PDGFRB platelet derived growth factor receptor beta [Homo sapiens (human)] - Gene

Summary

Official Symbol: PDGFRBprovided by HGNC
Official Full Name: platelet derived growth factor receptor betaprovided by HGNC
Primary source: HGNC:HGNC:8804
See related: Ensembl:ENSG00000113721 MIM:173410; AllianceGenome:HGNC:8804
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: IMF1; KOGS; IBGC4; JTK12; PDGFR; PENTT; CD140B; PDGFR1; PDGFR-1
Summary: The protein encoded by this gene is a cell surface tyrosine kinase receptor for members of the platelet-derived growth factor family. These growth factors are mitogens for cells of mesenchymal origin. The identity of the growth factor bound to a receptor monomer determines whether the functional receptor is a homodimer (PDGFB or PDGFD) or a heterodimer (PDGFA and PDGFB). This gene is essential for normal development of the cardiovascular system and aids in rearrangement of the actin cytoskeleton. This gene is flanked on chromosome 5 by the genes for granulocyte-macrophage colony-stimulating factor and macrophage-colony stimulating factor receptor; all three genes may be implicated in the 5-q syndrome. A translocation between chromosomes 5 and 12, that fuses this gene to that of the ETV6 gene, results in chronic myeloproliferative disorder with eosinophilia. [provided by RefSeq, Aug 2017]
Expression: Broad expression in gall bladder (RPKM 79.5), placenta (RPKM 61.0) and 21 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 5q32

Exon count:: 24

Annotation release	Status	Assembly	Chr	Location
110	current	GRCh38.p14 (GCF_000001405.40)	5	NC_000005.10 (150113839..150155845, complement)
110	current	T2T-CHM13v2.0 (GCF_009914755.1)	5	NC_060929.1 (150650431..150692448, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	5	NC_000005.9 (149493402..149535408, complement)

Chromosome 5 - NC_000005.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Penttinen syndrome-associated PDGFRB Val665Ala variant causes aberrant constitutive STAT1 signalling.
Title: Penttinen syndrome-associated PDGFRB Val665Ala variant causes aberrant constitutive STAT1 signalling.
PDGFRB is a potential prognostic biomarker and correlated with immune infiltrates in gastric cancer.
Title: PDGFRB is a potential prognostic biomarker and correlated with immune infiltrates in gastric cancer.
PDGFRbeta modulates aerobic glycolysis in osteosarcoma HOS cells via the PI3K/AKT/mTOR/c-Myc pathway.
Title: PDGFRβ modulates aerobic glycolysis in osteosarcoma HOS cells via the PI3K/AKT/mTOR/c-Myc pathway.
Diverse roles of tumor-stromal PDGFB-to-PDGFRbeta signaling in breast cancer growth and metastasis.
Title: Diverse roles of tumor-stromal PDGFB-to-PDGFRβ signaling in breast cancer growth and metastasis.
SWATH-MS identification of CXCL7, LBP, TGFbeta1 and PDGFRbeta as novel biomarkers in human systemic mastocytosis.
Title: SWATH-MS identification of CXCL7, LBP, TGFβ1 and PDGFRβ as novel biomarkers in human systemic mastocytosis.
Distinct functional classes of PDGFRB pathogenic variants in primary familial brain calcification.
Title: Distinct functional classes of PDGFRB pathogenic variants in primary familial brain calcification.
Somatic Mosaicism of a PDGFRB Activating Variant in Aneurysms of the Intracranial, Coronary, Aortic, and Radial Artery Vascular Beds.
Title: Somatic Mosaicism of a PDGFRB Activating Variant in Aneurysms of the Intracranial, Coronary, Aortic, and Radial Artery Vascular Beds.
Kosaki overgrowth syndrome due to a novel de novo PDGFRB variant.
Title: Kosaki overgrowth syndrome due to a novel de novo PDGFRB variant.
CircCDK14 Promotes Tumor Progression and Resists Ferroptosis in Glioma by Regulating PDGFRA.
Title: CircCDK14 Promotes Tumor Progression and Resists Ferroptosis in Glioma by Regulating PDGFRA.
PDGF-D-PDGFRbeta signaling enhances IL-15-mediated human natural killer cell survival.
Title: PDGF-D-PDGFRβ signaling enhances IL-15-mediated human natural killer cell survival.

