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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:VANGL1-CSDE1 (FusionGDB2 ID:97869)

Fusion Gene Summary for VANGL1-CSDE1

check button Fusion gene summary
Fusion gene informationFusion gene name: VANGL1-CSDE1
Fusion gene ID: 97869
HgeneTgene
Gene symbol

VANGL1

CSDE1

Gene ID

81839

7812

Gene nameVANGL planar cell polarity protein 1cold shock domain containing E1
SynonymsKITENIN|LPP2|STB2|STBM2D1S155E|UNR
Cytomap

1p13.1

1p13.2

Type of geneprotein-codingprotein-coding
Descriptionvang-like protein 1KAI1 C-terminal interacting tetraspaninloop-tail protein 2 homologstrabismus 2van Gogh-like protein 1vang-like 1 (van gogh, Drosophila)cold shock domain-containing protein E1N-ras upstream gene proteinNRAS-relatedcold shock domain containing E1, RNA bindingupstream of NRAS
Modification date2020032220200313
UniProtAcc.

O75534

Ensembl transtripts involved in fusion geneENST00000355485, ENST00000369510, 
ENST00000310260, ENST00000369509, 
ENST00000474344, 		ENST00000339438, 
ENST00000358528, ENST00000369530, 
ENST00000530886, ENST00000261443, 
ENST00000438362, ENST00000483407, 
ENST00000534699, 
Fusion gene scores* DoF score5 X 5 X 3=7518 X 14 X 7=1764
# samples 519
** MAII scorelog2(5/75*10)=-0.584962500721156
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(19/1764*10)=-3.21477923722657
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: VANGL1 [Title/Abstract] AND CSDE1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointVANGL1(116184707)-CSDE1(115292828), # samples:1
Anticipated loss of major functional domain due to fusion event.
* 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 VANGL1 (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 CSDE1 (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
ChimerDB4STADTCGA-BR-A4PE-01AVANGL1chr1

116184707

+CSDE1chr1

115292828

-


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Fusion Gene ORF analysis for VANGL1-CSDE1

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
5UTR-5UTRENST00000355485ENST00000339438VANGL1chr1

