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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:CDH1-PIK3C3 (FusionGDB2 ID:15039)

Fusion Gene Summary for CDH1-PIK3C3

check button Fusion gene summary
Fusion gene informationFusion gene name: CDH1-PIK3C3
Fusion gene ID: 15039
HgeneTgene
Gene symbol

CDH1

PIK3C3

Gene ID

51343

5289

Gene namefizzy and cell division cycle 20 related 1phosphatidylinositol 3-kinase catalytic subunit type 3
SynonymsCDC20C|CDH1|FZR|FZR2|HCDH|HCDH1VPS34|Vps34|hVps34
Cytomap

19p13.3

18q12.3

Type of geneprotein-codingprotein-coding
Descriptionfizzy-related protein homologCDC20 homolog 1CDC20-like 1bCDC20-like protein 1cdh1/Hct1 homologfizzy/cell division cycle 20 related 1phosphatidylinositol 3-kinase catalytic subunit type 3PI3-kinase type 3PI3K type 3PtdIns-3-kinase type 3phosphatidylinositol 3-kinase p100 subunitphosphoinositide-3-kinase, class 3
Modification date2020031320200327
UniProtAcc

P12830

.
Ensembl transtripts involved in fusion geneENST00000562836, ENST00000261769, 
ENST00000422392, 		ENST00000262039, 
ENST00000398870, ENST00000586545, 
ENST00000587328, ENST00000587402, 
ENST00000588156, ENST00000589056, 
ENST00000590220, ENST00000593098, 
Fusion gene scores* DoF score21 X 16 X 8=26885 X 5 X 2=50
# samples 295
** MAII scorelog2(29/2688*10)=-3.21240833276383
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(5/50*10)=0
Context

PubMed: CDH1 [Title/Abstract] AND PIK3C3 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointCDH1(68862159)-PIK3C3(39662333), # 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
HgeneCDH1

GO:0031145

anaphase-promoting complex-dependent catabolic process

18662541|21596315

HgeneCDH1

GO:0072425

signal transduction involved in G2 DNA damage checkpoint

18662541

HgeneCDH1

GO:1904668

positive regulation of ubiquitin protein ligase activity

11459826


check buttonFusion gene breakpoints across CDH1 (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 PIK3C3 (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-CD-A48C-01ACDH1chr16

68862159

+PIK3C3chr18

39662333

+


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Fusion Gene ORF analysis for CDH1-PIK3C3

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-3UTRENST00000562836ENST00000262039CDH1chr16

68862159

+PIK3C3chr18

39662333

+
3UTR-3UTRENST00000562836ENST00000398870CDH1chr16

68862159

+PIK3C3chr18

39662333

+
3UTR-intronENST00000562836ENST00000586545CDH1chr16

68862159

+PIK3C3chr18

39662333

+
3UTR-intronENST00000562836ENST00000587328CDH1chr16

68862159

+PIK3C3chr18

39662333

+
3UTR-intronENST00000562836ENST00000587402CDH1chr16

68862159

+PIK3C3chr18

39662333

+
3UTR-intronENST00000562836ENST00000588156CDH1chr16

68862159

+PIK3C3chr18

39662333

+
3UTR-intronENST00000562836ENST00000589056CDH1chr16

68862159

+PIK3C3chr18

39662333

+
3UTR-intronENST00000562836ENST00000590220CDH1chr16

68862159

+PIK3C3chr18

39662333

+
3UTR-intronENST00000562836ENST00000593098CDH1chr16

68862159

+PIK3C3chr18

39662333

+
5CDS-3UTRENST00000261769ENST00000262039CDH1chr16

68862159

+PIK3C3chr18

39662333

+
5CDS-3UTRENST00000261769ENST00000398870CDH1chr16

68862159

+PIK3C3chr18

39662333

+
5CDS-3UTRENST00000422392ENST00000262039CDH1chr16

68862159

+PIK3C3chr18

39662333

+
5CDS-3UTRENST00000422392ENST00000398870CDH1chr16

68862159

+PIK3C3chr18

39662333

+
5CDS-intronENST00000261769ENST00000586545CDH1chr16

68862159

+PIK3C3chr18

39662333

+
5CDS-intronENST00000261769ENST00000587328CDH1chr16

68862159

+PIK3C3chr18

39662333

+
5CDS-intronENST00000261769ENST00000587402CDH1chr16

68862159

+PIK3C3chr18

39662333

+
5CDS-intronENST00000261769ENST00000588156CDH1chr16

68862159

+PIK3C3chr18

39662333

+
5CDS-intronENST00000261769ENST00000589056CDH1chr16

68862159

+PIK3C3chr18

39662333

+
5CDS-intronENST00000261769ENST00000590220CDH1chr16

68862159

+PIK3C3chr18

39662333

+
5CDS-intronENST00000261769ENST00000593098CDH1chr16

68862159

+PIK3C3chr18

39662333

+
5CDS-intronENST00000422392ENST00000586545CDH1chr16

68862159

+PIK3C3chr18

39662333

+
5CDS-intronENST00000422392ENST00000587328CDH1chr16

68862159

+PIK3C3chr18

39662333

+
5CDS-intronENST00000422392ENST00000587402CDH1chr16

68862159

+PIK3C3chr18

39662333

+
5CDS-intronENST00000422392ENST00000588156CDH1chr16

68862159

+PIK3C3chr18

39662333

+
5CDS-intronENST00000422392ENST00000589056CDH1chr16

68862159

+PIK3C3chr18

39662333

+
5CDS-intronENST00000422392ENST00000590220CDH1chr16

68862159

+PIK3C3chr18

39662333

+
5CDS-intronENST00000422392ENST00000593098CDH1chr16

68862159

+PIK3C3chr18

39662333

+

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 CDH1-PIK3C3


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 CDH1-PIK3C3


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/:68862159/:39662333)
- 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
CDH1

P12830

.
FUNCTION: Cadherins are calcium-dependent cell adhesion proteins (PubMed:11976333). They preferentially interact with themselves in a homophilic manner in connecting cells; cadherins may thus contribute to the sorting of heterogeneous cell types. CDH1 is involved in mechanisms regulating cell-cell adhesions, mobility and proliferation of epithelial cells (PubMed:11976333). Has a potent invasive suppressor role. It is a ligand for integrin alpha-E/beta-7. {ECO:0000269|PubMed:11976333, ECO:0000269|PubMed:16417575}.; FUNCTION: E-Cad/CTF2 promotes non-amyloidogenic degradation of Abeta precursors. Has a strong inhibitory effect on APP C99 and C83 production. {ECO:0000269|PubMed:16417575}.; FUNCTION: (Microbial infection) Serves as a receptor for Listeria monocytogenes; internalin A (InlA) binds to this protein and promotes uptake of the bacteria. {ECO:0000269|PubMed:10406800, ECO:0000269|PubMed:17540170, ECO:0000269|PubMed:8601315}.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 CDH1-PIK3C3


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 CDH1-PIK3C3


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 CDH1-PIK3C3


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 CDH1-PIK3C3


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