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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:PPP2R2A-BNIP3L (FusionGDB2 ID:HG5520TG665)

Fusion Gene Summary for PPP2R2A-BNIP3L

check button Fusion gene summary
Fusion gene informationFusion gene name: PPP2R2A-BNIP3L
Fusion gene ID: hg5520tg665
HgeneTgene
Gene symbol

PPP2R2A

BNIP3L

Gene ID

5520

665

Gene nameprotein phosphatase 2 regulatory subunit BalphaBCL2 interacting protein 3 like
SynonymsB55A|B55ALPHA|PR52A|PR55A|PR55alphaBNIP3a|NIX
Cytomap('PPP2R2A')('BNIP3L')

8p21.2

8p21.2

Type of geneprotein-codingprotein-coding
Descriptionserine/threonine-protein phosphatase 2A 55 kDa regulatory subunit B alpha isoformprotein phosphatase 2, regulatory subunit B, alphaBCL2/adenovirus E1B 19 kDa protein-interacting protein 3-likeBCL2/adenovirus E1B 19 kDa protein-interacting protein 3ABCL2/adenovirus E1B 19-kd protein-interacting protein 3aBCL2/adenovirus E1B 19kDa interacting protein 3 likeNIP-3-like protein XNIP3
Modification date2020032720200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000523473, ENST00000315985, 
ENST00000380737, 
Fusion gene scores* DoF score17 X 13 X 9=19899 X 8 X 6=432
# samples 2911
** MAII scorelog2(29/1989*10)=-2.77791847081881
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(11/432*10)=-1.97352778863881
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: PPP2R2A [Title/Abstract] AND BNIP3L [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointPPP2R2A(26151256)-BNIP3L(26248758), # samples:3
Anticipated loss of major functional domain due to fusion event.PPP2R2A-BNIP3L seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF.
PPP2R2A-BNIP3L seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame ORF.
PPP2R2A-BNIP3L seems lost the major protein functional domain in Hgene partner, which is a cell metabolism gene due to the frame-shifted ORF.
PPP2R2A-BNIP3L seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
PPP2R2A-BNIP3L seems lost the major protein functional domain in Tgene partner, which is a tumor suppressor due to the frame-shifted ORF.
* 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
HgenePPP2R2A

GO:0006470

protein dephosphorylation

1849734

TgeneBNIP3L

GO:0043065

positive regulation of apoptotic process

9973195

TgeneBNIP3L

GO:0043066

negative regulation of apoptotic process

10381623

TgeneBNIP3L

GO:0051607

defense response to virus

9973195


check buttonFusion gene breakpoints across PPP2R2A (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure
check buttonFusion gene breakpoints across BNIP3L (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure

check button Fusion gene information
* 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
ChimerDB4BRCATCGA-AC-A6IWPPP2R2Achr8

26151256

+BNIP3Lchr8

26248758

+
ChimerDB4OVTCGA-13-1507PPP2R2Achr8

26151256

+BNIP3Lchr8

26248758

+
ChimerDB4OVTCGA-24-1564-01APPP2R2Achr8

26151256

+BNIP3Lchr8

26265516

+
ChimerDB4OVTCGA-24-1564PPP2R2Achr8

26151256

+BNIP3Lchr8

26265515

+
ChimerDB4OVTCGA-24-1843-01APPP2R2Achr8

26151256

+BNIP3Lchr8

26265516

+
ChimerDB4READTCGA-AF-6136PPP2R2Achr8

26151256

+BNIP3Lchr8

26248758

+


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Fusion Gene ORF analysis for PPP2R2A-BNIP3L

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
3UTR-3CDSENST00000523473ENST00000380629PPP2R2Achr8

