Gene: HLA-A
Alternate names for this Gene: HLAA
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. Hundreds of 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 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.
Gene is located in Chromosome: 6
Location in Chromosome : 6p22.1
Description of this Gene: major histocompatibility complex, class I, A
Type of Gene: protein-coding
rs2256543 in
HLA-A gene and
Adenocarcinoma of lung (disorder)
PMID 19836008 2009 A genome-wide association study of lung cancer identifies a region of chromosome 5p15 associated with risk for adenocarcinoma.
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HLA-A gene and
Age at menarche
PMID 25231870 2014 Parent-of-origin-specific allelic associations among 106 genomic loci for age at menarche.
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HLA-A gene and
Beta-2-microglobulin measurement
PMID 23417110 2013 Genome-wide association study identified the human leukocyte antigen region as a novel locus for plasma beta-2 microglobulin.
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HLA-A gene and
Bipolar Disorder
PMID 22688191 2012 Genome-wide association study in a Swedish population yields support for greater CNV and MHC involvement in schizophrenia compared with bipolar disorder.
rs28749114 in
HLA-A gene and
Blood Protein Measurement
PMID 29875488 2018 Genomic atlas of the human plasma proteome.
rs3893464 in
HLA-A gene and
Blood basophil count (lab test)
PMID 27863252 2016 The Allelic Landscape of Human Blood Cell Trait Variation and Links to Common Complex Disease.
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HLA-A gene and
Carcinoma of lung
PMID 28604730 2017 Large-scale association analysis identifies new lung cancer susceptibility loci and heterogeneity in genetic susceptibility across histological subtypes.
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HLA-A gene and
Chemical and Drug Induced Liver Injury
PMID 28043905 2017 Association of Liver Injury From Specific Drugs, or Groups of Drugs, With Polymorphisms in HLA and Other Genes in a Genome-Wide Association Study.
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HLA-A gene and
Child Development Disorders, Pervasive
PMID 28540026 2017 Meta-analysis of GWAS of over 16,000 individuals with autism spectrum disorder highlights a novel locus at 10q24.32 and a significant overlap with schizophrenia.
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HLA-A gene and
Cicatrix
PMID 31066027 2019 Shared Genetic Risk Factors Across Carbamazepine-Induced Hypersensitivity Reactions.
rs1061535 in
HLA-A gene and
Corpuscular Hemoglobin Concentration Mean
PMID 23222517 2012 Seventy-five genetic loci influencing the human red blood cell.
rs9260151 in
HLA-A gene and
Diabetes Mellitus, Insulin-Dependent
PMID 29404672 2018 Conditional analyses suggested that the three identified variants in the MHC region were independent of each other. rs9260151 and rs3135002 have been associated with type 1 diabetes, whereas rs559047 and rs61211515 have not been associated with a risk of developing type 1 diabetes.
rs3893464 in
HLA-A gene and
Eosinophil count procedure
PMID 27863252 2016 The Allelic Landscape of Human Blood Cell Trait Variation and Links to Common Complex Disease.
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HLA-A gene and
Esophageal Neoplasms
PMID 22960999 2012 Genome-wide association analyses of esophageal squamous cell carcinoma in Chinese identify multiple susceptibility loci and gene-environment interactions.
rs7749944 in
HLA-A gene and
Frontal fibrosing alopecia
PMID 30850646 2019 Genome-wide association study in frontal fibrosing alopecia identifies four susceptibility loci including HLA-B*07:02.
rs9260620 in
HLA-A gene and
Granulocyte count
PMID 27863252 2016 The Allelic Landscape of Human Blood Cell Trait Variation and Links to Common Complex Disease.
rs3893464 in
HLA-A gene and
Graves Disease
PMID 21900946 2011 Multivariate stepwise logistic regression analysis selected rs3893464, rs4313034, rs3132613, rs4248154, rs2273017, rs9394159 and rs4713693, as markers for independent risk loci for GD.
rs9260313 in
HLA-A gene and
Hematocrit procedure
PMID 27863252 2016 The Allelic Landscape of Human Blood Cell Trait Variation and Links to Common Complex Disease.
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HLA-A gene and
Hemoglobin measurement
PMID 27863252 2016 The Allelic Landscape of Human Blood Cell Trait Variation and Links to Common Complex Disease.
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HLA-A gene and
Insulin C-peptide measurement
PMID 29404672 2018 Meta-genome-wide association studies identify a locus on chromosome 1 and multiple variants in the MHC region for serum C-peptide in type 1 diabetes.
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HLA-A gene and
Intelligence
PMID 29844566 2018 Study of 300,486 individuals identifies 148 independent genetic loci influencing general cognitive function.
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HLA-A gene and
Lymphocyte Count measurement
PMID 22286170 2012 The combination of a genome-wide association study of lymphocyte count and analysis of gene expression data reveals novel asthma candidate genes.
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HLA-A gene and
Malignant neoplasm of lung
PMID 21725308 2011 A genome-wide association study identifies two new lung cancer susceptibility loci at 13q12.12 and 22q12.2 in Han Chinese.
