HLA-B

major histocompatibility complex, class I, B, the group of C1-set domain containing|Histocompatibility complex|MicroRNA protein coding host genes

Basic information

Region (hg38): 6:31353872-31367067

Previous symbols: [ "AS" ]

Links

ENSG00000234745 ∙ NCBI:3106 ∙ OMIM:142830 ∙ HGNC:4932 ∙ Uniprot:P01889 ∙ 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 importance related to a number of medications, including abacavir, allopurinol, carbamazepine, flucocloxacillin	General	3477129; 16415921; 16538176; 17258541; 19933789; 203459391; 21244392; 21428768; 21676164; 22348415; 22348435

ClinVar

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

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HLA-B 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				10	1	11
missense				5	4	9
nonsense						0
start loss						0
frameshift				3	5	8
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	0	18	10

Variants in HLA-B

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

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

Position	Type	Phenotype	Significance	ClinVar
6-31354498-C-A			Likely benign (Apr 11, 2018)
6-31355138-G-A			Benign (Jun 18, 2018)
6-31355144-A-G			Likely benign (Jul 01, 2022)
6-31355224-C-G			not provided (-)
6-31355378-C-T			Likely benign (Aug 01, 2024)
6-31355490-C-T		EBV-positive nodal T- and NK-cell lymphoma	Pathogenic (-)
6-31355564-G-A			Likely benign (Nov 01, 2022)
6-31356164-T-A			not provided (-)
6-31356245-TCC-T		HLA-B-related disorder	Benign (Dec 17, 2020)
6-31356248-G-T			Likely benign (May 01, 2024)
6-31356248-G-GTC		HLA-B-related disorder	Benign (Dec 17, 2020)
6-31356297-C-T			Likely benign (Jan 01, 2024)
6-31356367-T-G		HLA-B-related disorder	Benign (Dec 17, 2020)
6-31356389-G-A			Benign (Jul 01, 2024)
6-31356418-T-A			Likely benign (Jul 01, 2023)
6-31356418-T-G			Likely benign (Jun 01, 2024)
6-31356423-G-C		HLA-B-related disorder	Benign (Dec 17, 2020)
6-31356686-AC-GA			not provided (-)
6-31356687-C-T			not provided (-)
6-31356712-C-A		HLA-B-related disorder	Likely benign (Dec 17, 2020)
6-31356711-C-CGG		HLA-B-related disorder	Likely benign (Dec 17, 2020)
6-31356713-G-C			Likely benign (Jul 01, 2024)
6-31356716-C-A			Likely benign (May 01, 2023)
6-31356716-C-G			Likely benign (May 01, 2023)
6-31356716-CA-C		HLA-B-related disorder	Likely benign (Dec 17, 2020)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HLA-B	protein_coding	protein_coding	ENST00000412585	7	3317

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000386	0.957	27804	62749	35194	125747	0.530

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0112	196	196	1.00	0.00000977	2123
Missense in Polyphen		110	130.87	0.84052		1447
Synonymous	0.131	77	78.5	0.981	0.00000423	660
Loss of Function	1.85	10	18.6	0.538	8.04e-7	194

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	2.21	1.59
Ashkenazi Jewish	1.34	0.650
East Asian	0.861	0.520
Finnish	1.02	0.483
European (Non-Finnish)	1.17	0.496
Middle Eastern	0.861	0.520
South Asian	1.27	0.604
Other	1.16	0.515

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);Abacavir Pathway, Pharmacokinetics/Pharmacodynamics;Proteasome Degradation;Allograft Rejection;Type II interferon signaling (IFNG);Neutrophil degranulation;DAP12 interactions;Cytokine Signaling in Immune system;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;Interferon gamma signaling;Interferon alpha/beta signaling;Antigen Presentation: Folding, assembly and peptide loading of class I MHC;Interferon Signaling (Consensus)

Intolerance Scores

• loftool: 0.996
• rvis_EVS: 8.95
• rvis_percentile_EVS: 99.96

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.328

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.447

Gene Damage Prediction

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

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: signaling receptor binding;protein binding;peptide antigen binding