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PDGFRB (platelet-derived growth factor receptor, beta polypeptide)

Identity

Other namesBC032224
J03278
M21616
JTK12
PDGFR
CD140B
PDGFR1
PDGF-R-beta
HGNC (Hugo) PDGFRB
Location 5q31-q32
Location_base_pair Starts at 149493403 and ends at 149535422 bp from pter ( according to hg19-Feb_2009)  [Mapping]
Local_order MXI1 (MAX-interacting protein 1) is more telomeric. XPNPEP1 (X-prolylaminopeptidase 1) is more telomeric.
 
  Probe(s) - Courtesy Mariano Rocchi, Resources for Molecular Cytogenetics

DNA/RNA

 
  Genomic structure of PDGFRB. Black boxes indicate exons, small ones indicate untranslated exons.
Description 23 exons spanning 149.5 Mb on 5q31-q32. Transcription is from telomere to centromere.
Transcription 1 transcript in RefSeq encoding NP_002600. 1 transcript in EnsEMBL encoding ENSP00000261799.

Protein

Note PDGFRB; Beta platelet-derived growth factor receptor [Precursor]
 
  Schematic representation of PDGFRB. Ig-like domains: extracellular immunoglobulin-like domains involved in protein-ligand interaction, TM: transmembrane domain, Split-TK domain: RTK class III cytoplasmic kinase domain with an insertion of 70 to 100 hydrophilic residues.
Description Beta platelet-derived growth factor receptor precursor (PDGF-R-beta) (CD140b antigen).
Localisation Type I membrane protein.
Function is receptor that binds specifically to PDGFB and has a tyrosine-protein kinase activity. Is a cell surface tyrosine kinase receptor for members of the platelet-derived growth factor (PDGF) family. The PDGFR/PDGF system includes two receptors (PDGFRA and PDGFRB) and four ligands (, B, C and D). The receptors PDGFRA and PDGFRB are related in sequence and both are members of the class III subtype of receptor tyrosine kinases (RTKs). Other class III RTKs are CSF1R, KIT and FLT3. Mature PDGFRB consist of 1067 amino acids and can bind strongly to PDGF-BB and -DD homodimers, but weakly to AB heterodimers and not to PDGF-AA homodimer. The different ligands seem to induce different signals.
Homology PDGFRB presents homology in several species. It also belongs to GROWTH FACTOR RECEPTOR PRECURSOR EC_2.7.1.112 TYROSINE KINASE protein family.

Mutations

Germinal See SNPs at EnsEMBL (http://www.ensembl.org/Homo_sapiens/genesnpview?db=core&gene=ENSG00000113721).

Implicated in

Note Some rare gene fusions involving PDGFRB have been described in several patients with chronic myeloproliferative disorders (CMPD), myelodysplastic/myeloproliferative syndromes (MDS/MPD) and AML, often associated with eosinophilia and splenomegaly. Transformation to acute leukemia has been observed in a minor proportion of cases. Some of them respond to imatinib mesylate.
  
Entity t(1;5)(q23;q33)
Disease described in an 11 month old girl with myelodysplastic/myeloproliferative syndrome with eosinophilia
Prognosis bad
Cytogenetics t(1;5)(q23;q33)
Hybrid/Mutated Gene 5' PDE4DIP-PDGFRB 3'
Abnormal Protein PDE4DIP-PDGFRB
  
Entity t(1;3;5)(p36;p21;q33)
Note PDGFRB fusion partner unpublished. Translocation described in a patient with a chronic myeloproliferative disorder
Disease CMPD
Cytogenetics t(1;3;5)(p36;p21;q33)
Hybrid/Mutated Gene unidentified
Abnormal Protein unidentified.
  
Entity t(2;12;5)(q37;q22;q33)
Note PDGFRB fusion partner unpublished.
Disease Translocation described in a patient with a myelodysplastic syndrome
Cytogenetics t(2;12;5)(q37;q22;q33)
Hybrid/Mutated Gene unidentified.
Abnormal Protein unidentified.
  
Entity t(3;5)(p21;q31)
Note PDGFRB fusion partner unpublished.
Disease Translocation described in a patient with an atypical CML
Cytogenetics t(3;5)(p21;q31)
Hybrid/Mutated Gene unidentified.
Abnormal Protein unidentified.
  
