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Gene

BAP1

BRCA1 associated deubiquitinase 1

Summary

Cytogenetic location
3p21.1
Coordinates
Chromosome 3: 52,401,008–52,410,008 (GRCh38)
Exons
17 exons across 9 kb
Protein
729 amino acids
Inheritance
Autosomal dominant
Also known as
hucep-6, KIAA0272, UCHL2
MANE Select transcript
ENST00000460680.6NM_004656.4
Locus type
gene with protein product
  • Very high
  • Confident
  • Low
  • Very low

Reference genomeGRCh38

Positions on gene and variant pages follow this choice, in this browser.

Curated reports relevant to this gene

  • BAP1 Tumour Predisposition Syndrome

    • Autosomal dominant

      BAP1 variants that increase the risk of uveal and cutaneous melanoma, mesothelioma, renal cell carcinoma and other tumours.

      • ClinGen rates the link definitive
      • 5 GenCC submitters rate it definitive or strong
      What knowing changes

      Annual eye, skin and kidney checks are recommended, along with avoiding asbestos exposure; relatives can be offered testing.

  • Kidney Cancer

    • Primary or metastatic malignant neoplasm involving the kidney.

      • 1 GenCC submitter rates it definitive or strong

  • Urinary and Renal System Tumour

    • Urinary System Neoplasm

      A benign or malignant, primary or metastatic neoplasm involving the urinary system.

      • 1 GenCC submitter rates it definitive or strong

Inheritance

Autosomal dominant
One changed copy, from either parent, is enough. A parent who has one passes it on to each child with a one-in-two chance.

How BAP1 is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
Chromosome 3, with a bracket where BAP1 sits. BAP1 and 39 genes near it on chromosome 3, from 51,905,508 to 52,905,507.Chromosome 33p21.1p26.3p26.2p26.1p25.3p25.2p25.1p24.3p24.2p24.1p23p22.3p22.2p22.1p21.33p21.32p21.31p21.2p21.1p14.3p14.2p14.1p13p12.3p12.2p12.1p11.2p11.1q11.1q11.2q12.1q12.2q12.3q13.11q13.12q13.13q13.2q13.31q13.32q13.33q21.1q21.2q21.3q22.1q22.2q22.3q23q24q25.1q25.2q25.31q25.32q25.33q26.1q26.2q26.31q26.32q26.33q27.1q27.2q27.3q28q2952 Mb52.2 Mb52.4 Mb52.6 Mb52.8 MbRRP9: 51,933,425–51,941,946, reverse strandPARP3: 51,942,252–51,949,371, forward strandGPR62: 51,955,381–51,957,499, forward strandPCBP4: 51,957,448–51,974,630, reverse strandABHD14B: 51,968,510–51,983,409, reverse strandABHD14A: 51,971,426–51,982,398, forward strandABHD14AABHD14A-ACY1: 51,974,706–51,989,183, forward strandABHD14A-ACY1ACY1: 51,983,047–51,989,457, forward strandACY1RPL29: 51,993,522–51,996,021, reverse strandRPL29DUSP7: 52,048,919–52,056,577, reverse strandDUSP7POC1A: 52,074,590–52,154,746, reverse strandPOC1AALAS1: 52,198,085–52,214,620, forward strandTLR9: 52,221,080–52,225,651, reverse strandTLR9: 52,221,081–52,231,190, reverse strandTWF2: 52,228,612–52,246,788, reverse strandTWF2PPM1M: 52,245,741–52,250,616, forward strandPPM1MWDR82: 52,254,434–52,288,020, reverse strandWDR82GLYCTK: 52,286,945–52,295,273, forward strandGLYCTKDNAH1: 52,316,319–52,400,492, forward strandDNAH1BAP1: 52,401,008–52,410,008, reverse strandBAP1PHF7: 52,410,504–52,427,966, forward strandPHF7SEMA3G: 52,433,035–52,445,103, reverse strandSEMA3GTNNC1: 52,451,082–52,454,071, reverse strandTNNC1NISCH: 52,455,118–52,493,081, forward strandNISCHSTAB1: 52,495,331–52,524,512, forward strandSTAB1NT5DC2: 52,524,369–52,535,093, reverse strandNT5DC2UQCC5: 52,533,950–52,579,237, forward strandUQCC5PBRM1: 52,544,271–52,685,979, reverse strandPBRM1GNL3: 52,681,156–52,696,160, forward strandGNL3GLT8D1: 52,691,527–52,706,368, reverse strandGLT8D1SPCS1: 52,704,955–52,711,148, forward strandSPCS1NEK4: 52,708,444–52,770,973, reverse strandNEK4ITIH1: 52,777,559–52,792,068, forward strandITIH1ITIH3: 52,794,450–52,809,881, forward strandITIH3ITIH4: 52,812,918–52,831,069, reverse strandITIH4: 52,813,282–52,835,729, reverse strandMUSTN1: 52,833,113–52,835,222, reverse strandSTIMATE-MUSTN1: 52,833,121–52,897,562, reverse strandSTIMATE: 52,836,219–52,897,621, reverse strandSFMBT1: 52,903,345–53,046,750, reverse strandSFMBT1Diagram of BAP1: 17 exons on the reverse strand of chromosome 3Exon 17: 2 known disease-causing sitesExon 16: 10 known disease-causing sitesExon 15: 13 known disease-causing sitesExon 14: 24 known disease-causing sitesExon 13: 58 known disease-causing sitesExon 12: 19 known disease-causing sitesExon 11: 22 known disease-causing sitesExon 10: 21 known disease-causing sitesExon 9: 16 known disease-causing sitesExon 8: 19 known disease-causing sitesExon 7: 21 known disease-causing sitesExon 6: 8 known disease-causing sitesExon 5: 18 known disease-causing sitesExon 4: 26 known disease-causing sitesExon 3: 11 known disease-causing sitesExon 2: 5 known disease-causing sitesExon 1: 9 known disease-causing sitesExon 17: 52,401,008–52,402,421, 1,414 basesExon 16: 52,402,602–52,402,674, 73 basesExon 15: 52,402,779–52,402,871, 93 basesExon 14: 52,403,138–52,403,298, 161 basesExon 13: 52,403,416–52,403,894, 479 basesExon 12: 52,404,453–52,404,586, 134 basesExon 11: 52,405,110–52,405,294, 185 basesExon 10: 52,405,765–52,405,912, 148 basesExon 9: 52,406,253–52,406,376, 124 basesExon 8: 52,406,829–52,406,907, 79 basesExon 7: 52,407,174–52,407,316, 143 basesExon 6: 52,407,399–52,407,460, 62 basesExon 5: 52,407,958–52,408,077, 120 basesExon 4: 52,408,474–52,408,606, 133 basesExon 3: 52,409,554–52,409,608, 55 basesExon 2: 52,409,714–52,409,743, 30 basesExon 1: 52,409,842–52,410,008, 167 bases1716141210864215′3′

