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 | 6,603 | 472 | 6,104 |
| Samples | 1,339 | 184 | 1,149 |
| Peptides | 406 | 78 | 383 |
Function
CDKN2A · Cyclin dependent kinase inhibitor 2A
This gene generates several transcript variants which differ in their first exons. At least three alternatively spliced variants encoding distinct proteins have been reported, two of which encode structurally related isoforms known to function as inhibitors of CDK4 kinase. The remaining transcript includes an alternate first exon located 20 Kb upstream of the remainder of the gene; this transcript contains an alternate open reading frame (ARF) that specifies a protein which is structurally unrelated to the products of the other variants. This ARF product functions as a stabilizer of the tumor suppressor protein p53 as it can interact with, and sequester, the E3 ubiquitin-protein ligase MDM2, a protein responsible for the degradation of p53. In spite of the structural and functional differences, the CDK inhibitor isoforms and the ARF product encoded by this gene, through the regulatory roles of CDK4 and p53 in cell cycle G1 progression, share a common functionality in cell cycle G1 control. This gene is frequently mutated or deleted in a wide variety of tumors, and is known to be an important tumor suppressor gene. [provided by RefSeq, Sep 2012].
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 |
|---|---|---|---|
| ENST00000579755 | Q8N726 | 866 | 123 |
| ENST00000530628 | Q8N726 | 863 | 120 |
| ENST00000304494 | P42771 | 851 | 225 |
| ENST00000498124 | P42771-4 | 709 | 219 |
| ENST00000579122 | J3QRG6* | 673 | 201 |
| ENST00000497750 | K7ES20* | 537 | 152 |
| ENST00000479692 | K7ENC6* | 526 | 149 |
| ENST00000494262 | P42771-2 | 526 | 149 |
| ENST00000498628 | P42771-2 | 526 | 149 |
| ENST00000578845 | P42771-2 | 526 | 149 |
Gene Properties
Recurrent Mutations
All 123 amino-acid changes on canonical ENST00000579755 · 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 CDKN2A · cell line vs tissue
For each cancer type, the fraction of samples that carry at least one missense/complex mutation anywhere in CDKN2A – 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 |
|---|---|---|
| Oral Cavity Carcinoma | 6/54 11% | 0/0 0% |
| Esophageal Squamous Cell Carcinoma | 3/51 6% | 228/2550 9% |
| Other Solid Cancers | 1/94 1% | 131/1515 9% |
| Melanoma | 22/210 10% | 137/1899 7% |
| Squamous Cell Lung Carcinoma | 8/57 14% | 55/810 7% |
| Esophageal Carcinoma | 2/23 9% | 47/769 6% |
| Head and Neck Carcinoma | 6/85 7% | 95/1574 6% |
| Pancreatic Carcinoma | 8/89 9% | 95/1611 6% |
| T-Lymphoblastic Leukemia | 2/40 5% | 0/0 0% |
| T-Cell Non-Hodgkins Lymphoma | 1/26 4% | 0/0 0% |
| Non-Small Cell Lung Carcinoma | 25/304 8% | 38/1390 3% |
| Bladder Carcinoma | 4/58 7% | 32/956 3% |
| Chondrosarcoma | 0/14 0% | 3/75 4% |
| Glioblastoma | 3/98 3% | 0/0 0% |
| Cervical Carcinoma | 3/35 9% | 10/422 2% |
| Ovarian Carcinoma | 8/109 7% | 22/998 2% |
| Acute Myeloid Leukemia | 2/90 2% | 0/0 0% |
| Hodgkins Lymphoma | 1/16 6% | 2/122 2% |
| Gastric Carcinoma | 5/74 7% | 35/1809 2% |
| Biliary Tract Carcinoma | 1/54 2% | 20/950 2% |
| Plasma Cell Myeloma | 4/44 9% | 3/305 1% |
| Small Cell Lung Carcinoma | 0/9 0% | 15/752 2% |
| Hepatocellular Carcinoma | 3/46 7% | 40/2210 2% |
| Endometrial Carcinoma | 2/42 5% | 8/612 1% |
| Colorectal Carcinoma | 11/143 8% | 37/3239 1% |
| Pheochromocytoma and Paraganglioma | 0/0 0% | 1/71 1% |
| Neuroendocrine Tumour | 6/154 4% | 4/577 1% |
| Non-Cancerous | 7/104 7% | 4/830 0% |
| Other Sarcomas | 5/69 7% | 4/699 1% |
| Osteosarcoma | 2/45 4% | 0/166 0% |
Mutation Distribution
Where CDKN2A is mutated · all tissues, split by cell line vs tissue
How many mutations in CDKN2A 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 6,603 mutations in CDKN2A
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 |
|---|