HLA-A

protein-coding

major 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

NM_002116.8

Inheritance

AD

ClinVar variants

P:1U:50B:17

Top phenotype

Drug-induced toxicity, susceptibility to

gnomAD constraint

pLI —, LoF o/e 0.42

Max pathogenic AF

—

Genomic locus

chr6:29,941,260-29,949,572

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~8.3 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

Clinical Genomic Database (CGD)

Drug-induced toxicity, susceptibility toAD

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

Refs: 15743917; 17258541; 21149285; 21428768; 21428769Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to HLA-A variants in ClinVar

7 Conditions Cataloged
not specifiedTotal: 15
not providedTotal: 5
Abnormality of neuronal migrationTotal: 2
Susceptibility to severe cutaneous adverse reactionTotal: 2
EBV-positive nodal T- and NK-cell lymphomaTotal: 1
HLA-A-related conditionTotal: 1
Susceptibility to severe COVID-19Total: 1

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.

EffectPLPVUSLBBSum
synonymous
7
clinvar
2
clinvar
9
missense
26
clinvar
11
clinvar
2
clinvar
39
nonsense
0
start loss
0
frameshift
1
clinvar
2
clinvar
2
clinvar
5
splice donor/acceptor (+/-2bp)
15
clinvar
15
Total015015268
Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 74 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_002116.8RefSeqNP_002107.38MANE Select
ENST00000376809.10EnsemblENSP00000366005.58MANE Select
ENST00000376802.2EnsemblENSP00000365998.25Standard
ENST00000376802.3EnsemblENSP00000365998.25Standard

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: gnomAD

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-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense-0.09622142101.020.00001102195
Missense (PolyPhen)6794.2310.711021059
Synonymous0.6187986.30.9150.00000483674
Loss of Function2.36819.10.4188.27e-7199

Population LoF Frequency

PopulationCAFp-valueStatus
African0.210.14notable
Latino/Admixed American0.260.22notable
Ashkenazi Jewish0.220.19notable
East Asian0.510.44notable
Finnish0.160.13notable
European (Non-Finnish)0.190.15notable
South Asian0.340.31notable
Other0.240.20notable

dbNSFP Gene Annotations

Source: dbNSFP

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

AllRecessiveDominant
MendelianHighHighHigh
Primary ImmunodeficiencyHighHighHigh
CancerHighHighHigh
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