PMID 19654303 2009 Deciphering the impact of common genetic variation on lung cancer risk: a genome-wide association study.
rs2524005 in
HLA-A gene and
Mental disorders
PMID 22688191 2012 Genome-wide association study in a Swedish population yields support for greater CNV and MHC involvement in schizophrenia compared with bipolar disorder.
rs9260620 in
HLA-A gene and
Monocyte count procedure
PMID 27863252 2016 The Allelic Landscape of Human Blood Cell Trait Variation and Links to Common Complex Disease.
rs9260620 in
HLA-A gene and
Monocyte count result
PMID 27863252 2016 The Allelic Landscape of Human Blood Cell Trait Variation and Links to Common Complex Disease.
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HLA-A gene and
Multiple Sclerosis
PMID 22190364 2011 Genome-wide meta-analysis identifies novel multiple sclerosis susceptibility loci.
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HLA-A gene and
Myasthenia Gravis
PMID 26562150 2016 Genome-Wide Association Study of Late-Onset Myasthenia Gravis: Confirmation of TNFRSF11A and Identification of ZBTB10 and Three Distinct HLA Associations.
PMID 23055271 2012 Risk for myasthenia gravis maps to a (151) Pro→Ala change in TNIP1 and to human leukocyte antigen-B*08.
rs2517713 in
HLA-A gene and
Nasopharyngeal Neoplasms
PMID 19664746 2009 Genome-wide association study reveals multiple nasopharyngeal carcinoma-associated loci within the HLA region at chromosome 6p21.3.
PMID 20512145 2010 A genome-wide association study of nasopharyngeal carcinoma identifies three new susceptibility loci.
PMID 27436580 2016 An extended genome-wide association study identifies novel susceptibility loci for nasopharyngeal carcinoma.
rs2517713 in
HLA-A gene and
Nasopharyngeal carcinoma
PMID 19664746 2009 Genome-wide association study reveals multiple nasopharyngeal carcinoma-associated loci within the HLA region at chromosome 6p21.3.
PMID 20512145 2010 A genome-wide association study of nasopharyngeal carcinoma identifies three new susceptibility loci.
PMID 23209447 2012 The principal genetic determinants for nasopharyngeal carcinoma in China involve the HLA class I antigen recognition groove.
rs9260620 in
HLA-A gene and
Neutrophil count (procedure)
PMID 27863252 2016 The Allelic Landscape of Human Blood Cell Trait Variation and Links to Common Complex Disease.
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HLA-A gene and
Oral Ulcer
PMID 30837455 2019 Genome wide analysis for mouth ulcers identifies associations at immune regulatory loci.
rs2975009 in
HLA-A gene and
Platelet Count measurement
PMID 27863252 2016 The Allelic Landscape of Human Blood Cell Trait Variation and Links to Common Complex Disease.
rs7749944 in
HLA-A gene and
Postmenopausal frontal fibrosing alopecia
PMID 30850646 2019 Genome-wide association study in frontal fibrosing alopecia identifies four susceptibility loci including HLA-B*07:02.
rs2524005 in
HLA-A gene and
Psychotic Disorders
PMID 22688191 2012 Genome-wide association study in a Swedish population yields support for greater CNV and MHC involvement in schizophrenia compared with bipolar disorder.
rs17882753 in
HLA-A gene and
Reticulocyte count (procedure)
PMID 27863252 2016 The Allelic Landscape of Human Blood Cell Trait Variation and Links to Common Complex Disease.
rs111312615 in
HLA-A gene and
Schizophrenia
PMID 30285260 2019 Genome-Wide Association Study Detected Novel Susceptibility Genes for Schizophrenia and Shared Trans-Populations/Diseases Genetic Effect.
PMID 28540026 2017 Meta-analysis of GWAS of over 16,000 individuals with autism spectrum disorder highlights a novel locus at 10q24.32 and a significant overlap with schizophrenia.
PMID 22688191 2012 Genome-wide association study in a Swedish population yields support for greater CNV and MHC involvement in schizophrenia compared with bipolar disorder.
rs192543598 in
HLA-A gene and
Severe cutaneous adverse reactions (SMQ)
PMID 31066027 2019 Shared Genetic Risk Factors Across Carbamazepine-Induced Hypersensitivity Reactions.
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HLA-A gene and
Squamous cell carcinoma of lung
PMID 28604730 2017 Large-scale association analysis identifies new lung cancer susceptibility loci and heterogeneity in genetic susceptibility across histological subtypes.
rs1061539 in
HLA-A gene and
Varicosity
PMID 30566020 2018 Clinical and Genetic Determinants of Varicose Veins.
rs12206499 in
HLA-A gene and
Vitiligo
PMID 21326295 2011 Genome-wide analysis identifies a quantitative trait locus in the MHC class II region associated with generalized vitiligo age of onset.
PMID 22561518 2012 Genome-wide association analyses identify 13 new susceptibility loci for generalized vitiligo.
PMID 27723757 2016 Genome-wide association studies of autoimmune vitiligo identify 23 new risk loci and highlight key pathways and regulatory variants.
rs9260620 in
HLA-A gene and
White Blood Cell Count procedure
PMID 27863252 2016 The Allelic Landscape of Human Blood Cell Trait Variation and Links to Common Complex Disease.