PDGFB platelet derived growth factor subunit B [Homo sapiens (human)] - Gene

Summary

Official Symbol: PDGFBprovided by HGNC
Official Full Name: platelet derived growth factor subunit Bprovided by HGNC
Primary source: HGNC:HGNC:8800
See related: Ensembl:ENSG00000100311 MIM:190040; AllianceGenome:HGNC:8800
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: SIS; SSV; IBGC5; PDGF2; c-sis; PDGF-2
Summary: This gene encodes a member of the protein family comprised of both platelet-derived growth factors (PDGF) and vascular endothelial growth factors (VEGF). The encoded preproprotein is proteolytically processed to generate platelet-derived growth factor subunit B, which can homodimerize, or alternatively, heterodimerize with the related platelet-derived growth factor subunit A. These proteins bind and activate PDGF receptor tyrosine kinases, which play a role in a wide range of developmental processes. Mutations in this gene are associated with meningioma. Reciprocal translocations between chromosomes 22 and 17, at sites where this gene and that for collagen type 1, alpha 1 are located, are associated with dermatofibrosarcoma protuberans, a rare skin tumor. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Oct 2015]
Expression: Broad expression in placenta (RPKM 18.6), fat (RPKM 12.7) and 23 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 22q13.1

Exon count:: 9

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	22	NC_000022.11 (39223359..39244982, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	22	NC_060946.1 (39694033..39715652, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	22	NC_000022.10 (39619364..39640987, complement)

Chromosome 22 - NC_000022.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues 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?

Role of endothelial PDGFB in arterio-venous malformations pathogenesis.
Title: Role of endothelial PDGFB in arterio-venous malformations pathogenesis.
Small vessel disease in primary familial brain calcification with novel truncating PDGFB variants.
Title: Small vessel disease in primary familial brain calcification with novel truncating PDGFB variants.
Platelet-derived growth factor subunit-B mediating the effect of dickkopf-1 on acute myocardial infarction risk: a two-step Mendelian randomization study.
Title: Platelet-derived growth factor subunit-B mediating the effect of dickkopf-1 on acute myocardial infarction risk: a two-step Mendelian randomization study.
Cancer-Associated Fibroblasts Promote Lymphatic Metastasis in Cholangiocarcinoma via the PDGF-BB/PDGFR-beta Mediated Paracrine Signaling Network.
Title: Cancer-Associated Fibroblasts Promote Lymphatic Metastasis in Cholangiocarcinoma via the PDGF-BB/PDGFR-β Mediated Paracrine Signaling Network.
JAM-A Overexpression in Human Umbilical Cord-Derived Mesenchymal Stem Cells Accelerated the Angiogenesis of Diabetic Wound By Enhancing Both Paracrine Function and Survival of Mesenchymal Stem Cells.
Title: JAM-A Overexpression in Human Umbilical Cord-Derived Mesenchymal Stem Cells Accelerated the Angiogenesis of Diabetic Wound By Enhancing Both Paracrine Function and Survival of Mesenchymal Stem Cells.
Preosteoclast plays a pathogenic role in syndesmophyte formation of ankylosing spondylitis through the secreted PDGFB - GRB2/ERK/RUNX2 pathway.
Title: Preosteoclast plays a pathogenic role in syndesmophyte formation of ankylosing spondylitis through the secreted PDGFB - GRB2/ERK/RUNX2 pathway.
Platelet-Derived Growth Factor B Is a Key Element in the Pathological Bone Formation of Ankylosing Spondylitis.
Title: Platelet-Derived Growth Factor B Is a Key Element in the Pathological Bone Formation of Ankylosing Spondylitis.
The Role of Platelet-Derived Growth Factor in Focal Segmental Glomerulosclerosis.
Title: The Role of Platelet-Derived Growth Factor in Focal Segmental Glomerulosclerosis.
Primary familial brain calcification with mild phenotype due to a new PDGFB mutation.
Title: Primary familial brain calcification with mild phenotype due to a new PDGFB mutation.
Living with primary brain calcification with PDGFB variants: A qualitative study.
Title: Living with primary brain calcification with PDGFB variants: A qualitative study.

Submit: New GeneRIF Correction See all GeneRIFs (257)

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Basal ganglia calcification, idiopathic, 5 MedGen: C3809645 OMIM: 615483 GeneReviews: Primary Familial Brain Calcification	not available
Dermatofibrosarcoma protuberans MedGen: C3693482 OMIM: 607907 GeneReviews: Not available	not available
Familial meningioma MedGen: C3551915 OMIM: 607174 GeneReviews: MN1 C-Terminal Truncation Syndrome	not available
Idiopathic basal ganglia calcification 1 MedGen: C4551624 OMIM: 213600 GeneReviews: Primary Familial Brain Calcification	not available

Variation

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See Variation Viewer (GRCh37.p13)