Entity t(5;7)(q33;q11.2)
Disease Described in two patients with CMML/eosinophilia and CMML
Prognosis unknown.
Cytogenetics t(5;7)(q33;q11.2)
Hybrid/Mutated Gene 5' HIP1-PDGFRB 3'
Abnormal Protein HIP1-PDGFRB
  
Entity t(5;10)(q33;q22)
Disease Described in five cases with atypical CML.
Prognosis good, imatinib mesylate responsive disease.
Cytogenetics t(5;10)(q33;q22)
Hybrid/Mutated Gene 5' H4-PDGFRB 3'
Abnormal Protein H4-PDGFRB
  
Entity t(5;12)(q33;p13)
Disease Associated to atypical CML, AML, chronic myelomonocytic leukaemia (CMML), chronic eosinophilic leukaemia (CEL) or unclassified myeloproliferative disorders
Prognosis Good.
Cytogenetics t(5;12)(q33;p13)
Hybrid/Mutated Gene 5' ETV6-PDGFRB 3'
Abnormal Protein ETV6-PDGFRB
  
Entity t(5;14)(q33;q32)
Disease Described in a patient with AML and a t(7;11)(p15;p15) at initial diagnosis, who relapsed with a prominent eosinophilia, hepatosplenomegaly and t(5;14) as an additional cytogenetic abnormality.
Prognosis Good.
Cytogenetics t(5;14)(q33;q32)
Hybrid/Mutated Gene 5' TRIP11-PDGFRB 3'
Abnormal Protein TRIP11-PDGFRB
  
Entity t(5;14)(q33;q24)
Disease described in a patient with a chronic myeloproliferative disorder with eosinophilia
Prognosis Good, imatinib mesylate responsive disease.
Cytogenetics t(5;14)(q33;q24)
Hybrid/Mutated Gene 5' NIN-PDGFRB 3'
Abnormal Protein NIN-PDGFRB
  
Entity t(5;14)(q31;q32)
Disease described in a patient with a chronic myeloproliferative disorder with peripheral blood monocitosis
Prognosis Good, imatinib mesylate responsive disease.
Cytogenetics t(5;14)(q31;q32)
Hybrid/Mutated Gene 5' KIAA1509-PDGFRB 3'
Abnormal Protein 5' KIAA1509-PDGFRB 3'
  
Entity t(5;15)(q33;q22)
Disease described in a patient with a chronic myeloproliferative disorder with eosinophilia
Prognosis Imatinib mesylate responsive disease but the patient described resistance was developed.
Cytogenetics t(5;15)(q33;q22)
Hybrid/Mutated Gene 5' TP53BP1-PDGFRB 3'
Abnormal Protein TP53BP1-PDGFRB
  
Entity t(5;17)(q33;p11.2)
Disease JMML/CMML
Prognosis Good.
Cytogenetics t(5;17)(q33;p11.2)
Hybrid/Mutated Gene 5' HCMOGT-PDGFRB 3' fusion described in an 18 month old boy with juvenile myelomonocytic leukemia and eosinophilia
Abnormal Protein HCMOGT-PDGFRB
  
Entity t(5;17)(q33;p13)
Disease described in a patient with chronic myelomonocitic leukemia
Prognosis unknown.
Cytogenetics t(5;17)(q33;p13)
Hybrid/Mutated Gene 5' RABEP1-PDGFRB 3'
Abnormal Protein RABEP1-PDGFRB
  

Breakpoints

 

