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Center for Computational Systems Medicine
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Fusion Gene Summary

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Fusion Gene ORF analysis

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Fusion Genomic Features

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Fusion Protein Features

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Fusion Gene Sequence

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Fusion Gene PPI analysis

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Related Drugs

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Related Diseases

Fusion gene:BCR-PDGFRA (FusionGDB2 ID:9582)

Fusion Gene Summary for BCR-PDGFRA

check button Fusion gene summary
Fusion gene informationFusion gene name: BCR-PDGFRA
Fusion gene ID: 9582
HgeneTgene
Gene symbol

BCR

PDGFRA

Gene ID

613

5156

Gene nameBCR activator of RhoGEF and GTPaseplatelet derived growth factor receptor alpha
SynonymsALL|BCR1|CML|D22S11|D22S662|PHLCD140A|PDGFR-2|PDGFR2
Cytomap

22q11.23

4q12

Type of geneprotein-codingprotein-coding
Descriptionbreakpoint cluster region proteinBCR, RhoGEF and GTPase activating proteinBCR/FGFR1 chimera proteinFGFR1/BCR chimera proteinbreakpoint cluster regionrenal carcinoma antigen NY-REN-26platelet-derived growth factor receptor alphaCD140 antigen-like family member ACD140a antigenPDGF-R-alphaalpha-type platelet-derived growth factor receptorplatelet-derived growth factor receptor 2platelet-derived growth factor receptor, alpha polype
Modification date2020031320200329
UniProtAcc

P11274

P16234

Ensembl transtripts involved in fusion geneENST00000305877, ENST00000359540, 
ENST00000398512, ENST00000436990, 
ENST00000257290, ENST00000508170, 
Fusion gene scores* DoF score22 X 142 X 16=4998418 X 27 X 8=3888
# samples 16317
** MAII scorelog2(163/49984*10)=-4.93852248902354
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(17/3888*10)=-4.51542156746808
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: BCR [Title/Abstract] AND PDGFRA [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointBCR(23652041)-PDGFRA(55141056), # samples:2
Anticipated loss of major functional domain due to fusion event.
* DoF score (Degree of Frequency) = # partners X # break points X # cancer types
** MAII score (Major Active Isofusion Index) = log2(# samples/DoF score*10)

check button Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez
PartnerGeneGO IDGO termPubMed ID
HgeneBCR

GO:0090630

activation of GTPase activity

7479768

TgenePDGFRA

GO:0008284

positive regulation of cell proliferation

10806482

TgenePDGFRA

GO:0010544

negative regulation of platelet activation

8188664

TgenePDGFRA

GO:0018108

peptidyl-tyrosine phosphorylation

1646396|2536956|8188664

TgenePDGFRA

GO:0030335

positive regulation of cell migration

17470632

TgenePDGFRA

GO:0034614

cellular response to reactive oxygen species

24190966

TgenePDGFRA

GO:0038091

positive regulation of cell proliferation by VEGF-activated platelet derived growth factor receptor signaling pathway

17470632

TgenePDGFRA

GO:0046777

protein autophosphorylation

1646396|2536956|8188664

TgenePDGFRA

GO:0048008

platelet-derived growth factor receptor signaling pathway

2536956|10806482

TgenePDGFRA

GO:0048146

positive regulation of fibroblast proliferation

10806482


check buttonFusion gene breakpoints across BCR (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

check buttonFusion gene breakpoints across PDGFRA (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

check button Fusion gene information from two resources (ChiTars 5.0 and ChimerDB 4.0)
* All genome coordinats were lifted-over on hg19.
* Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser.
SourceDiseaseSampleHgeneHchrHbpHstrandTgeneTchrTbpTstrand
ChimerDB4chronic myeloproliferative disordersAY303970BCRchr22