HIV-1 interactions

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Protein interactions

Protein	Gene	Interaction	Pubs
Envelope surface glycoprotein gp120	env	Human primary pulmonary arterial endothelial cells (HPAEC) are treated with both HIV-1 Tat and gp120 resulting in increased ROS generation and PDGF-B expression	PubMed
	env	PDGFB protects neurons from gp120-induced cytotoxicity through an increased phosphorylation of both GSK-3beta and Bad, the downregulation of the proapoptotic protein Bax, and inhibition of gp120-induced release of mitochondrial cytochrome C	PubMed
	env	Gp120-mediated activation of caspase-3 is significantly reduced in cells pretreated with PDGF-B. PDGF-mediated protection against gp120 involves the phosphoinositide (PI)3-kinase/Akt pathway	PubMed
	env	Pretreatment with PDGFB reduces gp120-associated neurotoxicity and rescues neurite outgrowth	PubMed
Tat	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
	tat	HIV-1-Tat-mediated upregulation of platelet-derived growth factor (PDGF) B chain in astrocytes is regulated by activation of ERK1/2 and JNK MAPK signaling pathways and the downstream transcription factor early growth response 1 (Egr1)	PubMed
	tat	Human primary pulmonary arterial endothelial cells (HPAEC) are treated with both HIV-1 Tat and gp120 resulting in increased ROS generation and PDGF-B expression	PubMed
	tat	PDGF-BB-mediated protection against HIV-1 Tat and morphine-induced neuron apoptosis involves Akt activation	PubMed
	tat	PDGF-BB prevents mitochondria depolarization in human neurons exposed to HIV-1 Tat and morphine	PubMed
	tat	PDGF-BB inhibits NADPH oxidase-mediated reactive oxygen species production induced by HIV-1 Tat and morphine treatment in neuroblastoma cells	PubMed
	tat	PDGF-BB prevents caspase-3 activation induced by HIV-1 Tat and morphine in neuroblastoma cells	PubMed
	tat	PDGF-BB protects neurons against HIV-1 Tat and morphine-induced apoptosis by promoting Bcl2 and inhibiting Bax expression	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

PDGFB_1020 (e-PCR)
- UniSTS:277575

D22S1108 (e-PCR)
- UniSTS:13517

GDB:452638 (e-PCR)
- UniSTS:157403

GDB:190930 (e-PCR)
- UniSTS:155635

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables chemoattractant activity	IDA Inferred from Direct Assay more info	PubMed
enables collagen binding	IDA Inferred from Direct Assay more info	PubMed
enables growth factor activity	IDA Inferred from Direct Assay more info	PubMed
enables identical protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables platelet-derived growth factor binding	IPI Inferred from Physical Interaction more info	PubMed
enables platelet-derived growth factor receptor binding	EXP Inferred from Experiment more info	PubMed
enables platelet-derived growth factor receptor binding	IBA Inferred from Biological aspect of Ancestor more info
enables platelet-derived growth factor receptor binding	IDA Inferred from Direct Assay more info	PubMed
enables platelet-derived growth factor receptor binding	IPI Inferred from Physical Interaction more info	PubMed
enables platelet-derived growth factor receptor binding	NAS Non-traceable Author Statement more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein heterodimerization activity	IPI Inferred from Physical Interaction more info	PubMed
enables protein homodimerization activity	IDA Inferred from Direct Assay more info	PubMed
enables superoxide-generating NADPH oxidase activator activity	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in angiogenesis	IBA Inferred from Biological aspect of Ancestor more info
involved_in cell chemotaxis	IDA Inferred from Direct Assay more info	PubMed
involved_in cellular response to growth factor stimulus	IDA Inferred from Direct Assay more info	PubMed
involved_in cellular response to mycophenolic acid	ISS Inferred from Sequence or Structural Similarity more info
involved_in cellular response to platelet-derived growth factor stimulus	ISS Inferred from Sequence or Structural Similarity more info
involved_in embryonic placenta development	ISS Inferred from Sequence or Structural Similarity more info
involved_in gene expression	IDA Inferred from Direct Assay more info	PubMed
involved_in heart development	ISS Inferred from Sequence or Structural Similarity more info
NOT involved_in hemopoiesis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in interleukin-18-mediated signaling pathway	IDA Inferred from Direct Assay more info	PubMed
involved_in intracellular signal transduction	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in metanephric glomerular mesangial cell development	ISS Inferred from Sequence or Structural Similarity more info
involved_in monocyte chemotaxis	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of DNA-templated transcription	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of gene expression	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of miRNA transcription	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of phosphatidylinositol biosynthetic process	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of platelet activation	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of vascular associated smooth muscle cell differentiation	IDA Inferred from Direct Assay more info	PubMed
involved_in paracrine signaling	ISS Inferred from Sequence or Structural Similarity more info
involved_in peptidyl-tyrosine phosphorylation	IDA Inferred from Direct Assay more info	PubMed
involved_in platelet-derived growth factor receptor signaling pathway	IBA Inferred from Biological aspect of Ancestor more info
involved_in platelet-derived growth factor receptor signaling pathway	IDA Inferred from Direct Assay more info	PubMed
involved_in platelet-derived growth factor receptor signaling pathway	NAS Non-traceable Author Statement more info	PubMed
involved_in positive chemotaxis	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of DNA biosynthetic process	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of DNA-templated transcription	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of ERK1 and ERK2 cascade	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of ERK1 and ERK2 cascade	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of MAP kinase activity	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of MAPK cascade	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of blood vessel endothelial cell migration	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of calcium ion import	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of cell division	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of cell migration	IBA Inferred from Biological aspect of Ancestor 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	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of cell population proliferation	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of cell-substrate adhesion	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of chemotaxis	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of endothelial cell proliferation	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of fibroblast proliferation	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of gene expression	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of gene expression	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of glomerular filtration	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of glomerular mesangial cell proliferation	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of hyaluronan biosynthetic process	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of metanephric mesenchymal cell migration	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of metanephric mesenchymal cell migration by platelet-derived growth factor receptor-beta signaling pathway	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of miRNA transcription	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of mitotic nuclear division	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of protein autophosphorylation	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of reactive oxygen species metabolic process	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of smooth muscle cell migration	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of smooth muscle cell proliferation	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of smooth muscle cell proliferation	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of vascular associated smooth muscle cell dedifferentiation	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of vascular associated smooth muscle cell migration	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of vascular associated smooth muscle cell proliferation	IDA Inferred from Direct Assay more info	PubMed
involved_in protein phosphorylation	IDA Inferred from Direct Assay more info	PubMed
involved_in reactive oxygen species metabolic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in response to wounding	IDA Inferred from Direct Assay more info	PubMed
involved_in response to wounding	NAS Non-traceable Author Statement more info	PubMed

