Genatlas sheet

Selected-GenAtlas references	SOURCE	GeneCards	NCBI Gene	Swiss-Prot	Orphanet	Ensembl
Selected-GenAtlas references	HGNC	UniGene	Nucleotide	OMIM	Orphanet	UCSC

Home Page

FLASH GENE

Symbol

PDGFRB

contributors: mct/pgu - updated : 15-07-2016

HGNC name	platelet-derived growth factor receptor, beta polypeptide
HGNC id	8804

Corresponding disease

BGCI4	idiopathic basal ganglia calcification-4
IMF1	infantile myofibromatosis-1
PENTT	Penttinen type of premature aging syndrome

Location

5q32 Physical location : 149.493.402 - 149.535.422

Synonym name

beta platelet-derived growth factor receptor

soluble PDGFRb variant 1

CD140 antigen-like family member B

CD140b antigen

Synonym symbol(s)

PDGFR, JTK12, CD140B, PDGFR1, PDGF-R-beta, IBGC4,

EC.number

2.7.10.1

DNA

TYPE	functioning gene
STRUCTURE	42.02 kb 23 Exon(s)

10 Kb 5' upstream gene genomic sequence study

regulatory sequence	Promoter (CAAT box)
text structure	TP53 binds the proximal promoter containing the CCAAT motif ( Tp53 represses the PDGFRB promoter, facilitating the Tp53-induced apoptosis)
	GC-rich region (-165 to -139) of the promoter is crucial for basal promoter activity
	promoter region is extensively demethylated following differentiation, and represents a developmentally regulated, differentially methylated region linked to PDGFRB expression

MAPPING

cloned

linked

status

confirmed

Map

see CSF1R

RNA

TRANSCRIPTS	type	messenger

identification	nb exons	type	bp	product
identification	nb exons	type	bp	Protein	kDa	AA	specific expression	Year	Pubmed
	23	-	5718		-	1106	-	1995	7641887

EXPRESSION

Rna function	mRNA for PDGFRB only in 25p100 of the oocytes
Type	ubiquitous

expressed in

(based on citations)

organ(s)

System	Organ level 1	Organ level 2	Organ level 3	Organ level 4	Level	Pubmed	Species	Stage	Rna symbol
Endocrine	pancreas						Homo sapiens
Nervous	brain				highly		Homo sapiens
Reproductive	female system	ovary			highly
Respiratory	respiratory tract	larynx			highly
Skin/Tegument	skin						Homo sapiens	Fetal

tissue

System	Tissue	Tissue level 1	Tissue level 2	Level	Pubmed	Species	Stage	Rna symbol
Connective	bone			highly
Connective	interstitial	dermis				Homo sapiens	Fetal
Muscular	smooth	vessel				Homo sapiens

cells

System	Cell	Pubmed	Species	Stage	Rna symbol
Endocrine	islet cell (alpha,beta...)		Homo sapiens
Nervous	astrocyte		Homo sapiens
Nervous	neuron		Homo sapiens
not specific	fibroblast		Homo sapiens	Fetal

cell lineage

cell lines

fluid/secretion

at STAGE

physiological period

growth/childhood

Text

PDGFRB levels were markedly reduced in islet beta-cells at 6 weeks and 6 months of age, compared to neonatal islets

PROTEIN

PHYSICAL PROPERTIES

STRUCTURE

motifs/domains	five extracellular Ig-like motifs
	a transmembrane segment (1TM)
	a cytoplasmic split tyrosine kinase domain

mono polymer

homomer , heteromer , dimer

HOMOLOGY

Homologene

FAMILY	protein kinase superfamily
	Tyr protein kinase family
	CSF-1/PDGF receptor subfamily