23652041

PDGFRAchr4

55141056

ChiTaRS5.0N/AAY303970BCRchr22

23652041

+PDGFRAchr4

55141056

+


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Fusion Gene ORF analysis for BCR-PDGFRA

check button Open reading frame (ORF) analsis of fusion genes based on Ensembl gene isoform structure.
* Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser.
ORFHenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrand
intron-3CDSENST00000305877ENST00000257290BCRchr22

23652041

PDGFRAchr4

55141056

intron-intronENST00000305877ENST00000508170BCRchr22

23652041

PDGFRAchr4

55141056

intron-3CDSENST00000359540ENST00000257290BCRchr22

23652041

PDGFRAchr4

55141056

intron-intronENST00000359540ENST00000508170BCRchr22

23652041

PDGFRAchr4

55141056

intron-3CDSENST00000398512ENST00000257290BCRchr22

23652041

PDGFRAchr4

55141056

intron-intronENST00000398512ENST00000508170BCRchr22

23652041

PDGFRAchr4

55141056

3UTR-3CDSENST00000436990ENST00000257290BCRchr22

23652041

PDGFRAchr4

55141056

3UTR-intronENST00000436990ENST00000508170BCRchr22

23652041

PDGFRAchr4

55141056

intron-3CDSENST00000305877ENST00000257290BCRchr22

23652041

+PDGFRAchr4

55141056

+
intron-intronENST00000305877ENST00000508170BCRchr22

23652041

+PDGFRAchr4

55141056

+
intron-3CDSENST00000359540ENST00000257290BCRchr22

23652041

+PDGFRAchr4

55141056

+
intron-intronENST00000359540ENST00000508170BCRchr22

23652041

+PDGFRAchr4

55141056

+
intron-3CDSENST00000398512ENST00000257290BCRchr22

23652041

+PDGFRAchr4

55141056

+
intron-intronENST00000398512ENST00000508170BCRchr22

23652041

+PDGFRAchr4

55141056

+
3UTR-3CDSENST00000436990ENST00000257290BCRchr22

23652041

+PDGFRAchr4

55141056

+
3UTR-intronENST00000436990ENST00000508170BCRchr22

23652041

+PDGFRAchr4

55141056

+
5CDS-intronENST00000305877ENST00000508170BCRchr22

23615320

+PDGFRAchr4

55141007

+
5CDS-intronENST00000359540ENST00000508170BCRchr22

23615320

+PDGFRAchr4

55141007

+
In-frameENST00000305877ENST00000257290BCRchr22

23615320

+PDGFRAchr4

55141007

+
In-frameENST00000359540ENST00000257290BCRchr22

23615320

+PDGFRAchr4

55141007

+
intron-3CDSENST00000398512ENST00000257290BCRchr22

23615320

+PDGFRAchr4

55141007

+
intron-3CDSENST00000436990ENST00000257290BCRchr22

23615320

+PDGFRAchr4

55141007

+
intron-intronENST00000398512ENST00000508170BCRchr22

23615320

+PDGFRAchr4

55141007

+
intron-intronENST00000436990ENST00000508170BCRchr22

23615320

+PDGFRAchr4

55141007

+

check buttonORFfinder result based on the fusion transcript sequence of in-frame fusion genes.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandSeq length
(transcript)		BP loci
(transcript)		Predicted start
(transcript)		Predicted stop
(transcript)		Seq length
(amino acids)

check buttonDeepORF prediction of the coding potential based on the fusion transcript sequence of in-frame fusion genes. DeepORF is a coding potential classifier based on convolutional neural network by comparing the real Ribo-seq data. If the no-coding score < 0.5 and coding score > 0.5, then the in-frame fusion transcript is predicted as being likely translated.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandNo-coding scoreCoding score

