HLA-DMA
major histocompatibility complex, class II, DM alpha, the group of Histocompatibility complex|C1-set domain containing
Basic information
Region (hg38): 6:32948613-32969094
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-DMA 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 | |||||
| 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 | 1 |
Variants in HLA-DMA
This is a list of pathogenic ClinVar variants found in the HLA-DMA region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 6-32949723-A-G | Benign (Jun 05, 2018) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| HLA-DMA | protein_coding | protein_coding | ENST00000374843 | 5 | 20482 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.00238 | 0.933 | 123753 | 0 | 7 | 123760 | 0.0000283 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.879 | 116 | 146 | 0.795 | 0.00000827 | 1703 |
| Missense in Polyphen | 33 | 53.538 | 0.61638 | 662 | ||
| Synonymous | 0.485 | 57 | 61.9 | 0.921 | 0.00000396 | 529 |
| Loss of Function | 1.61 | 6 | 12.0 | 0.498 | 5.19e-7 | 126 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000123 | 0.000123 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000547 | 0.0000547 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00000923 | 0.00000900 |
| Middle Eastern | 0.0000547 | 0.0000547 |
| South Asian | 0.0000659 | 0.0000656 |
| 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;Exercise-induced Circadian Regulation;MHC class II antigen presentation;Immune System;Adaptive Immune System
(Consensus)
Recessive Scores
- pRec
- 0.0950
Intolerance Scores
- loftool
- 0.306
- rvis_EVS
- 0.75
- rvis_percentile_EVS
- 86.57
Haploinsufficiency Scores
- pHI
- 0.157
- hipred
- N
- hipred_score
- 0.436
- ghis
- 0.506
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.576
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-DMa
- Phenotype
- growth/size/body region 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); hematopoietic system phenotype; immune system phenotype;
Gene ontology
- Biological process
- peptide antigen assembly with MHC class II protein complex;immune response;antigen processing and presentation of exogenous peptide antigen via MHC class II
- Cellular component
- lysosomal membrane;cell surface;membrane;integral component of membrane;late endosome membrane;MHC class II protein complex;intracellular membrane-bounded organelle
- Molecular function
- MHC class II protein complex binding