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 | 1,846 | 284 | 1,542 |
| Samples | 797 | 157 | 630 |
| Peptides | 631 | 111 | 547 |
Function
COL9A1 · Collagen type IX alpha 1 chain
This gene encodes one of the three alpha chains of type IX collagen, which is a minor (5-20%) collagen component of hyaline cartilage. Type IX collagen is usually found in tissues containing type II collagen, a fibrillar collagen. Studies in knockout mice have shown that synthesis of the alpha 1 chain is essential for assembly of type IX collagen molecules, a heterotrimeric molecule, and that lack of type IX collagen is associated with early onset osteoarthritis. Mutations in this gene are associated with osteoarthritis in humans, with multiple epiphyseal dysplasia, 6, a form of chondrodysplasia, and with Stickler syndrome, a disease characterized by ophthalmic, orofacial, articular, and auditory defects. Two transcript variants that encode different isoforms have been identified for this gene. [provided by RefSeq, Jul 2008].
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.
Gene Properties
Recurrent Mutations
All 603 amino-acid changes on canonical ENST00000357250 · 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 COL9A1 · cell line vs tissue
For each cancer type, the fraction of samples that carry at least one missense/complex mutation anywhere in COL9A1 – 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 | 5/40 12% | 0/0 0% |
| Melanoma | 23/210 11% | 158/1899 8% |
| Chordoma | 1/7 14% | 0/13 0% |
| Other Solid Cancers | 5/94 5% | 67/1515 4% |
| Non-Small Cell Lung Carcinoma | 18/304 6% | 51/1390 4% |
| Squamous Cell Lung Carcinoma | 2/57 4% | 33/810 4% |
| Endometrial Carcinoma | 3/42 7% | 23/612 4% |
| Hodgkins Lymphoma | 4/16 25% | 0/122 0% |
| Adrenocortical Carcinoma | 0/3 0% | 3/112 3% |
| Small Cell Lung Carcinoma | 0/9 0% | 19/752 3% |
| Plasma Cell Myeloma | 3/44 7% | 5/305 2% |
| Chondrosarcoma | 2/14 14% | 0/75 0% |
| Acute Myeloid Leukemia | 2/90 2% | 0/0 0% |
| Colorectal Carcinoma | 16/143 11% | 54/3239 2% |
| Neuroendocrine Tumour | 12/154 8% | 3/577 1% |
| Glioblastoma | 2/98 2% | 0/0 0% |
| Gastric Carcinoma | 4/74 5% | 31/1809 2% |
| Other Sarcomas | 6/69 9% | 6/699 1% |
| Bladder Carcinoma | 0/58 0% | 14/956 1% |
| Ovarian Carcinoma | 4/109 4% | 9/998 1% |
| Cervical Carcinoma | 0/35 0% | 5/422 1% |
| Breast Carcinoma | 10/144 7% | 22/3264 1% |
| Hepatocellular Carcinoma | 1/46 2% | 20/2210 1% |
| Burkitts Lymphoma | 2/32 6% | 0/196 0% |
| Non-Cancerous | 2/104 2% | 6/830 1% |
| Esophageal Squamous Cell Carcinoma | 3/51 6% | 19/2550 1% |
| Gastrointestinal Stromal Tumour | 0/0 0% | 1/133 1% |
| Head and Neck Carcinoma | 0/85 0% | 12/1574 1% |
| Pancreatic Carcinoma | 3/89 3% | 9/1611 1% |
| Biliary Tract Carcinoma | 3/54 6% | 4/950 0% |
Mutation Distribution
Where COL9A1 is mutated · all tissues, split by cell line vs tissue
How many mutations in COL9A1 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 53 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 1,846 mutations in COL9A1
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 |
|---|