Gene Gene information from NCBI Gene database. Download as csv Download as pdf
Entrez ID	3134
Gene name	Major histocompatibility complex, class I, F
Gene symbol	HLA-F
Synonyms (NCBI Gene)	CDA12HLA-5.4HLA-CDA12HLAF
Chromosome	6
Chromosome location	6p22.1
Summary	This gene belongs to the HLA class I heavy chain paralogues. It encodes a non-classical heavy chain that forms a heterodimer with a beta-2 microglobulin light chain, with the heavy chain anchored in the membrane. Unlike most other HLA heavy chains, this m

19 Show/Hide all (19)

miRTarBase ID	miRNA	Experiments	Reference
MIRT438041	hsa-miR-324-3p	qRT-PCR	24367666
MIRT438038	hsa-miR-93-5p	qRT-PCR	24367666
MIRT438041	hsa-miR-324-3p	qRT-PCR	24367666
MIRT438038	hsa-miR-93-5p	qRT-PCR	24367666
MIRT1048556	hsa-miR-130a	CLIP-seq
MIRT1048557	hsa-miR-130b	CLIP-seq
MIRT1048558	hsa-miR-1827	CLIP-seq
MIRT1048559	hsa-miR-221	CLIP-seq
MIRT1048560	hsa-miR-222	CLIP-seq
MIRT1048561	hsa-miR-301a	CLIP-seq
MIRT1048562	hsa-miR-301b	CLIP-seq
MIRT1048563	hsa-miR-3666	CLIP-seq
MIRT1048564	hsa-miR-4295	CLIP-seq
MIRT1048565	hsa-miR-4316	CLIP-seq
MIRT1048566	hsa-miR-454	CLIP-seq
MIRT1048567	hsa-miR-519a	CLIP-seq
MIRT1048568	hsa-miR-519b-3p	CLIP-seq
MIRT1048569	hsa-miR-519c-3p	CLIP-seq
MIRT1048570	hsa-miR-548v	CLIP-seq

6 Show/Hide all (6)

Transcription factor	Regulation	Reference
CIITA	Unknown	11137213
HIVEP2	Unknown	1409593
MYC	Activation	8206526
MYCN	Unknown	8895520
NFKB1	Unknown	11137213;9725221
RELA	Unknown	11137213

52 Show/Hide all (52)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000139	Component	Golgi membrane	IDA	16709803
GO:0000139	Component	Golgi membrane	IEA
GO:0000139	Component	Golgi membrane	TAS
GO:0001916	Process	Positive regulation of T cell mediated cytotoxicity	IBA
GO:0001916	Process	Positive regulation of T cell mediated cytotoxicity	IMP	23851683
GO:0002376	Process	Immune system process	IEA
GO:0002474	Process	Antigen processing and presentation of peptide antigen via MHC class I	IEA
GO:0002476	Process	Antigen processing and presentation of endogenous peptide antigen via MHC class Ib	IBA
GO:0002476	Process	Antigen processing and presentation of endogenous peptide antigen via MHC class Ib	IDA	28636952
GO:0002477	Process	Antigen processing and presentation of exogenous peptide antigen via MHC class Ib	IDA	23851683
GO:0002486	Process	Antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent	IBA
GO:0002725	Process	Negative regulation of T cell cytokine production	IDA	24018270
GO:0002728	Process	Negative regulation of natural killer cell cytokine production	IDA	24018270
GO:0002729	Process	Positive regulation of natural killer cell cytokine production	IDA	27455421
GO:0005102	Function	Signaling receptor binding	IBA
GO:0005515	Function	Protein binding	IPI	10605026, 11169396, 20483783, 24018270, 27455421, 27649529, 28636952, 33961781
GO:0005615	Component	Extracellular space	IBA
GO:0005764	Component	Lysosome	IEA
GO:0005765	Component	Lysosomal membrane	IDA	23851683
GO:0005765	Component	Lysosomal membrane	IEA
GO:0005768	Component	Endosome	IEA
GO:0005783	Component	Endoplasmic reticulum	IDA	10605026
GO:0005886	Component	Plasma membrane	IDA	16709803, 23851683, 27455421
GO:0005886	Component	Plasma membrane	IEA
GO:0005886	Component	Plasma membrane	TAS
GO:0006955	Process	Immune response	IBA
GO:0009897	Component	External side of plasma membrane	IBA
GO:0009986	Component	Cell surface	IDA	20865824
GO:0012507	Component	ER to Golgi transport vesicle membrane	IEA
GO:0012507	Component	ER to Golgi transport vesicle membrane	TAS
GO:0016020	Component	Membrane	HDA	19946888
GO:0016020	Component	Membrane	IEA
GO:0030670	Component	Phagocytic vesicle membrane	IEA
GO:0030670	Component	Phagocytic vesicle membrane	TAS
GO:0030881	Function	Beta-2-microglobulin binding	IDA	28636952
GO:0031901	Component	Early endosome membrane	IDA	23851683
GO:0031901	Component	Early endosome membrane	IEA
GO:0031901	Component	Early endosome membrane	TAS
GO:0032398	Component	MHC class Ib protein complex	IDA	28636952
GO:0042605	Function	Peptide antigen binding	IBA
GO:0042605	Function	Peptide antigen binding	IDA	23851683, 28636952
GO:0042612	Component	MHC class I protein complex	IEA
GO:0043322	Process	Negative regulation of natural killer cell degranulation	IDA	24018270
GO:0043323	Process	Positive regulation of natural killer cell degranulation	IDA	27455421
GO:0045953	Process	Negative regulation of natural killer cell mediated cytotoxicity	IDA	24018270
GO:0046978	Function	TAP1 binding	IPI	10605026
GO:0046979	Function	TAP2 binding	IPI	10605026
GO:0055038	Component	Recycling endosome membrane	IEA
GO:0055038	Component	Recycling endosome membrane	TAS
GO:0071889	Function	14-3-3 protein binding	IDA	16709803
GO:0098553	Component	Lumenal side of endoplasmic reticulum membrane	IEA
GO:0098553	Component	Lumenal side of endoplasmic reticulum membrane	TAS

