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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:PRUNE2-HDAC9 (FusionGDB2 ID:69356)

Fusion Gene Summary for PRUNE2-HDAC9

check button Fusion gene summary
Fusion gene informationFusion gene name: PRUNE2-HDAC9
Fusion gene ID: 69356
HgeneTgene
Gene symbol

PRUNE2

HDAC9

Gene ID

158471

9734

Gene nameprune homolog 2 with BCH domainhistone deacetylase 9
SynonymsBMCC1|BNIPXL|C9orf65|KIAA0367HD7|HD7b|HD9|HDAC|HDAC7|HDAC7B|HDAC9B|HDAC9FL|HDRP|MITR
Cytomap

9q21.2

7p21.1

Type of geneprotein-codingprotein-coding
Descriptionprotein prune homolog 2BCH motif-containing molecule at the carboxyl terminal region 1BNIP2 motif containing molecule at the carboxyl terminal region 1BNIP2 motif-containing molecule at the C-terminal region 1olfaxintruncated PRUNE2histone deacetylase 9MEF-2 interacting transcription repressor (MITR) proteinhistone deacetylase 4/5-related proteinhistone deacetylase 7B
Modification date2020031320200322
UniProtAcc.

Q9UKV0

Ensembl transtripts involved in fusion geneENST00000376718, ENST00000428286, 
ENST00000223609, ENST00000376713, 
ENST00000443509, ENST00000466266, 
ENST00000405010, ENST00000406072, 
ENST00000428307, ENST00000456174, 
ENST00000476135, ENST00000524023, 
ENST00000401921, ENST00000406451, 
ENST00000417496, ENST00000432645, 
ENST00000441542, 
Fusion gene scores* DoF score9 X 11 X 6=59412 X 10 X 6=720
# samples 1012
** MAII scorelog2(10/594*10)=-2.57046293102604
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(12/720*10)=-2.58496250072116
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: PRUNE2 [Title/Abstract] AND HDAC9 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointPRUNE2(79318253)-HDAC9(18684294), # samples:2
Anticipated loss of major functional domain due to fusion event.PRUNE2-HDAC9 seems lost the major protein functional domain in Tgene partner, which is a epigenetic factor due to the frame-shifted ORF.
PRUNE2-HDAC9 seems lost the major protein functional domain in Tgene partner, which is a IUPHAR drug target 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
TgeneHDAC9

GO:0000122

negative regulation of transcription by RNA polymerase II

10655483|11535832

TgeneHDAC9

GO:0016575

histone deacetylation

11535832

TgeneHDAC9

GO:0032869

cellular response to insulin stimulus

19303849

TgeneHDAC9

GO:0034983

peptidyl-lysine deacetylation

11535832

TgeneHDAC9

GO:0042632

cholesterol homeostasis

28855441

TgeneHDAC9

GO:0045892

negative regulation of transcription, DNA-templated

11535832

TgeneHDAC9

GO:0050710

negative regulation of cytokine secretion

28855441

TgeneHDAC9

GO:0051005

negative regulation of lipoprotein lipase activity

28855441

TgeneHDAC9

GO:0070932

histone H3 deacetylation

12590135

TgeneHDAC9

GO:0070933

histone H4 deacetylation

12590135

TgeneHDAC9

GO:1990678

histone H4-K16 deacetylation

28855441


check buttonFusion gene breakpoints across PRUNE2 (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 HDAC9 (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
ChimerDB4KIRPTCGA-B9-A44B-01APRUNE2chr9

79318253

-HDAC9chr7

18684294

+


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Fusion Gene ORF analysis for PRUNE2-HDAC9

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-intronENST00000376718ENST00000405010PRUNE2chr9