CATEGORY

signaling cytokine growth factor , receptor

SUBCELLULAR LOCALIZATION	plasma membrane
	intracellular
	intracellular,cytoplasm,organelle,lumen
	intracellular,cytoplasm,organelle,lysosome
	intracellular,cytoplasm,cytosolic,vesicle
	intracellular,nucleus

basic FUNCTION	receptor tyrosine kinase, class III, phosphorylating Tyr residues at the C-terminus of PTPN11 creating a binding site for the SH2 domain of GRB2
	mitogen for mesenchyme-derived cells, including fibroblasts and smooth muscle
	phosphorylates GRK2 tyrosyl residues and thereby activates GRK2, which then serine-phosphorylates and desensitizes the PDGFRbeta
	PDGFRB signaling is crucial for neuroprotection, endogenous tissue repair, and functional recovery after stroke by targeting neurons,pericyte/vascular smooth muscle cells, and astrocytes
	required for the development of mesenchymal cell types, and plays a diverse role in the function of fibroblasts in tissue homeostasis and regeneration
	PDGFRB-mediated signaling plays a key role in morphine tolerance
	has an essential role in vascular progenitor cell signaling (pMID: 31031011)

CELLULAR PROCESS	cell life, proliferation/growth

PHYSIOLOGICAL PROCESS

PATHWAY

metabolism

signaling

PDGFRB-AKT1 signaling in brain pericytes may play various important roles leading to neuroprotection after ischemic stroke

a component

homodimerizing and heterodimerizing with PDGFRA

INTERACTION

DNA

RNA

small molecule	nucleotide,
	ATP

protein	binds specifically to PDGFRA and has a tyrosine-protein kinase activity
	interacting with NRP1 (influences ligand-induced PDGFRB homodimer signalling)
	important interactive relationship between SLC6A4 and the PDGFRB in the production of pulmonary artery smooth muscle cell proliferation triggered by PDGF that may be important in pulmonary hypertension (PH)
	LRP6 forms a complex with PDGFRB and promotes its degradation
	SH2B3 is a negative regulator of PDGFR signaling
	in aortic smooth muscle cells, TGM2 specifically amplifies the activation of PDGFRB and its multiple downstream signaling targets in response to PDGF-BB
	ETV6-PDGFRB antagonizes the effects of ETV6 and IRF8 on PTPN13 transcription
	PDGFRB/MAPK1 signalling pathway triggered by FGF2 plays an important role in the proliferation and migration of endothelial progenitor cells
	involved in angiogenesis and in the regulation of inorganic phosphate (Pi) transport in vascular smooth
	muscle cells via SLC20A1
	PDGFRB expression was upregulated by NOTCH3 ligand induction or by activated forms of the NOTCH3 receptor
	affects the intracellular sorting of activated PDGFRB and the migration, proliferation and tumorigenicity of cells stimulated by PDGF

cell & other

REGULATION

activated by

constitutively activated through amino-acid(s) substitution in a WW-like domain (phosphoserine- or phosphothreonine binding)

repressed by

ZNF24

Other	phosphorylated by PTPN11 controlling Ras GAP recruitement and Ras MAP kinase signaling in the heterodimeric configuration of PDGF receptors
	ligand-mediated stabilization of specific G-quadruplex structures in the promoter can modulate its transcription

ASSOCIATED DISORDERS

corresponding disease(s)

IMF1 , BGCI4 , PENTT , POGS

Other morbid association(s)

Type	Gene Modification	Chromosome rearrangement	Protein Function
tumoral			gain of function
in clear cell renal carcinoma with favourable outcome
tumoral	fusion	translocation	protein chimeric
t(5;12)(q33;p13) in myelodysplasia, myeloproliferative disorders (MPS), chronic myelocytic leukemia (CMLL), with fusion 5' - ETV66 - PDGFRB - 3'
constitutional	germinal mutation
gain of function mutation in the activation loop deregulates its kinase activity
tumoral	fusion	translocation
somatic traslocations in various hematological disorders resulting in PDGFRB/D10S170 fusion gene, PDGFRB/RABPT5 fusion gene, PDGFRB/HIP1 fusion gene and other partners genes
tumoral	fusion
with MYO18A in an eosinophilia-associated atypical myeloproliferative neoplasm with a t(5;17)(q33-34;q11.2)
tumoral	fusion
to SPTBN1 in imatinib-responsive atypical myeloproliferative disorders
constitutional	somatic mutation
in intracerebral fusiform aneurysms

Susceptibility

Variant & Polymorphism

Candidate gene

Marker

Therapy target

ANIMAL & CELL MODELS

PDGFRB inhibition selectively eliminates morphine tolerance in rats