Stats by Source
Total, split by cell line (COSMIC CL / DepMap / PubMed) vs tissue (COSMIC primary tissue)
Total = all mutations for this gene across every source.
Cell line = COSMIC Cell Lines Project + DepMap + PubMed.
Tissue = COSMIC primary-tissue (patient tumour) samples.
Total can exceed cell line + tissue: COSMIC tissue-derived models sit only in global, and a peptide can be shared across both.
| Total | Cell line | Tissue | |
|---|---|---|---|
| Mutations | 985 | 113 | 852 |
| Samples | 506 | 79 | 419 |
| Peptides | 358 | 49 | 319 |
Function
BAP1 · BRCA1 associated deubiquitinase 1
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].
Isoforms & Proteins
3 transcripts · UniProt mapping is sequence-verified (AA-safe)
Each Ensembl transcript (ENST) this gene is mutated on, with its matched UniProt accession.
The mapping is sequence-verified: the UniProt sequence is identical to the transcript translation, so amino-acid positions line up exactly. A * marks an unreviewed (TrEMBL) entry.
Counts are mutations and unique mutant peptides on each transcript.
| Transcript | UniProt | Mutations | Peptides |
|---|---|---|---|
| ENST00000460680 | Q92560 | 537 | 349 |
| ENST00000296288 | F8W6N3* | 447 | 317 |
| ENST00000615113 | A0A087WZR5* | 1 | 1 |
Gene Properties
Recurrent Mutations
All 349 amino-acid changes on canonical ENST00000460680 · needle height = samples · drag the mini-map to zoom
A lollipop / needle plot – the standard way to show recurrent mutations along a protein (as used by cBioPortal and MutationMapper).
X-axis = amino-acid position in the protein.
Needle height & head size = how often that exact amino-acid change was observed (its recurrence). Tall/large heads are mutational hotspots.
The most recurrent changes are labelled; hover any needle for the change, position and counts.
Mutation frequency across cancer types
% of samples with a missense/complex mutation in BAP1 · cell line vs tissue
For each cancer type, the fraction of samples that carry at least one missense/complex mutation anywhere in BAP1 – counted as distinct samples (a sample counts once no matter how many mutations it has).
Split into cell line and tissue; each cell shows mutated / total and the percentage. Cohorts with <20 samples are omitted. Ordered by combined frequency.
| Cancer type | Cell lines | Tissue samples |
|---|---|---|
| T-Lymphoblastic Leukemia | 9/40 22% | 0/0 0% |
| Mesothelioma | 3/62 5% | 10/165 6% |
| Endometrial Carcinoma | 6/42 14% | 23/612 4% |
| Acute Monocytic Leukemia | 0/1 0% | 1/25 4% |
| Kidney Carcinoma | 4/85 5% | 69/1862 4% |
| Hodgkins Lymphoma | 2/16 12% | 3/122 2% |
| Unknown | 0/10 0% | 1/29 3% |
| Bladder Carcinoma | 4/58 7% | 21/956 2% |
| Biliary Tract Carcinoma | 0/54 0% | 19/950 2% |
| Melanoma | 4/210 2% | 34/1899 2% |
| Colorectal Carcinoma | 16/143 11% | 38/3239 1% |
| Gastric Carcinoma | 0/74 0% | 28/1809 2% |
| Acute Myeloid Leukemia | 1/90 1% | 0/0 0% |
| Cervical Carcinoma | 0/35 0% | 5/422 1% |
| Non-Small Cell Lung Carcinoma | 3/304 1% | 15/1390 1% |
| Germ Cell Tumour | 1/25 4% | 1/169 1% |
| Ovarian Carcinoma | 1/109 1% | 10/998 1% |
| Neuroendocrine Tumour | 2/154 1% | 5/577 1% |
| Ewings Sarcoma | 2/63 3% | 1/262 0% |
| Adrenocortical Carcinoma | 0/3 0% | 1/112 1% |
| Plasma Cell Myeloma | 0/44 0% | 3/305 1% |
| Non-Cancerous | 3/104 3% | 5/830 1% |
| Hepatocellular Carcinoma | 0/46 0% | 19/2210 1% |
| Head and Neck Carcinoma | 3/85 4% | 10/1574 1% |
| Esophageal Carcinoma | 0/23 0% | 6/769 1% |
| Gastrointestinal Stromal Tumour | 0/0 0% | 1/133 1% |
| Other Solid Cancers | 0/94 0% | 10/1515 1% |
| Breast Carcinoma | 3/144 2% | 16/3264 0% |
| Pancreatic Carcinoma | 1/89 1% | 8/1611 0% |
| B-Cell Non-Hodgkins Lymphoma | 4/88 5% | 9/2534 0% |
Mutation Distribution
Where BAP1 is mutated · all tissues, split by cell line vs tissue
How many mutations in BAP1 were found in each tissue, across the whole database.
Each bar is a tissue (cell-line and tissue names are merged to the standard tissue), split into cell line and tissue (patient tumour) contributions.
This shows the cancer-context where this gene is recurrently altered.
GTEx Expression
Median TPM across 54 healthy tissues
Median gene expression (TPM) in normal, non-cancer human tissues from the GTEx project.
Useful for judging tumour specificity – a strong neoantigen target ideally comes from a gene with low expression in healthy tissues.
Scroll or drag the mini-axis below the chart to browse all tissues.
Mutations
All 985 mutations in BAP1
Every mutation record for this gene, across all samples and sources.
The Sample column links to the cell line (cell-line samples) or the tissue type (tissue samples).
Use the Type / Source filters, the search box, and column sorting to explore; each CAN-IMMUNE ID opens the full mutation & peptide view.
| ID | Sample | Transcript | AA Change | CDS | Type | Source | Mutant Peptide | Wild-type Peptide |
|---|