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 | 4,333 | 1,202 | 3,113 |
| Samples | 1,303 | 874 | 426 |
| Peptides | 319 | 90 | 245 |
Function
HLA-A · Major histocompatibility complex, class I, A
HLA-A belongs to the HLA class I heavy chain paralogues. This class I molecule is a heterodimer consisting of a heavy chain and a light chain (beta-2 microglobulin). The heavy chain is anchored in the membrane. Class I molecules play a central role in the immune system by presenting peptides derived from the endoplasmic reticulum lumen so that they can be recognized by cytotoxic T cells. They are expressed in nearly all cells. The heavy chain is approximately 45 kDa and its gene contains 8 exons. Exon 1 encodes the leader peptide, exons 2 and 3 encode the alpha1 and alpha2 domains, which both bind the peptide, exon 4 encodes the alpha3 domain, exon 5 encodes the transmembrane region, and exons 6 and 7 encode the cytoplasmic tail. Polymorphisms within exon 2 and exon 3 are responsible for the peptide binding specificity of each class one molecule. Typing for these polymorphisms is routinely done for bone marrow and kidney transplantation. More than 6000 HLA-A alleles have been described. The HLA system plays an important role in the occurrence and outcome of infectious diseases, including those caused by the malaria parasite, the human immunodeficiency virus (HIV), and the severe acute respiratory syndrome coronavirus (SARS-CoV). The structural spike and the nucleocapsid proteins of the novel coronavirus SARS-CoV-2, which causes coronavirus disease 2019 (COVID-19), are reported to contain multiple Class I epitopes with predicted HLA restrictions. Individual HLA genetic variation may help explain different immune responses to a virus across a population.[provided by RefSeq, Aug 2020].
Isoforms & Proteins
5 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 |
|---|---|---|---|
| ENST00000376809 | P04439 | 1,613 | 295 |
| ENST00000376806 | Q5SRN5* | 706 | 254 |
| ENST00000396634 | P04439 | 704 | 253 |
| ENST00000638375 | A0A1W2PS24* | 660 | 233 |
| ENST00000376802 | Q5SRN7* | 650 | 228 |
Gene Properties
Recurrent Mutations
All 295 amino-acid changes on canonical ENST00000376809 · 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-A · cell line vs tissue
For each cancer type, the fraction of samples that carry at least one missense/complex mutation anywhere in HLA-A – 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 |
|---|---|---|
| Acute Myeloid Leukemia | 32/90 36% | 0/0 0% |
| T-Cell Non-Hodgkins Lymphoma | 9/26 35% | 0/0 0% |
| Chronic Myelogenous Leukemia | 8/25 32% | 0/0 0% |
| Glioblastoma | 28/98 29% | 0/0 0% |
| Oral Cavity Carcinoma | 15/54 28% | 0/0 0% |
| T-Lymphoblastic Leukemia | 9/40 22% | 0/0 0% |
| Unknown | 5/10 50% | 0/29 0% |
| Mesothelioma | 18/62 29% | 1/165 1% |
| Osteosarcoma | 14/45 31% | 3/166 2% |
| Chondrosarcoma | 5/14 36% | 0/75 0% |
| Chordoma | 1/7 14% | 0/13 0% |
| Germ Cell Tumour | 9/25 36% | 0/169 0% |
| Ewings Sarcoma | 15/63 24% | 0/262 0% |
| Neuroendocrine Tumour | 32/154 21% | 1/577 0% |
| Biliary Tract Carcinoma | 24/54 44% | 21/950 2% |
| Other Solid Cancers | 41/94 44% | 30/1515 2% |
| Plasma Cell Myeloma | 13/44 30% | 2/305 1% |
| Non-Small Cell Lung Carcinoma | 55/304 18% | 17/1390 1% |
| Bladder Carcinoma | 17/58 29% | 23/956 2% |
| Rhabdomyosarcoma | 8/33 24% | 0/171 0% |
| Acute Monocytic Leukemia | 1/1 100% | 0/25 0% |
| Non-Cancerous | 28/104 27% | 8/830 1% |
| Endometrial Carcinoma | 17/42 40% | 7/612 1% |
| Thyroid Gland Carcinoma | 13/45 29% | 47/1592 3% |
| Hodgkins Lymphoma | 4/16 25% | 1/122 1% |
| Burkitts Lymphoma | 7/32 22% | 1/196 1% |
| Melanoma | 52/210 25% | 18/1899 1% |
| Cervical Carcinoma | 7/35 20% | 8/422 2% |
| Other Sarcomas | 21/69 30% | 2/699 0% |
| Head and Neck Carcinoma | 31/85 36% | 17/1574 1% |
Mutation Distribution
Where HLA-A is mutated · all tissues, split by cell line vs tissue
How many mutations in HLA-A 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 4,333 mutations in HLA-A
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 |
|---|