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PTPRF (protein tyrosine phosphatase, receptor type F)

Identity

Alias_namesLAR
Other aliasBNAH2
HGNC (Hugo) PTPRF
LocusID (NCBI) 5792
Atlas_Id 41929
Location 1p34.2  [Link to chromosome band 1p34]
Location_base_pair Starts at 43530860 and ends at 43623672 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)
CHD3 (17p13.1) / PTPRF (1p34.2)EGFR (7p11.2) / PTPRF (1p34.2)KDM4A (1p34.1) / PTPRF (1p34.2)
PSMC2 (7q22.1) / PTPRF (1p34.2)PTPRF (1p34.2) / B4GALT2 (1p34.1)PTPRF (1p34.2) / CFAP74 (1p36.33)
PTPRF (1p34.2) / GUCA2A (1p34.2)PTPRF (1p34.2) / HIVEP3 (1p34.2)PTPRF (1p34.2) / METTL16 (17p13.3)
PTPRF (1p34.2) / PDE4B (1p31.3)PTPRF (1p34.2) / PTPRF (1p34.2)PTPRF (1p34.2) / RPS6KA3 (Xp22.12)
SREBF1 (17p11.2) / PTPRF (1p34.2)KDM4A 1p34.1 / PTPRF 1p34.2PTPRF 1p34.2 C1orf222
PTPRF 1p34.2 / GUCA2A 1p34.2PTPRF 1p34.2 / HIVEP3 1p34.2PTPRF 1p34.2 / PDE4B 1p31.3

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) [ 7 ]
  t(1;1)(p31;p34) PTPRF/PDE4B
KDM4A/PTPRF (1p34)
PTPRF/GUCA2A (1p34)
PTPRF/HIVEP3 (1p34)
t(1;1)(p34;p36) PTPRF/CFAP74
t(1;17)(p34;p13) PTPRF/METTL16
t(X;1)(p22;p34) PTPRF/RPS6KA3