MIM	HGNC	e!Ensembl
143110	4963	ENSG00000204642

P30511

Protein name

HLA class I histocompatibility antigen, alpha chain F (CDA12) (HLA F antigen) (Leukocyte antigen F) (MHC class I antigen F)

Protein function

Non-classical major histocompatibility class Ib molecule postulated to play a role in immune surveillance, immune tolerance and inflammation. Functions in two forms, as a heterotrimeric complex with B2M/beta-2 microglobulin and a peptide (peptid

PDB

5IUE , 5KNM

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF00129	MHC_I	22 → 200	Class I Histocompatibility antigen, domains alpha 1 and 2	Domain
PF07654	C1-set	208 → 287	Immunoglobulin C1-set domain	Domain

Tissue specificity

TISSUE SPECIFICITY: Expressed in resting B cells (at protein level). Expressed in secondary lymphoid organs rich in B and T cells such as the tonsils, spleen, and thymus (at protein level) (PubMed:10605026, PubMed:11169396). Expressed in the endothelial c

Sequence

MAPRSLLLLLSGALALTDTWAGSHSLRYFSTAVSRPGRGEPRYIAVEYVDDTQFLRFDSD
AAIPRMEPREPWVEQEGPQYWEWTTGYAKANAQTDRVALRNLLRRYNQSEAGSHTLQGMN
GCDMGPDGRLLRGYHQHAYDGKDYISLNEDLRSWTAADTVAQITQRFYEAEEYAEEFRTY
LEGECLELLRRYLENGKETLQRADPPKAHVAHHPISDHEATLRCWALGFYPAEITLTWQR
DGEEQTQDTELVETRPAGDGTFQKWAAVVVPPGEEQRYTCHVQHEGLPQPLILRWEQSPQ
PTIPIVGIVAGLVVLGAVVTGAVVAAVMWRKKSSDRNRGSYSQAAV

Sequence length

346

Interactions

View interactions

KEGG Pathway	Reactome Pathway
Endocytosis	ER-Phagosome pathway
Phagosome	Endosomal/Vacuolar pathway
Cellular senescence	Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell
Cell adhesion molecules	Interferon gamma signaling
Antigen processing and presentation	Interferon alpha/beta signaling
Type I diabetes mellitus	Antigen Presentation: Folding, assembly and peptide loading of class I MHC
Human cytomegalovirus infection
Human papillomavirus infection
Human T-cell leukemia virus 1 infection
Kaposi sarcoma-associated herpesvirus infection
Herpes simplex virus 1 infection
Epstein-Barr virus infection
Human immunodeficiency virus 1 infection
Viral carcinogenesis
Autoimmune thyroid disease
Allograft rejection
Graft-versus-host disease
Viral myocarditis

