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 | 531 | 92 | 426 |
| Samples | 190 | 50 | 136 |
| Peptides | 161 | 30 | 130 |
Function
HLA-F · Major histocompatibility complex, class I, F
This gene belongs to the HLA class I heavy chain paralogues. It encodes a non-classical heavy chain that forms a heterodimer with a beta-2 microglobulin light chain, with the heavy chain anchored in the membrane. Unlike most other HLA heavy chains, this molecule is localized in the endoplasmic reticulum and Golgi apparatus, with a small amount present at the cell surface in some cell types. It contains a divergent peptide-binding groove, and is thought to bind a restricted subset of peptides for immune presentation. This gene exhibits few polymorphisms. Multiple transcript variants encoding different isoforms have been found for this gene. These variants lack a coding exon found in transcripts from other HLA paralogues due to an altered splice acceptor site, resulting in a shorter cytoplasmic domain. [provided by RefSeq, Jul 2008].
Isoforms & Proteins
4 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 148 amino-acid changes on canonical ENST00000259951 · 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 HLA-F · cell line vs tissue
For each cancer type, the fraction of samples that carry at least one missense/complex mutation anywhere in HLA-F – 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 |
|---|---|---|
| Chronic Myelogenous Leukemia | 4/25 16% | 0/0 0% |
| T-Lymphoblastic Leukemia | 2/40 5% | 0/0 0% |
| Endometrial Carcinoma | 4/42 10% | 7/612 1% |
| Cervical Carcinoma | 0/35 0% | 7/422 2% |
| Hodgkins Lymphoma | 2/16 12% | 0/122 0% |
| Osteosarcoma | 0/45 0% | 2/166 1% |
| Bladder Carcinoma | 0/58 0% | 9/956 1% |
| Gastric Carcinoma | 3/74 4% | 12/1809 1% |
| Colorectal Carcinoma | 10/143 7% | 17/3239 1% |
| Melanoma | 0/210 0% | 16/1899 1% |
| Ewings Sarcoma | 0/63 0% | 2/262 1% |
| Plasma Cell Myeloma | 1/44 2% | 1/305 0% |
| Thyroid Gland Carcinoma | 0/45 0% | 9/1592 1% |
| Neuroendocrine Tumour | 4/154 3% | 0/577 0% |
| Head and Neck Carcinoma | 0/85 0% | 9/1574 1% |
| Germ Cell Tumour | 1/25 4% | 0/169 0% |
| Rhabdomyosarcoma | 1/33 3% | 0/171 0% |
| Non-Small Cell Lung Carcinoma | 4/304 1% | 4/1390 0% |
| Squamous Cell Lung Carcinoma | 2/57 4% | 2/810 0% |
| Glioma | 0/52 0% | 7/2127 0% |
| Hepatocellular Carcinoma | 2/46 4% | 5/2210 0% |
| B-Cell Non-Hodgkins Lymphoma | 2/88 2% | 5/2534 0% |
| Ovarian Carcinoma | 2/109 2% | 1/998 0% |
| Breast Carcinoma | 3/144 2% | 6/3264 0% |
| Esophageal Carcinoma | 0/23 0% | 2/769 0% |
| Other Solid Cancers | 0/94 0% | 3/1515 0% |
| Kidney Carcinoma | 0/85 0% | 3/1862 0% |
| Prostate Carcinoma | 0/13 0% | 3/2105 0% |
| Small Cell Lung Carcinoma | 0/9 0% | 1/752 0% |
| Other Blood Cancers | 0/61 0% | 3/2725 0% |
Mutation Distribution
Where HLA-F is mutated · all tissues, split by cell line vs tissue
How many mutations in HLA-F 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 531 mutations in HLA-F
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 |
|---|