HLA-E
major histocompatibility complex, class I, E, the group of Histocompatibility complex|C1-set domain containing
Basic information
Region (hg38): 6:30489509-30494194
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-E 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 | 1 | |||||
| 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 | 1 | 0 |
Variants in HLA-E
This is a list of pathogenic ClinVar variants found in the HLA-E region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 6-30491353-A-C | Likely benign (Jul 29, 2018) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| HLA-E | protein_coding | protein_coding | ENST00000376630 | 7 | 4739 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0368 | 0.962 | 125726 | 0 | 17 | 125743 | 0.0000676 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.98 | 132 | 213 | 0.619 | 0.0000107 | 2306 |
| Missense in Polyphen | 48 | 99.076 | 0.48448 | 1067 | ||
| Synonymous | 1.58 | 76 | 95.6 | 0.795 | 0.00000555 | 731 |
| Loss of Function | 2.80 | 6 | 19.3 | 0.311 | 8.34e-7 | 207 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000154 | 0.000149 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.0000462 | 0.0000462 |
| European (Non-Finnish) | 0.0000556 | 0.0000527 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.000196 | 0.000196 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Preferably binds to a peptide derived from the signal sequence of most HLA-A, -B, -C and -G molecules.;
- 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;DAP12 signaling;DAP12 interactions;Cytokine Signaling in Immune system;Innate 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
- 0.533
- rvis_EVS
- 0.71
- rvis_percentile_EVS
- 85.53
Haploinsufficiency Scores
- pHI
- 0.162
- hipred
- Y
- hipred_score
- 0.519
- ghis
- 0.543
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.721
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-T-ps
- Phenotype
Gene ontology
- Biological process
- positive regulation of antibody-dependent cellular cytotoxicity;positive regulation of T cell mediated cytotoxicity;adaptive immune response;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;natural killer cell tolerance induction;regulation of natural killer cell mediated immunity;positive regulation of natural killer cell mediated immunity;positive regulation of natural killer cell cytokine production;immune response;antibacterial humoral response;positive regulation of interleukin-13 production;positive regulation of interleukin-4 production;positive regulation of TRAIL production;positive regulation of tumor necrosis factor production;positive regulation of natural killer cell proliferation;CD8-positive, alpha-beta T cell activation;protection from natural killer cell mediated cytotoxicity;innate immune response;negative regulation of natural killer cell mediated cytotoxicity;positive regulation of natural killer cell mediated cytotoxicity;regulation of immune response;defense response to Gram-positive bacterium;positive regulation of immunoglobulin secretion;interferon-gamma-mediated signaling pathway;type I interferon signaling pathway;positive regulation of CD8-positive, alpha-beta T cell proliferation;positive regulation of CD8-positive, alpha-beta T cell activation
- Cellular component
- Golgi membrane;extracellular space;plasma membrane;external side of plasma membrane;cell surface;ER to Golgi transport vesicle membrane;phagocytic vesicle membrane;early endosome membrane;MHC class Ib protein complex;MHC class I protein complex;recycling endosome membrane;extracellular exosome;integral component of lumenal side of endoplasmic reticulum membrane
- Molecular function
- signaling receptor binding;protein binding;beta-2-microglobulin binding;MHC class I protein binding;peptide antigen binding;T cell receptor binding;natural killer cell lectin-like receptor binding