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; AllianceGenome:HGNC:8803
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
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Genomic context

Location:: 4q12

Exon count:: 30

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	4	NC_000004.12 (54229293..54298245)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	4	NC_060928.1 (57718046..57786996)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	4	NC_000004.11 (55095460..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?

PDGFRA, KIT, and KDR Gene Amplification in Glioblastoma: Heterogeneity and Clinical Significance.
Title: PDGFRA, KIT, and KDR Gene Amplification in Glioblastoma: Heterogeneity and Clinical Significance.
Identification of an Activating PDGFRA Deletion in a Novel Sinonasal Soft Tissue Neoplasm.
Title: Identification of an Activating PDGFRA Deletion in a Novel Sinonasal Soft Tissue Neoplasm.
Isocitrate dehydrogenase 1 mutation drives leukemogenesis by PDGFRA activation due to insulator disruption in acute myeloid leukemia (AML).
Title: Isocitrate dehydrogenase 1 mutation drives leukemogenesis by PDGFRA activation due to insulator disruption in acute myeloid leukemia (AML).
Caveolin-1 expression predicts favourable outcome and correlates with PDGFRA mutations in gastrointestinal stromal tumours (GISTs).
Title: Caveolin-1 expression predicts favourable outcome and correlates with PDGFRA mutations in gastrointestinal stromal tumours (GISTs).
Clinicopathological and therapeutic analysis of PDGFRA mutated gastrointestinal stromal tumor.
Title: Clinicopathological and therapeutic analysis of PDGFRA mutated gastrointestinal stromal tumor.
Association of MTOR and PDGFRA gene polymorphisms with different degrees of myopia severity.
Title: Association of MTOR and PDGFRA gene polymorphisms with different degrees of myopia severity.
Association of genetic variants in PDGFRA with high myopia in the Han population of southwestern China.
Title: Association of genetic variants in PDGFRA with high myopia in the Han population of southwestern China.
PDGF/PDGFR: A Possible Molecular Target in Scleroderma Fibrosis.
Title: PDGF/PDGFR: A Possible Molecular Target in Scleroderma Fibrosis.
Platelet-Derived Growth Factor Receptor Type alpha Activation Drives Pulmonary Vascular Remodeling Via Progenitor Cell Proliferation and Induces Pulmonary Hypertension.
Title: Platelet-Derived Growth Factor Receptor Type α Activation Drives Pulmonary Vascular Remodeling Via Progenitor Cell Proliferation and Induces Pulmonary Hypertension.
EPHA2 mediates PDGFA activity and functions together with PDGFRA as prognostic marker and therapeutic target in glioblastoma.
Title: EPHA2 mediates PDGFA activity and functions together with PDGFRA as prognostic marker and therapeutic target in glioblastoma.

Submit: New GeneRIF Correction See all GeneRIFs (419)

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: C5193005 OMIM: 175510 GeneReviews: Not available	Compare labs

EBI 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. EBI GWAS Catalog EBI GWAS CatalogPubMed
Association of variants in FRAP1 and PDGFRA with corneal curvature in Asian populations from Singapore. EBI GWAS Catalog EBI GWAS CatalogPubMed
CMPK1 and RBP3 are associated with corneal curvature in Asian populations. EBI GWAS Catalog EBI GWAS CatalogPubMed
Common variants in the GDF5-UQCC region are associated with variation in human height. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study of hematological and biochemical traits in a Japanese population. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide meta-analysis of five Asian cohorts identifies PDGFRA as a susceptibility locus for corneal astigmatism. EBI GWAS Catalog EBI GWAS CatalogPubMed
Identification of a variant in KDR associated with serum VEGFR2 and pharmacodynamics of pazopanib. EBI GWAS Catalog EBI GWAS CatalogPubMed
Lupus nephritis susceptibility Loci in women with systemic lupus erythematosus. EBI GWAS Catalog EBI GWAS 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

Gene Ontology Provided by GOA

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

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

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

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

XP_047271722.1

EC 2.7.10.1

XP_047271723.1

EC 2.7.10.1

XP_054206134.1

EC 2.7.10.1

XP_054206135.1

EC 2.7.10.1

XP_054206136.1

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

B2RE69, E9PBH0, P16234, Q6P4H5, Q96KZ7, Q9UD28

Conserved Domains (4) summary

cd05105
Location:555 → 956

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

pfam13927
Location:28 → 100

Ig_3; Immunoglobulin domain

cd05859
Location:313 → 413

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

cd05861
Location:212 → 310

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
NM_001347830.2 → 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

B2RE69, E9PBH0, P16234, Q6P4H5, Q96KZ7, Q9UD28

Related

ENSP00000257290.5, ENST00000257290.10

Conserved Domains (4) summary

cd05105
Location:555 → 956

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

pfam13927
Location:28 → 100

Ig_3; Immunoglobulin domain

cd05859
Location:313 → 413

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

cd05861
Location:212 → 310

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

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000004.12 Reference GRCh38.p14 Primary Assembly

Range

54229293..54298245

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006714041.4 → 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_005265743.2 → 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

B2RE69, E9PBH0, P16234, Q6P4H5, Q96KZ7, Q9UD28

Conserved Domains (4) summary

cd05105
Location:555 → 956

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

pfam13927
Location:28 → 100

Ig_3; Immunoglobulin domain

cd05859
Location:313 → 413

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

cd05861
Location:212 → 310

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
XM_047415767.1 → XP_047271723.1 platelet-derived growth factor receptor alpha isoform X1

UniProtKB/Swiss-Prot

B2RE69, E9PBH0, P16234, Q6P4H5, Q96KZ7, Q9UD28
XM_047415766.1 → XP_047271722.1 platelet-derived growth factor receptor alpha isoform X1

UniProtKB/Swiss-Prot

B2RE69, E9PBH0, P16234, Q6P4H5, Q96KZ7, Q9UD28
XM_017008281.2 → XP_016863770.1 platelet-derived growth factor receptor alpha isoform X3

Alternate T2T-CHM13v2.0

Genomic

NC_060928.1 Alternate T2T-CHM13v2.0

Range

57718046..57786996

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054350160.1 → XP_054206135.1 platelet-derived growth factor receptor alpha isoform X2
XM_054350159.1 → XP_054206134.1 platelet-derived growth factor receptor alpha isoform X1

UniProtKB/Swiss-Prot

B2RE69, E9PBH0, P16234, Q6P4H5, Q96KZ7, Q9UD28
XM_054350161.1 → XP_054206136.1 platelet-derived growth factor receptor alpha isoform X3