HLA-A

major histocompatibility complex, class I, A, the group of Histocompatibility complex|C1-set domain containing

Basic information

Region (hg38): 6:29941260-29949572

Links

ENSG00000206503 ∙ NCBI:3105 ∙ OMIM:142800 ∙ HGNC:4931 ∙ Uniprot:P04439 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Drug-induced toxicity, susceptibility to	AD	Pharmacogenomic	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	General	15743917; 17258541; 21149285; 21428768; 21428769

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the HLA-A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HLA-A gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1		1
missense						0
nonsense						0
start loss						0
frameshift		1				1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1	1	2
non coding						0
Total	0	1	0	1	0

Variants in HLA-A

This is a list of pathogenic ClinVar variants found in the HLA-A region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
6-29941373-A-G			Uncertain significance (-)
6-29942594-C-T		-	no classification for the single variant (-)
6-29942772-G-A		EBV-positive nodal T- and NK-cell lymphoma	Likely benign (-)
6-29942863-C-T		-	no classification for the single variant (-)
6-29942944-G-A			Likely benign (Jan 01, 2024)
6-29942965-G-C		-	no classification for the single variant (-)
6-29942982-T-A		-	no classification for the single variant (-)
6-29942984-G-A		-	no classification for the single variant (-)
6-29942985-A-G		-	no classification for the single variant (-)
6-29942990-G-C		-	no classification for the single variant (-)
6-29942994-C-T		-	no classification for the single variant (-)
6-29942996-C-G		-	no classification for the single variant (-)
6-29942997-T-C		-	no classification for the single variant (-)
6-29943000-G-T		-	no classification for the single variant (-)
6-29943002-G-C		-	no classification for the single variant (-)
6-29943261-G-A			Likely benign (Jul 01, 2022)
6-29943287-A-G		-	no classification for the single variant (-)
6-29943307-G-A		Abnormality of neuronal migration	Benign (Oct 31, 2014)
6-29943309-T-C		-	no classification for the single variant (-)
6-29943321-T-C		-	no classification for the single variant (-)
6-29943337-G-A		-	no classification for the single variant (-)
6-29943372-C-T		-	no classification for the single variant (-)
6-29943426-A-C		-	no classification for the single variant (-)
6-29943448-A-G		-	no classification for the single variant (-)
6-29943451-A-T		-	no classification for the single variant (-)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HLA-A	protein_coding	protein_coding	ENST00000396634	8	4625

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00133	0.992	80841	5909	38993	125743	0.198

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0962	214	210	1.02	0.0000110	2195
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.466	0.393
Ashkenazi Jewish	0.223	0.194
East Asian	0.510	0.444
Finnish	0.158	0.132
European (Non-Finnish)	0.193	0.154
Middle Eastern	0.510	0.444
South Asian	0.342	0.307
Other	0.240	0.202

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in the presentation of foreign antigens to the immune system.
• Pathway: 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);Graft-versus-host disease - Homo sapiens (human);Viral myocarditis - Homo sapiens (human);Endocytosis - Homo sapiens (human);Autoimmune thyroid disease - Homo sapiens (human);Phagosome - Homo sapiens (human);HTLV-I infection - Homo sapiens (human);Natural killer cell mediated cytotoxicity - Homo sapiens (human);Viral carcinogenesis - Homo sapiens (human);Cellular senescence - Homo sapiens (human);Epstein-Barr virus infection - Homo sapiens (human);Human papillomavirus infection - Homo sapiens (human);Herpes simplex infection - Homo sapiens (human);Proteasome Degradation;Allograft Rejection;Neutrophil degranulation;Disease;ras-independent pathway in nk cell-mediated cytotoxicity;antigen processing and presentation;Cytokine Signaling in Immune system;Host Interactions of HIV factors;HIV Infection;Post-translational protein modification;Metabolism of proteins;Infectious disease;Innate Immune System;Immune System;Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell;Adaptive Immune System;Endosomal/Vacuolar pathway;Antigen processing-Cross presentation;Class I MHC mediated antigen processing & presentation;Nef mediated downregulation of MHC class I complex cell surface expression;Nef-mediates down modulation of cell surface receptors by recruiting them to clathrin adapters;The role of Nef in HIV-1 replication and disease pathogenesis;Interferon gamma signaling;Protein ubiquitination;Interferon alpha/beta signaling;Antigen Presentation: Folding, assembly and peptide loading of class I MHC;Downstream signaling in naïve CD8+ T cells;Interferon Signaling;AP-1 transcription factor network;TCR signaling in naïve CD8+ T cells;E3 ubiquitin ligases ubiquitinate target proteins;IL12-mediated signaling events (Consensus)

Intolerance Scores

• loftool: 0.944
• rvis_EVS: 8.93
• rvis_percentile_EVS: 99.96

Haploinsufficiency Scores

• pHI: 0.191
• hipred: N
• hipred_score: 0.466
• ghis: 0.527

Essentials

• essential_gene_CRISPR: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.657

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High

Mouse Genome Informatics

• Gene name: H2-Q7

Gene ontology

• 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;antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent;immune response;regulation of immune response;interferon-gamma-mediated signaling pathway;type I interferon signaling pathway
• Cellular component: Golgi membrane;extracellular space;endoplasmic reticulum;Golgi apparatus;plasma membrane;external side of plasma membrane;cell surface;ER to Golgi transport vesicle membrane;phagocytic vesicle membrane;early endosome membrane;MHC class I protein complex;recycling endosome membrane;integral component of lumenal side of endoplasmic reticulum membrane
• Molecular function: RNA binding;signaling receptor binding;protein binding;beta-2-microglobulin binding;peptide antigen binding