Submit: New GeneRIF Correction See all GeneRIFs (322)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Acroosteolysis-keloid-like lesions-premature aging syndrome MedGen: C1866182 OMIM: 601812 GeneReviews: Not available	Compare labs
Basal ganglia calcification, idiopathic, 4 MedGen: C3554321 OMIM: 615007 GeneReviews: Primary Familial Brain Calcification	Compare labs
Idiopathic basal ganglia calcification 1 MedGen: C4551624 OMIM: 213600 GeneReviews: Primary Familial Brain Calcification	Compare labs
Myeloproliferative disorder, chronic, with eosinophilia MedGen: C1851585 OMIM: 131440 GeneReviews: Not available	Compare labs
Myofibromatosis, infantile, 1 MedGen: C4551572 OMIM: 228550 GeneReviews: Not available	Compare labs
Skeletal overgrowth-craniofacial dysmorphism-hyperelastic skin-white matter lesions syndrome MedGen: C4225270 OMIM: 616592 GeneReviews: Not available	Compare labs

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Protein interactions

Protein	Gene	Interaction	Pubs
Tat	tat	HIV-1 Tat and cocaine treatment induces phosphorylation of PDGFR-beta at position Y934 without the requirement of PDGF binding in human pulmonary arterial smooth muscle cells	PubMed
	tat	HIV-1 Tat upregulates the expression of platelet-derived growth factor subunit B homodimer through activation of the PDGFR-B/MEK/NF-kappaB pathway in human brain microvascular pericytes	PubMed

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH69916 (e-PCR)
- UniSTS:6912

D5S2602 (e-PCR)
- UniSTS:56095

D5S2862 (e-PCR)
- UniSTS:38439

WI-18889 (e-PCR)
- UniSTS:44587

PDGFRB_1343 (e-PCR)
- UniSTS:277577

RH11092 (e-PCR)
- UniSTS:68426

WI-18300 (e-PCR)
- UniSTS:18664

Homology

Homologs of the PDGFRB gene: The PDGFRB gene is conserved in chimpanzee, Rhesus monkey, dog, cow, mouse, rat, chicken, zebrafish, and frog.
Orthologs from Annotation Pipeline: 447 organisms have orthologs with human gene PDGFRB
Orthologs

