Atlas of Genetics and Cytogenetics in Oncology and Haematology


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

Identity

Other aliasCDA12
HLA-5.4
HLA-CDA12
HLAF
HGNC (Hugo) HLA-F
LocusID (NCBI) 3134
Atlas_Id 53636
Location 6p22.1  [Link to chromosome band 6p22]
Location_base_pair Starts at 29723340 and ends at 29726526 bp from pter ( according to hg38-Dec_2013)
Fusion genes
(updated 2017)
Data from Atlas, Mitelman, Cosmic Fusion, Fusion Cancer, TCGA fusion databases with official HUGO symbols (see references in chromosomal bands)
AP1G2 (14q11.2) / HLA-F (6p22.1)GSN (9q33.2) / HLA-F (6p22.1)HLA-F (6p22.1) / CD300LB (17q25.1)
HLA-F (6p22.1) / COL1A1 (17q21.33)HLA-F (6p22.1) / MEF2C (5q14.3)HLA-L (6p22.1) / HLA-F (6p22.1)
GSN 9q33.2 / HLA-F 6p22.1

Note

Non-annotated gene. Preliminary data : if you are an author
who wish to write a full paper/card on this gene, go to  How to contribute

DNA/RNA

 


Other Solid tumors implicated (Data extracted from papers in the Atlas) [ 1 ]
  t(6;9)(p22;q33) GSN/HLA-F