External links

Nomenclature
HGNC (Hugo)PDGFRB   8804
Entrez_Gene (NCBI)PDGFRB  5159  platelet-derived growth factor receptor, beta polypeptide
Cards
AtlasPDGFRBID21ch5q32
GeneCards (Weizmann)PDGFRB
Ensembl (Hinxton)ENSG00000113721 [Gene_View]  PDGFRB [Vega]
AceView (NCBI)PDGFRB
Genatlas (Paris)PDGFRB
euGene (Indiana)5159
SOURCE (Stanford)NM_002609
Gene Expression (Array Express) ENSG00000113721
Genomic and cartography
GoldenPath (UCSC)PDGFRB  -     chr5:149493403-149535422 -  5q31-q32   [Description]    (hg19-Feb_2009)
EnsemblPDGFRB - 5q31-q32 [CytoView]
Mapping of homologs : NCBIPDGFRB [Mapview]
OMIM131440   173410   
Gene and transcription
Gene : Genbank (Entrez)AB209657 AI346188 AK293093 BC032224 CN268096
Reference sequence (RefSeq transcript) :SRSNM_002609
Reference transcript : EntrezNM_002609
RefSeq genomic : SRSAC_000048 AC_000137 NC_000005 NT_029289 NW_001838953 NW_922784
RefSeq genomic : EntrezAC_000048 AC_000137 NC_000005 NT_029289 NW_001838953 NW_922784
Consensus coding sequences : CCDS NCBIPDGFRB
Cluster EST : UnigeneHs.509067 [ SRS ] Hs.509067 [ NCBI ]
Alternative Splicing : Fast-db (Paris)12002
Protein : pattern, domain, 3D structure
Protein : UniProt/SwissProtP09619 (SRS) P09619 (Expasy) P09619 (Uniprot)
With graphics : InterProP09619
Splice isoforms : VarSplice FASTAP09619(VarSplice FASTA)
Domaine pattern : Prosite (SRS)IG_LIKE (PS50835)    PROTEIN_KINASE_ATP (PS00107)    PROTEIN_KINASE_DOM (PS50011)    PROTEIN_KINASE_TYR (PS00109)    RECEPTOR_TYR_KIN_III (PS00240)   
Domain pattern : Prosite (Expaxy)IG_LIKE (PS50835)    PROTEIN_KINASE_ATP (PS00107)    PROTEIN_KINASE_DOM (PS50011)    PROTEIN_KINASE_TYR (PS00109)    RECEPTOR_TYR_KIN_III (PS00240)   
Domains : Interpro (SRS)Ig-like    Ig-like_fold    Ig_sub    Ig_sub2    Immunoglobulin    Kinase-like_dom    Prot_kinase_cat_dom    Protein_kinase_ATP_BS    Ser-Thr/Tyr-Pkinase    Tyr_Pkinase_cat_dom    Tyr_prot_kinase    Tyr_prot_kinase_AS    Tyr_prot_kinase_CSF1/PDGF_rcpt    Tyr_prot_kinase_PDGF_rcpt_b    Tyr_prot_kinase_rcpt_3_CS    Tyr_prot_kinase_VEGFR_rcpt_N   
Domains : Interpro (EBI)Ig-like    Ig-like_fold    Ig_sub    Ig_sub2    Immunoglobulin    Kinase-like_dom    Prot_kinase_cat_dom    Protein_kinase_ATP_BS    Ser-Thr/Tyr-Pkinase    Tyr_Pkinase_cat_dom    Tyr_prot_kinase    Tyr_prot_kinase_AS    Tyr_prot_kinase_CSF1/PDGF_rcpt    Tyr_prot_kinase_PDGF_rcpt_b    Tyr_prot_kinase_rcpt_3_CS    Tyr_prot_kinase_VEGFR_rcpt_N   
Related proteins : CluSTrP09619
Domain families : Pfam SRSig (PF00047)    Pkinase_Tyr (PF07714)   
Domain families : Pfam Sangerig (PF00047)    Pkinase_Tyr (PF07714)   
Domain families : Pfam NCBIpfam00047    pfam07714   
Domain families : Smart EMBLIG (SM00409)  IGc2 (SM00408)  TyrKc (SM00219)  
Blocks (Seattle)P09619
Crystal structure of protein : PDB SRS1GQ5    1H9O    1LWP   
Crystal structure of protein : PDBSum1GQ5    1H9O    1LWP   
Crystal structure of protein : IMB1GQ5    1H9O    1LWP   
Crystal structure of protein : PDB RSDB1GQ5    1H9O    1LWP   
Human Protein AtlasENSG00000113721
HPRD01423
Protein Interaction databases
DIP (DOE-UCLA)P09619
IntAct (EBI)P09619
FunCoupENSG00000113721
Polymorphism : SNP, mutations, diseases
Single Nucleotide Polymorphism (SNP) : dbSNP NCBIPDGFRB
SNP : GeneSNP UtahPDGFRB
SNP : HGBasePDGFRB
Genetic variants : HAPMAPPDGFRB
Cancer Gene: CensusPDGFRB 
Somatic Mutations in Cancer : COSMICPDGFRB 
Translocation Breakpoints in Cancer : TICdbPDGFRB 
Mutations and Diseases : HGMDPDGFRB
Hereditary diseases : OMIM131440    173410   
Hereditary diseases : GENETests131440    173410   
Diseases : Genetic AssociationPDGFRB
General knowledge
Homologs : HomoloGenePDGFRB
Homology/Alignments : Family Browser UCSCPDGFRB
Phylogenetic Trees/Animal Genes : TreeFamPDGFRB
Catalytic activity : Enzyme2.7.10.1 [ Enzyme-Expasy ]   2.7.10.1 [ Enzyme-SRS ]   2.7.10.1 [ IntEnz-EBI ]   2.7.10.1 [ BRENDA ]   2.7.10.1 [ KEGG ]   
Chemical/Protein Interactions : CTD5159
Keywords Ontology : AmiGOnucleotide binding  in utero embryonic development  kidney development  tissue homeostasis  receptor activity  platelet activating factor receptor activity  platelet-derived growth factor receptor activity  platelet-derived growth factor beta-receptor activity  vascular endothelial growth factor receptor activity  platelet-derived growth factor receptor binding  protein binding  ATP binding  plasma membrane  integral to plasma membrane  nitrogen compound metabolic process  signal transduction  positive regulation of cell proliferation  membrane  transferase activity  peptidyl-tyrosine phosphorylation  growth factor binding  positive regulation of cell migration  protein amino acid autophosphorylation  platelet-derived growth factor receptor signaling pathway  vascular endothelial growth factor receptor signaling pathway  platelet-derived growth factor binding  skeletal system morphogenesis  smooth muscle tissue development  regulation of peptidyl-tyrosine phosphorylation  cell chemotaxis  
Keywords Ontology : EGO-EBInucleotide binding  in utero embryonic development  kidney development  tissue homeostasis  receptor activity  platelet activating factor receptor activity  platelet-derived growth factor receptor activity  platelet-derived growth factor beta-receptor activity  vascular endothelial growth factor receptor activity  platelet-derived growth factor receptor binding  protein binding  ATP binding  plasma membrane  integral to plasma membrane  nitrogen compound metabolic process  signal transduction  positive regulation of cell proliferation  membrane  transferase activity  peptidyl-tyrosine phosphorylation  growth factor binding  positive regulation of cell migration  protein amino acid autophosphorylation  platelet-derived growth factor receptor signaling pathway  vascular endothelial growth factor receptor signaling pathway  platelet-derived growth factor binding  skeletal system morphogenesis  smooth muscle tissue development  regulation of peptidyl-tyrosine phosphorylation  cell chemotaxis  
Pathways : BIOCARTA
Pathways : KEGGColorectal cancerCalcium signaling pathwayFocal adhesionMAPK signaling pathwayCytokine-cytokine receptor interactionRegulation of actin cytoskeletonGap junction
Other databases
Probes
Probes : ImagenesPDGFRB Related clones (RZPD - Berlin)
Literature
PubMed201 Pubmed reference(s) in Entrez
PubGenePDGFRB

