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 | 7,183 | 1,253 | 5,880 |
| Samples | 3,970 | 730 | 3,210 |
| Peptides | 3,704 | 635 | 3,191 |
Function
USH2A · Usherin
This gene encodes a protein that contains laminin EGF motifs, a pentaxin domain, and many fibronectin type III motifs. The protein is found in the basement membrane, and may be important in development and homeostasis of the inner ear and retina. Mutations within this gene have been associated with Usher syndrome type IIa and retinitis pigmentosa. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 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 2500 amino-acid changes on canonical ENST00000307340 · 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 USH2A · cell line vs tissue
For each cancer type, the fraction of samples that carry at least one missense/complex mutation anywhere in USH2A – 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 | 15/40 38% | 0/0 0% |
| T-Cell Non-Hodgkins Lymphoma | 7/26 27% | 0/0 0% |
| Non-Small Cell Lung Carcinoma | 132/304 43% | 319/1390 23% |
| Squamous Cell Lung Carcinoma | 22/57 39% | 197/810 24% |
| Acute Myeloid Leukemia | 22/90 24% | 0/0 0% |
| Melanoma | 59/210 28% | 421/1899 22% |
| Oral Cavity Carcinoma | 12/54 22% | 0/0 0% |
| Chronic Myelogenous Leukemia | 5/25 20% | 0/0 0% |
| Endometrial Carcinoma | 23/42 55% | 95/612 16% |
| Glioblastoma | 17/98 17% | 0/0 0% |
| Small Cell Lung Carcinoma | 1/9 11% | 124/752 16% |
| Other Solid Cancers | 12/94 13% | 186/1515 12% |
| Neuroendocrine Tumour | 60/154 39% | 28/577 5% |
| Gastric Carcinoma | 17/74 23% | 207/1809 11% |
| Colorectal Carcinoma | 52/143 36% | 296/3239 9% |
| Cervical Carcinoma | 7/35 20% | 34/422 8% |
| Rhabdomyosarcoma | 11/33 33% | 7/171 4% |
| Hodgkins Lymphoma | 5/16 31% | 7/122 6% |
| Esophageal Squamous Cell Carcinoma | 16/51 31% | 198/2550 8% |
| Head and Neck Carcinoma | 12/85 14% | 121/1574 8% |
| Esophageal Carcinoma | 3/23 13% | 57/769 7% |
| Plasma Cell Myeloma | 14/44 32% | 11/305 4% |
| Bladder Carcinoma | 11/58 19% | 61/956 6% |
| Ovarian Carcinoma | 16/109 15% | 59/998 6% |
| Osteosarcoma | 11/45 24% | 2/166 1% |
| Other Sarcomas | 11/69 16% | 36/699 5% |
| Thymic Epithelial Tumor | 0/0 0% | 2/39 5% |
| Unknown | 1/10 10% | 1/29 3% |
| Chordoma | 0/7 0% | 1/13 8% |
| Hepatocellular Carcinoma | 6/46 13% | 102/2210 5% |
Mutation Distribution
Where USH2A is mutated · all tissues, split by cell line vs tissue
How many mutations in USH2A 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 53 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 7,183 mutations in USH2A
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 |
|---|