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 | 1,764 | 274 | 1,457 |
| Samples | 1,491 | 230 | 1,246 |
| Peptides | 926 | 158 | 813 |
Function
PRDM9 · PR/SET domain 9
The protein encoded by this gene is a zinc finger protein with histone methyltransferase activity that catalyzes histone H3 lysine 4 trimethylation (H3K4me3) during meiotic prophase. This protein contains multiple domains, including a Kruppel-associated box (KRAB) domain, an SSX repression domain (SSXRD), a PRD1-BF1 and RIZ homologous region, a subclass of SET (PR/SET) domain, and a tandem array of C2H2 zinc fingers. The zinc finger array recognizes a short sequence motif, leading to local H3K4me3, and meiotic recombination hotspot activity. The observed allelic variation alters the DNA-binding sequence specificity of the protein, resulting in distinct meiotic recombination hotspots amongst individuals and populations. Multiple alternate alleles of this gene have been described. [provided by RefSeq, Jul 2015].
Isoforms & Proteins
2 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 |
|---|---|---|---|
| ENST00000296682 | Q9NQV7 | 1,759 | 922 |
| ENST00000709929 | A0A0U1RQY2* | 5 | 5 |
Gene Properties
Recurrent Mutations
All 964 amino-acid changes on canonical ENST00000296682 · 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 PRDM9 · cell line vs tissue
For each cancer type, the fraction of samples that carry at least one missense/complex mutation anywhere in PRDM9 – 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% |
| Squamous Cell Lung Carcinoma | 18/57 32% | 73/810 9% |
| Non-Small Cell Lung Carcinoma | 42/304 14% | 135/1390 10% |
| Melanoma | 19/210 9% | 194/1899 10% |
| Endometrial Carcinoma | 11/42 26% | 44/612 7% |
| Gastrointestinal Stromal Tumour | 0/0 0% | 10/133 8% |
| Glioblastoma | 7/98 7% | 0/0 0% |
| Small Cell Lung Carcinoma | 0/9 0% | 43/752 6% |
| Other Solid Cancers | 4/94 4% | 80/1515 5% |
| Neuroendocrine Tumour | 24/154 16% | 14/577 2% |
| Colorectal Carcinoma | 24/143 17% | 144/3239 4% |
| Gastric Carcinoma | 6/74 8% | 77/1809 4% |
| T-Cell Non-Hodgkins Lymphoma | 1/26 4% | 0/0 0% |
| Esophageal Carcinoma | 2/23 9% | 28/769 4% |
| Head and Neck Carcinoma | 6/85 7% | 56/1574 4% |
| Oral Cavity Carcinoma | 2/54 4% | 0/0 0% |
| Esophageal Squamous Cell Carcinoma | 5/51 10% | 63/2550 2% |
| Bladder Carcinoma | 3/58 5% | 20/956 2% |
| Hodgkins Lymphoma | 2/16 12% | 1/122 1% |
| Germ Cell Tumour | 3/25 12% | 1/169 1% |
| Cervical Carcinoma | 0/35 0% | 9/422 2% |
| Rhabdomyosarcoma | 0/33 0% | 4/171 2% |
| Osteosarcoma | 1/45 2% | 3/166 2% |
| Ovarian Carcinoma | 6/109 6% | 15/998 2% |
| Glioma | 2/52 4% | 38/2127 2% |
| Other Sarcomas | 3/69 4% | 11/699 2% |
| Hepatocellular Carcinoma | 2/46 4% | 35/2210 2% |
| Biliary Tract Carcinoma | 3/54 6% | 11/950 1% |
| Thyroid Gland Carcinoma | 1/45 2% | 20/1592 1% |
| B-Cell Non-Hodgkins Lymphoma | 9/88 10% | 23/2534 1% |
Mutation Distribution
Where PRDM9 is mutated · all tissues, split by cell line vs tissue
How many mutations in PRDM9 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 2 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 1,764 mutations in PRDM9
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 |
|---|