26151256

+BNIP3Lchr8

26248758

+
3UTR-3CDSENST00000523473ENST00000380629PPP2R2Achr8

26151256

+BNIP3Lchr8

26265516

+
3UTR-3CDSENST00000523473ENST00000380629PPP2R2Achr8

26151256

+BNIP3Lchr8

26265515

+
3UTR-3CDSENST00000523473ENST00000518611PPP2R2Achr8

26151256

+BNIP3Lchr8

26265516

+
3UTR-3CDSENST00000523473ENST00000518611PPP2R2Achr8

26151256

+BNIP3Lchr8

26265515

+
3UTR-3CDSENST00000523473ENST00000520409PPP2R2Achr8

26151256

+BNIP3Lchr8

26265516

+
3UTR-3CDSENST00000523473ENST00000520409PPP2R2Achr8

26151256

+BNIP3Lchr8

26265515

+
3UTR-3CDSENST00000523473ENST00000523515PPP2R2Achr8

26151256

+BNIP3Lchr8

26265516

+
3UTR-3CDSENST00000523473ENST00000523515PPP2R2Achr8

26151256

+BNIP3Lchr8

26265515

+
3UTR-3UTRENST00000523473ENST00000521254PPP2R2Achr8

26151256

+BNIP3Lchr8

26265516

+
3UTR-3UTRENST00000523473ENST00000521254PPP2R2Achr8

26151256

+BNIP3Lchr8

26265515

+
3UTR-5UTRENST00000523473ENST00000518611PPP2R2Achr8

26151256

+BNIP3Lchr8

26248758

+
3UTR-5UTRENST00000523473ENST00000520409PPP2R2Achr8

26151256

+BNIP3Lchr8

26248758

+
3UTR-5UTRENST00000523473ENST00000523515PPP2R2Achr8

26151256

+BNIP3Lchr8

26248758

+
3UTR-intronENST00000523473ENST00000521254PPP2R2Achr8

26151256

+BNIP3Lchr8

26248758

+
5CDS-3UTRENST00000315985ENST00000521254PPP2R2Achr8

26151256

+BNIP3Lchr8

26265516

+
5CDS-3UTRENST00000315985ENST00000521254PPP2R2Achr8

26151256

+BNIP3Lchr8

26265515

+
5CDS-3UTRENST00000380737ENST00000521254PPP2R2Achr8

26151256

+BNIP3Lchr8

26265516

+
5CDS-3UTRENST00000380737ENST00000521254PPP2R2Achr8

26151256

+BNIP3Lchr8

26265515

+
5CDS-5UTRENST00000315985ENST00000518611PPP2R2Achr8

26151256

+BNIP3Lchr8

26248758

+
5CDS-5UTRENST00000315985ENST00000520409PPP2R2Achr8

26151256

+BNIP3Lchr8

26248758

+
5CDS-5UTRENST00000315985ENST00000523515PPP2R2Achr8

26151256

+BNIP3Lchr8

26248758

+
5CDS-5UTRENST00000380737ENST00000518611PPP2R2Achr8

26151256

+BNIP3Lchr8

26248758

+
5CDS-5UTRENST00000380737ENST00000520409PPP2R2Achr8

26151256

+BNIP3Lchr8

26248758

+
5CDS-5UTRENST00000380737ENST00000523515PPP2R2Achr8

26151256

+BNIP3Lchr8

26248758

+
5CDS-intronENST00000315985ENST00000521254PPP2R2Achr8

26151256

+BNIP3Lchr8

26248758

+
5CDS-intronENST00000380737ENST00000521254PPP2R2Achr8

26151256

+BNIP3Lchr8

26248758

+
Frame-shiftENST00000315985ENST00000380629PPP2R2Achr8

26151256

+BNIP3Lchr8

26265516

+
Frame-shiftENST00000315985ENST00000380629PPP2R2Achr8

26151256

+BNIP3Lchr8

26265515

+
Frame-shiftENST00000315985ENST00000518611PPP2R2Achr8

26151256

+BNIP3Lchr8

26265516

+
Frame-shiftENST00000315985ENST00000518611PPP2R2Achr8

26151256

+BNIP3Lchr8

26265515

+
Frame-shiftENST00000315985ENST00000520409PPP2R2Achr8

26151256

+BNIP3Lchr8

26265516

+
Frame-shiftENST00000315985ENST00000520409PPP2R2Achr8

26151256

+BNIP3Lchr8

26265515

+
Frame-shiftENST00000315985ENST00000523515PPP2R2Achr8

26151256

+BNIP3Lchr8

26265516

+
Frame-shiftENST00000315985ENST00000523515PPP2R2Achr8

26151256

+BNIP3Lchr8

26265515

+
Frame-shiftENST00000380737ENST00000380629PPP2R2Achr8

26151256

+BNIP3Lchr8

26265516

+
Frame-shiftENST00000380737ENST00000380629PPP2R2Achr8

26151256

+BNIP3Lchr8

26265515

+
Frame-shiftENST00000380737ENST00000518611PPP2R2Achr8

26151256

+BNIP3Lchr8

26265516

+
Frame-shiftENST00000380737ENST00000518611PPP2R2Achr8

26151256

+BNIP3Lchr8

26265515

+
Frame-shiftENST00000380737ENST00000520409PPP2R2Achr8

26151256

+BNIP3Lchr8

26265516

+
Frame-shiftENST00000380737ENST00000520409PPP2R2Achr8

26151256

+BNIP3Lchr8

26265515

+
Frame-shiftENST00000380737ENST00000523515PPP2R2Achr8

26151256

+BNIP3Lchr8

26265516

+
Frame-shiftENST00000380737ENST00000523515PPP2R2Achr8

26151256

+BNIP3Lchr8

26265515

+
In-frameENST00000315985ENST00000380629PPP2R2Achr8

26151256

+BNIP3Lchr8

26248758

+
In-frameENST00000380737ENST00000380629PPP2R2Achr8

26151256

+BNIP3Lchr8

26248758

+

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 PPP2R2A-BNIP3L


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)
PPP2R2Achr826151256+BNIP3Lchr826248758+6.52E-101
PPP2R2Achr826151256+BNIP3Lchr826248758+6.52E-101
PPP2R2Achr826151256+BNIP3Lchr826265515+3.14E-081
PPP2R2Achr826151256+BNIP3Lchr826265515+3.14E-081
PPP2R2Achr826151256+BNIP3Lchr826248758+6.52E-101
PPP2R2Achr826151256+BNIP3Lchr826248758+6.52E-101
PPP2R2Achr826151256+BNIP3Lchr826265515+3.14E-081
PPP2R2Achr826151256+BNIP3Lchr826265515+3.14E-081

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.
genomic feature

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.
genomic feature of top 1%

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Fusion Protein Features for PPP2R2A-BNIP3L


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/chr8:26151256/chr8:26248758)
- 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
..
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}.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
TgeneBNIP3Lchr8:26151256chr8:26248758ENST0000038062906126_14833220.0MotifNote=BH3
TgeneBNIP3Lchr8:26151256chr8:26248758ENST0000038062906188_20833220.0TransmembraneHelical

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgenePPP2R2Achr8:26151256chr8:26248758ENST00000315985+210175_21337458.0RepeatNote=WD 3
HgenePPP2R2Achr8:26151256chr8:26248758ENST00000315985+210224_26437458.0RepeatNote=WD 4
HgenePPP2R2Achr8:26151256chr8:26248758ENST00000315985+21026_6537458.0RepeatNote=WD 1
HgenePPP2R2Achr8:26151256chr8:26248758ENST00000315985+210283_32137458.0RepeatNote=WD 5
HgenePPP2R2Achr8:26151256chr8:26248758ENST00000315985+210338_37937458.0RepeatNote=WD 6
HgenePPP2R2Achr8:26151256chr8:26248758ENST00000315985+210414_44637458.0RepeatNote=WD 7
HgenePPP2R2Achr8:26151256chr8:26248758ENST00000315985+21091_13237458.0RepeatNote=WD 2
HgenePPP2R2Achr8:26151256chr8:26248758ENST00000380737+210175_21327448.0RepeatNote=WD 3
HgenePPP2R2Achr8:26151256chr8:26248758ENST00000380737+210224_26427448.0RepeatNote=WD 4
HgenePPP2R2Achr8:26151256chr8:26248758ENST00000380737+21026_6527448.0RepeatNote=WD 1
HgenePPP2R2Achr8:26151256chr8:26248758ENST00000380737+210283_32127448.0RepeatNote=WD 5
HgenePPP2R2Achr8:26151256chr8:26248758ENST00000380737+210338_37927448.0RepeatNote=WD 6
HgenePPP2R2Achr8:26151256chr8:26248758ENST00000380737+210414_44627448.0RepeatNote=WD 7
HgenePPP2R2Achr8:26151256chr8:26248758ENST00000380737+21091_13227448.0RepeatNote=WD 2


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Fusion Gene Sequence for PPP2R2A-BNIP3L


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 PPP2R2A-BNIP3L


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 PPP2R2A-BNIP3L


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 PPP2R2A-BNIP3L


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgenePPP2R2AC0013990Pathological accumulation of air in tissues1CTD_human
HgenePPP2R2AC0033578Prostatic Neoplasms1CTD_human
HgenePPP2R2AC0376358Malignant neoplasm of prostate1CTD_human
HgenePPP2R2AC1257806Chromosomal Instability1CTD_human
HgenePPP2R2AC1449861Micronuclei, Chromosome-Defective1CTD_human
HgenePPP2R2AC1449862Micronuclei, Genotoxicant-Induced1CTD_human