Human Gene BAP1 (ENST00000460680.6) from GENCODE V44
  Description: Homo sapiens BRCA1 associated protein 1 (BAP1), mRNA. (from RefSeq NM_004656)
RefSeq Summary (NM_004656): 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].
Gencode Transcript: ENST00000460680.6
Gencode Gene: ENSG00000163930.10
Transcript (Including UTRs)
   Position: hg38 chr3:52,401,008-52,410,008 Size: 9,001 Total Exon Count: 17 Strand: -
Coding Region
   Position: hg38 chr3:52,402,288-52,409,878 Size: 7,591 Coding Exon Count: 17 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesGeneReviewsMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr3:52,401,008-52,410,008)mRNA (may differ from genome)Protein (729 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGencodeGeneCards

-  Comments and Description Text from UniProtKB
DESCRIPTION: RecName: Full=Ubiquitin carboxyl-terminal hydrolase BAP1; EC=; AltName: Full=BRCA1-associated protein 1; AltName: Full=Cerebral protein 6;
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).
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.
INTERACTION: P38398:BRCA1; NbExp=3; IntAct=EBI-1791447, EBI-349905; P38398-5:BRCA1; NbExp=2; IntAct=EBI-1791447, EBI-2015072;
SUBCELLULAR LOCATION: Cytoplasm. Nucleus. Note=Mainly nuclear. Binds to chromatin.
TISSUE SPECIFICITY: Highly expressed in testis, placenta and ovary. Expressed in breast.
PTM: Phosphorylated upon DNA damage, probably by ATM or ATR.
DISEASE: Defects in BAP1 may be a cause of 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.
DISEASE: Defects in BAP1 are a cause of tumor predisposition syndrome (TPDS) [MIM:614327]. TPDS is 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.
SIMILARITY: Belongs to the peptidase C12 family. BAP1 subfamily.
SEQUENCE CAUTION: Sequence=BAA13401.2; Type=Erroneous initiation; Note=Translation N-terminally shortened;

-  Primer design for this transcript

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Click here to load the transcript sequence and exon structure into Primer3Plus

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To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3

-  MalaCards Disease Associations
  MalaCards Gene Search: BAP1
Diseases sorted by gene-association score: tumor predisposition syndrome* (1388), bap1 tumor predisposition syndrome* (418), uveal melanoma* (230), nevus of ota (18), pleural cancer (16), ocular melanoma (13), bainbridge-ropers syndrome (13), malignant melanoma, somatic* (11), malignant pleural mesothelioma (7), rhabdoid meningioma (6), clear cell renal cell carcinoma (6), peritoneum cancer (5), malignant conjunctival melanoma (5), melanoma (4), sensory system cancer (1)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 104.25 RPKM in Testis
Total median expression: 1524.43 RPKM

View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -60.90130-0.468 Picture PostScript Text
3' UTR -538.001280-0.420 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR001578 - Peptidase_C12

Pfam Domains:
PF01088 - Ubiquitin carboxyl-terminal hydrolase, family 1

ModBase Predicted Comparative 3D Structure on Q92560
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
Genome BrowserGenome BrowserGenome BrowserGenome BrowserNo orthologNo ortholog
Gene Details     
Gene Sorter     
Protein SequenceProtein SequenceProtein SequenceProtein Sequence  

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003682 chromatin binding
GO:0004843 thiol-dependent ubiquitin-specific protease activity
GO:0005515 protein binding
GO:0008233 peptidase activity
GO:0008234 cysteine-type peptidase activity
GO:0016787 hydrolase activity
GO:0036459 thiol-dependent ubiquitinyl hydrolase activity

Biological Process:
GO:0001558 regulation of cell growth
GO:0006325 chromatin organization
GO:0006464 cellular protein modification process
GO:0006508 proteolysis
GO:0006511 ubiquitin-dependent protein catabolic process
GO:0008285 negative regulation of cell proliferation
GO:0010035 response to inorganic substance
GO:0016579 protein deubiquitination
GO:0035520 monoubiquitinated protein deubiquitination
GO:0035522 monoubiquitinated histone H2A deubiquitination
GO:0050727 regulation of inflammatory response
GO:0051726 regulation of cell cycle
GO:0061519 macrophage homeostasis
GO:0071108 protein K48-linked deubiquitination
GO:1900015 regulation of cytokine production involved in inflammatory response
GO:1903955 positive regulation of protein targeting to mitochondrion