Evidence Score: ★☆☆☆☆ Gene-disease association found in Text Mining only ★★☆☆☆ Found in Text Mining and Unknown/Other Associations ★★★☆☆ Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆ ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★ ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Phenotype Name	Clinical Significance	Source	Reference	Evidence Score
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal. Show/Hide Unknown Diseases (13)
COLORECTAL CANCER	—	GWAS catalog	29228715	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
GASTRIC CANCER	—	GWAS catalog	33002439	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
GASTRIC CARCINOMA	—	GWAS catalog	33002439	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
GOUT	—	GWAS catalog	33356394	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
HYPOTHYROIDISM	—	GWAS catalog	38368726	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
LYMPHEDEMA	—	GWAS catalog	37146673	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MULTIPLE SCLEROSIS	—	GWAS catalog	19525953	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PROSTATE CARCINOMA	—	GWAS catalog	22219177	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PSORIASIS	—	GWAS catalog	39885523	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PSORIATIC ARTHRITIS	—	GWAS catalog	30552173	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
RHEUMATOID ARTHRITIS	—	GWAS catalog	36762574, 38368726	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
STEVENS-JOHNSON SYNDROME	—	GWAS catalog	33574277	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
TOXIC EPIDERMAL NECROLYSIS	—	GWAS catalog	33574277	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Disease Name	Disease (Merged)	Source	PMID	Evidence Score
Associations from Text Mining Disease associations identified through text mining Show/Hide Text Mining Associations (36)
Adenocarcinoma of large intestine	Colorectal Cancer	GWASCAT_DG	29228715	★★★★★ ★☆☆☆☆ Found in Text Mining only
Amyotrophic Lateral Sclerosis	Amyotrophic Lateral Sclerosis	BEFREE	26928464	★★★★★ ★☆☆☆☆ Found in Text Mining only
Arthritis, Psoriatic	Psoriatic Arthritis	GWASCAT_DG	30552173	★★★★★ ★☆☆☆☆ Found in Text Mining only
Autoimmune Diseases	Autoimmune Diseases	BEFREE	31134067	★★★★★ ★☆☆☆☆ Found in Text Mining only
Avellino corneal dystrophy	Avellino Corneal Dystrophy	BEFREE	19622345	★★★★★ ★☆☆☆☆ Found in Text Mining only
Behcet Syndrome	Behcet Syndrome	BEFREE	24821759	★★★★★ ★☆☆☆☆ Found in Text Mining only
Bladder Neoplasm	Bladder Neoplasm	BEFREE	29749526	★★★★★ ★☆☆☆☆ Found in Text Mining only
Carcinoma of bladder	Bladder carcinoma	BEFREE	29749526	★★★★★ ★☆☆☆☆ Found in Text Mining only
Colorectal Carcinoma	Colorectal Cancer	GWASCAT_DG	29228715	★★★★★ ★☆☆☆☆ Found in Text Mining only
Colorectal Carcinoma	Colorectal Cancer	BEFREE	30984346	★★★★★ ★☆☆☆☆ Found in Text Mining only
Colorectal Neoplasms	Colorectal Neoplasms	GWASCAT_DG	29228715	★★★★★ ★☆☆☆☆ Found in Text Mining only
Coronary Artery Disease	Coronary artery disease	BEFREE	26780503	★★★★★ ★☆☆☆☆ Found in Text Mining only
Glioblastoma	Glioblastoma	BEFREE	30755240	★★★★★ ★☆☆☆☆ Found in Text Mining only
Glioblastoma Multiforme	Glioblastoma	BEFREE	30755240	★★★★★ ★☆☆☆☆ Found in Text Mining only
Glioma	Glioma	BEFREE	30755240	★★★★★ ★☆☆☆☆ Found in Text Mining only
Hemochromatosis	Hemochromatosis	BEFREE	7847378	★★★★★ ★☆☆☆☆ Found in Text Mining only
HEMOCHROMATOSIS, TYPE 1	Hemochromatosis	BEFREE	7847378, 9032645	★★★★★ ★☆☆☆☆ Found in Text Mining only
Hereditary hemochromatosis	Hereditary Hemochromatosis	BEFREE	8518796	★★★★★ ★☆☆☆☆ Found in Text Mining only
Idiopathic generalized epilepsy	Epilepsy	BEFREE	10402495	★★★★★ ★☆☆☆☆ Found in Text Mining only
Juvenile Myoclonic Epilepsy	Myoclonic Epilepsy	BEFREE	9933300	★★★★★ ★☆☆☆☆ Found in Text Mining only
Liver carcinoma	Liver carcinoma	BEFREE	22015712, 29790184	★★★★★ ★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of large intestine	Colorectal Neoplasms	GWASCAT_DG	29228715	★★★★★ ★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of stomach	Stomach Neoplasms	BEFREE	23542057, 25862890	★★★★★ ★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of urinary bladder	Urinary bladder cancer	BEFREE	29749526	★★★★★ ★☆☆☆☆ Found in Text Mining only
Malignant Neoplasms	Malignant Neoplasm	BEFREE	15515436, 16455204, 29749526, 30031767	★★★★★ ★☆☆☆☆ Found in Text Mining only
Malignant tumor of colon	Colonic Neoplasms	GWASCAT_DG	29228715	★★★★★ ★☆☆☆☆ Found in Text Mining only
melanoma	Melanoma	BEFREE	7989117	★★★★★ ★☆☆☆☆ Found in Text Mining only
Multiple Sclerosis	Multiple Sclerosis	GWASDB_DG	17660530, 19525953	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Multiple Sclerosis	Multiple Sclerosis	GWASCAT_DG	19525953	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Narcolepsy	Narcolepsy	GWASDB_DG	19629137	★★★★★ ★☆☆☆☆ Found in Text Mining only
Nasopharyngeal carcinoma	Nasopharyngeal Carcinoma	BEFREE	19664746	★★★★★ ★☆☆☆☆ Found in Text Mining only
Neoplasms	Neoplasms	BEFREE	22544725	★★★★★ ★☆☆☆☆ Found in Text Mining only
Squamous cell carcinoma of esophagus	Esophagus Neoplasm	BEFREE	22544725	★★★★★ ★☆☆☆☆ Found in Text Mining only
Stomach Carcinoma	Stomach Carcinoma	BEFREE	23542057, 25862890	★★★★★ ★☆☆☆☆ Found in Text Mining only
Vitiligo	Vitiligo	BEFREE	21847675	★★★★★ ★☆☆☆☆ Found in Text Mining only
VITILIGO-ASSOCIATED MULTIPLE AUTOIMMUNE DISEASE SUSCEPTIBILITY 1 (finding)	Vitiligo-associated SYSTEMIC LUPUS ERYTHEMATOSUS	BEFREE	21847675	★★★★★ ★☆☆☆☆ Found in Text Mining only

