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.

rs16896742 in HLA-A gene and Age at menarche PMID 25231870 2014 Parent-of-origin-specific allelic associations among 106 genomic loci for age at menarche.

rs9260489 in 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.

rs2524005 in 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.

rs115729734 in 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.

rs114577328 in 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.

rs111312615 in 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.

rs192543598 in 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.

rs1655900 in 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.

rs9260313 in HLA-A gene and Hemoglobin measurement PMID 27863252 2016 The Allelic Landscape of Human Blood Cell Trait Variation and Links to Common Complex Disease.

rs9260151 in 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.

rs2523933 in HLA-A gene and Intelligence PMID 29844566 2018 Study of 300,486 individuals identifies 148 independent genetic loci influencing general cognitive function.

rs2508037 in 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.

rs1655902 in 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.

rs9260489 in HLA-A gene and Multiple Sclerosis PMID 22190364 2011 Genome-wide meta-analysis identifies novel multiple sclerosis susceptibility loci.

rs150881176 in 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.

rs41546314 in 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.

rs147097402 in 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.