Exons of the gene's MANE Select transcript (release v1.5), from NCBI and EMBL-EBI, on the GRCh38 reference genome.

Chromosome bands from UCSC's GRCh38 ideogram (2022-10-29).

Nearby genes from Ensembl release 116, on GRCh38.

Exons make up 3.6 kb of the gene's 9 kb; 2,190 of those bases code for the protein.

How a genome test reads BAP1

359

positions in BAP1 where ClinVar classes a change as pathogenic or likely pathogenic

None of them falls in a region short reads find hard.

A whole genome covers all 9 kb of BAP1, introns included, not only the 3.6 kb of exons.

Where this comes from

  • HGNC: the gene's symbol, name, other symbols and location.
  • MANE Select v1.5, from NCBI and EMBL-EBI: the transcript, its exons and coding sequence.
  • GenCC and ClinGen, released 2026-10-16: which conditions the gene is linked to, and how strongly.
  • The ACMG secondary findings list, SF v3.2.
  • ClinVar and the GIAB stratifications: known disease-causing sites, and the regions short reads find hard.
  • The Human Phenotype Ontology, release 2026-09-01: the traits linked to the gene. Find out more at hpo.jax.org.
  • Data release 2026.10.16-c6eea6bf.

Cite this page

APA

Dante Labs. (n.d.). BAP1 gene: BRCA1 associated deubiquitinase 1. Retrieved 17 October 2026, from https://dantelabs.com/genes/bap1

Vancouver

Dante Labs. BAP1 gene: BRCA1 associated deubiquitinase 1 [Internet]. [cited 17 October 2026]. Available from: https://dantelabs.com/genes/bap1

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