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 | 377 | 65 | 308 |
| Samples | 131 | 30 | 99 |
| Peptides | 99 | 23 | 80 |
Function
APEX1 · Apurinic/apyrimidinic endodeoxyribonuclease 1
The APEX gene encodes the major AP endonuclease in human cells. It encodes the APEX endonuclease, a DNA repair enzyme with apurinic/apyrimidinic (AP) activity. Such AP activity sites occur frequently in DNA molecules by spontaneous hydrolysis, by DNA damaging agents or by DNA glycosylases that remove specific abnormal bases. The AP sites are the most frequent pre-mutagenic lesions that can prevent normal DNA replication. Splice variants have been found for this gene; all encode the same protein. Disruptions in the biological functions related to APEX are associated with many various malignancies and neurodegenerative diseases.[provided by RefSeq, Dec 2019].
Isoforms & Proteins
4 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.
Gene Properties
Recurrent Mutations
All 91 amino-acid changes on canonical ENST00000216714 · 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 APEX1 · cell line vs tissue
For each cancer type, the fraction of samples that carry at least one missense/complex mutation anywhere in APEX1 – 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 | 2/40 5% | 0/0 0% |
| Gastrointestinal Stromal Tumour | 0/0 0% | 3/133 2% |
| Oral Cavity Carcinoma | 1/54 2% | 0/0 0% |
| Endometrial Carcinoma | 2/42 5% | 5/612 1% |
| Colorectal Carcinoma | 6/143 4% | 19/3239 1% |
| Melanoma | 4/210 2% | 10/1899 1% |
| Non-Small Cell Lung Carcinoma | 5/304 2% | 5/1390 0% |
| Bladder Carcinoma | 0/58 0% | 6/956 1% |
| Gastric Carcinoma | 0/74 0% | 11/1809 1% |
| Osteosarcoma | 0/45 0% | 1/166 1% |
| Cervical Carcinoma | 0/35 0% | 2/422 0% |
| Other Sarcomas | 2/69 3% | 1/699 0% |
| Head and Neck Carcinoma | 0/85 0% | 6/1574 0% |
| Squamous Cell Lung Carcinoma | 1/57 2% | 2/810 0% |
| Glioma | 0/52 0% | 7/2127 0% |
| Ewings Sarcoma | 0/63 0% | 1/262 0% |
| Plasma Cell Myeloma | 0/44 0% | 1/305 0% |
| Ovarian Carcinoma | 2/109 2% | 1/998 0% |
| Small Cell Lung Carcinoma | 1/9 11% | 1/752 0% |
| Hepatocellular Carcinoma | 0/46 0% | 5/2210 0% |
| Breast Carcinoma | 1/144 1% | 4/3264 0% |
| Neuroendocrine Tumour | 1/154 1% | 0/577 0% |
| Non-Cancerous | 0/104 0% | 1/830 0% |
| Biliary Tract Carcinoma | 0/54 0% | 1/950 0% |
| Prostate Carcinoma | 0/13 0% | 2/2105 0% |
| Other Blood Cancers | 0/61 0% | 2/2725 0% |
| Other Solid Cancers | 1/94 1% | 0/1515 0% |
| Pancreatic Carcinoma | 0/89 0% | 1/1611 0% |
| Kidney Carcinoma | 1/85 1% | 0/1862 0% |
| B-Lymphoblastic Leukemia | 0/55 0% | 1/2640 0% |
Mutation Distribution
Where APEX1 is mutated · all tissues, split by cell line vs tissue
How many mutations in APEX1 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 377 mutations in APEX1
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 |
|---|