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

Summary

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: mouse all
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Genomic context

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_000003.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
BAP1 promotes osteoclast function by metabolic reprogramming.
Title: BAP1 promotes osteoclast function by metabolic reprogramming.
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.
BAP1 as a guardian of genome stability: implications in human cancer.
Title: BAP1 as a guardian of genome stability: implications in human cancer.
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.
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.
Two unique BAP1 pathogenic variants identified in the same family by panel cascade testing.
Title: Two unique BAP1 pathogenic variants identified in the same family by panel cascade testing.
BAP1 and PTEN mutations shape the immunological landscape of clear cell renal cell carcinoma and reveal the intertumoral heterogeneity of T cell suppression: a proof-of-concept study.
Title: BAP1 and PTEN mutations shape the immunological landscape of clear cell renal cell carcinoma and reveal the intertumoral heterogeneity of T cell suppression: a proof-of-concept study.
Organoid models of fibrolamellar carcinoma mutations reveal hepatocyte transdifferentiation through cooperative BAP1 and PRKAR2A loss.
Title: Organoid models of fibrolamellar carcinoma mutations reveal hepatocyte transdifferentiation through cooperative BAP1 and PRKAR2A loss.
BAP1-deficient meningioma presenting with trabecular architecture and cytokeratin expression: a report of two cases and review of the literature.
Title: BAP1-deficient meningioma presenting with trabecular architecture and cytokeratin expression: a report of two cases and review of the literature.

Submit: New GeneRIF Correction See all GeneRIFs (310)

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 EBI GWAS CatalogPubMed
Large-scale genome-wide association analysis of bipolar disorder identifies a new susceptibility locus near ODZ4. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D3S3975 (e-PCR)
- UniSTS:8864

D1S3697 (e-PCR)
- UniSTS:474275

D3S3829 (e-PCR)
- UniSTS:63694

SHGC-76996 (e-PCR)
- UniSTS:53212

RH135811 (e-PCR)
- UniSTS:209631

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 more info	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

EC 3.4.19.12

NP_004647.1

EC 3.4.19.12

XP_011532451.1

EC 3.4.19.12

XP_011532452.1

EC 3.4.19.12

XP_011532453.1

EC 3.4.19.12

XP_011532454.1

EC 3.4.19.12

XP_047305000.1

EC 3.4.19.12

XP_054204030.1

EC 3.4.19.12

XP_054204031.1

EC 3.4.19.12

XP_054204032.1

EC 3.4.19.12

XP_054204033.1

EC 3.4.19.12

XP_054204034.1

EC 3.4.19.12

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

NG_031859.1 RefSeqGene

Range

4889..13990

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GenBank, FASTA, Sequence Viewer (Graphics), LRG_529

mRNA and Protein(s)

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
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

NC_000003.12 Reference GRCh38.p14 Primary Assembly

Range

52401008..52410008 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

NC_060927.1 Alternate T2T-CHM13v2.0

Range

52433990..52442989 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054348059.1 → XP_054204034.1 ubiquitin carboxyl-terminal hydrolase BAP1 isoform X5
XM_054348057.1 → XP_054204032.1 ubiquitin carboxyl-terminal hydrolase BAP1 isoform X3
XM_054348058.1 → XP_054204033.1 ubiquitin carboxyl-terminal hydrolase BAP1 isoform X4
XM_054348056.1 → XP_054204031.1 ubiquitin carboxyl-terminal hydrolase BAP1 isoform X2
XM_054348055.1 → XP_054204030.1 ubiquitin carboxyl-terminal hydrolase BAP1 isoform X1