External links

Nomenclature
HGNC (Hugo)HLA-F   4963
Cards
Entrez_Gene (NCBI)HLA-F  3134  major histocompatibility complex, class I, F
AliasesCDA12; HLA-5.4; HLA-CDA12; HLAF
GeneCards (Weizmann)HLA-F
Ensembl hg19 (Hinxton)ENSG00000204642 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000204642 [Gene_View]  ENSG00000204642 [Sequence]  chr6:29723340-29726526 [Contig_View]  HLA-F [Vega]
ICGC DataPortalENSG00000204642
TCGA cBioPortalHLA-F
AceView (NCBI)HLA-F
Genatlas (Paris)HLA-F
WikiGenes3134
SOURCE (Princeton)HLA-F
Genetics Home Reference (NIH)HLA-F
Genomic and cartography
GoldenPath hg38 (UCSC)HLA-F  -     chr6:29723340-29726526 +  6p22.1   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)HLA-F  -     6p22.1   [Description]    (hg19-Feb_2009)
EnsemblHLA-F - 6p22.1 [CytoView hg19]  HLA-F - 6p22.1 [CytoView hg38]
Mapping of homologs : NCBIHLA-F [Mapview hg19]  HLA-F [Mapview hg38]
OMIM143110   
Gene and transcription
Genbank (Entrez)AK096962 AK125274 AK225185 AK298704 AK300090
RefSeq transcript (Entrez)NM_001098478 NM_001098479 NM_018950
RefSeq genomic (Entrez)NC_000006 NG_012009 NT_113891 NT_167245 NT_167246 NT_167247 NT_167248 NT_167249
Consensus coding sequences : CCDS (NCBI)HLA-F
Cluster EST : UnigeneHs.519972 [ NCBI ]
CGAP (NCI)Hs.519972
Alternative Splicing GalleryENSG00000204642
Gene ExpressionHLA-F [ NCBI-GEO ]   HLA-F [ EBI - ARRAY_EXPRESS ]   HLA-F [ SEEK ]   HLA-F [ MEM ]
Gene Expression Viewer (FireBrowse)HLA-F [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevestigatorExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)3134
GTEX Portal (Tissue expression)HLA-F
Human Protein AtlasENSG00000204642-HLA-F [pathology]   [cell]   [tissue]
Protein : pattern, domain, 3D structure
UniProt/SwissProtP30511   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtP30511  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProP30511
Splice isoforms : SwissVarP30511
PhosPhoSitePlusP30511
Domaine pattern : Prosite (Expaxy)IG_LIKE (PS50835)    IG_MHC (PS00290)   
Domains : Interpro (EBI)Ig-like_dom    Ig-like_dom_sf    Ig-like_fold    Ig/MHC_CS    Ig_C1-set    MHC_I-like_Ag-recog    MHC_I-like_Ag-recog_sf    MHC_I/II-like_Ag-recog    MHC_I_a_a1/a2   
Domain families : Pfam (Sanger)C1-set (PF07654)    MHC_I (PF00129)   
Domain families : Pfam (NCBI)pfam07654    pfam00129   
Domain families : Smart (EMBL)IGc1 (SM00407)  
Conserved Domain (NCBI)HLA-F
DMDM Disease mutations3134
Blocks (Seattle)HLA-F
PDB (SRS)5IUE    5KNM   
PDB (PDBSum)5IUE    5KNM   
PDB (IMB)5IUE    5KNM   
PDB (RSDB)5IUE    5KNM   
Structural Biology KnowledgeBase5IUE    5KNM   
SCOP (Structural Classification of Proteins)5IUE    5KNM   
CATH (Classification of proteins structures)5IUE    5KNM   
SuperfamilyP30511
Human Protein Atlas [tissue]ENSG00000204642-HLA-F [tissue]
Peptide AtlasP30511
HPRD00884
IPIIPI00936104   IPI00973471   IPI00980648   IPI00941498   IPI00909988   IPI00942068   IPI01020882   IPI01022363   IPI01018860   IPI01022027   IPI01021477   IPI00953287   IPI01021154   IPI00973577   IPI00871578   IPI00294547   IPI00658058   IPI00657681   IPI00657949   IPI00657742   IPI00893670   IPI00939439   IPI00893968   IPI00893546   IPI00853015   IPI00893656   
Protein Interaction databases
DIP (DOE-UCLA)P30511
IntAct (EBI)P30511
FunCoupENSG00000204642
BioGRIDHLA-F
STRING (EMBL)HLA-F
ZODIACHLA-F
Ontologies - Pathways
QuickGOP30511
Ontology : AmiGOGolgi membrane  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  signaling receptor binding  protein binding  endoplasmic reticulum  plasma membrane  plasma membrane  immune response  cell surface  ER to Golgi transport vesicle membrane  membrane  phagocytic vesicle membrane  early endosome membrane  peptide antigen binding  MHC class I protein complex  TAP1 binding  TAP2 binding  regulation of immune response  recycling endosome membrane  interferon-gamma-mediated signaling pathway  type I interferon signaling pathway  integral component of lumenal side of endoplasmic reticulum membrane  
Ontology : EGO-EBIGolgi membrane  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  signaling receptor binding  protein binding  endoplasmic reticulum  plasma membrane  plasma membrane  immune response  cell surface  ER to Golgi transport vesicle membrane  membrane  phagocytic vesicle membrane  early endosome membrane  peptide antigen binding  MHC class I protein complex  TAP1 binding  TAP2 binding  regulation of immune response  recycling endosome membrane  interferon-gamma-mediated signaling pathway  type I interferon signaling pathway  integral component of lumenal side of endoplasmic reticulum membrane  
Pathways : KEGGEndocytosis    Phagosome    Cell adhesion molecules (CAMs)    Antigen processing and presentation    Type I diabetes mellitus    HTLV-I infection    Herpes simplex infection    Epstein-Barr virus infection    Viral carcinogenesis    Autoimmune thyroid disease    Allograft rejection    Graft-versus-host disease    Viral myocarditis   
NDEx NetworkHLA-F
Atlas of Cancer Signalling NetworkHLA-F
Wikipedia pathwaysHLA-F
Orthology - Evolution
OrthoDB3134
GeneTree (enSembl)ENSG00000204642
Phylogenetic Trees/Animal Genes : TreeFamHLA-F
HOVERGENP30511
HOGENOMP30511
Homologs : HomoloGeneHLA-F
Homology/Alignments : Family Browser (UCSC)HLA-F
Gene fusions - Rearrangements
Fusion : MitelmanGSN/HLA-F [9q33.2/6p22.1]  [t(6;9)(p22;q33)]  
Fusion PortalGSN 9q33.2 HLA-F 6p22.1 LUAD
Fusion Cancer (Beijing)HLA-L [6p22.1]  -  HLA-F [6p22.1]  [FUSC000231]  [FUSC000231]  [FUSC000231]  [FUSC000231]  [FUSC000231]
Fusion : QuiverHLA-F
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerHLA-F [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)HLA-F
dbVarHLA-F
ClinVarHLA-F
1000_GenomesHLA-F 
Exome Variant ServerHLA-F
ExAC (Exome Aggregation Consortium)ENSG00000204642
GNOMAD BrowserENSG00000204642
Varsome BrowserHLA-F
Genetic variants : HAPMAP3134
Genomic Variants (DGV)HLA-F [DGVbeta]
DECIPHERHLA-F [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisHLA-F 
Mutations
ICGC Data PortalHLA-F 
TCGA Data PortalHLA-F 
Broad Tumor PortalHLA-F
OASIS PortalHLA-F [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICHLA-F  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDHLA-F
LOVD (Leiden Open Variation Database)Whole genome datasets
LOVD (Leiden Open Variation Database)LOVD - Leiden Open Variation Database
LOVD (Leiden Open Variation Database)LOVD 3.0 shared installation
BioMutasearch HLA-F
DgiDB (Drug Gene Interaction Database)HLA-F
DoCM (Curated mutations)HLA-F (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)HLA-F (select a term)
intoGenHLA-F
Cancer3DHLA-F(select the gene name)
Impact of mutations[PolyPhen2] [Provean] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM143110   
Orphanet
DisGeNETHLA-F
MedgenHLA-F
Genetic Testing Registry HLA-F
NextProtP30511 [Medical]
TSGene3134
GENETestsHLA-F
Target ValidationHLA-F
Huge Navigator HLA-F [HugePedia]
snp3D : Map Gene to Disease3134
BioCentury BCIQHLA-F
ClinGenHLA-F
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD3134
Chemical/Pharm GKB GenePA35082
Clinical trialHLA-F
Miscellaneous
canSAR (ICR)HLA-F (select the gene name)
Probes
Litterature
PubMed124 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineHLA-F
EVEXHLA-F
GoPubMedHLA-F
iHOPHLA-F
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

Search in all EBI   NCBI

© Atlas of Genetics and Cytogenetics in Oncology and Haematology
indexed on : Tue Nov 6 11:11:13 CET 2018

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