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Fusion Genomic Features for BCR-PDGFRA


check buttonFusionAI prediction of the potential fusion gene breakpoint based on the pre-mature RNA sequence context (+/- 5kb of individual partner genes, total 20kb length sequence). FusionAI is a fusion gene breakpoint classifier based on convolutional neural network by comparing the fusion positive and negative sequence context of ~ 20K fusion gene data. From here, we can have the relative potentency of the 20K genomic sequence how individual sequnce will be likely used as the gene fusion breakpoints.
HgeneHchrHbpHstrandTgeneTchrTbpTstrand1-pp (fusion gene breakpoint)

check buttonDistribution of 44 human genomic features loci across 20kb length fusion breakpoint regions. We integrated a total of 44 different types of human genomic feature loci information across five big categories including virus integration sites, repeats, structural variants, chromatin states, and gene expression regulation. More details are in help page.

check buttonDistribution of 44 human genomic features loci across 20kb length fusion breakpoint regions that are ovelapped with the top 1% feature importance score regions. More details are in help page.

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Fusion Protein Features for BCR-PDGFRA


check button Go to

FGviewer for the breakpoints of chr22:23615320-chr4:55141007

.
- FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels.
FGviewer

check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
BCR

P11274

PDGFRA

P16234

FUNCTION: Protein with a unique structure having two opposing regulatory activities toward small GTP-binding proteins. The C-terminus is a GTPase-activating protein (GAP) domain which stimulates GTP hydrolysis by RAC1, RAC2 and CDC42. Accelerates the intrinsic rate of GTP hydrolysis of RAC1 or CDC42, leading to down-regulation of the active GTP-bound form (PubMed:7479768, PubMed:1903516, PubMed:17116687). The central Dbl homology (DH) domain functions as guanine nucleotide exchange factor (GEF) that modulates the GTPases CDC42, RHOA and RAC1. Promotes the conversion of CDC42, RHOA and RAC1 from the GDP-bound to the GTP-bound form (PubMed:7479768, PubMed:23940119). The amino terminus contains an intrinsic kinase activity (PubMed:1657398). Functions as an important negative regulator of neuronal RAC1 activity (By similarity). Regulates macrophage functions such as CSF1-directed motility and phagocytosis through the modulation of RAC1 activity (PubMed:17116687). Plays a major role as a RHOA GEF in keratinocytes being involved in focal adhesion formation and keratinocyte differentiation (PubMed:23940119). {ECO:0000250|UniProtKB:Q6PAJ1, ECO:0000269|PubMed:1657398, ECO:0000269|PubMed:17116687, ECO:0000269|PubMed:1903516, ECO:0000269|PubMed:23940119, ECO:0000269|PubMed:7479768}.FUNCTION: Tyrosine-protein kinase that acts as a cell-surface receptor for PDGFA, PDGFB and PDGFC and plays an essential role in the regulation of embryonic development, cell proliferation, survival and chemotaxis. Depending on the context, promotes or inhibits cell proliferation and cell migration. Plays an important role in the differentiation of bone marrow-derived mesenchymal stem cells. Required for normal skeleton development and cephalic closure during embryonic development. Required for normal development of the mucosa lining the gastrointestinal tract, and for recruitment of mesenchymal cells and normal development of intestinal villi. Plays a role in cell migration and chemotaxis in wound healing. Plays a role in platelet activation, secretion of agonists from platelet granules, and in thrombin-induced platelet aggregation. Binding of its cognate ligands - homodimeric PDGFA, homodimeric PDGFB, heterodimers formed by PDGFA and PDGFB or homodimeric PDGFC -leads to the activation of several signaling cascades; the response depends on the nature of the bound ligand and is modulated by the formation of heterodimers between PDGFRA and PDGFRB. Phosphorylates PIK3R1, PLCG1, and PTPN11. Activation of PLCG1 leads to the production of the cellular signaling molecules diacylglycerol and inositol 1,4,5-trisphosphate, mobilization of cytosolic Ca(2+) and the activation of protein kinase C. Phosphorylates PIK3R1, the regulatory subunit of phosphatidylinositol 3-kinase, and thereby mediates activation of the AKT1 signaling pathway. Mediates activation of HRAS and of the MAP kinases MAPK1/ERK2 and/or MAPK3/ERK1. Promotes activation of STAT family members STAT1, STAT3 and STAT5A and/or STAT5B. Receptor signaling is down-regulated by protein phosphatases that dephosphorylate the receptor and its down-stream effectors, and by rapid internalization of the activated receptor. {ECO:0000269|PubMed:10734113, ECO:0000269|PubMed:10947961, ECO:0000269|PubMed:11297552, ECO:0000269|PubMed:12522257, ECO:0000269|PubMed:1646396, ECO:0000269|PubMed:17087943, ECO:0000269|PubMed:1709159, ECO:0000269|PubMed:17141222, ECO:0000269|PubMed:20972453, ECO:0000269|PubMed:21224473, ECO:0000269|PubMed:21596750, ECO:0000269|PubMed:2554309, ECO:0000269|PubMed:8188664, ECO:0000269|PubMed:8760137, ECO:0000269|PubMed:8943348}.

