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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:VGLL4-UPF2 (FusionGDB2 ID:98084)

Fusion Gene Summary for VGLL4-UPF2

check button Fusion gene summary
Fusion gene informationFusion gene name: VGLL4-UPF2
Fusion gene ID: 98084
HgeneTgene
Gene symbol

VGLL4

UPF2

Gene ID

9686

26019

Gene namevestigial like family member 4UPF2 regulator of nonsense mediated mRNA decay
SynonymsVGL-4HUPF2|RENT2|smg-3
Cytomap

3p25.3-p25.2

10p14

Type of geneprotein-codingprotein-coding
Descriptiontranscription cofactor vestigial-like protein 4Vestigial-like 4vestigial like 4regulator of nonsense transcripts 2FRS2/UPF2/LEMD3 fusionLEMD3/UPF2 fusionUPF2 regulator of nonsense transcripts homolognonsense mRNA reducing factor 2smg-3 homolog, nonsense mediated mRNA decay factorup-frameshift suppressor 2 homologyeast Upf2p h
Modification date2020031320200329
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000273038, ENST00000404339, 
ENST00000413604, ENST00000424529, 
ENST00000430365, ENST00000451674, 
ENST00000480288, 		ENST00000460569, 
ENST00000356352, ENST00000357604, 
ENST00000397053, 
Fusion gene scores* DoF score18 X 13 X 11=25748 X 12 X 4=384
# samples 3011
** MAII scorelog2(30/2574*10)=-3.10097764772482
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(11/384*10)=-1.8036027871965
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: VGLL4 [Title/Abstract] AND UPF2 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointVGLL4(11744445)-UPF2(12021164), # samples:3
Anticipated loss of major functional domain due to fusion event.VGLL4-UPF2 seems lost the major protein functional domain in Tgene partner, which is a cell metabolism gene due to the frame-shifted ORF.
VGLL4-UPF2 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

check buttonFusion gene breakpoints across VGLL4 (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 UPF2 (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
ChimerDB4BLCATCGA-XF-A8HD-01AVGLL4chr3

11744444

-UPF2chr10

12009452

-
ChimerDB4BLCATCGA-XF-A8HD-01AVGLL4chr3

11744444

-UPF2chr10

12021163

-
ChimerDB4BLCATCGA-XF-A8HD-01AVGLL4chr3

11744445

-UPF2chr10

12009453

-
ChimerDB4BLCATCGA-XF-A8HD-01AVGLL4chr3

11744445

-UPF2chr10

12021164

-


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Fusion Gene ORF analysis for VGLL4-UPF2

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-intronENST00000273038ENST00000460569VGLL4chr3

