PDGFRA platelet derived growth factor receptor alpha [Homo sapiens (human)] - Gene

Summary

Official Symbol: PDGFRAprovided by HGNC
Official Full Name: platelet derived growth factor receptor alphaprovided by HGNC
Primary source: HGNC:HGNC:8803
See related: Ensembl:ENSG00000134853 MIM:173490
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: CD140A; PDGFR2; PDGFR-2
Summary: This gene encodes 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 or a heterodimer, composed of both platelet-derived growth factor receptor alpha and beta polypeptides. Studies suggest that this gene plays a role in organ development, wound healing, and tumor progression. Mutations in this gene have been associated with idiopathic hypereosinophilic syndrome, somatic and familial gastrointestinal stromal tumors, and a variety of other cancers. [provided by RefSeq, Mar 2012]
Expression: Ubiquitous expression in ovary (RPKM 74.4), brain (RPKM 24.8) and 20 other tissues See more
Orthologs: mouse all

Genomic context

Location:: 4q12

Exon count:: 28

Annotation release	Status	Assembly	Chr	Location
109.20200228	current	GRCh38.p13 (GCF_000001405.39)	4	NC_000004.12 (54229127..54298247)
105	previous assembly	GRCh37.p13 (GCF_000001405.25)	4	NC_000004.11 (55095264..55164412)

Chromosome 4 - NC_000004.12 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?

Primary/secondary KIT/PDGFRA mutations, BRAF mutations and SDH defects in gastrointestinal stromal tumors cause drug resistance.
Title: Gastrointestinal stromal tumors - Summary of mutational status of the primary/secondary KIT/PDGFRA mutations, BRAF mutations and SDH defects.
Induced pluripotent stem cell-derived mesenchymal stromal cells (iMSCs) are functionally and genetically different from bone marrow-derived mesenchymal stromal cells (BM-MSCs): iMSCs express very high levels of both KDR and MSX2 compared with BM-MSCs, while BM-MSCs had significantly higher levels of PDGFRalpha.
Title: Induced Pluripotent Stem Cell-Derived Mesenchymal Stromal Cells Are Functionally and Genetically Different From Bone Marrow-Derived Mesenchymal Stromal Cells.
PDGFRA-mutant gastrointestinal stromal tumors harbor more immune cells with increased cytolytic activity when compared to KIT-mutant gastrointestinal stromal tumor cells
Title: Differential immune profiles distinguish the mutational subtypes of gastrointestinal stromal tumor.
-derived growth factor receptor (PDGFR)alpha- and PDGFRbeta- expressing perivascular cell populations were identified as leptin producing within skeletal muscle of mice and humans. Furthermore, in response to 2 weeks of high-fat feeding, PDGFRbeta+ but not PDGFRalpha+ cells increased leptin production.
Title: Leptin is a physiological regulator of skeletal muscle angiogenesis and is locally produced by PDGFRα and PDGFRβ expressing perivascular cells.
PDGFRalpha signaling is essential for cardiac fibroblast maintenance.
Title: Platelet-derived growth factor receptor-α is essential for cardiac fibroblast survival.
Nine gastrointestinal stromal tumors (16%) had mutations of the PDGFRA gene.
Title: Malignancies associated with GIST: a retrospective study with molecular analysis of KIT and PDGFRA.
Circulating tumor DNA (CtDNA) harboring tumor-specific c-Kit protooncogene (cKIT) or platelet derived growth factor receptor alpha (PDGFRA) mutations was detected in in gastrointestinal stromal tumor (GIST).
Title: Circulating cKIT and PDGFRA DNA indicates disease activity in Gastrointestinal Stromal Tumor (GIST).
Interactions between cadherin-11 and PDGFRalpha signaling link cell adhesion and cell proliferation.
Title: Interactions between cadherin-11 and platelet-derived growth factor receptor-alpha signaling link cell adhesion and proliferation.
miR3423p was proposed to inhibit the proliferation, migration, invasion and G1/S phase transition of HTR8/SVneo cells by suppressing PDGFRA.
Title: miR‑342‑3p suppresses cell migration and invasion in preeclampsia by targeting platelet‑derived growth factor receptor α.
PDGFRA/Pdgfra gene is regulated by at least seven first exons in human and mouse.
Title: Platelet-derived growth factor receptor α gene is regulated by multiple first exons.

