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 | 479 | 111 | 357 |
| Samples | 206 | 53 | 146 |
| Peptides | 137 | 32 | 106 |
Function
UPF3A · UPF3A regulator of nonsense mediated mRNA decay
This gene encodes a protein that is part of a post-splicing multiprotein complex involved in both mRNA nuclear export and mRNA surveillance. The encoded protein is one of two functional homologs to yeast Upf3p. mRNA surveillance detects exported mRNAs with truncated open reading frames and initiates nonsense-mediated mRNA decay (NMD). When translation ends upstream from the last exon-exon junction, this triggers NMD to degrade mRNAs containing premature stop codons. This protein binds to the mRNA and remains bound after nuclear export, acting as a nucleocytoplasmic shuttling protein. It forms with Y14 a complex that binds specifically 20 nt upstream of exon-exon junctions. This gene is located on the long arm of chromosome 13. Several splice variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2017].
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.
| Transcript | UniProt | Mutations | Peptides |
|---|---|---|---|
| ENST00000375299 | Q9H1J1 | 215 | 131 |
| ENST00000351487 | Q9H1J1-2 | 189 | 114 |
| ENST00000492270 | A0A087WZ33* | 75 | 22 |
Gene Properties
Recurrent Mutations
All 131 amino-acid changes on canonical ENST00000375299 · 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 UPF3A · cell line vs tissue
For each cancer type, the fraction of samples that carry at least one missense/complex mutation anywhere in UPF3A – 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 |
|---|---|---|
| Chordoma | 1/7 14% | 0/13 0% |
| Unknown | 1/10 10% | 0/29 0% |
| T-Lymphoblastic Leukemia | 1/40 2% | 0/0 0% |
| Glioblastoma | 2/98 2% | 0/0 0% |
| Oral Cavity Carcinoma | 1/54 2% | 0/0 0% |
| Thyroid Gland Carcinoma | 0/45 0% | 29/1592 2% |
| Endometrial Carcinoma | 2/42 5% | 9/612 1% |
| Non-Small Cell Lung Carcinoma | 19/304 6% | 9/1390 1% |
| Melanoma | 1/210 0% | 15/1899 1% |
| Gastric Carcinoma | 2/74 3% | 11/1809 1% |
| Squamous Cell Lung Carcinoma | 2/57 4% | 4/810 0% |
| Colorectal Carcinoma | 5/143 4% | 18/3239 1% |
| Cervical Carcinoma | 0/35 0% | 3/422 1% |
| Neuroendocrine Tumour | 2/154 1% | 2/577 0% |
| Germ Cell Tumour | 0/25 0% | 1/169 1% |
| Esophageal Carcinoma | 0/23 0% | 4/769 1% |
| Burkitts Lymphoma | 0/32 0% | 1/196 1% |
| Other Solid Cancers | 1/94 1% | 5/1515 0% |
| Pancreatic Carcinoma | 2/89 2% | 4/1611 0% |
| Hepatocellular Carcinoma | 2/46 4% | 6/2210 0% |
| Bladder Carcinoma | 0/58 0% | 3/956 0% |
| Breast Carcinoma | 2/144 1% | 7/3264 0% |
| Head and Neck Carcinoma | 2/85 2% | 2/1574 0% |
| Medulloblastoma | 0/0 0% | 1/450 0% |
| Biliary Tract Carcinoma | 0/54 0% | 2/950 0% |
| Esophageal Squamous Cell Carcinoma | 1/51 2% | 4/2550 0% |
| Ovarian Carcinoma | 0/109 0% | 2/998 0% |
| B-Cell Non-Hodgkins Lymphoma | 2/88 2% | 2/2534 0% |
| Glioma | 0/52 0% | 3/2127 0% |
| Neuroblastoma | 1/87 1% | 1/1331 0% |
Mutation Distribution
Where UPF3A is mutated · all tissues, split by cell line vs tissue
How many mutations in UPF3A 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 479 mutations in UPF3A
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 |
|---|