Cellular Component:
GO:0005622 intracellular
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0035517 PR-DUB complex

-  Descriptions from all associated GenBank mRNAs
  KJ897824 - Synthetic construct Homo sapiens clone ccsbBroadEn_07218 BAP1 gene, encodes complete protein.
LF333775 - JP 2014500723-A/141278: Polycomb-Associated Non-Coding RNAs.
MA569352 - JP 2018138019-A/141278: Polycomb-Associated Non-Coding RNAs.
LF209993 - JP 2014500723-A/17496: Polycomb-Associated Non-Coding RNAs.
MA445570 - JP 2018138019-A/17496: Polycomb-Associated Non-Coding RNAs.
AY130008 - Homo sapiens MU-MB-17.261 mRNA, partial cds.
LF214009 - JP 2014500723-A/21512: Polycomb-Associated Non-Coding RNAs.
MA449586 - JP 2018138019-A/21512: Polycomb-Associated Non-Coding RNAs.
AF045581 - Homo sapiens BRCA1 associated protein 1 (BAP1) mRNA, complete cds.
AK092725 - Homo sapiens cDNA FLJ35406 fis, clone SKNSH2007429, highly similar to Ubiquitin carboxyl-terminal hydrolase BAP1 (EC
AK094499 - Homo sapiens cDNA FLJ37180 fis, clone BRALZ2001038, highly similar to Homo sapiens BRCA1 associated protein 1 (BAP1) mRNA.
AK225494 - Homo sapiens mRNA for BRCA1 associated protein-1 variant, clone: JTH08468.
D87462 - Homo sapiens mRNA for KIAA0272 gene.
BX647318 - Homo sapiens mRNA; cDNA DKFZp686N04275 (from clone DKFZp686N04275).
JD333126 - Sequence 314150 from Patent EP1572962.
JD177936 - Sequence 158960 from Patent EP1572962.
JD427866 - Sequence 408890 from Patent EP1572962.
JD438089 - Sequence 419113 from Patent EP1572962.
JD452535 - Sequence 433559 from Patent EP1572962.
JD474091 - Sequence 455115 from Patent EP1572962.
JD514206 - Sequence 495230 from Patent EP1572962.
JD399994 - Sequence 381018 from Patent EP1572962.
JD416653 - Sequence 397677 from Patent EP1572962.
JD525577 - Sequence 506601 from Patent EP1572962.
JD527624 - Sequence 508648 from Patent EP1572962.
JD102594 - Sequence 83618 from Patent EP1572962.
JD243860 - Sequence 224884 from Patent EP1572962.
JD423738 - Sequence 404762 from Patent EP1572962.
JD549621 - Sequence 530645 from Patent EP1572962.
AB002534 - Homo sapiens hucep-13 mRNA for cerebral protein-13, complete cds.
JD147682 - Sequence 128706 from Patent EP1572962.
JD290341 - Sequence 271365 from Patent EP1572962.
JD334873 - Sequence 315897 from Patent EP1572962.
JD425685 - Sequence 406709 from Patent EP1572962.
JD393387 - Sequence 374411 from Patent EP1572962.
AK295395 - Homo sapiens cDNA FLJ54103 complete cds, highly similar to Ubiquitin carboxyl-terminal hydrolase BAP1 (EC
CQ873779 - Sequence 198 from Patent WO2004076622.
DD413616 - Regulation of Mammalian Cells.
JD322409 - Sequence 303433 from Patent EP1572962.
JD555373 - Sequence 536397 from Patent EP1572962.
JD041114 - Sequence 22138 from Patent EP1572962.
JD478722 - Sequence 459746 from Patent EP1572962.
BC001596 - Homo sapiens BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase), mRNA (cDNA clone MGC:1530 IMAGE:3543914), complete cds.
JD372748 - Sequence 353772 from Patent EP1572962.
AK307274 - Homo sapiens cDNA, FLJ97222.
JD446223 - Sequence 427247 from Patent EP1572962.
JD231047 - Sequence 212071 from Patent EP1572962.
JD081498 - Sequence 62522 from Patent EP1572962.
JD392535 - Sequence 373559 from Patent EP1572962.
JD040952 - Sequence 21976 from Patent EP1572962.
AK292608 - Homo sapiens cDNA FLJ75117 complete cds, highly similar to Homo sapiens BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase) (BAP1), mRNA.
JD079669 - Sequence 60693 from Patent EP1572962.
JD210763 - Sequence 191787 from Patent EP1572962.
JD498168 - Sequence 479192 from Patent EP1572962.
JD347113 - Sequence 328137 from Patent EP1572962.
D88812 - Homo sapiens hucep-6 mRNA for cerebral protein-6, complete cds.
AB383829 - Synthetic construct DNA, clone: pF1KSDA0272, Homo sapiens BAP1 gene for ubiquitin carboxyl-terminal hydrolase BAP1, complete cds, without stop codon, in Flexi system.
DQ892545 - Synthetic construct clone IMAGE:100005175; FLH187353.01X; RZPDo839G0572D BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase) (BAP1) gene, encodes complete protein.
DQ895756 - Synthetic construct Homo sapiens clone IMAGE:100010216; FLH187349.01L; RZPDo839G0562D BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase) (BAP1) gene, encodes complete protein.
JD024823 - Sequence 5847 from Patent EP1572962.
LF333774 - JP 2014500723-A/141277: Polycomb-Associated Non-Coding RNAs.
MA569351 - JP 2018138019-A/141277: Polycomb-Associated Non-Coding RNAs.
LF333773 - JP 2014500723-A/141276: Polycomb-Associated Non-Coding RNAs.
MA569350 - JP 2018138019-A/141276: Polycomb-Associated Non-Coding RNAs.
LF333772 - JP 2014500723-A/141275: Polycomb-Associated Non-Coding RNAs.
MA569349 - JP 2018138019-A/141275: Polycomb-Associated Non-Coding RNAs.
LF333771 - JP 2014500723-A/141274: Polycomb-Associated Non-Coding RNAs.
MA569348 - JP 2018138019-A/141274: Polycomb-Associated Non-Coding RNAs.
DQ583738 - Homo sapiens piRNA piR-50850, complete sequence.
CU674778 - Synthetic construct Homo sapiens gateway clone IMAGE:100020041 5' read BAP1 mRNA.
LF333768 - JP 2014500723-A/141271: Polycomb-Associated Non-Coding RNAs.
MA569345 - JP 2018138019-A/141271: Polycomb-Associated Non-Coding RNAs.
DQ593715 - Homo sapiens piRNA piR-33827, complete sequence.
LF333767 - JP 2014500723-A/141270: Polycomb-Associated Non-Coding RNAs.
MA569344 - JP 2018138019-A/141270: Polycomb-Associated Non-Coding RNAs.
LF333766 - JP 2014500723-A/141269: Polycomb-Associated Non-Coding RNAs.
MA569343 - JP 2018138019-A/141269: Polycomb-Associated Non-Coding RNAs.
JD187473 - Sequence 168497 from Patent EP1572962.
JD485482 - Sequence 466506 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q92560 (Reactome details) participates in the following event(s):