79318253

-HDAC9chr7

18684294

+
5CDS-intronENST00000376718ENST00000406072PRUNE2chr9

79318253

-HDAC9chr7

18684294

+
5CDS-intronENST00000376718ENST00000428307PRUNE2chr9

79318253

-HDAC9chr7

18684294

+
5CDS-intronENST00000376718ENST00000456174PRUNE2chr9

79318253

-HDAC9chr7

18684294

+
5CDS-intronENST00000376718ENST00000476135PRUNE2chr9

79318253

-HDAC9chr7

18684294

+
5CDS-intronENST00000376718ENST00000524023PRUNE2chr9

79318253

-HDAC9chr7

18684294

+
5CDS-intronENST00000428286ENST00000405010PRUNE2chr9

79318253

-HDAC9chr7

18684294

+
5CDS-intronENST00000428286ENST00000406072PRUNE2chr9

79318253

-HDAC9chr7

18684294

+
5CDS-intronENST00000428286ENST00000428307PRUNE2chr9

79318253

-HDAC9chr7

18684294

+
5CDS-intronENST00000428286ENST00000456174PRUNE2chr9

79318253

-HDAC9chr7

18684294

+
5CDS-intronENST00000428286ENST00000476135PRUNE2chr9

79318253

-HDAC9chr7

18684294

+
5CDS-intronENST00000428286ENST00000524023PRUNE2chr9

79318253

-HDAC9chr7

18684294

+
Frame-shiftENST00000376718ENST00000401921PRUNE2chr9

79318253

-HDAC9chr7

18684294

+
Frame-shiftENST00000376718ENST00000406451PRUNE2chr9

79318253

-HDAC9chr7

18684294

+
Frame-shiftENST00000376718ENST00000417496PRUNE2chr9

79318253

-HDAC9chr7

18684294

+
Frame-shiftENST00000376718ENST00000432645PRUNE2chr9

79318253

-HDAC9chr7

18684294

+
Frame-shiftENST00000376718ENST00000441542PRUNE2chr9

79318253

-HDAC9chr7

18684294

+
Frame-shiftENST00000428286ENST00000401921PRUNE2chr9

79318253

-HDAC9chr7

18684294

+
Frame-shiftENST00000428286ENST00000406451PRUNE2chr9

79318253

-HDAC9chr7

18684294

+
Frame-shiftENST00000428286ENST00000417496PRUNE2chr9

79318253

-HDAC9chr7

18684294

+
Frame-shiftENST00000428286ENST00000432645PRUNE2chr9

79318253

-HDAC9chr7

18684294

+
Frame-shiftENST00000428286ENST00000441542PRUNE2chr9

79318253

-HDAC9chr7

18684294

+
intron-3CDSENST00000223609ENST00000401921PRUNE2chr9

79318253

-HDAC9chr7

18684294

+
intron-3CDSENST00000223609ENST00000406451PRUNE2chr9

79318253

-HDAC9chr7

18684294

+
intron-3CDSENST00000223609ENST00000417496PRUNE2chr9

79318253

-HDAC9chr7

18684294

+
intron-3CDSENST00000223609ENST00000432645PRUNE2chr9

79318253

-HDAC9chr7

18684294

+
intron-3CDSENST00000223609ENST00000441542PRUNE2chr9

79318253

-HDAC9chr7

18684294

+
intron-3CDSENST00000376713ENST00000401921PRUNE2chr9

79318253

-HDAC9chr7

18684294

+
intron-3CDSENST00000376713ENST00000406451PRUNE2chr9

79318253

-HDAC9chr7

18684294

+
intron-3CDSENST00000376713ENST00000417496PRUNE2chr9

79318253

-HDAC9chr7

18684294

+
intron-3CDSENST00000376713ENST00000432645PRUNE2chr9

79318253

-HDAC9chr7

18684294

+
intron-3CDSENST00000376713ENST00000441542PRUNE2chr9

79318253

-HDAC9chr7

18684294

+
intron-3CDSENST00000443509ENST00000401921PRUNE2chr9

79318253

-HDAC9chr7

18684294

+
intron-3CDSENST00000443509ENST00000406451PRUNE2chr9

79318253

-HDAC9chr7

18684294

+
intron-3CDSENST00000443509ENST00000417496PRUNE2chr9

79318253

-HDAC9chr7

18684294

+
intron-3CDSENST00000443509ENST00000432645PRUNE2chr9

79318253

-HDAC9chr7

18684294

+
intron-3CDSENST00000443509ENST00000441542PRUNE2chr9

79318253

-HDAC9chr7

18684294

+
intron-3CDSENST00000466266ENST00000401921PRUNE2chr9

79318253

-HDAC9chr7

18684294

+
intron-3CDSENST00000466266ENST00000406451PRUNE2chr9

79318253

-HDAC9chr7

18684294

+
intron-3CDSENST00000466266ENST00000417496PRUNE2chr9

79318253

-HDAC9chr7

18684294

+
intron-3CDSENST00000466266ENST00000432645PRUNE2chr9

79318253

-HDAC9chr7

18684294

+
intron-3CDSENST00000466266ENST00000441542PRUNE2chr9

79318253

-HDAC9chr7

18684294

+
intron-intronENST00000223609ENST00000405010PRUNE2chr9

