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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:BCAR1-PGA5 (FusionGDB2 ID:9161)

Fusion Gene Summary for BCAR1-PGA5

check button Fusion gene summary
Fusion gene informationFusion gene name: BCAR1-PGA5
Fusion gene ID: 9161
HgeneTgene
Gene symbol

BCAR1

PGA5

Gene ID

9564

5222

Gene nameBCAR1 scaffold protein, Cas family memberpepsinogen A5
SynonymsCAS|CAS1|CASS1|CRKAS|P130CasPg5
Cytomap

16q23.1

11q12.2

Type of geneprotein-codingprotein-coding
Descriptionbreast cancer anti-estrogen resistance protein 1BCAR1, Cas family scaffold proteinBCAR1, Cas family scaffolding proteinCas scaffolding protein family member 1Crk-associated substrate p130Caspepsin A-5Pepsin A-4Pepsinogen-4pepsin Apepsinogen 5, group I (pepsinogen A)pepsinogen-5
Modification date2020032720200313
UniProtAcc

P56945

.
Ensembl transtripts involved in fusion geneENST00000162330, ENST00000393420, 
ENST00000393422, ENST00000418647, 
ENST00000420641, ENST00000535626, 
ENST00000538440, ENST00000542031, 
ENST00000546196, ENST00000566982, 
ENST00000312403, ENST00000451616, 
ENST00000541528, 
Fusion gene scores* DoF score4 X 4 X 5=8012 X 25 X 5=1500
# samples 613
** MAII scorelog2(6/80*10)=-0.415037499278844
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(13/1500*10)=-3.52837897235479
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: BCAR1 [Title/Abstract] AND PGA5 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointBCAR1(75297845)-PGA5(61017138), # samples:1
BCAR1(75297845)-PGA5(60997388), # samples:1
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
HgeneBCAR1

GO:0007015

actin filament organization

16105984

HgeneBCAR1

GO:0007229

integrin-mediated signaling pathway

8649368

HgeneBCAR1

GO:0010595

positive regulation of endothelial cell migration

21245381

HgeneBCAR1

GO:0016477

cell migration

9425168

HgeneBCAR1

GO:0030335

positive regulation of cell migration

9472046

HgeneBCAR1

GO:0050851

antigen receptor-mediated signaling pathway

10587647

HgeneBCAR1

GO:0050853

B cell receptor signaling pathway

9020138

HgeneBCAR1

GO:0086100

endothelin receptor signaling pathway

19086031


check buttonFusion gene breakpoints across BCAR1 (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 PGA5 (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
ChimerDB4ESCATCGA-L5-A4OJBCAR1chr16

75297845

-PGA5chr11

60997388

+
ChimerDB4ESCATCGA-L5-A4OJBCAR1chr16

75297845

-PGA5chr11

61017138

+


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Fusion Gene ORF analysis for BCAR1-PGA5

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-3CDSENST00000162330ENST00000312403BCAR1chr16