Submit: New GeneRIF Correction See all GeneRIFs (383)

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
Idiopathic hypereosinophilic syndrome MedGen: C0206141 OMIM: 607685 GeneReviews: Not available	Compare labs
Polyps, multiple and recurrent inflammatory fibroid, gastrointestinal MedGen: C1868000 OMIM: 175510 GeneReviews: Not available	not available

NHGRI GWAS Catalog

Description
A genome-wide association study for corneal curvature identifies the platelet-derived growth factor receptor &#x003b1; gene as a quantitative trait locus for eye size in white Europeans. NHGRI GWA Catalog NHGRI GWA CatalogPubMed
Association of variants in FRAP1 and PDGFRA with corneal curvature in Asian populations from Singapore. NHGRI GWA Catalog NHGRI GWA CatalogPubMed
CMPK1 and RBP3 are associated with corneal curvature in Asian populations. NHGRI GWA Catalog NHGRI GWA CatalogPubMed
Common variants in the GDF5-UQCC region are associated with variation in human height. NHGRI GWA Catalog NHGRI GWA CatalogPubMed
Genome-wide association study of hematological and biochemical traits in a Japanese population. NHGRI GWA Catalog NHGRI GWA CatalogPubMed
Genome-wide meta-analysis of five Asian cohorts identifies PDGFRA as a susceptibility locus for corneal astigmatism. NHGRI GWA Catalog NHGRI GWA CatalogPubMed
Identification of a variant in KDR associated with serum VEGFR2 and pharmacodynamics of pazopanib. NHGRI GWA Catalog NHGRI GWA CatalogPubMed
Lupus nephritis susceptibility Loci in women with systemic lupus erythematosus. NHGRI GWA Catalog NHGRI GWA CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

G43580 (e-PCR)
- UniSTS:95026

PDGFRA__1207 (e-PCR)
- UniSTS:277576

PDGFRA__v331 (e-PCR)
- UniSTS:277576

D4S1394 (e-PCR)
- UniSTS:79704

SHGC-85185 (e-PCR)
- UniSTS:104030

G34454 (e-PCR)
- UniSTS:2145

RH68733 (e-PCR)
- UniSTS:12701

GDB:626067 (e-PCR)
- UniSTS:158383

GDB:626070 (e-PCR)
- UniSTS:158384

SHGC-8069 (e-PCR)
- UniSTS:83678

Homology

Homologs of the PDGFRA gene: The PDGFRA gene is conserved in chimpanzee, Rhesus monkey, dog, cow, mouse, rat, chicken, zebrafish, C.elegans, and frog.
Orthologs from Annotation Pipeline: 320 organisms have orthologs with human gene PDGFRA
Orthologs