R-HSA-5689630 BAP1 binds BAP1-interacting complex
R-HSA-5689649 BAP1 binds BRCA1:BARD1
R-HSA-5690785 BAP1 binds Ub-HCFC1
R-HSA-5690759 BAP1:Ub-HCFC1 deubiquitinates BAP1:Ub-HCFC1
R-HSA-5690790 Histone H2A is dubiquitinated by the PR-DUB complex
R-HSA-5689603 UCH proteinases
R-HSA-5688426 Deubiquitination
R-HSA-597592 Post-translational protein modification
R-HSA-392499 Metabolism of proteins

-  Other Names for This Gene
  Alternate Gene Symbols: A8K993, BAP1_HUMAN, ENST00000460680.1, ENST00000460680.2, ENST00000460680.3, ENST00000460680.4, ENST00000460680.5, hucep-6, KIAA0272, NM_004656, Q6LEM0, Q7Z5E8, Q92560, uc003ddx.1, uc003ddx.2, uc003ddx.3, uc003ddx.4, uc003ddx.5, uc003ddx.6
UCSC ID: ENST00000460680.6
RefSeq Accession: NM_004656
Protein: Q92560 (aka BAP1_HUMAN)
CCDS: CCDS2853.1

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene BAP1:
bap1-tpds (BAP1 Tumor Predisposition Syndrome)

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.