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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:BNIP3-PPP2R2D (FusionGDB2 ID:HG664TG55844)

Fusion Gene Summary for BNIP3-PPP2R2D

check button Fusion gene summary
Fusion gene informationFusion gene name: BNIP3-PPP2R2D
Fusion gene ID: hg664tg55844
HgeneTgene
Gene symbol

BNIP3

PPP2R2D

Gene ID

664

55844

Gene nameBCL2 interacting protein 3protein phosphatase 2 regulatory subunit Bdelta
SynonymsNIP3B55D|B55delta|MDS026
Cytomap('BNIP3')('PPP2R2D')

10q26.3

10q26.3

Type of geneprotein-codingprotein-coding
DescriptionBCL2/adenovirus E1B 19 kDa protein-interacting protein 3BCL2/adenovirus E1B 19kDa interacting protein 3BCL2/adenovirus E1B interacting protein 3nineteen kD interacting protein-3serine/threonine-protein phosphatase 2A 55 kDa regulatory subunit B delta isoformPP2A subunit B isoform B55-deltaPP2A subunit B isoform PR55-deltaPP2A subunit B isoform R2-deltaPP2A subunit B isoform deltaprotein phosphatase 2 regulatory subunit B, d
Modification date2020031320200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000368636, ENST00000540159, 
ENST00000368636, ENST00000540159, 
Fusion gene scores* DoF score3 X 3 X 3=276 X 7 X 3=126
# samples 37
** MAII scorelog2(3/27*10)=0.15200309344505
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
log2(7/126*10)=-0.84799690655495
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: BNIP3 [Title/Abstract] AND PPP2R2D [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointBNIP3(133795265)-PPP2R2D(133769188), # samples:1
Anticipated loss of major functional domain due to fusion event.BNIP3-PPP2R2D seems lost the major protein functional domain in Hgene partner, which is a essential gene 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
HgeneBNIP3

GO:0008626

granzyme-mediated apoptotic signaling pathway

9396766

HgeneBNIP3

GO:0010637

negative regulation of mitochondrial fusion

20436456

HgeneBNIP3

GO:0043065

positive regulation of apoptotic process

9973195|10381623

HgeneBNIP3

GO:0043068

positive regulation of programmed cell death

10891486

HgeneBNIP3

GO:0043243

positive regulation of protein complex disassembly

20436456

HgeneBNIP3

GO:0043653

mitochondrial fragmentation involved in apoptotic process

20436456

HgeneBNIP3

GO:0045837

negative regulation of membrane potential

10891486

HgeneBNIP3

GO:0046902

regulation of mitochondrial membrane permeability

10891486

HgeneBNIP3

GO:0051607

defense response to virus

9973195

HgeneBNIP3

GO:0072593

reactive oxygen species metabolic process

10891486

HgeneBNIP3

GO:0090141

positive regulation of mitochondrial fission

20436456

HgeneBNIP3

GO:0090200

positive regulation of release of cytochrome c from mitochondria

20436456

HgeneBNIP3

GO:0097345

mitochondrial outer membrane permeabilization

18371312



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
ChimerDB4CESCTCGA-ZJ-A8QO-01ABNIP3chr10

133795265

-PPP2R2Dchr10

133769188

+


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Fusion Gene ORF analysis for BNIP3-PPP2R2D

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
5CDS-3UTRENST00000368636ENST00000470416BNIP3chr10

133795265

-PPP2R2Dchr10

133769188

+
5CDS-3UTRENST00000540159ENST00000470416BNIP3chr10

133795265

-PPP2R2Dchr10

133769188

+
Frame-shiftENST00000368636ENST00000422256BNIP3chr10

133795265

-PPP2R2Dchr10

133769188

+
Frame-shiftENST00000540159ENST00000422256BNIP3chr10

133795265

-PPP2R2Dchr10

133769188

+

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 BNIP3-PPP2R2D


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)
BNIP3chr10133795264-PPP2R2Dchr10133769187+1.01E-060.9999989
BNIP3chr10133795264-PPP2R2Dchr10133769187+1.01E-060.9999989


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 BNIP3-PPP2R2D


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/:133795265/:133769188)
- 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

- 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 BNIP3-PPP2R2D


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 BNIP3-PPP2R2D


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 BNIP3-PPP2R2D


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 BNIP3-PPP2R2D


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneBNIP3C0024623Malignant neoplasm of stomach1CTD_human
HgeneBNIP3C0026764Multiple Myeloma1CTD_human
HgeneBNIP3C0033578Prostatic Neoplasms1CTD_human
HgeneBNIP3C0038356Stomach Neoplasms1CTD_human
HgeneBNIP3C0376358Malignant neoplasm of prostate1CTD_human
HgeneBNIP3C0677050Manganese Poisoning1CTD_human
HgeneBNIP3C1708349Hereditary Diffuse Gastric Cancer1CTD_human