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables ATP binding	IEA Inferred from Electronic Annotation more info
enables enzyme binding	IPI Inferred from Physical Interaction more info	PubMed
enables growth factor binding	IBA Inferred from Biological aspect of Ancestor more info	PubMed
enables phosphatidylinositol 3-kinase binding	IEA Inferred from Electronic Annotation more info
enables platelet activating factor receptor activity	TAS Traceable Author Statement more info	PubMed
enables platelet-derived growth factor beta-receptor activity	IBA Inferred from Biological aspect of Ancestor more info	PubMed
enables platelet-derived growth factor beta-receptor activity	IDA Inferred from Direct Assay more info	PubMed
enables platelet-derived growth factor beta-receptor activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables platelet-derived growth factor binding	IBA Inferred from Biological aspect of Ancestor more info	PubMed
enables platelet-derived growth factor binding	IDA Inferred from Direct Assay more info	PubMed
enables platelet-derived growth factor binding	IPI Inferred from Physical Interaction more info	PubMed
enables platelet-derived growth factor receptor activity	TAS Traceable Author Statement more info	PubMed
enables platelet-derived growth factor receptor binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein kinase binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein tyrosine kinase activity	IDA Inferred from Direct Assay more info	PubMed
enables signaling receptor binding	IPI Inferred from Physical Interaction more info	PubMed
enables transmembrane receptor protein tyrosine kinase activity	IBA Inferred from Biological aspect of Ancestor more info	PubMed
enables vascular endothelial growth factor binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in G protein-coupled receptor signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in aging	IEA Inferred from Electronic Annotation more info
involved_in angiogenesis	IBA Inferred from Biological aspect of Ancestor more info	PubMed
involved_in aorta morphogenesis	ISS Inferred from Sequence or Structural Similarity more info
involved_in cardiac myofibril assembly	ISS Inferred from Sequence or Structural Similarity more info
involved_in cell chemotaxis	IBA Inferred from Biological aspect of Ancestor more info	PubMed
involved_in cell chemotaxis	IDA Inferred from Direct Assay more info	PubMed
involved_in cell migration	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in cell migration involved in coronary angiogenesis	ISS Inferred from Sequence or Structural Similarity more info
involved_in cell migration involved in vasculogenesis	ISS Inferred from Sequence or Structural Similarity more info
involved_in cellular response to platelet-derived growth factor stimulus	IEA Inferred from Electronic Annotation more info
involved_in glycosaminoglycan biosynthetic process	IEA Inferred from Electronic Annotation more info
involved_in inner ear development	IEA Inferred from Electronic Annotation more info
involved_in lung growth	IEA Inferred from Electronic Annotation more info
involved_in male gonad development	IEA Inferred from Electronic Annotation more info
involved_in metanephric S-shaped body morphogenesis	IEA Inferred from Electronic Annotation more info
involved_in metanephric comma-shaped body morphogenesis	IEA Inferred from Electronic Annotation more info
involved_in metanephric glomerular capillary formation	ISS Inferred from Sequence or Structural Similarity more info
involved_in metanephric glomerular mesangial cell proliferation involved in metanephros development	ISS Inferred from Sequence or Structural Similarity more info
involved_in metanephric mesenchymal cell migration	IEA Inferred from Electronic Annotation more info
involved_in metanephric mesenchyme development	IEA Inferred from Electronic Annotation more info
involved_in multicellular organism development	IBA Inferred from Biological aspect of Ancestor more info	PubMed
involved_in negative regulation of apoptotic process	IEA Inferred from Electronic Annotation more info
involved_in peptidyl-tyrosine phosphorylation	IDA Inferred from Direct Assay more info	PubMed
involved_in phosphatidylinositol metabolic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in phosphatidylinositol-mediated signaling	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in platelet-derived growth factor receptor signaling pathway	IDA Inferred from Direct Assay more info	PubMed
involved_in platelet-derived growth factor receptor-beta signaling pathway	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of DNA biosynthetic process	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of ERK1 and ERK2 cascade	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of ERK1 and ERK2 cascade	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of MAP kinase activity	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of Rho protein signal transduction	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of apoptotic process	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of calcium ion import	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of cell migration	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of cell population proliferation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of cell proliferation by VEGF-activated platelet derived growth factor receptor signaling pathway	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of chemotaxis	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of collagen biosynthetic process	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of fibroblast proliferation	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of hepatic stellate cell activation	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of kinase activity	IBA Inferred from Biological aspect of Ancestor more info	PubMed
involved_in positive regulation of metanephric mesenchymal cell migration by platelet-derived growth factor receptor-beta signaling pathway	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of mitotic nuclear division	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of phosphatidylinositol 3-kinase activity	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of phosphatidylinositol 3-kinase signaling	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of phospholipase C activity	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of phosphoprotein phosphatase activity	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of reactive oxygen species metabolic process	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of smooth muscle cell migration	IBA Inferred from Biological aspect of Ancestor more info	PubMed
involved_in positive regulation of smooth muscle cell migration	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of smooth muscle cell migration	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of smooth muscle cell proliferation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of smooth muscle cell proliferation	ISS Inferred from Sequence or Structural Similarity more info
involved_in protein autophosphorylation	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of actin cytoskeleton organization	ISS Inferred from Sequence or Structural Similarity more info
involved_in response to estradiol	IEA Inferred from Electronic Annotation more info
involved_in response to estrogen	IEA Inferred from Electronic Annotation more info
involved_in response to fluid shear stress	IEA Inferred from Electronic Annotation more info
involved_in response to hydrogen peroxide	IEA Inferred from Electronic Annotation more info
involved_in response to hyperoxia	IEA Inferred from Electronic Annotation more info
involved_in response to retinoic acid	IEA Inferred from Electronic Annotation more info
involved_in response to toxic substance	IEA Inferred from Electronic Annotation more info
involved_in retina vasculature development in camera-type eye	ISS Inferred from Sequence or Structural Similarity more info
involved_in signal transduction	IDA Inferred from Direct Assay more info	PubMed
involved_in smooth muscle cell chemotaxis	ISS Inferred from Sequence or Structural Similarity more info
involved_in transmembrane receptor protein tyrosine kinase signaling pathway	IBA Inferred from Biological aspect of Ancestor more info	PubMed
involved_in wound healing	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in Golgi apparatus	IDA Inferred from Direct Assay more info
located_in apical plasma membrane	ISS Inferred from Sequence or Structural Similarity more info
located_in cell surface	IEA Inferred from Electronic Annotation more info
located_in cytoplasm	ISS Inferred from Sequence or Structural Similarity more info
located_in cytoplasmic vesicle	IEA Inferred from Electronic Annotation more info
located_in focal adhesion	HDA more info	PubMed
is_active_in integral component of plasma membrane	IBA Inferred from Biological aspect of Ancestor more info	PubMed
located_in intracellular membrane-bounded organelle	IDA Inferred from Direct Assay more info
located_in intrinsic component of plasma membrane	IDA Inferred from Direct Assay more info	PubMed
located_in lysosomal lumen	IEA Inferred from Electronic Annotation more info
located_in membrane	HDA more info	PubMed
located_in membrane	IDA Inferred from Direct Assay more info	PubMed
located_in nucleus	ISS Inferred from Sequence or Structural Similarity more info
located_in plasma membrane	TAS Traceable Author Statement more info
part_of receptor complex	IBA Inferred from Biological aspect of Ancestor more info	PubMed