116184707

+CSDE1chr1

115292828

-
5UTR-5UTRENST00000355485ENST00000358528VANGL1chr1

116184707

+CSDE1chr1

115292828

-
5UTR-5UTRENST00000355485ENST00000369530VANGL1chr1

116184707

+CSDE1chr1

115292828

-
5UTR-5UTRENST00000355485ENST00000530886VANGL1chr1

116184707

+CSDE1chr1

115292828

-
5UTR-5UTRENST00000369510ENST00000339438VANGL1chr1

116184707

+CSDE1chr1

115292828

-
5UTR-5UTRENST00000369510ENST00000358528VANGL1chr1

116184707

+CSDE1chr1

115292828

-
5UTR-5UTRENST00000369510ENST00000369530VANGL1chr1

116184707

+CSDE1chr1

115292828

-
5UTR-5UTRENST00000369510ENST00000530886VANGL1chr1

116184707

+CSDE1chr1

115292828

-
5UTR-intronENST00000355485ENST00000261443VANGL1chr1

116184707

+CSDE1chr1

115292828

-
5UTR-intronENST00000355485ENST00000438362VANGL1chr1

116184707

+CSDE1chr1

115292828

-
5UTR-intronENST00000355485ENST00000483407VANGL1chr1

116184707

+CSDE1chr1

115292828

-
5UTR-intronENST00000355485ENST00000534699VANGL1chr1

116184707

+CSDE1chr1

115292828

-
5UTR-intronENST00000369510ENST00000261443VANGL1chr1

116184707

+CSDE1chr1

115292828

-
5UTR-intronENST00000369510ENST00000438362VANGL1chr1

116184707

+CSDE1chr1

115292828

-
5UTR-intronENST00000369510ENST00000483407VANGL1chr1

116184707

+CSDE1chr1

115292828

-
5UTR-intronENST00000369510ENST00000534699VANGL1chr1

116184707

+CSDE1chr1

115292828

-
intron-5UTRENST00000310260ENST00000339438VANGL1chr1

116184707

+CSDE1chr1

115292828

-
intron-5UTRENST00000310260ENST00000358528VANGL1chr1

116184707

+CSDE1chr1

115292828

-
intron-5UTRENST00000310260ENST00000369530VANGL1chr1

116184707

+CSDE1chr1

115292828

-
intron-5UTRENST00000310260ENST00000530886VANGL1chr1

116184707

+CSDE1chr1

115292828

-
intron-5UTRENST00000369509ENST00000339438VANGL1chr1

116184707

+CSDE1chr1

115292828

-
intron-5UTRENST00000369509ENST00000358528VANGL1chr1

116184707

+CSDE1chr1

115292828

-
intron-5UTRENST00000369509ENST00000369530VANGL1chr1

116184707

+CSDE1chr1

115292828

-
intron-5UTRENST00000369509ENST00000530886VANGL1chr1

116184707

+CSDE1chr1

115292828

-
intron-5UTRENST00000474344ENST00000339438VANGL1chr1

116184707

+CSDE1chr1

115292828

-
intron-5UTRENST00000474344ENST00000358528VANGL1chr1

116184707

+CSDE1chr1

115292828

-
intron-5UTRENST00000474344ENST00000369530VANGL1chr1

116184707

+CSDE1chr1

115292828

-
intron-5UTRENST00000474344ENST00000530886VANGL1chr1

116184707

+CSDE1chr1

115292828

-
intron-intronENST00000310260ENST00000261443VANGL1chr1

116184707

+CSDE1chr1

115292828

-
intron-intronENST00000310260ENST00000438362VANGL1chr1

116184707

+CSDE1chr1

115292828

-
intron-intronENST00000310260ENST00000483407VANGL1chr1

116184707

+CSDE1chr1

115292828

-
intron-intronENST00000310260ENST00000534699VANGL1chr1

116184707

+CSDE1chr1

115292828

-
intron-intronENST00000369509ENST00000261443VANGL1chr1

116184707

+CSDE1chr1

115292828

-
intron-intronENST00000369509ENST00000438362VANGL1chr1

116184707

+CSDE1chr1

115292828

-
intron-intronENST00000369509ENST00000483407VANGL1chr1

116184707

+CSDE1chr1

115292828

-
intron-intronENST00000369509ENST00000534699VANGL1chr1

116184707

+CSDE1chr1

115292828

-
intron-intronENST00000474344ENST00000261443VANGL1chr1

116184707

+CSDE1chr1

115292828

-
intron-intronENST00000474344ENST00000438362VANGL1chr1

116184707

+CSDE1chr1

115292828

-
intron-intronENST00000474344ENST00000483407VANGL1chr1

116184707

+CSDE1chr1

115292828

-
intron-intronENST00000474344ENST00000534699VANGL1chr1

116184707

+CSDE1chr1

115292828

-

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 VANGL1-CSDE1


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 VANGL1-CSDE1


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/:116184707/:115292828)
- 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
.CSDE1

O75534

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: RNA-binding protein involved in translationally coupled mRNA turnover (PubMed:11051545, PubMed:15314026). Implicated with other RNA-binding proteins in the cytoplasmic deadenylation/translational and decay interplay of the FOS mRNA mediated by the major coding-region determinant of instability (mCRD) domain (PubMed:11051545, PubMed:15314026). Required for efficient formation of stress granules (PubMed:29395067). {ECO:0000269|PubMed:11051545, ECO:0000269|PubMed:15314026, ECO:0000269|PubMed:29395067}.; FUNCTION: (Microbial infection) Required for internal initiation of translation of human rhinovirus RNA. {ECO:0000269|PubMed:10049359}.

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 VANGL1-CSDE1


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 VANGL1-CSDE1


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 VANGL1-CSDE1


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 VANGL1-CSDE1


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