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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:VHL-CPNE9 (FusionGDB2 ID:97419)

Fusion Gene Summary for VHL-CPNE9

check button Fusion gene summary
Fusion gene informationFusion gene name: VHL-CPNE9
Fusion gene ID: 97419
HgeneTgene
Gene symbol

VHL

CPNE9

Gene ID

7428

151835

Gene namevon Hippel-Lindau tumor suppressorcopine family member 9
SynonymsHRCA1|RCA1|VHL1|pVHL-
Cytomap

3p25.3

3p25.3

Type of geneprotein-codingprotein-coding
Descriptionvon Hippel-Lindau disease tumor suppressorelongin binding proteinprotein G7von Hippel-Lindau tumor suppressor, E3 ubiquitin protein ligasecopine-9copine IXcopine family member IXcopine-like protein
Modification date2020032720200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000256474, ENST00000345392, 
ENST00000477538, 		ENST00000383832, 
ENST00000383831, 
Fusion gene scores* DoF score5 X 5 X 3=752 X 5 X 2=20
# samples 83
** MAII scorelog2(8/75*10)=0.0931094043914815
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0		log2(3/20*10)=0.584962500721156
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context

PubMed: VHL [Title/Abstract] AND CPNE9 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointVHL(10183871)-CPNE9(9767632), # samples:1
VHL(10183871)-CPNE9(9771190), # samples:1
VHL(10183871)-CPNE9(9767633), # samples:1
VHL(10183871)-CPNE9(9771191), # samples:1
Anticipated loss of major functional domain due to fusion event.VHL-CPNE9 seems lost the major protein functional domain in Hgene partner, which is a CGC due to the frame-shifted ORF.
VHL-CPNE9 seems lost the major protein functional domain in Hgene partner, which is a tumor suppressor due to the frame-shifted ORF.
VHL-CPNE9 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
HgeneVHL

GO:0016567

protein ubiquitination

24899725

HgeneVHL

GO:0061428

negative regulation of transcription from RNA polymerase II promoter in response to hypoxia

11641274

TgeneCPNE9

GO:1903861

positive regulation of dendrite extension

23999003


check buttonFusion gene breakpoints across VHL (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 CPNE9 (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
ChimerDB4OVTCGA-31-1953VHLchr3

10183871

+CPNE9chr3

9767632

+
ChimerDB4OVTCGA-31-1953VHLchr3

10183871

+CPNE9chr3

9771190

+
ChimerDB4OVTCGA-31-1953-01AVHLchr3

10183871

+CPNE9chr3

9767633

+
ChimerDB4OVTCGA-31-1953-01AVHLchr3

10183871

+CPNE9chr3

9771191

+


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Fusion Gene ORF analysis for VHL-CPNE9

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
Frame-shiftENST00000256474ENST00000383832VHLchr3