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
ATP binding	IEA Inferred from Electronic Annotation more info
growth factor binding	IBA Inferred from Biological aspect of Ancestor more info	PubMed
platelet-derived growth factor alpha-receptor activity	IBA Inferred from Biological aspect of Ancestor more info	PubMed
platelet-derived growth factor alpha-receptor activity	IDA Inferred from Direct Assay more info	PubMed
platelet-derived growth factor alpha-receptor activity	IMP Inferred from Mutant Phenotype more info	PubMed
platelet-derived growth factor binding	IBA Inferred from Biological aspect of Ancestor more info	PubMed
platelet-derived growth factor binding	IDA Inferred from Direct Assay more info	PubMed
platelet-derived growth factor binding	IPI Inferred from Physical Interaction more info	PubMed
platelet-derived growth factor receptor binding	IPI Inferred from Physical Interaction more info	PubMed
protein binding	IPI Inferred from Physical Interaction more info	PubMed
protein homodimerization activity	IDA Inferred from Direct Assay more info	PubMed
protein kinase activity	IDA Inferred from Direct Assay more info	PubMed
protein-containing complex binding	IEA Inferred from Electronic Annotation more info
transmembrane receptor protein tyrosine kinase activity	IBA Inferred from Biological aspect of Ancestor more info	PubMed
transmembrane receptor protein tyrosine kinase activity	IDA Inferred from Direct Assay more info	PubMed
vascular endothelial growth factor binding	IPI Inferred from Physical Interaction more info	PubMed
vascular endothelial growth factor-activated receptor activity	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
Leydig cell differentiation	IEA Inferred from Electronic Annotation more info
MAPK cascade	TAS Traceable Author Statement more info
adrenal gland development	IEA Inferred from Electronic Annotation more info
cardiac myofibril assembly	ISS Inferred from Sequence or Structural Similarity more info
cell activation	TAS Traceable Author Statement more info	PubMed
cell chemotaxis	IMP Inferred from Mutant Phenotype more info	PubMed
cellular response to amino acid stimulus	IEA Inferred from Electronic Annotation more info
cellular response to reactive oxygen species	IDA Inferred from Direct Assay more info	PubMed
embryonic cranial skeleton morphogenesis	IBA Inferred from Biological aspect of Ancestor more info	PubMed
embryonic cranial skeleton morphogenesis	ISS Inferred from Sequence or Structural Similarity more info
embryonic digestive tract morphogenesis	ISS Inferred from Sequence or Structural Similarity more info
embryonic skeletal system morphogenesis	ISS Inferred from Sequence or Structural Similarity more info
estrogen metabolic process	IEA Inferred from Electronic Annotation more info
extracellular matrix organization	IEA Inferred from Electronic Annotation more info
face morphogenesis	IEA Inferred from Electronic Annotation more info
hematopoietic progenitor cell differentiation	IBA Inferred from Biological aspect of Ancestor more info	PubMed
in utero embryonic development	IEA Inferred from Electronic Annotation more info
lung development	IEA Inferred from Electronic Annotation more info
luteinization	ISS Inferred from Sequence or Structural Similarity more info
male genitalia development	IEA Inferred from Electronic Annotation more info
metanephric glomerular capillary formation	ISS Inferred from Sequence or Structural Similarity more info
multicellular organism development	IBA Inferred from Biological aspect of Ancestor more info	PubMed
negative regulation of platelet activation	IDA Inferred from Direct Assay more info	PubMed
odontogenesis of dentin-containing tooth	IEA Inferred from Electronic Annotation more info
peptidyl-tyrosine phosphorylation	IDA Inferred from Direct Assay more info	PubMed
phosphatidylinositol-mediated signaling	IMP Inferred from Mutant Phenotype more info	PubMed
platelet aggregation	IMP Inferred from Mutant Phenotype more info	PubMed
platelet-derived growth factor receptor signaling pathway	IDA Inferred from Direct Assay more info	PubMed
platelet-derived growth factor receptor-alpha signaling pathway	IMP Inferred from Mutant Phenotype more info	PubMed
positive regulation of ERK1 and ERK2 cascade	IMP Inferred from Mutant Phenotype more info	PubMed
positive regulation of cell migration	IDA Inferred from Direct Assay more info	PubMed
positive regulation of cell migration	IMP Inferred from Mutant Phenotype more info	PubMed
positive regulation of cell proliferation	IDA Inferred from Direct Assay more info	PubMed
positive regulation of cell proliferation	IMP Inferred from Mutant Phenotype more info	PubMed
positive regulation of cell proliferation by VEGF-activated platelet derived growth factor receptor signaling pathway	IDA Inferred from Direct Assay more info	PubMed
positive regulation of cytosolic calcium ion concentration	IMP Inferred from Mutant Phenotype more info	PubMed
positive regulation of fibroblast proliferation	IDA Inferred from Direct Assay more info	PubMed
positive regulation of kinase activity	IBA Inferred from Biological aspect of Ancestor more info	PubMed
positive regulation of phosphatidylinositol 3-kinase activity	IMP Inferred from Mutant Phenotype more info	PubMed
positive regulation of phosphatidylinositol 3-kinase signaling	TAS Traceable Author Statement more info	PubMed
positive regulation of phospholipase C activity	IMP Inferred from Mutant Phenotype more info	PubMed
positive regulation of protein kinase B signaling	TAS Traceable Author Statement more info
protein autophosphorylation	IDA Inferred from Direct Assay more info	PubMed
regulation of actin cytoskeleton reorganization	TAS Traceable Author Statement more info	PubMed
regulation of chemotaxis	IMP Inferred from Mutant Phenotype more info	PubMed
regulation of mesenchymal stem cell differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
retina vasculature development in camera-type eye	ISS Inferred from Sequence or Structural Similarity more info
roof of mouth development	IEA Inferred from Electronic Annotation more info
signal transduction involved in regulation of gene expression	IEA Inferred from Electronic Annotation more info
transmembrane receptor protein tyrosine kinase signaling pathway	IBA Inferred from Biological aspect of Ancestor more info	PubMed
viral process	IEA Inferred from Electronic Annotation more info
wound healing	ISS Inferred from Sequence or Structural Similarity more info

