HLA-G

major histocompatibility complex, class I, G, the group of Histocompatibility complex|C1-set domain containing

Basic information

Region (hg38): 6:29826966-29831125

Links

ENSG00000204632 ∙ NCBI:3135 ∙ OMIM:142871 ∙ HGNC:4964 ∙ Uniprot:P17693 ∙ 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-G gene.

• not provided (6 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HLA-G 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				3	3	6
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	3	3

Variants in HLA-G

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

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

Position	Type	Phenotype	Significance	ClinVar
6-29828078-C-G			Likely benign (Dec 31, 2019)
6-29828150-G-A			Benign (Jul 06, 2018)
6-29828210-G-A			Benign (Jul 18, 2018)
6-29828571-C-T			Benign (Jun 08, 2018)
6-29829503-G-A			Likely benign (Aug 21, 2018)
6-29829644-G-A			Likely benign (Apr 01, 2023)
6-29830804-G-GATTTGTTCATGCCT		Post-COVID-19 disorder	Likely risk allele (Oct 27, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HLA-G	protein_coding	protein_coding	ENST00000428701	6	4159

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.36e-11	0.0530	121440	68	4240	125748	0.0173

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.230	198	207	0.955	0.0000112	2163
Missense in Polyphen		96	95.449	1.0058		1084
Synonymous	-0.520	95	88.8	1.07	0.00000534	672
Loss of Function	0.105	17	17.5	0.973	7.59e-7	183

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0852	0.0814
Ashkenazi Jewish	0.0238	0.0236
East Asian	0.0195	0.0194
Finnish	0.00268	0.00268
European (Non-Finnish)	0.0141	0.0137
Middle Eastern	0.0195	0.0194
South Asian	0.0144	0.0143
Other	0.0202	0.0202

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in the presentation of foreign antigens to the immune system. Plays a role in maternal tolerance of the fetus by mediating protection from the deleterious effects of natural killer cells, cytotoxic T-lymphocytes, macrophages and mononuclear cells.
• Pathway: Antigen processing and presentation - Homo sapiens (human);Cell adhesion molecules (CAMs) - Homo sapiens (human);Type I diabetes mellitus - Homo sapiens (human);Kaposi,s sarcoma-associated herpesvirus infection - Homo sapiens (human);Allograft rejection - Homo sapiens (human);Graft-versus-host disease - Homo sapiens (human);Viral myocarditis - Homo sapiens (human);Endocytosis - Homo sapiens (human);Autoimmune thyroid disease - Homo sapiens (human);Phagosome - Homo sapiens (human);HTLV-I infection - Homo sapiens (human);Natural killer cell mediated cytotoxicity - Homo sapiens (human);Viral carcinogenesis - Homo sapiens (human);Cellular senescence - Homo sapiens (human);Epstein-Barr virus infection - Homo sapiens (human);Human papillomavirus infection - Homo sapiens (human);Herpes simplex infection - Homo sapiens (human);Proteasome Degradation;Allograft Rejection;Cytokine Signaling in Immune system;Immune System;Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell;Adaptive Immune System;Endosomal/Vacuolar pathway;Antigen processing-Cross presentation;Class I MHC mediated antigen processing & presentation;Interferon gamma signaling;Interferon alpha/beta signaling;Antigen Presentation: Folding, assembly and peptide loading of class I MHC;Interferon Signaling (Consensus)

Intolerance Scores

• loftool: 0.834
• rvis_EVS: 0.09
• rvis_percentile_EVS: 60.47

Haploinsufficiency Scores

• pHI: 0.106
• hipred: N
• hipred_score: 0.238
• ghis: 0.431

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.439

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-M3
• Phenotype: homeostasis/metabolism phenotype; hematopoietic system phenotype; immune system phenotype

Gene ontology

• Biological process: negative regulation of T cell mediated cytotoxicity;positive regulation of T cell mediated cytotoxicity;peripheral B cell tolerance induction;antigen processing and presentation of peptide antigen via MHC class I;antigen processing and presentation of endogenous peptide antigen via MHC class Ib;antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent;antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent;antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent;positive regulation of tolerance induction;positive regulation of T cell tolerance induction;positive regulation of natural killer cell cytokine production;immune response-inhibiting cell surface receptor signaling pathway;immune response;cellular defense response;negative regulation of angiogenesis;positive regulation of interleukin-12 production;negative regulation of T cell proliferation;protection from natural killer cell mediated cytotoxicity;positive regulation of regulatory T cell differentiation;negative regulation of natural killer cell mediated cytotoxicity;regulation of immune response;negative regulation of immune response;negative regulation of protein kinase B signaling;interferon-gamma-mediated signaling pathway;type I interferon signaling pathway;positive regulation of macrophage cytokine production;protein homotrimerization;negative regulation of G0 to G1 transition;positive regulation of endothelial cell apoptotic process;positive regulation of cellular senescence;negative regulation of dendritic cell differentiation
• Cellular component: Golgi membrane;extracellular region;extracellular space;early endosome;plasma membrane;external side of plasma membrane;ER to Golgi transport vesicle membrane;membrane;phagocytic vesicle membrane;early endosome membrane;cis-Golgi network membrane;MHC class I protein complex;recycling endosome membrane;integral component of lumenal side of endoplasmic reticulum membrane
• Molecular function: signaling receptor binding;protein binding;peptide antigen binding;CD8 receptor binding;identical protein binding;protein homodimerization activity