check buttonRetention analysis result of each fusion partner protein across 39 protein features of UniProt such as six molecule processing features, 13 region features, four site features, six amino acid modification features, two natural variation features, five experimental info features, and 3 secondary structure features. Here, because of limited space for viewing, we only show the protein feature retention information belong to the 13 regional features. All retention annotation result can be downloaded at

download page


* Minus value of BPloci means that the break pointn is located before the CDS.
- In-frame and retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note


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Fusion Gene Sequence for BCR-PDGFRA


check button For in-frame fusion transcripts, we provide the fusion transcript sequences and fusion amino acid sequences. To have fusion amino acid sequence, we ran ORFfinder and chose the longest ORF among the all predicted ones.

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Fusion Gene PPI Analysis for BCR-PDGFRA


check button Go to ChiPPI (Chimeric Protein-Protein interactions) to see the chimeric PPI interaction in

ChiPPI page.


check button Protein-protein interactors with each fusion partner protein in wild-type (BIOGRID-3.4.160)
HgeneHgene's interactorsTgeneTgene's interactors


check button - Retained PPIs in in-frame fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenStill interaction with


check button - Lost PPIs in in-frame fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


check button - Retained PPIs, but lost function due to frame-shift fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


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Related Drugs for BCR-PDGFRA


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status
HgeneBCRP11274DB00619ImatinibInhibitorSmall moleculeApproved
HgeneBCRP11274DB00619ImatinibInhibitorSmall moleculeApproved
HgeneBCRP11274DB00619ImatinibInhibitorSmall moleculeApproved
HgeneBCRP11274DB06616BosutinibInhibitorSmall moleculeApproved
HgeneBCRP11274DB06616BosutinibInhibitorSmall moleculeApproved
HgeneBCRP11274DB06616BosutinibInhibitorSmall moleculeApproved
HgeneBCRP11274DB01254DasatinibSmall moleculeApproved|Investigational
HgeneBCRP11274DB01254DasatinibSmall moleculeApproved|Investigational
HgeneBCRP11274DB01254DasatinibSmall moleculeApproved|Investigational
HgeneBCRP11274DB08901PonatinibInhibitorSmall moleculeApproved|Investigational
HgeneBCRP11274DB08901PonatinibInhibitorSmall moleculeApproved|Investigational
HgeneBCRP11274DB08901PonatinibInhibitorSmall moleculeApproved|Investigational
TgenePDGFRAP16234DB00619ImatinibAntagonistSmall moleculeApproved
TgenePDGFRAP16234DB00619ImatinibAntagonistSmall moleculeApproved
TgenePDGFRAP16234DB00619ImatinibAntagonistSmall moleculeApproved
TgenePDGFRAP16234DB06589PazopanibInhibitorSmall moleculeApproved
