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 | 4,316 | 508 | 3,793 |
| Samples | 840 | 159 | 674 |
| Peptides | 691 | 119 | 588 |
Function
BRCA1 · BRCA1 DNA repair associated
This gene encodes a 190 kD nuclear phosphoprotein that plays a role in maintaining genomic stability, and it also acts as a tumor suppressor. The BRCA1 gene contains 22 exons spanning about 110 kb of DNA. The encoded protein combines with other tumor suppressors, DNA damage sensors, and signal transducers to form a large multi-subunit protein complex known as the BRCA1-associated genome surveillance complex (BASC). This gene product associates with RNA polymerase II, and through the C-terminal domain, also interacts with histone deacetylase complexes. This protein thus plays a role in transcription, DNA repair of double-stranded breaks, and recombination. Mutations in this gene are responsible for approximately 40% of inherited breast cancers and more than 80% of inherited breast and ovarian cancers. Alternative splicing plays a role in modulating the subcellular localization and physiological function of this gene. Many alternatively spliced transcript variants, some of which are disease-associated mutations, have been described for this gene, but the full-length natures of only some of these variants has been described. A related pseudogene, which is also located on chromosome 17, has been identified. [provided by RefSeq, May 2020].
Isoforms & Proteins
10 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 |
|---|---|---|---|
| ENST00000357654 | P38398 | 1,047 | 635 |
| ENST00000471181 | P38398-7 | 964 | 606 |
| ENST00000493795 | P38398-8 | 933 | 584 |
| ENST00000491747 | P38398-3 | 371 | 251 |
| ENST00000352993 | P38398-5 | 356 | 239 |
| ENST00000468300 | P38398-6 | 350 | 233 |
| ENST00000591534 | K7EPC7* | 198 | 114 |
| ENST00000586385 | C6YB45* | 68 | 53 |
| ENST00000591849 | K7EJW3* | 27 | 22 |
| ENST00000497488 | C9IZW4* | 2 | 2 |
Gene Properties
Recurrent Mutations
All 635 amino-acid changes on canonical ENST00000357654 · 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 BRCA1 · cell line vs tissue
For each cancer type, the fraction of samples that carry at least one missense/complex mutation anywhere in BRCA1 – 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 |
|---|---|---|
| Gastrointestinal Stromal Tumour | 0/0 0% | 29/133 22% |
| T-Lymphoblastic Leukemia | 8/40 20% | 0/0 0% |
| Chronic Myelogenous Leukemia | 3/25 12% | 0/0 0% |
| Endometrial Carcinoma | 6/42 14% | 30/612 5% |
| Bladder Carcinoma | 7/58 12% | 40/956 4% |
| Melanoma | 10/210 5% | 81/1899 4% |
| Non-Small Cell Lung Carcinoma | 26/304 9% | 38/1390 3% |
| Cervical Carcinoma | 2/35 6% | 15/422 4% |
| Oral Cavity Carcinoma | 2/54 4% | 0/0 0% |
| Glioblastoma | 3/98 3% | 0/0 0% |
| Neuroendocrine Tumour | 12/154 8% | 9/577 2% |
| Squamous Cell Lung Carcinoma | 3/57 5% | 20/810 2% |
| Colorectal Carcinoma | 14/143 10% | 71/3239 2% |
| Other Solid Cancers | 5/94 5% | 32/1515 2% |
| Acute Myeloid Leukemia | 2/90 2% | 0/0 0% |
| Gastric Carcinoma | 8/74 11% | 29/1809 2% |
| Mesothelioma | 1/62 2% | 3/165 2% |
| Biliary Tract Carcinoma | 1/54 2% | 15/950 2% |
| Small Cell Lung Carcinoma | 2/9 22% | 10/752 1% |
| Esophageal Squamous Cell Carcinoma | 7/51 14% | 33/2550 1% |
| Head and Neck Carcinoma | 3/85 4% | 22/1574 1% |
| Rhabdomyosarcoma | 0/33 0% | 3/171 2% |
| Hodgkins Lymphoma | 0/16 0% | 2/122 2% |
| Hepatocellular Carcinoma | 3/46 7% | 29/2210 1% |
| Non-Cancerous | 1/104 1% | 11/830 1% |
| Esophageal Carcinoma | 0/23 0% | 10/769 1% |
| Breast Carcinoma | 2/144 1% | 39/3264 1% |
| Meningioma | 1/3 33% | 2/252 1% |
| Other Sarcomas | 0/69 0% | 9/699 1% |
| Glioma | 0/52 0% | 24/2127 1% |
Mutation Distribution
Where BRCA1 is mutated · all tissues, split by cell line vs tissue
How many mutations in BRCA1 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 4,316 mutations in BRCA1
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 |
|---|