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 | 3,024 | 378 | 2,624 |
| Samples | 1,009 | 162 | 839 |
| Peptides | 640 | 122 | 564 |
Function
PCDHA13 · Protocadherin alpha 13
This gene is a member of the protocadherin alpha gene cluster, one of three related gene clusters tandemly linked on chromosome five that demonstrate an unusual genomic organization similar to that of B-cell and T-cell receptor gene clusters. The alpha gene cluster is composed of 15 cadherin superfamily genes related to the mouse CNR genes and consists of 13 highly similar and 2 more distantly related coding sequences. The tandem array of 15 N-terminal exons, or variable exons, are followed by downstream C-terminal exons, or constant exons, which are shared by all genes in the cluster. The large, uninterrupted N-terminal exons each encode six cadherin ectodomains while the C-terminal exons encode the cytoplasmic domain. These neural cadherin-like cell adhesion proteins are integral plasma membrane proteins that most likely play a critical role in the establishment and function of specific cell-cell connections in the brain. Alternative splicing has been observed and additional variants have been suggested but their full-length nature has yet to be determined. [provided by RefSeq, Jul 2008].
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 614 amino-acid changes on canonical ENST00000289272 · 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 PCDHA13 · cell line vs tissue
For each cancer type, the fraction of samples that carry at least one missense/complex mutation anywhere in PCDHA13 – 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 | 13/40 32% | 0/0 0% |
| Chronic Myelogenous Leukemia | 6/25 24% | 0/0 0% |
| Melanoma | 16/210 8% | 150/1899 8% |
| Oral Cavity Carcinoma | 4/54 7% | 0/0 0% |
| Endometrial Carcinoma | 12/42 29% | 34/612 6% |
| Other Solid Cancers | 5/94 5% | 77/1515 5% |
| Colorectal Carcinoma | 32/143 22% | 133/3239 4% |
| Cervical Carcinoma | 3/35 9% | 16/422 4% |
| Gastric Carcinoma | 6/74 8% | 71/1809 4% |
| Non-Small Cell Lung Carcinoma | 12/304 4% | 34/1390 2% |
| Esophageal Carcinoma | 0/23 0% | 21/769 3% |
| Plasma Cell Myeloma | 1/44 2% | 7/305 2% |
| Hodgkins Lymphoma | 3/16 19% | 0/122 0% |
| Head and Neck Carcinoma | 4/85 5% | 30/1574 2% |
| Squamous Cell Lung Carcinoma | 0/57 0% | 17/810 2% |
| Bladder Carcinoma | 1/58 2% | 18/956 2% |
| Retinoblastoma | 1/27 4% | 0/30 0% |
| Non-Cancerous | 2/104 2% | 14/830 2% |
| Hepatocellular Carcinoma | 2/46 4% | 31/2210 1% |
| Other Sarcomas | 4/69 6% | 7/699 1% |
| Small Cell Lung Carcinoma | 0/9 0% | 10/752 1% |
| Esophageal Squamous Cell Carcinoma | 1/51 2% | 31/2550 1% |
| Biliary Tract Carcinoma | 0/54 0% | 12/950 1% |
| Chondrosarcoma | 1/14 7% | 0/75 0% |
| Acute Myeloid Leukemia | 1/90 1% | 0/0 0% |
| Ovarian Carcinoma | 4/109 4% | 8/998 1% |
| Pancreatic Carcinoma | 6/89 7% | 12/1611 1% |
| Prostate Carcinoma | 2/13 15% | 20/2105 1% |
| Glioblastoma | 1/98 1% | 0/0 0% |
| Osteosarcoma | 1/45 2% | 1/166 1% |
Mutation Distribution
Where PCDHA13 is mutated · all tissues, split by cell line vs tissue
How many mutations in PCDHA13 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 46 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 3,024 mutations in PCDHA13
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 |
|---|