External links

Nomenclature
HGNC (Hugo)PTPRF   9670
Cards
Entrez_Gene (NCBI)PTPRF  5792  protein tyrosine phosphatase, receptor type F
AliasesBNAH2; LAR
GeneCards (Weizmann)PTPRF
Ensembl hg19 (Hinxton)ENSG00000142949 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000142949 [Gene_View]  ENSG00000142949 [Sequence]  chr1:43530860-43623672 [Contig_View]  PTPRF [Vega]
ICGC DataPortalENSG00000142949
TCGA cBioPortalPTPRF
AceView (NCBI)PTPRF
Genatlas (Paris)PTPRF
WikiGenes5792
SOURCE (Princeton)PTPRF
Genetics Home Reference (NIH)PTPRF
Genomic and cartography
GoldenPath hg38 (UCSC)PTPRF  -     chr1:43530860-43623672 +  1p34.2   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)PTPRF  -     1p34.2   [Description]    (hg19-Feb_2009)
EnsemblPTPRF - 1p34.2 [CytoView hg19]  PTPRF - 1p34.2 [CytoView hg38]
Mapping of homologs : NCBIPTPRF [Mapview hg19]  PTPRF [Mapview hg38]
OMIM179590   616001   
Gene and transcription
Genbank (Entrez)AB177856 AB177857 AB209478 AB621807 AK023775
RefSeq transcript (Entrez)NM_001329137 NM_001329138 NM_001329139 NM_001329140 NM_002840 NM_130440
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)PTPRF
Cluster EST : UnigeneHs.272062 [ NCBI ]
CGAP (NCI)Hs.272062
Alternative Splicing GalleryENSG00000142949
Gene ExpressionPTPRF [ NCBI-GEO ]   PTPRF [ EBI - ARRAY_EXPRESS ]   PTPRF [ SEEK ]   PTPRF [ MEM ]
Gene Expression Viewer (FireBrowse)PTPRF [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevestigatorExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)5792
GTEX Portal (Tissue expression)PTPRF
Human Protein AtlasENSG00000142949-PTPRF [pathology]   [cell]   [tissue]
Protein : pattern, domain, 3D structure
UniProt/SwissProtP10586   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtP10586  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProP10586
Splice isoforms : SwissVarP10586
Catalytic activity : Enzyme3.1.3.48 [ Enzyme-Expasy ]   3.1.3.483.1.3.48 [ IntEnz-EBI ]   3.1.3.48 [ BRENDA ]   3.1.3.48 [ KEGG ]   
PhosPhoSitePlusP10586
Domaine pattern : Prosite (Expaxy)FN3 (PS50853)    IG_LIKE (PS50835)    TYR_PHOSPHATASE_1 (PS00383)    TYR_PHOSPHATASE_2 (PS50056)    TYR_PHOSPHATASE_PTP (PS50055)   
Domains : Interpro (EBI)FN3_dom    FN3_sf    Ig-like_dom    Ig-like_dom_sf    Ig-like_fold    Ig_I-set    Ig_sub    Ig_sub2    Prot-tyrosine_phosphatase-like    PTPase_domain    Tyr_Pase_AS    Tyr_Pase_cat    TYR_PHOSPHATASE_dom   
Domain families : Pfam (Sanger)fn3 (PF00041)    I-set (PF07679)    Y_phosphatase (PF00102)   
Domain families : Pfam (NCBI)pfam00041    pfam07679    pfam00102   
Domain families : Smart (EMBL)FN3 (SM00060)  IG (SM00409)  IGc2 (SM00408)  PTPc (SM00194)  PTPc_motif (SM00404)  
Conserved Domain (NCBI)PTPRF
DMDM Disease mutations5792
Blocks (Seattle)PTPRF
PDB (SRS)1LAR    2DJU    2DN7    2EDX    2EDY    2YD5    2YD8    4N5U   
PDB (PDBSum)1LAR    2DJU    2DN7    2EDX    2EDY    2YD5    2YD8    4N5U   
PDB (IMB)1LAR    2DJU    2DN7    2EDX    2EDY    2YD5    2YD8    4N5U   
PDB (RSDB)1LAR    2DJU    2DN7    2EDX    2EDY    2YD5    2YD8    4N5U   
Structural Biology KnowledgeBase1LAR    2DJU    2DN7    2EDX    2EDY    2YD5    2YD8    4N5U   
SCOP (Structural Classification of Proteins)1LAR    2DJU    2DN7    2EDX    2EDY    2YD5    2YD8    4N5U   
CATH (Classification of proteins structures)1LAR    2DJU    2DN7    2EDX    2EDY    2YD5    2YD8    4N5U   
SuperfamilyP10586
Human Protein Atlas [tissue]ENSG00000142949-PTPRF [tissue]
Peptide AtlasP10586
HPRD01552
IPIIPI00107831   IPI00465186   IPI00853550   IPI00853169   IPI00384626   IPI00655814   IPI00480183   IPI01019036   
Protein Interaction databases
DIP (DOE-UCLA)P10586
IntAct (EBI)P10586
FunCoupENSG00000142949
BioGRIDPTPRF
STRING (EMBL)PTPRF
ZODIACPTPRF
Ontologies - Pathways
QuickGOP10586