Related Gene	Shared Diseases	Shared Disease Names	Shared Pathways	Shared Pathway Names	Shared Evidence Sources	Shared Evidence Names
HLA-C	4	["Psoriatic arthritis","Gastric cancer","Stevens-johnson syndrome","Toxic epidermal necrolysis"]	23	["Endocytosis","Phagosome","Cellular senescence","Cell adhesion molecules","Antigen processing and presentation","Type I diabetes mellitus","Human cytomegalovirus infection","Human T-cell leukemia virus 1 infection","Kaposi sarcoma-associated herpesvirus infection","Herpes simplex virus 1 infection","Epstein-Barr virus infection","Human immunodeficiency virus 1 infection"]	4	["GWAS catalog (Gastric cancer)","GWAS catalog (Psoriatic arthritis)","GWAS catalog (Stevens-johnson syndrome)","GWAS catalog (Toxic epidermal necrolysis)"]
NIPAL2	2	["Stevens-johnson syndrome","Toxic epidermal necrolysis"]	0	[]	2	["GWAS catalog (Stevens-johnson syndrome)","GWAS catalog (Toxic epidermal necrolysis)"]
SELENOK	2	["Stevens-johnson syndrome","Toxic epidermal necrolysis"]	0	[]	2	["GWAS catalog (Stevens-johnson syndrome)","GWAS catalog (Toxic epidermal necrolysis)"]
ZC3H12D	2	["Stevens-johnson syndrome","Toxic epidermal necrolysis"]	0	[]	2	["GWAS catalog (Stevens-johnson syndrome)","GWAS catalog (Toxic epidermal necrolysis)"]
HLA-B	4	["Psoriatic arthritis","Gastric cancer","Stevens-johnson syndrome","Toxic epidermal necrolysis"]	23	["Endocytosis","Phagosome","Cellular senescence","Cell adhesion molecules","Antigen processing and presentation","Type I diabetes mellitus","Human cytomegalovirus infection","Human T-cell leukemia virus 1 infection","Kaposi sarcoma-associated herpesvirus infection","Herpes simplex virus 1 infection","Epstein-Barr virus infection","Human immunodeficiency virus 1 infection"]	2	["GWAS catalog (Gastric cancer)","GWAS catalog (Psoriatic arthritis)"]

HLA-F (major histocompatibility complex, class I, F)

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