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

Summary

Official Symbol: BAP1provided by HGNC
Official Full Name: BRCA1 associated deubiquitinase 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_2024_08	current	GRCh38.p14 (GCF_000001405.40)	3	NC_000003.12 (52401008..52410008, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	3	NC_060927.1 (52433990..52442989, complement)
RS_2024_09	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 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?

Clinical and genetic characteristics of BAP1-mutated non-uveal and uveal melanoma.
Title: Clinical and genetic characteristics of BAP1-mutated non-uveal and uveal melanoma.
The elusive BAP1 mutation in pediatric melanocytic tumors.
Title: The elusive BAP1 mutation in pediatric melanocytic tumors.
Benign splenic lesions in BAP1-tumor predisposition syndrome: a case series.
Title: Benign splenic lesions in BAP1-tumor predisposition syndrome: a case series.
Protein and mRNA Expression in Uveal Melanoma Cell Lines Are Related to GNA and BAP1 Mutation Status.
Title: Protein and mRNA Expression in Uveal Melanoma Cell Lines Are Related to GNA and BAP1 Mutation Status.
Saturation genome editing of BAP1 functionally classifies somatic and germline variants.
Title: Saturation genome editing of BAP1 functionally classifies somatic and germline variants.
[Clinicopathological features of BAP1 mutated clear cell renal cell carcinoma].
Title: [Clinicopathological features of BAP1 mutated clear cell renal cell carcinoma].
ITGB2-ICAM1 axis promotes liver metastasis in BAP1-mutated uveal melanoma with retained hypoxia and ECM signatures.
Title: ITGB2-ICAM1 axis promotes liver metastasis in BAP1-mutated uveal melanoma with retained hypoxia and ECM signatures.
Slow proliferation of BAP1-deficient uveal melanoma cells is associated with reduced S6 signaling and resistance to nutrient stress.
Title: Slow proliferation of BAP1-deficient uveal melanoma cells is associated with reduced S6 signaling and resistance to nutrient stress.
BAP1 controls mesenchymal stem cell migration by inhibiting the ERK signaling pathway.
Title: BAP1 controls mesenchymal stem cell migration by inhibiting the ERK signaling pathway.
The BAP1 nuclear deubiquitinase is involved in the nonhomologous end-joining pathway of double-strand DNA repair through interaction with DNA-PK.
Title: The BAP1 nuclear deubiquitinase is involved in the nonhomologous end-joining pathway of double-strand DNA repair through interaction with DNA-PK.

Submit: New GeneRIF Correction See all GeneRIFs (325)

Phenotypes

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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

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 heterochromatin formation	IBA Inferred from Biological aspect of Ancestor 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	IDA Inferred from Direct Assay more info	PubMed
involved_in protein deubiquitination	TAS Traceable Author Statement more info
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 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
located_in chromosome	IEA Inferred from Electronic Annotation more info
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; BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase); cerebral protein 6; cerebral protein-13; ubiquitin carboxy-terminal hydrolase L2

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_2024_08

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