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 | 647 | 75 | 562 |
| Samples | 323 | 48 | 269 |
| Peptides | 268 | 37 | 228 |
Function
VPS39 · VPS39 subunit of HOPS complex
This gene encodes a protein that may promote clustering and fusion of late endosomes and lysosomes. The protein may also act as an adaptor protein that modulates the transforming growth factor-beta response by coupling the transforming growth factor-beta receptor complex to the Smad pathway. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2014].
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.
Gene Properties
Recurrent Mutations
All 255 amino-acid changes on canonical ENST00000318006 · 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 VPS39 · cell line vs tissue
For each cancer type, the fraction of samples that carry at least one missense/complex mutation anywhere in VPS39 – 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 | 5/42 12% | 13/612 2% |
| T-Lymphoblastic Leukemia | 1/40 2% | 0/0 0% |
| Hodgkins Lymphoma | 0/16 0% | 3/122 2% |
| Melanoma | 2/210 1% | 43/1899 2% |
| Squamous Cell Lung Carcinoma | 2/57 4% | 11/810 1% |
| Colorectal Carcinoma | 9/143 6% | 33/3239 1% |
| Gastric Carcinoma | 0/74 0% | 22/1809 1% |
| Chondrosarcoma | 1/14 7% | 0/75 0% |
| Bladder Carcinoma | 2/58 3% | 9/956 1% |
| Ewings Sarcoma | 1/63 2% | 2/262 1% |
| Other Solid Cancers | 1/94 1% | 13/1515 1% |
| Plasma Cell Myeloma | 1/44 2% | 2/305 1% |
| Hepatocellular Carcinoma | 1/46 2% | 16/2210 1% |
| Head and Neck Carcinoma | 3/85 4% | 9/1574 1% |
| Non-Small Cell Lung Carcinoma | 2/304 1% | 9/1390 1% |
| Thyroid Gland Carcinoma | 2/45 4% | 8/1592 0% |
| Breast Carcinoma | 3/144 2% | 15/3264 0% |
| Germ Cell Tumour | 0/25 0% | 1/169 1% |
| Other Sarcomas | 0/69 0% | 4/699 1% |
| Biliary Tract Carcinoma | 1/54 2% | 4/950 0% |
| Glioma | 0/52 0% | 10/2127 0% |
| Ovarian Carcinoma | 1/109 1% | 4/998 0% |
| Cervical Carcinoma | 0/35 0% | 2/422 0% |
| Esophageal Squamous Cell Carcinoma | 0/51 0% | 11/2550 0% |
| Kidney Carcinoma | 0/85 0% | 8/1862 0% |
| Neuroendocrine Tumour | 1/154 1% | 2/577 0% |
| B-Cell Non-Hodgkins Lymphoma | 4/88 5% | 6/2534 0% |
| Non-Cancerous | 0/104 0% | 3/830 0% |
| Small Cell Lung Carcinoma | 1/9 11% | 1/752 0% |
| Esophageal Carcinoma | 0/23 0% | 2/769 0% |
Mutation Distribution
Where VPS39 is mutated · all tissues, split by cell line vs tissue
How many mutations in VPS39 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 647 mutations in VPS39
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 |
|---|