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 | 399 | 49 | 340 |
| Samples | 97 | 22 | 72 |
| Peptides | 68 | 10 | 56 |
Function
VPS29 · VPS29 retromer complex component
This gene belongs to a group of vacuolar protein sorting (VPS) genes that, when functionally impaired, disrupt the efficient delivery of vacuolar hydrolases. The protein encoded by this gene is a component of a large multimeric complex, termed the retromer complex, which is involved in retrograde transport of proteins from endosomes to the trans-Golgi network. This VPS protein may be involved in the formation of the inner shell of the retromer coat for retrograde vesicles leaving the prevacuolar compartment. Alternative splice variants encoding different isoforms and representing non-protein coding transcripts have been found for this gene. [provided by RefSeq, Aug 2013].
Isoforms & Proteins
7 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 55 amino-acid changes on canonical ENST00000549578 · 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 VPS29 · cell line vs tissue
For each cancer type, the fraction of samples that carry at least one missense/complex mutation anywhere in VPS29 – 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 |
|---|---|---|
| Endometrial Carcinoma | 2/42 5% | 8/612 1% |
| Hodgkins Lymphoma | 2/16 12% | 0/122 0% |
| Melanoma | 1/210 0% | 11/1899 1% |
| Colorectal Carcinoma | 4/143 3% | 15/3239 0% |
| Germ Cell Tumour | 1/25 4% | 0/169 0% |
| Bladder Carcinoma | 0/58 0% | 3/956 0% |
| Head and Neck Carcinoma | 0/85 0% | 5/1574 0% |
| Glioma | 0/52 0% | 6/2127 0% |
| Ovarian Carcinoma | 2/109 2% | 1/998 0% |
| Gastric Carcinoma | 0/74 0% | 5/1809 0% |
| Small Cell Lung Carcinoma | 0/9 0% | 2/752 0% |
| Esophageal Squamous Cell Carcinoma | 2/51 4% | 4/2550 0% |
| Squamous Cell Lung Carcinoma | 0/57 0% | 2/810 0% |
| Medulloblastoma | 0/0 0% | 1/450 0% |
| Cervical Carcinoma | 0/35 0% | 1/422 0% |
| Biliary Tract Carcinoma | 0/54 0% | 2/950 0% |
| Other Sarcomas | 0/69 0% | 1/699 0% |
| Esophageal Carcinoma | 1/23 4% | 0/769 0% |
| Non-Small Cell Lung Carcinoma | 0/304 0% | 2/1390 0% |
| Pancreatic Carcinoma | 1/89 1% | 1/1611 0% |
| Other Solid Cancers | 1/94 1% | 1/1515 0% |
| Breast Carcinoma | 2/144 1% | 2/3264 0% |
| B-Cell Non-Hodgkins Lymphoma | 2/88 2% | 0/2534 0% |
| Kidney Carcinoma | 0/85 0% | 1/1862 0% |
| Prostate Carcinoma | 0/13 0% | 1/2105 0% |
| Hepatocellular Carcinoma | 1/46 2% | 0/2210 0% |
Mutation Distribution
Where VPS29 is mutated · all tissues, split by cell line vs tissue
How many mutations in VPS29 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 399 mutations in VPS29
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 |
|---|