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 | 3,434 | 470 | 2,886 |
| Samples | 1,472 | 250 | 1,201 |
| Peptides | 1,381 | 196 | 1,184 |
Function
VPS13D · Vacuolar protein sorting 13 homolog D
This gene encodes a protein belonging to the vacuolar-protein-sorting-13 gene family. In yeast, vacuolar-protein-sorting-13 proteins are involved in trafficking of membrane proteins between the trans-Golgi network and the prevacuolar compartment. While several transcript variants may exist for this gene, the full-length natures of only two have been described to date. These two represent the major variants of this gene and encode distinct isoforms. [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 1368 amino-acid changes on canonical ENST00000620676 · 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 VPS13D · cell line vs tissue
For each cancer type, the fraction of samples that carry at least one missense/complex mutation anywhere in VPS13D – 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-Cell Non-Hodgkins Lymphoma | 4/26 15% | 0/0 0% |
| Acute Myeloid Leukemia | 11/90 12% | 0/0 0% |
| Endometrial Carcinoma | 15/42 36% | 63/612 10% |
| Oral Cavity Carcinoma | 5/54 9% | 0/0 0% |
| Melanoma | 20/210 10% | 165/1899 9% |
| Chronic Myelogenous Leukemia | 2/25 8% | 0/0 0% |
| T-Lymphoblastic Leukemia | 3/40 8% | 0/0 0% |
| Other Solid Cancers | 10/94 11% | 90/1515 6% |
| Gastric Carcinoma | 11/74 15% | 92/1809 5% |
| Cervical Carcinoma | 5/35 14% | 20/422 5% |
| Squamous Cell Lung Carcinoma | 6/57 11% | 40/810 5% |
| Non-Small Cell Lung Carcinoma | 26/304 9% | 61/1390 4% |
| Colorectal Carcinoma | 37/143 26% | 131/3239 4% |
| Bladder Carcinoma | 1/58 2% | 47/956 5% |
| Hodgkins Lymphoma | 1/16 6% | 5/122 4% |
| Acute Monocytic Leukemia | 0/1 0% | 1/25 4% |
| Head and Neck Carcinoma | 5/85 6% | 53/1574 3% |
| Germ Cell Tumour | 1/25 4% | 5/169 3% |
| Glioblastoma | 3/98 3% | 0/0 0% |
| Neuroendocrine Tumour | 13/154 8% | 9/577 2% |
| Thymic Epithelial Tumor | 0/0 0% | 1/39 3% |
| Unknown | 0/10 0% | 1/29 3% |
| Esophageal Squamous Cell Carcinoma | 2/51 4% | 64/2550 3% |
| Small Cell Lung Carcinoma | 1/9 11% | 18/752 2% |
| Biliary Tract Carcinoma | 3/54 6% | 22/950 2% |
| Hepatocellular Carcinoma | 2/46 4% | 49/2210 2% |
| Thyroid Gland Carcinoma | 4/45 9% | 33/1592 2% |
| Chondrosarcoma | 2/14 14% | 0/75 0% |
| Other Sarcomas | 3/69 4% | 14/699 2% |
| Non-Cancerous | 1/104 1% | 18/830 2% |
Mutation Distribution
Where VPS13D is mutated · all tissues, split by cell line vs tissue
How many mutations in VPS13D 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 3,434 mutations in VPS13D
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 |
|---|