TgenePDGFRAP16234DB06589PazopanibInhibitorSmall moleculeApproved
TgenePDGFRAP16234DB06589PazopanibInhibitorSmall moleculeApproved
TgenePDGFRAP16234DB08896RegorafenibInhibitorSmall moleculeApproved
TgenePDGFRAP16234DB08896RegorafenibInhibitorSmall moleculeApproved
TgenePDGFRAP16234DB08896RegorafenibInhibitorSmall moleculeApproved
TgenePDGFRAP16234DB09079NintedanibInhibitorSmall moleculeApproved
TgenePDGFRAP16234DB09079NintedanibInhibitorSmall moleculeApproved
TgenePDGFRAP16234DB09079NintedanibInhibitorSmall moleculeApproved
TgenePDGFRAP16234DB10772Foreskin keratinocyte (neonatal)AgonistBiotechApproved
TgenePDGFRAP16234DB10772Foreskin keratinocyte (neonatal)AgonistBiotechApproved
TgenePDGFRAP16234DB10772Foreskin keratinocyte (neonatal)AgonistBiotechApproved
TgenePDGFRAP16234DB14840RipretinibInhibitorSmall moleculeApproved
TgenePDGFRAP16234DB14840RipretinibInhibitorSmall moleculeApproved
TgenePDGFRAP16234DB14840RipretinibInhibitorSmall moleculeApproved
TgenePDGFRAP16234DB00102BecaplerminBiotechApproved|Investigational
TgenePDGFRAP16234DB00102BecaplerminBiotechApproved|Investigational
TgenePDGFRAP16234DB00102BecaplerminBiotechApproved|Investigational
TgenePDGFRAP16234DB01268SunitinibInhibitorSmall moleculeApproved|Investigational
TgenePDGFRAP16234DB01268SunitinibInhibitorSmall moleculeApproved|Investigational
TgenePDGFRAP16234DB01268SunitinibInhibitorSmall moleculeApproved|Investigational
TgenePDGFRAP16234DB06043OlaratumabAntagonistBiotechApproved|Investigational
TgenePDGFRAP16234DB06043OlaratumabAntagonistBiotechApproved|Investigational
TgenePDGFRAP16234DB06043OlaratumabAntagonistBiotechApproved|Investigational
TgenePDGFRAP16234DB06595MidostaurinAntagonist|InhibitorSmall moleculeApproved|Investigational
TgenePDGFRAP16234DB06595MidostaurinAntagonist|InhibitorSmall moleculeApproved|Investigational
TgenePDGFRAP16234DB06595MidostaurinAntagonist|InhibitorSmall moleculeApproved|Investigational
TgenePDGFRAP16234DB08901PonatinibInhibitorSmall moleculeApproved|Investigational
TgenePDGFRAP16234DB08901PonatinibInhibitorSmall moleculeApproved|Investigational
TgenePDGFRAP16234DB08901PonatinibInhibitorSmall moleculeApproved|Investigational
TgenePDGFRAP16234DB09078LenvatinibInhibitorSmall moleculeApproved|Investigational
TgenePDGFRAP16234DB09078LenvatinibInhibitorSmall moleculeApproved|Investigational
TgenePDGFRAP16234DB09078LenvatinibInhibitorSmall moleculeApproved|Investigational
TgenePDGFRAP16234DB12010FostamatinibInhibitorSmall moleculeApproved|Investigational
TgenePDGFRAP16234DB12010FostamatinibInhibitorSmall moleculeApproved|Investigational
TgenePDGFRAP16234DB12010FostamatinibInhibitorSmall moleculeApproved|Investigational
TgenePDGFRAP16234DB12147ErdafitinibSubstrateSmall moleculeApproved|Investigational
TgenePDGFRAP16234DB12147ErdafitinibSubstrateSmall moleculeApproved|Investigational
TgenePDGFRAP16234DB12147ErdafitinibSubstrateSmall moleculeApproved|Investigational