75297845

-PGA5chr11

61017138

+
intron-3CDSENST00000162330ENST00000451616BCAR1chr16

75297845

-PGA5chr11

61017138

+
intron-3CDSENST00000393420ENST00000312403BCAR1chr16

75297845

-PGA5chr11

61017138

+
intron-3CDSENST00000393420ENST00000451616BCAR1chr16

75297845

-PGA5chr11

61017138

+
intron-3CDSENST00000393422ENST00000312403BCAR1chr16

75297845

-PGA5chr11

61017138

+
intron-3CDSENST00000393422ENST00000451616BCAR1chr16

75297845

-PGA5chr11

61017138

+
intron-3CDSENST00000418647ENST00000312403BCAR1chr16

75297845

-PGA5chr11

61017138

+
intron-3CDSENST00000418647ENST00000451616BCAR1chr16

75297845

-PGA5chr11

61017138

+
intron-3CDSENST00000420641ENST00000312403BCAR1chr16

75297845

-PGA5chr11

61017138

+
intron-3CDSENST00000420641ENST00000451616BCAR1chr16

75297845

-PGA5chr11

61017138

+
intron-3CDSENST00000535626ENST00000312403BCAR1chr16

75297845

-PGA5chr11

61017138

+
intron-3CDSENST00000535626ENST00000451616BCAR1chr16

75297845

-PGA5chr11

61017138

+
intron-3CDSENST00000538440ENST00000312403BCAR1chr16

75297845

-PGA5chr11

61017138

+
intron-3CDSENST00000538440ENST00000451616BCAR1chr16

75297845

-PGA5chr11

61017138

+
intron-3CDSENST00000542031ENST00000312403BCAR1chr16

75297845

-PGA5chr11

61017138

+
intron-3CDSENST00000542031ENST00000451616BCAR1chr16

75297845

-PGA5chr11

61017138

+
intron-3CDSENST00000546196ENST00000312403BCAR1chr16

75297845

-PGA5chr11

61017138

+
intron-3CDSENST00000546196ENST00000451616BCAR1chr16

75297845

-PGA5chr11

61017138

+
intron-3CDSENST00000566982ENST00000312403BCAR1chr16

75297845

-PGA5chr11

61017138

+
intron-3CDSENST00000566982ENST00000451616BCAR1chr16

75297845

-PGA5chr11

61017138

+
intron-5UTRENST00000162330ENST00000541528BCAR1chr16

75297845

-PGA5chr11

61017138

+
intron-5UTRENST00000393420ENST00000541528BCAR1chr16

75297845

-PGA5chr11

61017138

+
intron-5UTRENST00000393422ENST00000541528BCAR1chr16

75297845

-PGA5chr11

61017138

+
intron-5UTRENST00000418647ENST00000541528BCAR1chr16

75297845

-PGA5chr11

61017138

+
intron-5UTRENST00000420641ENST00000541528BCAR1chr16

75297845

-PGA5chr11

61017138

+
intron-5UTRENST00000535626ENST00000541528BCAR1chr16

75297845

-PGA5chr11

61017138

+
intron-5UTRENST00000538440ENST00000541528BCAR1chr16

75297845

-PGA5chr11

61017138

+
intron-5UTRENST00000542031ENST00000541528BCAR1chr16

75297845

-PGA5chr11

61017138

+
intron-5UTRENST00000546196ENST00000541528BCAR1chr16

75297845

-PGA5chr11

61017138

+
intron-5UTRENST00000566982ENST00000541528BCAR1chr16

75297845

-PGA5chr11

61017138

+
intron-intronENST00000162330ENST00000312403BCAR1chr16

75297845

-PGA5chr11

60997388

+
intron-intronENST00000162330ENST00000451616BCAR1chr16

75297845

-PGA5chr11

60997388

+
intron-intronENST00000162330ENST00000541528BCAR1chr16

75297845

-PGA5chr11

60997388

+
intron-intronENST00000393420ENST00000312403BCAR1chr16

75297845

-PGA5chr11

60997388

+
intron-intronENST00000393420ENST00000451616BCAR1chr16

75297845

-PGA5chr11

60997388

+
intron-intronENST00000393420ENST00000541528BCAR1chr16

75297845

-PGA5chr11

60997388

+
intron-intronENST00000393422ENST00000312403BCAR1chr16

75297845

-PGA5chr11

60997388

+
intron-intronENST00000393422ENST00000451616BCAR1chr16

75297845

-PGA5chr11

60997388

+
intron-intronENST00000393422ENST00000541528BCAR1chr16

75297845

-PGA5chr11

60997388

+
intron-intronENST00000418647ENST00000312403BCAR1chr16

75297845

-PGA5chr11

60997388

+
intron-intronENST00000418647ENST00000451616BCAR1chr16

75297845

-PGA5chr11

60997388

+
intron-intronENST00000418647ENST00000541528BCAR1chr16

75297845

-PGA5chr11

60997388

+
intron-intronENST00000420641ENST00000312403BCAR1chr16

75297845

-PGA5chr11

60997388

+
intron-intronENST00000420641ENST00000451616BCAR1chr16

75297845

-PGA5chr11

60997388

+
intron-intronENST00000420641ENST00000541528BCAR1chr16

75297845

-PGA5chr11

