The gene spans 9.0 kb and is composed of 17 exons.

Transcription start is 115 bp upstream of first ATG of the BAP1 ORF.

No pseudogene reported.

Human BAP1 is 729 amino acids with a molecular weight of 90 kDa. The amino-terminal 240 amino acids show homology to ubiquitin C-terminal hydrolases (UCH).
BAP1 also contains a region of extreme acidity (amino acids 396 to 408), multiple potential phosphorylation sites and N-linked glycosylation sites. The C-terminal region contains two putative nuclear localization signals.
BAP1 binds to the RING finger domain of BRCA1 through its carboxyl-terminal region (594-657 amino acids). Domain comprised by residues 182-365 of BAP1 interacts with the RING finger domain of BARD1. Interaction of BAP1 with HCF-1 (host cell factor 1; HCFC1) is dependent on the NHNY sequence resembling the HCF-binding motif (HBM).

BAP1 is expressed in a variety of human adult tissues. High expression was detected in testis, placenta and ovary, with varying levels detected in other tissues. Expression of BAP1 in normal human breast tissue was also detected.
Analysis conducted in mice revealed that Bap1 expression is up-regulated in the breast during puberty, pregnancy and as a result of parity.
BAP1 mRNA level is significantly increased in MCF10a cell line following genistein treatment, an isoflavone found in soya and proposed to prevent breast cancer.

BAP1 is a nuclear-localized ubiquitin carboxy-terminal hydrolase.

BAP1 enhances BRCA1-mediated inhibition of breast cancer cell growth and may serve as a regulator/effector of BRCA1 growth control/differentiation pathways. BAP1 interacts with HCF-1, a transcriptional cofactor found in a number of important regulatory complexes. Bap1 may help to control cell proliferation by regulating HCF-1 protein levels and by associating with genes involved in the G1-S transition.
The BRCA1/BARD1 complex possess a dual E3 ubiquitin ligase activity, promotes its own ubiquitination and targets other proteins. Although BAP1 associates with BRCA1, it does not appear to function in the deubiquitylation of the BRCA1/BARD1 complex. BAP1 inhibits the E3 ligase activity of BRCA1/BARD1 by binding the RING finger domain of BARD1 and possesses deubiquitination activity toward ubiquitin chains catalyzed by BRCA1/BARD1.
BAP1 and BRCA1/BARD1 may coordinately regulate ubiquitination during the DNA damage response and the cell cycle, BAP1 being phosphorylated by ATM and ATR in response to DNA damage and BAP1 inhibition causing S-phase retardation.
It was also proposed that specific regions and UCH activity of BAP1 play an essential role in TCR.
In the cytoplasm, BAP1 has recently been shown to localize at the endoplasmic reticulum, where it binds, deubiquitylates, and stabilizes type 3 inositol-1,4,5-trisphosphate receptor (IP3R3). This binding modulates calcium (Ca2+) release from the endoplasmic reticulum into the cytosol and mitochondria, promoting apoptosis.

The amino-terminal 240 amino acids show significant homology to a class of thiol proteases, designated UCH, which are implicated in the proteolytic processing of ubiquitin.

The mutation of a residue predicted to disrupt the helical nature of the extreme C-terminal region of BAP1 abolishes the BAP1/BRCA1 interaction.
BAP1 can suppress tumorigenicity of lung cancer cells in athymic nude mice.
Deubiquitinating activity and nuclear localization are both required for BAP1-mediated tumor suppression. Moreover, BAP1-mediated growth suppression is independent of wild-type BRCA1.
Squamous-cell carcinomas and large-cell undifferentiated carcinomas showed LOH for a 3p21-22 locus.
Large rearrangements, deletions, and missense mutations of the BAP1 locus have been found in lung and sporadic breast tumors and in lung cancer cell lines.
Heterozygous germline mutations of Bap1 in mice predispose to tumor formation, providing in vivo evidence that Bap1 Is a bona fide tumor suppressor. Bap1+/- mice followed for up to 20 months of age demonstrated that haploinsufficient mutant mice exhibited a markedly higher incidence and accelerated onset of asbestos-induced malignant mesothelioma when compared with similarly-exposed wild-type littermates.