Bibliography

Fusion of PDGF receptor beta to a novel ets-like gene, tel, in chronic myelomonocytic leukemia with t(5;12) chromosomal translocation.
Golub TR, Barker GF, Lovett M, Gilliland DG
Cell. 1994 ; 77 (2) : 307-316.
PMID 8168137
 
Fusion of the platelet-derived growth factor receptor beta to a novel gene CEV14 in acute myelogenous leukemia after clonal evolution.
Abe A, Emi N, Tanimoto M, Terasaki H, Marunouchi T, Saito H
Blood. 1997 ; 90 (11) : 4271-4277.
PMID 9373237
 
Fusion of Huntingtin interacting protein 1 to platelet-derived growth factor beta receptor (PDGFbetaR) in chronic myelomonocytic leukemia with t(5;7)(q33;q11.2).
Ross TS, Bernard OA, Berger R, Gilliland DG
Blood. 1998 ; 91 (12) : 4419-4426.
PMID 9616134
 
Fusion of H4/D10S170 to the platelet-derived growth factor receptor beta in BCR-ABL-negative myeloproliferative disorders with a t(5;10)(q33;q21).
Kulkarni S, Heath C, Parker S, Chase A, Iqbal S, Pocock CF, Kaeda J, Cwynarski K, Goldman JM, Cross NC
Cancer research. 2000 ; 60 (13) : 3592-3598.
PMID 10910073
 
Rabaptin-5 is a novel fusion partner to platelet-derived growth factor beta receptor in chronic myelomonocytic leukemia.
Magnusson MK, Meade KE, Brown KE, Arthur DC, Krueger LA, Barrett AJ, Dunbar CE
Blood. 2001 ; 98 (8) : 2518-2525.
PMID 11588050
 
H4(D10S170), a gene frequently rearranged in papillary thyroid carcinoma, is fused to the platelet-derived growth factor receptor beta gene in atypical chronic myeloid leukemia with t(5;10)(q33;q22).
Schwaller J, Anastasiadou E, Cain D, Kutok J, Wojiski S, Williams IR, LaStarza R, Crescenzi B, Sternberg DW, Andreasson P, Schiavo R, Siena S, Mecucci C, Gilliland DG
Blood. 2001 ; 97 (12) : 3910-3918.
PMID 11389034
 