60997388

+
intron-intronENST00000535626ENST00000312403BCAR1chr16

75297845

-PGA5chr11

60997388

+
intron-intronENST00000535626ENST00000451616BCAR1chr16

75297845

-PGA5chr11

60997388

+
intron-intronENST00000535626ENST00000541528BCAR1chr16

75297845

-PGA5chr11

60997388

+
intron-intronENST00000538440ENST00000312403BCAR1chr16

75297845

-PGA5chr11

60997388

+
intron-intronENST00000538440ENST00000451616BCAR1chr16

75297845

-PGA5chr11

60997388

+
intron-intronENST00000538440ENST00000541528BCAR1chr16

75297845

-PGA5chr11

60997388

+
intron-intronENST00000542031ENST00000312403BCAR1chr16

75297845

-PGA5chr11

60997388

+
intron-intronENST00000542031ENST00000451616BCAR1chr16

75297845

-PGA5chr11

60997388

+
intron-intronENST00000542031ENST00000541528BCAR1chr16

75297845

-PGA5chr11

60997388

+
intron-intronENST00000546196ENST00000312403BCAR1chr16

75297845

-PGA5chr11

60997388

+
intron-intronENST00000546196ENST00000451616BCAR1chr16

75297845

-PGA5chr11

60997388

+
intron-intronENST00000546196ENST00000541528BCAR1chr16

75297845

-PGA5chr11

60997388

+
intron-intronENST00000566982ENST00000312403BCAR1chr16

75297845

-PGA5chr11

60997388

+
intron-intronENST00000566982ENST00000451616BCAR1chr16

75297845

-PGA5chr11

60997388

+
intron-intronENST00000566982ENST00000541528BCAR1chr16

75297845

-PGA5chr11

60997388

+

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 BCAR1-PGA5


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 BCAR1-PGA5


check button Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/:75297845/:61017138)
- FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels.
- How to search
1. Put your fusion gene symbol.
2. Press the tab key until there will be shown the breakpoint information filled.
4. Go down and press 'Search' tab twice.
4. Go down to have the hyperlink of the search result.
5. Click the hyperlink.
6. See the FGviewer result for your fusion gene.
FGviewer

check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
BCAR1

P56945

.
FUNCTION: Docking protein which plays a central coordinating role for tyrosine kinase-based signaling related to cell adhesion (PubMed:12832404, PubMed:12432078). Implicated in induction of cell migration and cell branching (PubMed:12432078, PubMed:12832404, PubMed:17038317). Involved in the BCAR3-mediated inhibition of TGFB signaling (By similarity). {ECO:0000250|UniProtKB:Q61140, ECO:0000269|PubMed:12432078, ECO:0000269|PubMed:12832404, ECO:0000269|PubMed:17038317}.FUNCTION: Transcriptional activator which is required for calcium-dependent dendritic growth and branching in cortical neurons. Recruits CREB-binding protein (CREBBP) to nuclear bodies. Component of the CREST-BRG1 complex, a multiprotein complex that regulates promoter activation by orchestrating a calcium-dependent release of a repressor complex and a recruitment of an activator complex. In resting neurons, transcription of the c-FOS promoter is inhibited by BRG1-dependent recruitment of a phospho-RB1-HDAC1 repressor complex. Upon calcium influx, RB1 is dephosphorylated by calcineurin, which leads to release of the repressor complex. At the same time, there is increased recruitment of CREBBP to the promoter by a CREST-dependent mechanism, which leads to transcriptional activation. The CREST-BRG1 complex also binds to the NR2B promoter, and activity-dependent induction of NR2B expression involves a release of HDAC1 and recruitment of CREBBP (By similarity). {ECO:0000250}.

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 BCAR1-PGA5


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 BCAR1-PGA5


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 BCAR1-PGA5


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

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Related Diseases for BCAR1-PGA5


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource