HLA-DMB
Basic information
Region (hg38): 6:32934629-32941028
Links
Phenotypes
GenCC
Source:
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-DMB 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-DMB | protein_coding | protein_coding | ENST00000418107 | 6 | 6442 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.00246 | 0.936 | 125731 | 0 | 11 | 125742 | 0.0000437 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 1.59 | 89 | 142 | 0.626 | 0.00000730 | 1682 |
Missense in Polyphen | 15 | 44.051 | 0.34052 | 551 | ||
Synonymous | 0.184 | 57 | 58.8 | 0.970 | 0.00000315 | 536 |
Loss of Function | 1.63 | 6 | 12.1 | 0.495 | 5.95e-7 | 133 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.0000615 | 0.0000615 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.00 | 0.00 |
Finnish | 0.00 | 0.00 |
European (Non-Finnish) | 0.0000735 | 0.0000703 |
Middle Eastern | 0.00 | 0.00 |
South Asian | 0.0000656 | 0.0000653 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Plays a critical role in catalyzing the release of class II-associated invariant chain peptide (CLIP) from newly synthesized MHC class II molecules and freeing the peptide binding site for acquisition of antigenic peptides. In B-cells, the interaction between HLA-DM and MHC class II molecules is regulated by HLA-DO. {ECO:0000269|PubMed:16547258, ECO:0000269|PubMed:8849454, ECO:0000269|PubMed:9768757}.;
- 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
- 0.0690
Intolerance Scores
- loftool
- 0.705
- rvis_EVS
- 1.04
- rvis_percentile_EVS
- 91.21
Haploinsufficiency Scores
- pHI
- 0.0445
- hipred
- N
- hipred_score
- 0.180
- ghis
- 0.514
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.663
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-DMb2
- Phenotype
Gene ontology
- Biological process
- MHC class II protein complex assembly;peptide antigen assembly with MHC class II protein complex;immune response;antigen processing and presentation of exogenous peptide antigen via MHC class II;positive regulation of T cell proliferation;positive regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell
- Cellular component
- lysosomal membrane;integral component of membrane;late endosome membrane;MHC class II protein complex
- Molecular function
- protein binding;MHC class II protein complex binding