Component	Evidence Code	Pubs
Golgi apparatus	ISS Inferred from Sequence or Structural Similarity more info
cell	IEA Inferred from Electronic Annotation more info
cell junction	IDA Inferred from Direct Assay more info
cilium	ISS Inferred from Sequence or Structural Similarity more info
cytoplasm	ISS Inferred from Sequence or Structural Similarity more info
external side of plasma membrane	IEA Inferred from Electronic Annotation more info
integral component of plasma membrane	IBA Inferred from Biological aspect of Ancestor more info	PubMed
integral component of plasma membrane	IDA Inferred from Direct Assay more info	PubMed
intrinsic component of plasma membrane	IDA Inferred from Direct Assay more info	PubMed
membrane	HDA more info	PubMed
microvillus	IEA Inferred from Electronic Annotation more info
nucleoplasm	IDA Inferred from Direct Assay more info
nucleus	ISS Inferred from Sequence or Structural Similarity more info
plasma membrane	IDA Inferred from Direct Assay more info
plasma membrane	TAS Traceable Author Statement more info
protein-containing complex	IDA Inferred from Direct Assay more info	PubMed
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 alpha

Names: CD140 antigen-like family member A; CD140a antigen; PDGF-R-alpha; alpha-type platelet-derived growth factor receptor; platelet-derived growth factor receptor 2; platelet-derived growth factor receptor, alpha polypeptide

NP_001334756.1

EC 2.7.10.1

NP_001334757.1

EC 2.7.10.1

NP_001334758.1

EC 2.7.10.1

NP_001334759.1

EC 2.7.10.1

NP_006197.1

EC 2.7.10.1

XP_005265800.1

EC 2.7.10.1

XP_006714104.1

EC 2.7.10.1

XP_016863770.1

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_009250.1 RefSeqGene

Range

5001..74149

Download

GenBank, FASTA, Sequence Viewer (Graphics), LRG_309

mRNA and Protein(s)

NM_001347827.2 → NP_001334756.1 platelet-derived growth factor receptor alpha isoform 2 precursor

Status: REVIEWED

Description

Transcript Variant: This variant (2) includes an alternate 3' terminal exon, which results in a frameshift and an early stop codon compared to variant 1. The encoded isoform (2) is shorter and has a distinct C-terminus compared to isoform 1.

