HLA-A
protein-codingmajor histocompatibility complex, class I, A, the group of Histocompatibility complex|C1-set domain containing
Gene summary
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]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~8.3 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
Clinical Genomic Database (CGD)
Manifestation: General
Intervention: Pharmacogenomic
Rationale: Susceptibility to adverse reactions (including Stevens-Johnson syndrome), may have pharmacogenomic relevance related to a number of medications, including allopurinol, carbamazepine; HIV disease, progression in
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to HLA-A variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_002116.8. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 7 | 2 | 9 | |||
| missense | 26 | 11 | 2 | 39 | ||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 1 | 2 | 2 | 5 | ||
| splice donor/acceptor (+/-2bp) | 15 | 15 | ||||
| Total | 0 | 1 | 50 | 15 | 2 | 68 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_002107.3 | 8 | MANE Select | |
| Ensembl | ENSP00000366005.5 | 8 | MANE Select | |
| Ensembl | ENSP00000365998.2 | 5 | Standard | |
| Ensembl | ENSP00000365998.2 | 5 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Antigen processing and presentation - Homo sapiens (human)
- Cell adhesion molecules (CAMs) - Homo sapiens (human)
- Type I diabetes mellitus - Homo sapiens (human)
- Kaposi,s sarcoma-associated herpesvirus infection - Homo sapiens (human)
- Allograft rejection - Homo sapiens (human)
Biological Process
- positive regulation of T cell mediated cytotoxicity
- antigen processing and presentation of peptide antigen via MHC class I
- antigen processing and presentation of endogenous peptide antigen via MHC class Ib
- antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent
- antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent
Molecular Function
- RNA binding
- signaling receptor binding
- protein binding
- beta-2-microglobulin binding
- peptide antigen binding
Cellular Component
- Golgi membrane
- extracellular space
- endoplasmic reticulum
- Golgi apparatus
- plasma membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000396634
- Coding exons
- 8
- Length
- 4625
- Individuals with no LoFs
- 80841
- Homozygous LoFs
- 5909
- Heterozygous LoFs
- 38993
- Defined
- 125743
- p
- 0.198
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.0962 | 214 | 210 | 1.02 | 0.0000110 | 2195 |
| Missense (PolyPhen) | 67 | 94.231 | 0.71102 | 1059 | ||
| Synonymous | 0.618 | 79 | 86.3 | 0.915 | 0.00000483 | 674 |
| Loss of Function | 2.36 | 8 | 19.1 | 0.418 | 8.27e-7 | 199 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.21 | 0.14 | notable |
| Latino/Admixed American | 0.26 | 0.22 | notable |
| Ashkenazi Jewish | 0.22 | 0.19 | notable |
| East Asian | 0.51 | 0.44 | notable |
| Finnish | 0.16 | 0.13 | notable |
| European (Non-Finnish) | 0.19 | 0.15 | notable |
| South Asian | 0.34 | 0.31 | notable |
| Other | 0.24 | 0.20 | notable |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Involved in the presentation of foreign antigens to the immune system.;
Intolerance Scores
- LoFtool
- 0.944
- RVIS EVS
- 8.93
- RVIS percentile EVS
- 99.96
Essentials
- Essential (CRISPR)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.657
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | High | High | High |
| Primary Immunodeficiency | High | High | High |
| Cancer | High | High | High |