



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