11744444

-UPF2chr10

12009452

-
5CDS-intronENST00000273038ENST00000460569VGLL4chr3

11744444

-UPF2chr10

12021163

-
5CDS-intronENST00000273038ENST00000460569VGLL4chr3

11744445

-UPF2chr10

12009453

-
5CDS-intronENST00000273038ENST00000460569VGLL4chr3

11744445

-UPF2chr10

12021164

-
5UTR-3CDSENST00000404339ENST00000356352VGLL4chr3

11744444

-UPF2chr10

12009452

-
5UTR-3CDSENST00000404339ENST00000356352VGLL4chr3

11744444

-UPF2chr10

12021163

-
5UTR-3CDSENST00000404339ENST00000356352VGLL4chr3

11744445

-UPF2chr10

12009453

-
5UTR-3CDSENST00000404339ENST00000356352VGLL4chr3

11744445

-UPF2chr10

12021164

-
5UTR-3CDSENST00000404339ENST00000357604VGLL4chr3

11744444

-UPF2chr10

12009452

-
5UTR-3CDSENST00000404339ENST00000357604VGLL4chr3

11744444

-UPF2chr10

12021163

-
5UTR-3CDSENST00000404339ENST00000357604VGLL4chr3

11744445

-UPF2chr10

12009453

-
5UTR-3CDSENST00000404339ENST00000357604VGLL4chr3

11744445

-UPF2chr10

12021164

-
5UTR-3CDSENST00000404339ENST00000397053VGLL4chr3

11744444

-UPF2chr10

12009452

-
5UTR-3CDSENST00000404339ENST00000397053VGLL4chr3

11744444

-UPF2chr10

12021163

-
5UTR-3CDSENST00000404339ENST00000397053VGLL4chr3

11744445

-UPF2chr10

12009453

-
5UTR-3CDSENST00000404339ENST00000397053VGLL4chr3

11744445

-UPF2chr10

12021164

-
5UTR-intronENST00000404339ENST00000460569VGLL4chr3

11744444

-UPF2chr10

12009452

-
5UTR-intronENST00000404339ENST00000460569VGLL4chr3

11744444

-UPF2chr10

12021163

-
5UTR-intronENST00000404339ENST00000460569VGLL4chr3

11744445

-UPF2chr10

12009453

-
5UTR-intronENST00000404339ENST00000460569VGLL4chr3

11744445

-UPF2chr10

12021164

-
Frame-shiftENST00000273038ENST00000356352VGLL4chr3

11744444

-UPF2chr10

12009452

-
Frame-shiftENST00000273038ENST00000356352VGLL4chr3

11744444

-UPF2chr10

12021163

-
Frame-shiftENST00000273038ENST00000356352VGLL4chr3

11744445

-UPF2chr10

12009453

-
Frame-shiftENST00000273038ENST00000356352VGLL4chr3

11744445

-UPF2chr10

12021164

-
Frame-shiftENST00000273038ENST00000357604VGLL4chr3

11744444

-UPF2chr10

12009452

-
Frame-shiftENST00000273038ENST00000357604VGLL4chr3

11744444

-UPF2chr10

12021163

-
Frame-shiftENST00000273038ENST00000357604VGLL4chr3

11744445

-UPF2chr10

12009453

-
Frame-shiftENST00000273038ENST00000357604VGLL4chr3

11744445

-UPF2chr10

12021164

-
Frame-shiftENST00000273038ENST00000397053VGLL4chr3

11744444

-UPF2chr10

12009452

-
Frame-shiftENST00000273038ENST00000397053VGLL4chr3

11744444

-UPF2chr10

12021163

-
Frame-shiftENST00000273038ENST00000397053VGLL4chr3

11744445

-UPF2chr10

12009453

-
Frame-shiftENST00000273038ENST00000397053VGLL4chr3

11744445

-UPF2chr10

12021164

-
intron-3CDSENST00000413604ENST00000356352VGLL4chr3

11744444

-UPF2chr10

12009452

-
intron-3CDSENST00000413604ENST00000356352VGLL4chr3

11744444

-UPF2chr10

12021163

-
intron-3CDSENST00000413604ENST00000356352VGLL4chr3

11744445

-UPF2chr10

12009453

-
intron-3CDSENST00000413604ENST00000356352VGLL4chr3

11744445

-UPF2chr10

12021164

-
intron-3CDSENST00000413604ENST00000357604VGLL4chr3

11744444

-UPF2chr10

12009452

-
intron-3CDSENST00000413604ENST00000357604VGLL4chr3

11744444

-UPF2chr10

12021163

-
intron-3CDSENST00000413604ENST00000357604VGLL4chr3

11744445

-UPF2chr10

12009453

-
intron-3CDSENST00000413604ENST00000357604VGLL4chr3

11744445

-UPF2chr10

12021164

-
intron-3CDSENST00000413604ENST00000397053VGLL4chr3