Ontology : AmiGOprotein tyrosine phosphatase activity  protein tyrosine phosphatase activity  transmembrane receptor protein tyrosine phosphatase activity  plasma membrane  integral component of plasma membrane  cell adhesion  transmembrane receptor protein tyrosine phosphatase signaling pathway  heparin binding  cell migration  neuron projection regeneration  peptidyl-tyrosine dephosphorylation  chondroitin sulfate proteoglycan binding  neuron projection  neuronal cell body  protein-containing complex binding  regulation of axon regeneration  cell adhesion molecule binding  extracellular exosome  negative regulation of receptor binding  
Ontology : EGO-EBIprotein tyrosine phosphatase activity  protein tyrosine phosphatase activity  transmembrane receptor protein tyrosine phosphatase activity  plasma membrane  integral component of plasma membrane  cell adhesion  transmembrane receptor protein tyrosine phosphatase signaling pathway  heparin binding  cell migration  neuron projection regeneration  peptidyl-tyrosine dephosphorylation  chondroitin sulfate proteoglycan binding  neuron projection  neuronal cell body  protein-containing complex binding  regulation of axon regeneration  cell adhesion molecule binding  extracellular exosome  negative regulation of receptor binding  
Pathways : KEGGCell adhesion molecules (CAMs)    Adherens junction    Insulin signaling pathway   
NDEx NetworkPTPRF
Atlas of Cancer Signalling NetworkPTPRF
Wikipedia pathwaysPTPRF
Orthology - Evolution
OrthoDB5792
GeneTree (enSembl)ENSG00000142949
Phylogenetic Trees/Animal Genes : TreeFamPTPRF
HOVERGENP10586
HOGENOMP10586
Homologs : HomoloGenePTPRF
Homology/Alignments : Family Browser (UCSC)PTPRF
Gene fusions - Rearrangements
Fusion : MitelmanKDM4A/PTPRF [1p34.1/1p34.2]  [t(1;1)(p34;p34)]  
Fusion : MitelmanPTPRF/CFAP74 [1p34.2/1p36.33]  [t(1;1)(p34;p36)]  
Fusion : MitelmanPTPRF/GUCA2A [1p34.2/1p34.2]  [t(1;1)(p34;p34)]  
Fusion : MitelmanPTPRF/HIVEP3 [1p34.2/1p34.2]  [t(1;1)(p34;p34)]  
Fusion : MitelmanPTPRF/METTL16 [1p34.2/17p13.3]  [t(1;17)(p34;p13)]  
Fusion : MitelmanPTPRF/PDE4B [1p34.2/1p31.3]  [t(1;1)(p31;p34)]  
Fusion : MitelmanPTPRF/RPS6KA3 [1p34.2/Xp22.12]  [t(X;1)(p22;p34)]  
Fusion PortalKDM4A 1p34.1 PTPRF 1p34.2 BRCA
Fusion PortalPTPRF 1p34.2 C1orf222 SKCM
Fusion PortalPTPRF 1p34.2 GUCA2A 1p34.2 BRCA
Fusion PortalPTPRF 1p34.2 HIVEP3 1p34.2 BRCA
Fusion PortalPTPRF 1p34.2 PDE4B 1p31.3 BRCA
Fusion : QuiverPTPRF
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerPTPRF [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)PTPRF
dbVarPTPRF
ClinVarPTPRF
1000_GenomesPTPRF 
Exome Variant ServerPTPRF
ExAC (Exome Aggregation Consortium)ENSG00000142949
GNOMAD BrowserENSG00000142949
Varsome BrowserPTPRF
Genetic variants : HAPMAP5792
Genomic Variants (DGV)PTPRF [DGVbeta]
DECIPHERPTPRF [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisPTPRF 
Mutations
ICGC Data PortalPTPRF 
TCGA Data PortalPTPRF 
Broad Tumor PortalPTPRF
OASIS PortalPTPRF [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICPTPRF  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDPTPRF
intOGen PortalPTPRF
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 PTPRF
DgiDB (Drug Gene Interaction Database)PTPRF
DoCM (Curated mutations)PTPRF (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)PTPRF (select a term)
intoGenPTPRF
Cancer3DPTPRF(select the gene name)
Impact of mutations[PolyPhen2] [Provean] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM179590    616001   
Orphanet18113   
DisGeNETPTPRF
MedgenPTPRF
Genetic Testing Registry PTPRF
NextProtP10586 [Medical]
TSGene5792
GENETestsPTPRF
Target ValidationPTPRF
Huge Navigator PTPRF [HugePedia]
snp3D : Map Gene to Disease5792
BioCentury BCIQPTPRF
ClinGenPTPRF
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD5792
Chemical/Pharm GKB GenePA34015
Clinical trialPTPRF
Miscellaneous
canSAR (ICR)PTPRF (select the gene name)
Probes
Litterature
PubMed80 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMinePTPRF
EVEXPTPRF
GoPubMedPTPRF
iHOPPTPRF
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

Search in all EBI   NCBI

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indexed on : Mon Aug 27 11:47:15 CEST 2018

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