79318253

-HDAC9chr7

18684294

+
intron-intronENST00000223609ENST00000406072PRUNE2chr9

79318253

-HDAC9chr7

18684294

+
intron-intronENST00000223609ENST00000428307PRUNE2chr9

79318253

-HDAC9chr7

18684294

+
intron-intronENST00000223609ENST00000456174PRUNE2chr9

79318253

-HDAC9chr7

18684294

+
intron-intronENST00000223609ENST00000476135PRUNE2chr9

79318253

-HDAC9chr7

18684294

+
intron-intronENST00000223609ENST00000524023PRUNE2chr9

79318253

-HDAC9chr7

18684294

+
intron-intronENST00000376713ENST00000405010PRUNE2chr9

79318253

-HDAC9chr7

18684294

+
intron-intronENST00000376713ENST00000406072PRUNE2chr9

79318253

-HDAC9chr7

18684294

+
intron-intronENST00000376713ENST00000428307PRUNE2chr9

79318253

-HDAC9chr7

18684294

+
intron-intronENST00000376713ENST00000456174PRUNE2chr9

79318253

-HDAC9chr7

18684294

+
intron-intronENST00000376713ENST00000476135PRUNE2chr9

79318253

-HDAC9chr7

18684294

+
intron-intronENST00000376713ENST00000524023PRUNE2chr9

79318253

-HDAC9chr7

18684294

+
intron-intronENST00000443509ENST00000405010PRUNE2chr9

79318253

-HDAC9chr7

18684294

+
intron-intronENST00000443509ENST00000406072PRUNE2chr9

79318253

-HDAC9chr7

18684294

+
intron-intronENST00000443509ENST00000428307PRUNE2chr9

79318253

-HDAC9chr7

18684294

+
intron-intronENST00000443509ENST00000456174PRUNE2chr9

79318253

-HDAC9chr7

18684294

+
intron-intronENST00000443509ENST00000476135PRUNE2chr9

79318253

-HDAC9chr7

18684294

+
intron-intronENST00000443509ENST00000524023PRUNE2chr9

79318253

-HDAC9chr7

18684294

+
intron-intronENST00000466266ENST00000405010PRUNE2chr9

79318253

-HDAC9chr7

18684294

+
intron-intronENST00000466266ENST00000406072PRUNE2chr9

79318253

-HDAC9chr7

18684294

+
intron-intronENST00000466266ENST00000428307PRUNE2chr9

79318253

-HDAC9chr7

18684294

+
intron-intronENST00000466266ENST00000456174PRUNE2chr9

79318253

-HDAC9chr7

18684294

+
intron-intronENST00000466266ENST00000476135PRUNE2chr9

79318253

-HDAC9chr7

18684294

+
intron-intronENST00000466266ENST00000524023PRUNE2chr9

79318253

-HDAC9chr7

18684294

+

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 PRUNE2-HDAC9


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)
PRUNE2chr979318252-HDAC9chr718684293+0.0018745970.9981254
PRUNE2chr979318252-HDAC9chr718684293+0.0018745970.9981254

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.
genomic feature of top 1%

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Fusion Protein Features for PRUNE2-HDAC9


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/:79318253/:18684294)
- 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
.HDAC9

Q9UKV0

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: Responsible for the deacetylation of lysine residues on the N-terminal part of the core histones (H2A, H2B, H3 and H4). Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events. Represses MEF2-dependent transcription.; FUNCTION: Isoform 3 lacks active site residues and therefore is catalytically inactive. Represses MEF2-dependent transcription by recruiting HDAC1 and/or HDAC3. Seems to inhibit skeletal myogenesis and to be involved in heart development. Protects neurons from apoptosis, both by inhibiting JUN phosphorylation by MAPK10 and by repressing JUN transcription via HDAC1 recruitment to JUN promoter.

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 PRUNE2-HDAC9


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 PRUNE2-HDAC9


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 PRUNE2-HDAC9


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 PRUNE2-HDAC9


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