Source sequence(s)

AC098587, AC138779, BU737962

Related

ENSP00000424218.1, ENST00000509490.5
NM_001347828.2 → NP_001334757.1 platelet-derived growth factor receptor alpha isoform 3

Status: REVIEWED

Description

Transcript Variant: This variant (3) contains a novel 5' UTR and 5' coding region compared to variant 1. The encoded isoform (3) is longer, has a distinct N-terminus and lacks a predicted signal peptide compared to isoform 1.

Source sequence(s)

AC098587, AC138779, FN174599
NM_001347829.2 → NP_001334758.1 platelet-derived growth factor receptor alpha isoform 1 precursor

Status: REVIEWED

Description

Transcript Variant: This variant (5) differs in the 5' UTR compared to variant 1. Both variants 1 and 5 encode the same isoform (1).

Source sequence(s)

AC098587, AC138779, FN174599

Consensus CDS

CCDS3495.1

UniProtKB/Swiss-Prot

P16234
NM_001347830.1 → NP_001334759.1 platelet-derived growth factor receptor alpha isoform 4

Status: REVIEWED

Description

Transcript Variant: This variant (4) contains a novel 5' UTR and 5' coding region compared to variant 1. The encoded isoform (3) is longer, has a distinct N-terminus and lacks a predicted signal peptide compared to isoform 1.

Source sequence(s)

AC098587, AC138779, FN174599
NM_006206.6 → NP_006197.1 platelet-derived growth factor receptor alpha isoform 1 precursor

See identical proteins and their annotated locations for NP_006197.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).

Source sequence(s)

AC098587, DA678599, FN174599, M21574

Consensus CDS

CCDS3495.1

UniProtKB/Swiss-Prot

P16234

Related

ENSP00000257290.5, ENST00000257290.10

Conserved Domains (6) summary

cd04972
Location:415 → 497

Ig_TrkABC_d4; Fourth domain (immunoglobulin-like) of Trk receptors TrkA, TrkB and TrkC

cd05859
Location:313 → 413

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

cd05861
Location:228 → 311

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

cd05105
Location:555 → 956

PTKc_PDGFR_alpha; Catalytic domain of the Protein Tyrosine Kinase, Platelet Derived Growth Factor Receptor alpha

smart00409
Location:223 → 293

IG; Immunoglobulin

pfam07714
Location:593 → 953

Pkinase_Tyr; Protein tyrosine kinase

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.

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

Reference GRCh38.p13 Primary Assembly

Genomic

NC_000004.12 Reference GRCh38.p13 Primary Assembly

Range

54229127..54298247

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006714041.3 → XP_006714104.1 platelet-derived growth factor receptor alpha isoform X2

Conserved Domains (6) summary

cd04972
Location:440 → 522

Ig_TrkABC_d4; Fourth domain (immunoglobulin-like) of Trk receptors TrkA, TrkB and TrkC

cd05859
Location:338 → 438

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

cd05861
Location:253 → 336

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

smart00410
Location:248 → 318

IG_like; Immunoglobulin like

cl11960
Location:63 → 137

Ig; Immunoglobulin domain

cl21453
Location:580 → 797

PKc_like; Protein Kinases, catalytic domain
XM_005265743.1 → XP_005265800.1 platelet-derived growth factor receptor alpha isoform X1

See identical proteins and their annotated locations for XP_005265800.1

UniProtKB/Swiss-Prot

P16234

Conserved Domains (6) summary

cd04972
Location:415 → 497

Ig_TrkABC_d4; Fourth domain (immunoglobulin-like) of Trk receptors TrkA, TrkB and TrkC

cd05859
Location:313 → 413

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

cd05861
Location:228 → 311

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

cd05105
Location:555 → 956

PTKc_PDGFR_alpha; Catalytic domain of the Protein Tyrosine Kinase, Platelet Derived Growth Factor Receptor alpha

smart00409
Location:223 → 293

IG; Immunoglobulin

pfam07714
Location:593 → 953

Pkinase_Tyr; Protein tyrosine kinase
XM_017008281.1 → XP_016863770.1 platelet-derived growth factor receptor alpha isoform X3