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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:ATP5C1-VCAN (FusionGDB2 ID:HG509TG1462)

Fusion Gene Summary for ATP5C1-VCAN

check button Fusion gene summary
Fusion gene informationFusion gene name: ATP5C1-VCAN
Fusion gene ID: hg509tg1462
HgeneTgene
Gene symbol

ATP5C1

VCAN

Gene ID

509

1462

Gene nameATP synthase F1 subunit gammaversican
SynonymsATP5C|ATP5C1|ATP5CL1CSPG2|ERVR|GHAP|PG-M|WGN|WGN1
Cytomap('ATP5C1')('VCAN')

10p14

5q14.2-q14.3

Type of geneprotein-codingprotein-coding
DescriptionATP synthase subunit gamma, mitochondrialATP synthase gamma chain, mitochondrialATP synthase, H+ transporting, mitochondrial F1 complex, gamma polypeptide 1F-ATPase gamma subunitmitochondrial ATP synthase, gamma subunit 1versican core proteinchondroitin sulfate proteoglycan core protein 2glial hyaluronate-binding proteinlarge fibroblast proteoglycanversican proteoglycan
Modification date2020032020200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000493053, ENST00000335698, 
ENST00000356708, ENST00000541227, 
Fusion gene scores* DoF score10 X 8 X 7=5603 X 3 X 3=27
# samples 113
** MAII scorelog2(11/560*10)=-2.34792330342031
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(3/27*10)=0.15200309344505
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context

PubMed: ATP5C1 [Title/Abstract] AND VCAN [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointATP5C1(7841157)-VCAN(82832825), # samples:1
Anticipated loss of major functional domain due to fusion event.ATP5C1-VCAN seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
ATP5C1-VCAN seems lost the major protein functional domain in Tgene partner, which is a cell metabolism gene due to the frame-shifted ORF.
ATP5C1-VCAN seems lost the major protein functional domain in Tgene 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
HgeneATP5C1

GO:0042776

mitochondrial ATP synthesis coupled proton transport

12110673



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
ChimerDB4LAMLTCGA-AB-2965ATP5C1chr10

7841157

+VCANchr5

82832825

+


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Fusion Gene ORF analysis for ATP5C1-VCAN

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-3CDSENST00000493053ENST00000265077ATP5C1chr10

7841157

+VCANchr5

82832825

+
3UTR-3UTRENST00000493053ENST00000513016ATP5C1chr10

7841157

+VCANchr5

82832825

+
3UTR-intronENST00000493053ENST00000342785ATP5C1chr10

7841157

+VCANchr5

82832825

+
3UTR-intronENST00000493053ENST00000343200ATP5C1chr10

7841157

+VCANchr5

82832825

+
3UTR-intronENST00000493053ENST00000502527ATP5C1chr10

7841157

+VCANchr5

82832825

+
3UTR-intronENST00000493053ENST00000512590ATP5C1chr10

7841157

+VCANchr5

82832825

+
3UTR-intronENST00000493053ENST00000513984ATP5C1chr10

7841157

+VCANchr5

82832825

+
5CDS-3UTRENST00000335698ENST00000513016ATP5C1chr10

7841157

+VCANchr5

82832825

+
5CDS-3UTRENST00000356708ENST00000513016ATP5C1chr10

7841157

+VCANchr5

82832825

+
5CDS-3UTRENST00000541227ENST00000513016ATP5C1chr10

7841157

+VCANchr5

82832825

+
5CDS-intronENST00000335698ENST00000342785ATP5C1chr10

7841157

+VCANchr5

82832825

+
5CDS-intronENST00000335698ENST00000343200ATP5C1chr10

7841157

+VCANchr5

82832825

+
5CDS-intronENST00000335698ENST00000502527ATP5C1chr10

7841157

+VCANchr5

82832825

+
5CDS-intronENST00000335698ENST00000512590ATP5C1chr10

7841157

+VCANchr5

82832825

+
5CDS-intronENST00000335698ENST00000513984ATP5C1chr10

7841157

+VCANchr5

82832825

+
5CDS-intronENST00000356708ENST00000342785ATP5C1chr10

7841157

+VCANchr5

82832825

+
5CDS-intronENST00000356708ENST00000343200ATP5C1chr10

7841157

+VCANchr5

82832825

+
5CDS-intronENST00000356708ENST00000502527ATP5C1chr10

7841157

+VCANchr5

82832825

+
5CDS-intronENST00000356708ENST00000512590ATP5C1chr10

7841157

+VCANchr5

82832825

+
5CDS-intronENST00000356708ENST00000513984ATP5C1chr10

7841157

+VCANchr5

82832825

+
5CDS-intronENST00000541227ENST00000342785ATP5C1chr10

7841157

+VCANchr5

82832825

+
5CDS-intronENST00000541227ENST00000343200ATP5C1chr10

7841157

+VCANchr5

82832825

+
5CDS-intronENST00000541227ENST00000502527ATP5C1chr10

7841157

+VCANchr5

82832825

+
5CDS-intronENST00000541227ENST00000512590ATP5C1chr10

7841157

+VCANchr5

82832825

+
5CDS-intronENST00000541227ENST00000513984ATP5C1chr10

7841157

+VCANchr5

82832825

+
Frame-shiftENST00000335698ENST00000265077ATP5C1chr10

7841157

+VCANchr5

82832825

+
Frame-shiftENST00000356708ENST00000265077ATP5C1chr10

7841157

+VCANchr5

82832825

+
Frame-shiftENST00000541227ENST00000265077ATP5C1chr10

7841157

+VCANchr5

82832825

+

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 ATP5C1-VCAN


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)
ATP5C1chr107841157+VCANchr582832825+9.71E-050.99990296
ATP5C1chr107841157+VCANchr582832825+9.71E-050.99990296


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 ATP5C1-VCAN


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/:7841157/:82832825)
- 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 ATP5C1-VCAN


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 ATP5C1-VCAN


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 ATP5C1-VCAN


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 ATP5C1-VCAN


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneC0010606Adenoid Cystic Carcinoma1CTD_human
TgeneC0014175Endometriosis1CTD_human
TgeneC0036095Salivary Gland Neoplasms1CTD_human
TgeneC0220636Malignant neoplasm of salivary gland1CTD_human
TgeneC0269102Endometrioma1CTD_human