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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:CLINT1-PDLIM5 (FusionGDB2 ID:17148)

Fusion Gene Summary for CLINT1-PDLIM5

check button Fusion gene summary
Fusion gene informationFusion gene name: CLINT1-PDLIM5
Fusion gene ID: 17148
HgeneTgene
Gene symbol

CLINT1

PDLIM5

Gene ID

9685

10611

Gene nameclathrin interactor 1PDZ and LIM domain 5
SynonymsCLINT|ENTH|EPN4|EPNRENH|ENH1|L9|LIM
Cytomap

5q33.3

4q22.3

Type of geneprotein-codingprotein-coding
Descriptionclathrin interactor 1clathrin interacting protein localized in the trans-Golgi regionenthoprotinepsin 4epsin-related proteinepsinRPDZ and LIM domain protein 5enigma homologenigma-like LIM domain proteinenigma-like PDZ and LIM domains protein
Modification date2020031320200313
UniProtAcc

Q14677

.
Ensembl transtripts involved in fusion geneENST00000411809, ENST00000523908, 
ENST00000296951, ENST00000523094, 
ENST00000530742, 		ENST00000317968, 
ENST00000318007, ENST00000359265, 
ENST00000380180, ENST00000437932, 
ENST00000450793, ENST00000504489, 
ENST00000508216, ENST00000512274, 
ENST00000514743, ENST00000538141, 
ENST00000542407, ENST00000380176, 
Fusion gene scores* DoF score6 X 7 X 4=16815 X 18 X 7=1890
# samples 921
** MAII scorelog2(9/168*10)=-0.900464326449086
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(21/1890*10)=-3.16992500144231
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: CLINT1 [Title/Abstract] AND PDLIM5 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointCLINT1(157285938)-PDLIM5(95376398), # 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 CLINT1 (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 PDLIM5 (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-A4PD-01ACLINT1chr5

157285938

-PDLIM5chr4

95376398

+


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Fusion Gene ORF analysis for CLINT1-PDLIM5

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-5UTRENST00000411809ENST00000317968CLINT1chr5

