HLA-DOB
major histocompatibility complex, class II, DO beta, the group of C1-set domain containing|Histocompatibility complex
Basic information
Region (hg38): 6:32812762-32820466
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the HLA-DOB 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 | 0 | |||||
| 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 | 0 |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| HLA-DOB | protein_coding | protein_coding | ENST00000438763 | 6 | 4286 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.00000192 | 0.461 | 125602 | 0 | 146 | 125748 | 0.000581 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.177 | 136 | 142 | 0.958 | 0.00000704 | 1764 |
| Missense in Polyphen | 45 | 52.83 | 0.85179 | 691 | ||
| Synonymous | -0.356 | 61 | 57.6 | 1.06 | 0.00000308 | 545 |
| Loss of Function | 0.659 | 10 | 12.5 | 0.799 | 6.22e-7 | 137 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000727 | 0.000695 |
| Ashkenazi Jewish | 0.000400 | 0.000397 |
| East Asian | 0.000109 | 0.000109 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00108 | 0.00106 |
| Middle Eastern | 0.000109 | 0.000109 |
| South Asian | 0.0000329 | 0.0000327 |
| Other | 0.000658 | 0.000652 |
dbNSFP
Source:
- 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
- 0.123
Intolerance Scores
- loftool
- 0.729
- rvis_EVS
- 0.73
- rvis_percentile_EVS
- 86.08
Haploinsufficiency Scores
- pHI
- 0.119
- hipred
- N
- hipred_score
- 0.112
- ghis
- 0.535
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.724
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-Ob
- Phenotype
- neoplasm; hematopoietic system phenotype; immune system 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
- Cellular component
- lysosome;lysosomal membrane;endosome membrane;integral component of membrane;MHC class II protein complex
- Molecular function
- MHC class II protein complex binding;MHC class II receptor activity