HLA-F
major histocompatibility complex, class I, F, the group of C1-set domain containing|Histocompatibility complex
Basic information
Region (hg38): 6:29722775-29738528
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-F 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 | 2 | |||||
| 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 | 2 | 0 |
Variants in HLA-F
This is a list of pathogenic ClinVar variants found in the HLA-F region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 6-29725272-C-T | Likely benign (Nov 01, 2023) | |||
| 6-29725284-C-G | Likely benign (Nov 01, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| HLA-F | protein_coding | protein_coding | ENST00000259951 | 7 | 15754 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0000328 | 0.947 | 125597 | 0 | 151 | 125748 | 0.000601 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.10 | 207 | 257 | 0.806 | 0.0000137 | 2847 |
| Missense in Polyphen | 73 | 93.332 | 0.78216 | 1014 | ||
| Synonymous | 0.369 | 101 | 106 | 0.954 | 0.00000592 | 886 |
| Loss of Function | 1.78 | 10 | 18.2 | 0.550 | 7.91e-7 | 191 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000548 | 0.000485 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00684 | 0.00682 |
| Finnish | 0.0000464 | 0.0000462 |
| European (Non-Finnish) | 0.0000914 | 0.0000879 |
| Middle Eastern | 0.00684 | 0.00682 |
| South Asian | 0.000100 | 0.0000980 |
| Other | 0.000332 | 0.000326 |
dbNSFP
Source:
- Function
- FUNCTION: Involved in the presentation of foreign antigens to the immune system.;
- 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);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
- 0.947
- rvis_EVS
- 1.39
- rvis_percentile_EVS
- 94.67
Haploinsufficiency Scores
- pHI
- 0.0980
- hipred
- N
- hipred_score
- 0.227
- ghis
- 0.515
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.803
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Gm7030
- Phenotype
Gene ontology
- Biological process
- positive regulation of T cell mediated cytotoxicity;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;immune response;regulation of immune response;interferon-gamma-mediated signaling pathway;type I interferon signaling pathway
- Cellular component
- Golgi membrane;extracellular space;endoplasmic reticulum;plasma membrane;external side of plasma membrane;cell surface;ER to Golgi transport vesicle membrane;membrane;phagocytic vesicle membrane;early endosome 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;TAP1 binding;TAP2 binding