10183871

+CPNE9chr3

9767632

+
Frame-shiftENST00000256474ENST00000383831VHLchr3

10183871

+CPNE9chr3

9767632

+
Frame-shiftENST00000345392ENST00000383832VHLchr3

10183871

+CPNE9chr3

9767632

+
Frame-shiftENST00000345392ENST00000383831VHLchr3

10183871

+CPNE9chr3

9767632

+
intron-3CDSENST00000477538ENST00000383832VHLchr3

10183871

+CPNE9chr3

9767632

+
intron-3CDSENST00000477538ENST00000383831VHLchr3

10183871

+CPNE9chr3

9767632

+
Frame-shiftENST00000256474ENST00000383832VHLchr3

10183871

+CPNE9chr3

9771190

+
5CDS-intronENST00000256474ENST00000383831VHLchr3

10183871

+CPNE9chr3

9771190

+
Frame-shiftENST00000345392ENST00000383832VHLchr3

10183871

+CPNE9chr3

9771190

+
5CDS-intronENST00000345392ENST00000383831VHLchr3

10183871

+CPNE9chr3

9771190

+
intron-3CDSENST00000477538ENST00000383832VHLchr3

10183871

+CPNE9chr3

9771190

+
intron-intronENST00000477538ENST00000383831VHLchr3

10183871

+CPNE9chr3

9771190

+
Frame-shiftENST00000256474ENST00000383832VHLchr3

10183871

+CPNE9chr3

9767633

+
Frame-shiftENST00000256474ENST00000383831VHLchr3

10183871

+CPNE9chr3

9767633

+
Frame-shiftENST00000345392ENST00000383832VHLchr3

10183871

+CPNE9chr3

9767633

+
Frame-shiftENST00000345392ENST00000383831VHLchr3

10183871

+CPNE9chr3

9767633

+
intron-3CDSENST00000477538ENST00000383832VHLchr3

10183871

+CPNE9chr3

9767633

+
intron-3CDSENST00000477538ENST00000383831VHLchr3

10183871

+CPNE9chr3

9767633

+
Frame-shiftENST00000256474ENST00000383832VHLchr3

10183871

+CPNE9chr3

9771191

+
5CDS-intronENST00000256474ENST00000383831VHLchr3

10183871

+CPNE9chr3

9771191

+
Frame-shiftENST00000345392ENST00000383832VHLchr3

10183871

+CPNE9chr3

9771191

+
5CDS-intronENST00000345392ENST00000383831VHLchr3

10183871

+CPNE9chr3

9771191

+
intron-3CDSENST00000477538ENST00000383832VHLchr3

10183871

+CPNE9chr3

9771191

+
intron-intronENST00000477538ENST00000383831VHLchr3

10183871

+CPNE9chr3

9771191

+

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 VHL-CPNE9


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)
VHLchr310183871+CPNE9chr39767632+1.70E-111
VHLchr310183871+CPNE9chr39771190+2.60E-101
VHLchr310183871+CPNE9chr39767632+1.70E-111
VHLchr310183871+CPNE9chr39771190+2.60E-101
VHLchr310183871+CPNE9chr39767632+1.70E-111
VHLchr310183871+CPNE9chr39771190+2.60E-101
VHLchr310183871+CPNE9chr39767632+1.70E-111
VHLchr310183871+CPNE9chr39771190+2.60E-101

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 VHL-CPNE9


check button Go to

FGviewer for the breakpoints of :-:

.
- 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
..
FUNCTION: Might normally function as a transcriptional repressor. EWS-fusion-proteins (EFPS) may play a role in the tumorigenic process. They may disturb gene expression by mimicking, or interfering with the normal function of CTD-POLII within the transcription initiation complex. They may also contribute to an aberrant activation of the fusion protein target genes.FUNCTION: Might normally function as a transcriptional repressor. EWS-fusion-proteins (EFPS) may play a role in the tumorigenic process. They may disturb gene expression by mimicking, or interfering with the normal function of CTD-POLII within the transcription initiation complex. They may also contribute to an aberrant activation of the fusion protein target genes.

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 VHL-CPNE9


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 VHL-CPNE9


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 VHL-CPNE9


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 VHL-CPNE9


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneVHLC0019562Von Hippel-Lindau Syndrome19CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
HgeneVHLC1708353Hereditary Paraganglioma-Pheochromocytoma Syndrome12CLINGEN
HgeneVHLC0279702Conventional (Clear Cell) Renal Cell Carcinoma11CGI;CTD_human;GENOMICS_ENGLAND;UNIPROT
HgeneVHLC0007134Renal Cell Carcinoma10CTD_human;GENOMICS_ENGLAND
HgeneVHLC1266042Chromophobe Renal Cell Carcinoma9CTD_human
HgeneVHLC1266043Sarcomatoid Renal Cell Carcinoma9CTD_human
HgeneVHLC1266044Collecting Duct Carcinoma of the Kidney9CTD_human
HgeneVHLC1306837Papillary Renal Cell Carcinoma9CTD_human
HgeneVHLC0031511Pheochromocytoma5CGI;CTD_human;GENOMICS_ENGLAND;UNIPROT
HgeneVHLC1837915ERYTHROCYTOSIS, FAMILIAL, 25CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
HgeneVHLC0001430Adenoma1CTD_human
HgeneVHLC0007097Carcinoma1CTD_human
HgeneVHLC0022665Kidney Neoplasm1CGI;CTD_human
HgeneVHLC0024121Lung Neoplasms1CTD_human
HgeneVHLC0027708Nephroblastoma1CTD_human
HgeneVHLC0030421Paraganglioma1GENOMICS_ENGLAND
HgeneVHLC0032461Polycythemia1GENOMICS_ENGLAND
HgeneVHLC0040053Thrombosis1GENOMICS_ENGLAND
HgeneVHLC0042345Varicosity1GENOMICS_ENGLAND
HgeneVHLC0205646Adenoma, Basal Cell1CTD_human
HgeneVHLC0205647Follicular adenoma1CTD_human
HgeneVHLC0205648Adenoma, Microcystic1CTD_human
HgeneVHLC0205649Adenoma, Monomorphic1CTD_human
HgeneVHLC0205650Papillary adenoma1CTD_human
HgeneVHLC0205651Adenoma, Trabecular1CTD_human
HgeneVHLC0205696Anaplastic carcinoma1CTD_human
HgeneVHLC0205697Carcinoma, Spindle-Cell1CTD_human
HgeneVHLC0205698Undifferentiated carcinoma1CTD_human
HgeneVHLC0205699Carcinomatosis1CTD_human
HgeneVHLC0242379Malignant neoplasm of lung1CTD_human;UNIPROT
HgeneVHLC0346647Malignant neoplasm of pancreas1GENOMICS_ENGLAND
HgeneVHLC0431718Multiple renal cysts1GENOMICS_ENGLAND
HgeneVHLC0740457Malignant neoplasm of kidney1CGI;CTD_human;GENOMICS_ENGLAND
HgeneVHLC1257877Pheochromocytoma, Extra-Adrenal1CTD_human
HgeneVHLC1332243Adenocarcinoma of ampulla of Vater1GENOMICS_ENGLAND
HgeneVHLC1527405Erythrocytosis1GENOMICS_ENGLAND
HgeneVHLC1860392Renal hemangioblastoma1GENOMICS_ENGLAND
HgeneVHLC2930471Bilateral Wilms Tumor1CTD_human
HgeneVHLC2973725Pulmonary arterial hypertension1GENOMICS_ENGLAND
HgeneVHLC3203102Idiopathic pulmonary arterial hypertension1GENOMICS_ENGLAND