157285938

-PDLIM5chr4

95376398

+
5CDS-5UTRENST00000411809ENST00000318007CLINT1chr5

157285938

-PDLIM5chr4

95376398

+
5CDS-5UTRENST00000411809ENST00000359265CLINT1chr5

157285938

-PDLIM5chr4

95376398

+
5CDS-5UTRENST00000411809ENST00000380180CLINT1chr5

157285938

-PDLIM5chr4

95376398

+
5CDS-5UTRENST00000411809ENST00000437932CLINT1chr5

157285938

-PDLIM5chr4

95376398

+
5CDS-5UTRENST00000411809ENST00000450793CLINT1chr5

157285938

-PDLIM5chr4

95376398

+
5CDS-5UTRENST00000411809ENST00000504489CLINT1chr5

157285938

-PDLIM5chr4

95376398

+
5CDS-5UTRENST00000411809ENST00000508216CLINT1chr5

157285938

-PDLIM5chr4

95376398

+
5CDS-5UTRENST00000411809ENST00000512274CLINT1chr5

157285938

-PDLIM5chr4

95376398

+
5CDS-5UTRENST00000411809ENST00000514743CLINT1chr5

157285938

-PDLIM5chr4

95376398

+
5CDS-5UTRENST00000411809ENST00000538141CLINT1chr5

157285938

-PDLIM5chr4

95376398

+
5CDS-5UTRENST00000411809ENST00000542407CLINT1chr5

157285938

-PDLIM5chr4

95376398

+
5CDS-5UTRENST00000523908ENST00000317968CLINT1chr5

157285938

-PDLIM5chr4

95376398

+
5CDS-5UTRENST00000523908ENST00000318007CLINT1chr5

157285938

-PDLIM5chr4

95376398

+
5CDS-5UTRENST00000523908ENST00000359265CLINT1chr5

157285938

-PDLIM5chr4

95376398

+
5CDS-5UTRENST00000523908ENST00000380180CLINT1chr5

157285938

-PDLIM5chr4

95376398

+
5CDS-5UTRENST00000523908ENST00000437932CLINT1chr5

157285938

-PDLIM5chr4

95376398

+
5CDS-5UTRENST00000523908ENST00000450793CLINT1chr5

157285938

-PDLIM5chr4

95376398

+
5CDS-5UTRENST00000523908ENST00000504489CLINT1chr5

157285938

-PDLIM5chr4

95376398

+
5CDS-5UTRENST00000523908ENST00000508216CLINT1chr5

157285938

-PDLIM5chr4

95376398

+
5CDS-5UTRENST00000523908ENST00000512274CLINT1chr5

157285938

-PDLIM5chr4

95376398

+
5CDS-5UTRENST00000523908ENST00000514743CLINT1chr5

157285938

-PDLIM5chr4

95376398

+
5CDS-5UTRENST00000523908ENST00000538141CLINT1chr5

157285938

-PDLIM5chr4

95376398

+
5CDS-5UTRENST00000523908ENST00000542407CLINT1chr5

157285938

-PDLIM5chr4

95376398

+
5CDS-intronENST00000411809ENST00000380176CLINT1chr5

157285938

-PDLIM5chr4

95376398

+
5CDS-intronENST00000523908ENST00000380176CLINT1chr5

157285938

-PDLIM5chr4

95376398

+
5UTR-5UTRENST00000296951ENST00000317968CLINT1chr5

157285938

-PDLIM5chr4

95376398

+
5UTR-5UTRENST00000296951ENST00000318007CLINT1chr5

157285938

-PDLIM5chr4

95376398

+
5UTR-5UTRENST00000296951ENST00000359265CLINT1chr5

157285938

-PDLIM5chr4

95376398

+
5UTR-5UTRENST00000296951ENST00000380180CLINT1chr5

157285938

-PDLIM5chr4

95376398

+
5UTR-5UTRENST00000296951ENST00000437932CLINT1chr5

157285938

-PDLIM5chr4

95376398

+
5UTR-5UTRENST00000296951ENST00000450793CLINT1chr5

157285938

-PDLIM5chr4

95376398

+
5UTR-5UTRENST00000296951ENST00000504489CLINT1chr5

157285938

-PDLIM5chr4

95376398

+
5UTR-5UTRENST00000296951ENST00000508216CLINT1chr5

157285938

-PDLIM5chr4

95376398

+
5UTR-5UTRENST00000296951ENST00000512274CLINT1chr5

157285938

-PDLIM5chr4

95376398

+
5UTR-5UTRENST00000296951ENST00000514743CLINT1chr5

157285938

-PDLIM5chr4

95376398

+
5UTR-5UTRENST00000296951ENST00000538141CLINT1chr5

157285938

-PDLIM5chr4

95376398

+
5UTR-5UTRENST00000296951ENST00000542407CLINT1chr5

157285938

-PDLIM5chr4

95376398

+
5UTR-intronENST00000296951ENST00000380176CLINT1chr5

157285938

-PDLIM5chr4

95376398

+
intron-5UTRENST00000523094ENST00000317968CLINT1chr5

157285938

-PDLIM5chr4

95376398

+
intron-5UTRENST00000523094ENST00000318007CLINT1chr5

157285938

-PDLIM5chr4

95376398

+
intron-5UTRENST00000523094ENST00000359265CLINT1chr5

157285938

-PDLIM5chr4

95376398

+
intron-5UTRENST00000523094ENST00000380180CLINT1chr5

157285938

-PDLIM5chr4

95376398

+
intron-5UTRENST00000523094ENST00000437932CLINT1chr5

157285938

-PDLIM5chr4

95376398

+
intron-5UTRENST00000523094ENST00000450793CLINT1chr5

157285938

-PDLIM5chr4

95376398

+
intron-5UTRENST00000523094ENST00000504489CLINT1chr5

157285938

-PDLIM5chr4

95376398

+
intron-5UTRENST00000523094ENST00000508216CLINT1chr5

157285938

-PDLIM5chr4

95376398

+
intron-5UTRENST00000523094ENST00000512274CLINT1chr5

157285938

-PDLIM5chr4

95376398

+
intron-5UTRENST00000523094ENST00000514743CLINT1chr5

157285938

-PDLIM5chr4

95376398

+
intron-5UTRENST00000523094ENST00000538141CLINT1chr5

157285938

-PDLIM5chr4

95376398

+
intron-5UTRENST00000523094ENST00000542407CLINT1chr5

157285938

-PDLIM5chr4

95376398

+
intron-5UTRENST00000530742ENST00000317968CLINT1chr5

157285938

-PDLIM5chr4

95376398

+
intron-5UTRENST00000530742ENST00000318007CLINT1chr5

157285938

-PDLIM5chr4

95376398

+
intron-5UTRENST00000530742ENST00000359265CLINT1chr5

157285938

-PDLIM5chr4

95376398

+
intron-5UTRENST00000530742ENST00000380180CLINT1chr5

157285938

-PDLIM5chr4

95376398

+
intron-5UTRENST00000530742ENST00000437932CLINT1chr5

157285938

-PDLIM5chr4

95376398

+
intron-5UTRENST00000530742ENST00000450793CLINT1chr5

157285938

-PDLIM5chr4

95376398

+
intron-5UTRENST00000530742ENST00000504489CLINT1chr5

157285938

-PDLIM5chr4

95376398

+
intron-5UTRENST00000530742ENST00000508216CLINT1chr5

157285938

-PDLIM5chr4

95376398

+
intron-5UTRENST00000530742ENST00000512274CLINT1chr5

157285938

-PDLIM5chr4

95376398

+
intron-5UTRENST00000530742ENST00000514743CLINT1chr5

157285938

-PDLIM5chr4

95376398

+
intron-5UTRENST00000530742ENST00000538141CLINT1chr5

157285938

-PDLIM5chr4

95376398

+
intron-5UTRENST00000530742ENST00000542407CLINT1chr5

157285938

-PDLIM5chr4

95376398

+
intron-intronENST00000523094ENST00000380176CLINT1chr5

157285938

-PDLIM5chr4

95376398

+
intron-intronENST00000530742ENST00000380176CLINT1chr5

157285938

-PDLIM5chr4

95376398

+

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 CLINT1-PDLIM5


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)
CLINT1chr5157285937-PDLIM5chr495376395+0.0028202030.99717987
CLINT1chr5157285937-PDLIM5chr495376395+0.0028202030.99717987

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.
genomic feature of top 1%

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Fusion Protein Features for CLINT1-PDLIM5


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/:157285938/:95376398)
- 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
CLINT1

Q14677

.
FUNCTION: Binds to membranes enriched in phosphatidylinositol 4,5-bisphosphate (PtdIns(4,5)P2). May have a role in transport via clathrin-coated vesicles from the trans-Golgi network to endosomes. Stimulates clathrin assembly. {ECO:0000269|PubMed:12429846, ECO:0000269|PubMed:12538641}.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 CLINT1-PDLIM5


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 CLINT1-PDLIM5


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 CLINT1-PDLIM5


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 CLINT1-PDLIM5


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