HLA-DMA

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

Basic information

Region (hg38): 6:32948612-32969094

Links

ENSG00000204257

∙ NCBI:3108 ∙ OMIM:142855 ∙ HGNC:4934 ∙ Uniprot:P28067 ∙ 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-DMA gene.

not provided (1 variants)

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 clinvar	1
missense						0
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region ? Intron variants in splice region, excluding donor/acceptor (+/-2bp)						0
non coding ? UTR, intron and other, non coding variants						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)	789590

GnomAD

Source: gnomAD

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: dbNSFP

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