General protein information

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Preferred Names: platelet-derived growth factor receptor beta

Names: Activated tyrosine kinase PDGFRB; CD140 antigen-like family member B; NDEL1-PDGFRB; PDGF-R-beta; PDGFR-beta; beta-type platelet-derived growth factor receptor; platelet-derived growth factor receptor 1; platelet-derived growth factor receptor, beta polypeptide

NP_001341945.1

EC 2.7.10.1

NP_001341946.1

EC 2.7.10.1

NP_002600.1

EC 2.7.10.1

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

NG_023367.1 RefSeqGene

Range

5001..47021

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001355016.2 → NP_001341945.1 platelet-derived growth factor receptor beta isoform 2

Status: REVIEWED

Description

Transcript Variant: This variant (2) differs in the 5' UTR and coding sequence compared to variant 1. The resulting isoform (2) is shorter at the N-terminus compared to isoform 1.

Source sequence(s)

AC005895, AC011382

Conserved Domains (5) summary

cd05107
Location:498 → 889

PTKc_PDGFR_beta; Catalytic domain of the Protein Tyrosine Kinase, Platelet Derived Growth Factor Receptor beta

cd00096
Location:367 → 375

Ig; Ig strand B [structural motif]

cd05859
Location:250 → 351

Ig4_PDGFR; Fourth immunoglobulin (Ig)-like domain of platelet-derived growth factor receptor (PDGFR)

cd05861
Location:148 → 247

IgI_PDGFR-alphabeta; Immunoglobulin (Ig)-like domain of platelet-derived growth factor (PDGF) receptors (R), alpha and beta; member of the I-set of IgSF domains

cl11960
Location:367 → 455

Ig; Immunoglobulin domain
NM_001355017.2 → NP_001341946.1 platelet-derived growth factor receptor beta isoform 3

Status: REVIEWED

Description

Transcript Variant: This variant (3) uses an alternate splice junction compared to variant 1. The resulting isoform (3) has a shorter and distinct N-terminus compared to isoform 1.

Source sequence(s)

AC005895, AC011382

Conserved Domains (4) summary

cd05107
Location:401 → 792

PTKc_PDGFR_beta; Catalytic domain of the Protein Tyrosine Kinase, Platelet Derived Growth Factor Receptor beta

cd05859
Location:153 → 254

Ig4_PDGFR; Fourth immunoglobulin (Ig)-like domain of platelet-derived growth factor receptor (PDGFR)

cd05861
Location:67 → 151

Ig_PDGFR-alphabeta; Immunoglobulin (Ig)-like domain of platelet-derived growth factor (PDGF) receptors (R), alpha (CD140a), and beta (CD140b)

cl11960
Location:264 → 362

Ig; Immunoglobulin domain
NM_002609.4 → NP_002600.1 platelet-derived growth factor receptor beta isoform 1 precursor

See identical proteins and their annotated locations for NP_002600.1

Status: REVIEWED

Source sequence(s)

AC005895, AC011382

Consensus CDS

CCDS4303.1

UniProtKB/Swiss-Prot

P09619, Q8N5L4

UniProtKB/TrEMBL

Q59F04

Related

ENSP00000261799.4, ENST00000261799.9

Conserved Domains (8) summary

cd05107
Location:562 → 953

PTKc_PDGFR_beta; Catalytic domain of the Protein Tyrosine Kinase, Platelet Derived Growth Factor Receptor beta

cd05859
Location:314 → 415

Ig4_PDGFR-alpha; Fourth immunoglobulin (Ig)-like domain of platelet-derived growth factor receptor (PDGFR) alpha

cd05861
Location:228 → 312

Ig1_PDGFR-alphabeta; Frst immunoglobulin (Ig)-like domain of platelet-derived growth factor (PDGF) receptors (R), alpha (CD140a), and beta (CD140b)

smart00409
Location:40 → 110

IG; Immunoglobulin

smart00410
Location:222 → 310

IG_like; Immunoglobulin like

pfam00047
Location:37 → 114

ig; Immunoglobulin domain

pfam07714
Location:600 → 953

Pkinase_Tyr; Protein tyrosine kinase

cl11960
Location:425 → 523

Ig; Immunoglobulin domain

RNA

NR_149150.2 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (4) lacks most of the exons found in variant 1. This variant is represented as non-coding because it lacks the entire coding region found in variant 1.

Source sequence(s)

AC005895