11744444

-UPF2chr10

12009452

-
intron-3CDSENST00000413604ENST00000397053VGLL4chr3

11744444

-UPF2chr10

12021163

-
intron-3CDSENST00000413604ENST00000397053VGLL4chr3

11744445

-UPF2chr10

12009453

-
intron-3CDSENST00000413604ENST00000397053VGLL4chr3

11744445

-UPF2chr10

12021164

-
intron-3CDSENST00000424529ENST00000356352VGLL4chr3

11744444

-UPF2chr10

12009452

-
intron-3CDSENST00000424529ENST00000356352VGLL4chr3

11744444

-UPF2chr10

12021163

-
intron-3CDSENST00000424529ENST00000356352VGLL4chr3

11744445

-UPF2chr10

12009453

-
intron-3CDSENST00000424529ENST00000356352VGLL4chr3

11744445

-UPF2chr10

12021164

-
intron-3CDSENST00000424529ENST00000357604VGLL4chr3

11744444

-UPF2chr10

12009452

-
intron-3CDSENST00000424529ENST00000357604VGLL4chr3

11744444

-UPF2chr10

12021163

-
intron-3CDSENST00000424529ENST00000357604VGLL4chr3

11744445

-UPF2chr10

12009453

-
intron-3CDSENST00000424529ENST00000357604VGLL4chr3

11744445

-UPF2chr10

12021164

-
intron-3CDSENST00000424529ENST00000397053VGLL4chr3

11744444

-UPF2chr10

12009452

-
intron-3CDSENST00000424529ENST00000397053VGLL4chr3

11744444

-UPF2chr10

12021163

-
intron-3CDSENST00000424529ENST00000397053VGLL4chr3

11744445

-UPF2chr10

12009453

-
intron-3CDSENST00000424529ENST00000397053VGLL4chr3

11744445

-UPF2chr10

12021164

-
intron-3CDSENST00000430365ENST00000356352VGLL4chr3

11744444

-UPF2chr10

12009452

-
intron-3CDSENST00000430365ENST00000356352VGLL4chr3

11744444

-UPF2chr10

12021163

-
intron-3CDSENST00000430365ENST00000356352VGLL4chr3

11744445

-UPF2chr10

12009453

-
intron-3CDSENST00000430365ENST00000356352VGLL4chr3

11744445

-UPF2chr10

12021164

-
intron-3CDSENST00000430365ENST00000357604VGLL4chr3

11744444

-UPF2chr10

12009452

-
intron-3CDSENST00000430365ENST00000357604VGLL4chr3

11744444

-UPF2chr10

12021163

-
intron-3CDSENST00000430365ENST00000357604VGLL4chr3

11744445

-UPF2chr10

12009453

-
intron-3CDSENST00000430365ENST00000357604VGLL4chr3

11744445

-UPF2chr10

12021164

-
intron-3CDSENST00000430365ENST00000397053VGLL4chr3

11744444

-UPF2chr10

12009452

-
intron-3CDSENST00000430365ENST00000397053VGLL4chr3

11744444

-UPF2chr10

12021163

-
intron-3CDSENST00000430365ENST00000397053VGLL4chr3

11744445

-UPF2chr10

12009453

-
intron-3CDSENST00000430365ENST00000397053VGLL4chr3

11744445

-UPF2chr10

12021164

-
intron-3CDSENST00000451674ENST00000356352VGLL4chr3

11744444

-UPF2chr10

12009452

-
intron-3CDSENST00000451674ENST00000356352VGLL4chr3

11744444

-UPF2chr10

12021163

-
intron-3CDSENST00000451674ENST00000356352VGLL4chr3

11744445

-UPF2chr10

12009453

-
intron-3CDSENST00000451674ENST00000356352VGLL4chr3

11744445

-UPF2chr10

12021164

-
intron-3CDSENST00000451674ENST00000357604VGLL4chr3

11744444

-UPF2chr10

12009452

-
intron-3CDSENST00000451674ENST00000357604VGLL4chr3

11744444

-UPF2chr10

12021163

-
intron-3CDSENST00000451674ENST00000357604VGLL4chr3

11744445

-UPF2chr10

12009453

-
intron-3CDSENST00000451674ENST00000357604VGLL4chr3

11744445

-UPF2chr10

12021164

-
intron-3CDSENST00000451674ENST00000397053VGLL4chr3

11744444

-UPF2chr10

12009452

-
intron-3CDSENST00000451674ENST00000397053VGLL4chr3

11744444

-UPF2chr10

12021163

-
intron-3CDSENST00000451674ENST00000397053VGLL4chr3

11744445

-UPF2chr10

12009453

-
intron-3CDSENST00000451674ENST00000397053VGLL4chr3

11744445

-UPF2chr10