Response to imatinib mesylate in patients with chronic myeloproliferative diseases with rearrangements of the platelet-derived growth factor receptor beta.
Apperley JF, Gardembas M, Melo JV, Russell-Jones R, Bain BJ, Baxter EJ, Chase A, Chessells JM, Colombat M, Dearden CE, Dimitrijevic S, Mahon FX, Marin D, Nikolova Z, Olavarria E, Silberman S, Schultheis B, Cross NC, Goldman JM
The New England journal of medicine. 2002 ; 347 (7) : 481-487.
PMID 12181402
 
Myeloproliferative disorders with translocations of chromosome 5q31-35: role of the platelet-derived growth factor receptor Beta.
Steer EJ, Cross NC
Acta haematologica. 2002 ; 107 (2) : 113-122.
PMID 11919393
 
Novel translocations that disrupt the platelet-derived growth factor receptor beta (PDGFRB) gene in BCR-ABL-negative chronic myeloproliferative disorders.
Baxter EJ, Kulkarni S, Vizmanos JL, Jaju R, Martinelli G, Testoni N, Hughes G, Salamanchuk Z, Calasanz MJ, Lahortiga I, Pocock CF, Dang R, Fidler C, Wainscoat JS, Boultwood J, Cross NC
British journal of haematology. 2003 ; 120 (2) : 251-256.
PMID 12542482
 
Imatinib mesylate elicits positive clinical response in atypical chronic myeloid leukemia involving the platelet-derived growth factor receptor beta.
Garcia JL, Font de Mora J, Hernandez JM, Queizan JA, Gutierrez NC, Hernandez JM, San Miguel JF
Blood. 2003 ; 102 (7) : 2699-2700.
PMID 14504072
 
Sensitivity to imatinib but low frequency of the TEL/PDGFRbeta fusion protein in chronic myelomonocytic leukemia.
Gunby RH, Cazzaniga G, Tassi E, Le Coutre P, Pogliani E, Specchia G, Biondi A, Gambacorti-Passerini C
Haematologica. 2003 ; 88 (4) : 408-415.
PMID 12681968
 
Cloning of the t(1;5)(q23;q33) in a myeloproliferative disorder associated with eosinophilia: involvement of PDGFRB and response to imatinib.
Wilkinson K, Velloso ER, Lopes LF, Lee C, Aster JC, Shipp MA, Aguiar RC
Blood. 2003 ; 102 (12) : 4187-4190.
PMID 12907457
 
p53-Binding protein 1 is fused to the platelet-derived growth factor receptor beta in a patient with a t(5;15)(q33;q22) and an imatinib-responsive eosinophilic myeloproliferative disorder.
Grand FH, Burgstaller S, Kˆºhr T, Baxter EJ, Webersinke G, Thaler J, Chase AJ, Cross NC
Cancer research. 2004 ; 64 (20) : 7216-7219.
PMID 15492236
 
Oncogenic derivatives of platelet-derived growth factor receptors.
Jones AV, Cross NC
Cellular and molecular life sciences : CMLS. 2004 ; 61 (23) : 2912-2923.
PMID 15583853
 
HCMOGT-1 is a novel fusion partner to PDGFRB in juvenile myelomonocytic leukemia with t(5;17)(q33;p11.2).
Morerio C, Acquila M, Rosanda C, Rapella A, Dufour C, Locatelli F, Maserati E, Pasquali F, Panarello C
Cancer research. 2004 ; 64 (8) : 2649-2651.
PMID 15087372
 
NIN, a gene encoding a CEP110-like centrosomal protein, is fused to PDGFRB in a patient with a t(5;14)(q33;q24) and an imatinib-responsive myeloproliferative disorder.
Vizmanos JL, Novo FJ, Romˆ°n JP, Baxter EJ, Lahortiga I, Larrˆ°yoz MJ, Odero MD, Giraldo P, Calasanz MJ, Cross NC
Cancer research. 2004 ; 64 (8) : 2673-2676.
PMID 15087377
 
KIAA1509 is a novel PDGFRB fusion partner in imatinib-responsive myeloproliferative disease associated with a t(5;14)(q33;q32).
Levine RL, Wadleigh M, Sternberg DW, Wlodarska I, Galinsky I, Stone RM, DeAngelo DJ, Gilliland DG, Cools J
Leukemia : official journal of the Leukemia Society of America, Leukemia Research Fund, U.K. 2005 ; 19 (1) : 27-30.
PMID 15496975
 
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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Contributor(s)

Written07-2005José Luis Vizmanos

Citation

This paper should be referenced as such :
Vizmanos JL . PDGFRB (platelet-derived growth factor receptor, beta polypeptide). Atlas Genet Cytogenet Oncol Haematol. July 2005 .
URL : http://AtlasGeneticsOncology.org/Genes/PDGFRBID21ch5q32.html

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indexed on : Thu Jul 15 14:49:50 CEST 2010
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