HLA-DOA

major histocompatibility complex, class II, DO alpha, the group of Histocompatibility complex|C1-set domain containing

Basic information

Region (hg38): 6:33004182-33009591

Previous symbols: [ "HLA-DZA", "HLA-DNA" ]

Links

ENSG00000204252

∙ NCBI:3111 ∙ OMIM:142930 ∙ HGNC:4936 ∙ Uniprot:P06340 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HLA-DOA 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					2 clinvar	2
missense						0
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	0	0	2

Variants in HLA-DOA

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

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

Position	Type	Phenotype	Significance	ClinVar
6-33007564-C-T			Benign (Jun 21, 2018)	792038
6-33008236-G-A			Benign (Dec 31, 2019)	768080

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HLA-DOA	protein_coding	protein_coding	ENST00000229829	5	5435

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.98e-10	0.0239	123451	1	116	123568	0.000474

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.470	141	158	0.895	0.00000966	1603
Missense in Polyphen		65	65.363	0.99445		685
Synonymous	1.08	57	68.4	0.834	0.00000449	526
Loss of Function	-0.812	13	10.2	1.27	4.36e-7	108

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000554	0.000554
Ashkenazi Jewish	0.00	0.00
East Asian	0.00460	0.00455
Finnish	0.00	0.00
European (Non-Finnish)	0.0000816	0.0000811
Middle Eastern	0.00460	0.00455
South Asian	0.000165	0.000164
Other	0.000165	0.000164

dbNSFP

Source: dbNSFP

Function: FUNCTION: Important modulator in the HLA class II restricted antigen presentation pathway by interaction with the HLA-DM molecule in B-cells. Modifies peptide exchange activity of HLA-DM.;
Pathway: Antigen processing and presentation - Homo sapiens (human);Cell adhesion molecules (CAMs) - Homo sapiens (human);Type I diabetes mellitus - Homo sapiens (human);Allograft rejection - Homo sapiens (human);Graft-versus-host disease - Homo sapiens (human);Viral myocarditis - Homo sapiens (human);Influenza A - Homo sapiens (human);Systemic lupus erythematosus - Homo sapiens (human);Autoimmune thyroid disease - Homo sapiens (human);Inflammatory bowel disease (IBD) - Homo sapiens (human);Phagosome - Homo sapiens (human);Asthma - Homo sapiens (human);HTLV-I infection - Homo sapiens (human);Staphylococcus aureus infection - Homo sapiens (human);Tuberculosis - Homo sapiens (human);Th17 cell differentiation - Homo sapiens (human);Th1 and Th2 cell differentiation - Homo sapiens (human);Leishmaniasis - Homo sapiens (human);Toxoplasmosis - Homo sapiens (human);Rheumatoid arthritis - Homo sapiens (human);Hematopoietic cell lineage - Homo sapiens (human);Intestinal immune network for IgA production - Homo sapiens (human);Herpes simplex infection - Homo sapiens (human);Allograft Rejection;MHC class II antigen presentation;Immune System;Adaptive Immune System (Consensus)

Recessive Scores

pRec: 0.0932

Intolerance Scores

loftool: 0.763
rvis_EVS: 0.66
rvis_percentile_EVS: 84.44

Haploinsufficiency Scores

pHI: 0.185
hipred: N
hipred_score: 0.139
ghis: 0.448

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: N
gene_indispensability_score: 0.458

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

Gene name: H2-Oa
Phenotype: mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); normal phenotype; hematopoietic system phenotype; embryo phenotype; immune system phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); growth/size/body region phenotype; cellular phenotype; craniofacial phenotype;

Gene ontology

Biological process: negative regulation of antigen processing and presentation of peptide antigen via MHC class II;immune response;antigen processing and presentation of exogenous peptide antigen via MHC class II;regulation of T cell differentiation
Cellular component: lysosomal membrane;plasma membrane;endosome membrane;integral component of membrane;MHC class II protein complex
Molecular function: protein binding;MHC class II protein complex binding;MHC class II receptor activity