Component	Evidence Code	Pubs
located_in Golgi lumen	TAS Traceable Author Statement more info
located_in Golgi membrane	TAS Traceable Author Statement more info
located_in basolateral plasma membrane	ISS Inferred from Sequence or Structural Similarity more info
located_in cell surface	IDA Inferred from Direct Assay more info	PubMed
located_in collagen-containing extracellular matrix	HDA more info	PubMed
located_in cytoplasm	ISS Inferred from Sequence or Structural Similarity more info
located_in endoplasmic reticulum lumen	TAS Traceable Author Statement more info
located_in extracellular region	NAS Non-traceable Author Statement more info	PubMed
located_in extracellular region	TAS Traceable Author Statement more info
is_active_in extracellular space	IBA Inferred from Biological aspect of Ancestor more info
located_in platelet alpha granule lumen	TAS Traceable Author Statement more info
part_of platelet-derived growth factor complex	IPI Inferred from Physical Interaction more info	PubMed

General protein information

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Preferred Names: platelet-derived growth factor subunit B

Names: PDGF subunit B; PDGF, B chain; becaplermin; epididymis secretory sperm binding protein; platelet-derived growth factor 2; platelet-derived growth factor B chain; platelet-derived growth factor beta polypeptide (simian sarcoma viral (v-sis) oncogene homolog); platelet-derived growth factor, beta polypeptide (oncogene SIS); proto-oncogene c-Sis

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_012111.1 RefSeqGene

Range

4971..26594

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_002608.4 → NP_002599.1 platelet-derived growth factor subunit B isoform 1 preproprotein

See identical proteins and their annotated locations for NP_002599.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1), which contains a signal peptide.

Source sequence(s)

BC029822, BC077725, CD386140, M12783, X02811, Z81010

Consensus CDS

CCDS13987.1

UniProtKB/Swiss-Prot

G3XAG8, P01127, P78431, Q15354, Q6FHE7, Q9UF23

UniProtKB/TrEMBL

A0A384NYY3

Related

ENSP00000330382.6, ENST00000331163.11

Conserved Domains (2) summary

pfam00341
Location:97 → 180

PDGF; PDGF/VEGF domain

pfam04692
Location:21 → 93

PDGF_N; Platelet-derived growth factor, N terminal region
NM_033016.3 → NP_148937.1 platelet-derived growth factor subunit B isoform 2

See identical proteins and their annotated locations for NP_148937.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) contains an alternate 5' terminal exon, resulting in the use of an alternate start codon compared to variant (1). The encoded isoform (2) has a shorter and distinct N-terminus, and lacks a signal peptide compared to isoform 1. It is not known whether this isoform (2) is proteolytically processed in the same manner as isoform (1).

Source sequence(s)

BC029822, M12783, X83705, Z81010

Consensus CDS

CCDS33650.1

UniProtKB/Swiss-Prot

P01127

Related

ENSP00000370963.4, ENST00000381551.8

Conserved Domains (2) summary

pfam00341
Location:82 → 165

PDGF; PDGF/VEGF domain

pfam04692
Location:7 → 78

PDGF_N; Platelet-derived growth factor, N terminal region

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000022.11 Reference GRCh38.p14 Primary Assembly

Range

39223359..39244982 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047441394.1 → XP_047297350.1 platelet-derived growth factor subunit B isoform X1
XM_047441393.1 → XP_047297349.1 platelet-derived growth factor subunit B isoform X1

Alternate T2T-CHM13v2.0

Genomic

NC_060946.1 Alternate T2T-CHM13v2.0

Range

39694033..39715652 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054325676.1 → XP_054181651.1 platelet-derived growth factor subunit B isoform X1
XM_054325675.1 → XP_054181650.1 platelet-derived growth factor subunit B isoform X1