12021164

-
intron-3CDSENST00000480288ENST00000356352VGLL4chr3

11744444

-UPF2chr10

12009452

-
intron-3CDSENST00000480288ENST00000356352VGLL4chr3

11744444

-UPF2chr10

12021163

-
intron-3CDSENST00000480288ENST00000356352VGLL4chr3

11744445

-UPF2chr10

12009453

-
intron-3CDSENST00000480288ENST00000356352VGLL4chr3

11744445

-UPF2chr10

12021164

-
intron-3CDSENST00000480288ENST00000357604VGLL4chr3

11744444

-UPF2chr10

12009452

-
intron-3CDSENST00000480288ENST00000357604VGLL4chr3

11744444

-UPF2chr10

12021163

-
intron-3CDSENST00000480288ENST00000357604VGLL4chr3

11744445

-UPF2chr10

12009453

-
intron-3CDSENST00000480288ENST00000357604VGLL4chr3

11744445

-UPF2chr10

12021164

-
intron-3CDSENST00000480288ENST00000397053VGLL4chr3

11744444

-UPF2chr10

12009452

-
intron-3CDSENST00000480288ENST00000397053VGLL4chr3

11744444

-UPF2chr10

12021163

-
intron-3CDSENST00000480288ENST00000397053VGLL4chr3

11744445

-UPF2chr10

12009453

-
intron-3CDSENST00000480288ENST00000397053VGLL4chr3

11744445

-UPF2chr10

12021164

-
intron-intronENST00000413604ENST00000460569VGLL4chr3

11744444

-UPF2chr10

12009452

-
intron-intronENST00000413604ENST00000460569VGLL4chr3

11744444

-UPF2chr10

12021163

-
intron-intronENST00000413604ENST00000460569VGLL4chr3

11744445

-UPF2chr10

12009453

-
intron-intronENST00000413604ENST00000460569VGLL4chr3

11744445

-UPF2chr10

12021164

-
intron-intronENST00000424529ENST00000460569VGLL4chr3

11744444

-UPF2chr10

12009452

-
intron-intronENST00000424529ENST00000460569VGLL4chr3

11744444

-UPF2chr10

12021163

-
intron-intronENST00000424529ENST00000460569VGLL4chr3

11744445

-UPF2chr10

12009453

-
intron-intronENST00000424529ENST00000460569VGLL4chr3

11744445

-UPF2chr10

12021164

-
intron-intronENST00000430365ENST00000460569VGLL4chr3

11744444

-UPF2chr10

12009452

-
intron-intronENST00000430365ENST00000460569VGLL4chr3

11744444

-UPF2chr10

12021163

-
intron-intronENST00000430365ENST00000460569VGLL4chr3

11744445

-UPF2chr10

12009453

-
intron-intronENST00000430365ENST00000460569VGLL4chr3

11744445

-UPF2chr10

12021164

-
intron-intronENST00000451674ENST00000460569VGLL4chr3

11744444

-UPF2chr10

12009452

-
intron-intronENST00000451674ENST00000460569VGLL4chr3

11744444

-UPF2chr10

12021163

-
intron-intronENST00000451674ENST00000460569VGLL4chr3

11744445

-UPF2chr10

12009453

-
intron-intronENST00000451674ENST00000460569VGLL4chr3

11744445

-UPF2chr10

12021164

-
intron-intronENST00000480288ENST00000460569VGLL4chr3

11744444

-UPF2chr10

12009452

-
intron-intronENST00000480288ENST00000460569VGLL4chr3

11744444

-UPF2chr10

12021163

-
intron-intronENST00000480288ENST00000460569VGLL4chr3

11744445

-UPF2chr10

12009453

-
intron-intronENST00000480288ENST00000460569VGLL4chr3

11744445

-UPF2chr10

12021164

-

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 VGLL4-UPF2


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)

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 VGLL4-UPF2


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/:11744445/:12021164)
- 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 VGLL4-UPF2


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 VGLL4-UPF2


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 VGLL4-UPF2


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 VGLL4-UPF2


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