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Related Diseases for BCR-PDGFRA


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneBCRC0005586Bipolar Disorder4PSYGENET
HgeneBCRC0023473Myeloid Leukemia, Chronic3CTD_human;ORPHANET
HgeneBCRC0005699Blast Phase1CTD_human
HgeneBCRC0006413Burkitt Lymphoma1ORPHANET
HgeneBCRC0023893Liver Cirrhosis, Experimental1CTD_human
HgeneBCRC0027022Myeloproliferative disease1CTD_human
HgeneBCRC0027540Necrosis1CTD_human
HgeneBCRC0027659Neoplasms, Experimental1CTD_human
HgeneBCRC0041696Unipolar Depression1PSYGENET
HgeneBCRC1269683Major Depressive Disorder1PSYGENET
HgeneBCRC1292769Precursor B-cell lymphoblastic leukemia1ORPHANET
TgenePDGFRAC0238198Gastrointestinal Stromal Tumors10CGI;CLINGEN;CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
TgenePDGFRAC3179349Gastrointestinal Stromal Sarcoma9CLINGEN;CTD_human;ORPHANET
TgenePDGFRAC0346421Chronic eosinophilic leukemia4ORPHANET
TgenePDGFRAC0206141Idiopathic Hypereosinophilic Syndrome3CTD_human;GENOMICS_ENGLAND
TgenePDGFRAC0006413Burkitt Lymphoma2ORPHANET
TgenePDGFRAC0206142Eosinophilic leukemia2CTD_human
TgenePDGFRAC0206143Loeffler's Endocarditis2CTD_human
TgenePDGFRAC1292769Precursor B-cell lymphoblastic leukemia2ORPHANET
TgenePDGFRAC1540912Hypereosinophilic syndrome2CGI;CTD_human
TgenePDGFRAC0008925Cleft Palate1CTD_human
TgenePDGFRAC0015923Fetal Alcohol Syndrome1PSYGENET
TgenePDGFRAC0018801Heart failure1CTD_human
TgenePDGFRAC0018802Congestive heart failure1CTD_human
TgenePDGFRAC0023212Left-Sided Heart Failure1CTD_human
TgenePDGFRAC0023893Liver Cirrhosis, Experimental1CTD_human
TgenePDGFRAC0024115Lung diseases1CTD_human
TgenePDGFRAC0025149Medulloblastoma1CTD_human
TgenePDGFRAC0035238Congenital abnormality of respiratory system1CTD_human
TgenePDGFRAC0038219Status Dysraphicus1CTD_human
TgenePDGFRAC0080178Spina Bifida1CTD_human
TgenePDGFRAC0205833Medullomyoblastoma1CTD_human
TgenePDGFRAC0206637Mesenchymal Chondrosarcoma1CTD_human
TgenePDGFRAC0235527Heart Failure, Right-Sided1CTD_human
TgenePDGFRAC0266508Rachischisis1CTD_human
TgenePDGFRAC0278510Childhood Medulloblastoma1CTD_human
TgenePDGFRAC0278876Adult Medulloblastoma1CTD_human
TgenePDGFRAC0376634Craniofacial Abnormalities1CTD_human
TgenePDGFRAC0751291Desmoplastic Medulloblastoma1CTD_human
TgenePDGFRAC1275668Melanotic medulloblastoma1CTD_human
TgenePDGFRAC1837218Cleft palate, isolated1CTD_human
TgenePDGFRAC1959583Myocardial Failure1CTD_human
TgenePDGFRAC1961112Heart Decompensation1CTD_human
TgenePDGFRAC2718076Fetal Mummification1CTD_human
TgenePDGFRAC2985290Fetal Alcohol Spectrum Disorders1PSYGENET
TgenePDGFRAC4545381Myeloid and/or lymphoid neoplasm associated with platelet derived growth factor receptor alpha rearrangement1ORPHANET