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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:TRIO-CLIC5 (FusionGDB2 ID:93532)

Fusion Gene Summary for TRIO-CLIC5

check button Fusion gene summary
Fusion gene informationFusion gene name: TRIO-CLIC5
Fusion gene ID: 93532
HgeneTgene
Gene symbol

TRIO

CLIC5

Gene ID

7204

53405

Gene nametrio Rho guanine nucleotide exchange factorchloride intracellular channel 5
SynonymsARHGEF23|MEBAS|MRD44|tgatDFNB102|DFNB103|MST130|MSTP130
Cytomap

5p15.2

6p21.1

Type of geneprotein-codingprotein-coding
Descriptiontriple functional domain proteinPTPRF-interacting proteintriple functional domain (PTPRF interacting)chloride intracellular channel protein 5
Modification date2020031320200313
UniProtAcc

TRIOBP

Q9NZA1

Ensembl transtripts involved in fusion geneENST00000344204, ENST00000537187, 
ENST00000509967, ENST00000515710, 
ENST00000344135, 		ENST00000339561, 
ENST00000185206, ENST00000544153, 
ENST00000486570, 
Fusion gene scores* DoF score34 X 28 X 12=114242 X 3 X 2=12
# samples 353
** MAII scorelog2(35/11424*10)=-5.02856915219677
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(3/12*10)=1.32192809488736
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context

PubMed: TRIO [Title/Abstract] AND CLIC5 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointTRIO(14420130)-CLIC5(45922981), # samples:2
Anticipated loss of major functional domain due to fusion event.TRIO-CLIC5 seems lost the major protein functional domain in Hgene partner, which is a kinase due to the frame-shifted ORF.
TRIO-CLIC5 seems lost the major protein functional domain in Hgene partner, which is a IUPHAR drug target 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
TgeneCLIC5

GO:0006821

chloride transport

10793131


check buttonFusion gene breakpoints across TRIO (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 CLIC5 (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
ChimerDB4SKCMTCGA-EB-A44Q-06ATRIOchr5

14420130

+CLIC5chr6

45922981

-
ChimerDB4SKCMTCGA-EB-A44Q-06ATRIOchr5

14420130

-CLIC5chr6

45922981

-


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Fusion Gene ORF analysis for TRIO-CLIC5

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
Frame-shiftENST00000344204ENST00000339561TRIOchr5

14420130

+CLIC5chr6

45922981

-
Frame-shiftENST00000344204ENST00000185206TRIOchr5

14420130

+CLIC5chr6

45922981

-
Frame-shiftENST00000344204ENST00000544153TRIOchr5

14420130

+CLIC5chr6

45922981

-
5CDS-intronENST00000344204ENST00000486570TRIOchr5

14420130

+CLIC5chr6

45922981

-
Frame-shiftENST00000537187ENST00000339561TRIOchr5

14420130

+CLIC5chr6

45922981

-
Frame-shiftENST00000537187ENST00000185206TRIOchr5

14420130

+CLIC5chr6

45922981

-
Frame-shiftENST00000537187ENST00000544153TRIOchr5

14420130

+CLIC5chr6

45922981

-
5CDS-intronENST00000537187ENST00000486570TRIOchr5

14420130

+CLIC5chr6

45922981

-
intron-3CDSENST00000509967ENST00000339561TRIOchr5

14420130

+CLIC5chr6

45922981

-
intron-3CDSENST00000509967ENST00000185206TRIOchr5

14420130

+CLIC5chr6

45922981

-
intron-3CDSENST00000509967ENST00000544153TRIOchr5

14420130

+CLIC5chr6

45922981

-
intron-intronENST00000509967ENST00000486570TRIOchr5

14420130

+CLIC5chr6

45922981

-
intron-3CDSENST00000515710ENST00000339561TRIOchr5

14420130

+CLIC5chr6

45922981

-
intron-3CDSENST00000515710ENST00000185206TRIOchr5

14420130

+CLIC5chr6

45922981

-
intron-3CDSENST00000515710ENST00000544153TRIOchr5

14420130

+CLIC5chr6

45922981

-
intron-intronENST00000515710ENST00000486570TRIOchr5

14420130

+CLIC5chr6

45922981

-
intron-3CDSENST00000344135ENST00000339561TRIOchr5

14420130

+CLIC5chr6

45922981

-
intron-3CDSENST00000344135ENST00000185206TRIOchr5

14420130

+CLIC5chr6

45922981

-
intron-3CDSENST00000344135ENST00000544153TRIOchr5

14420130

+CLIC5chr6

45922981

-
intron-intronENST00000344135ENST00000486570TRIOchr5

14420130

+CLIC5chr6

45922981

-

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 TRIO-CLIC5


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 TRIO-CLIC5


check button Go to

FGviewer for the breakpoints of :-:

.
- FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels.
FGviewer

check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
TRIO

TRIOBP

CLIC5

Q9NZA1

2365FUNCTION: Required for normal hearing (PubMed:24781754). It is necessary for the formation of stereocilia in the inner ear and normal development of the organ of Corti (By similarity). Can insert into membranes and form poorly selective ion channels that may also transport chloride ions. May play a role in the regulation of transepithelial ion absorption and secretion. Is required for the development and/or maintenance of the proper glomerular endothelial cell and podocyte architecture (PubMed:15184393, PubMed:18028448, PubMed:20335315). Plays a role in formation of the lens suture in the eye, which is important for normal optical properties of the lens (By similarity). {ECO:0000250|UniProtKB:Q8BXK9, ECO:0000269|PubMed:15184393, ECO:0000269|PubMed:18028448, ECO:0000269|PubMed:20335315, ECO:0000269|PubMed:24781754}.

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 TRIO-CLIC5


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 TRIO-CLIC5


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 TRIO-CLIC5


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 TRIO-CLIC5


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneTRIOC4310740MENTAL RETARDATION, AUTOSOMAL DOMINANT 442CTD_human;ORPHANET;UNIPROT
HgeneTRIOC0023467Leukemia, Myelocytic, Acute1CTD_human
HgeneTRIOC0023903Liver neoplasms1CTD_human
HgeneTRIOC0026998Acute Myeloid Leukemia, M11CTD_human
HgeneTRIOC0032927Precancerous Conditions1CTD_human
HgeneTRIOC0282313Condition, Preneoplastic1CTD_human
HgeneTRIOC0345904Malignant neoplasm of liver1CTD_human
HgeneTRIOC1535926Neurodevelopmental Disorders1CTD_human
HgeneTRIOC1879321Acute Myeloid Leukemia (AML-M2)1CTD_human
TgeneCLIC5C1846647DEAFNESS, AUTOSOMAL RECESSIVE (disorder)3CLINGEN
TgeneCLIC5C4015050DEAFNESS, AUTOSOMAL RECESSIVE 1031CTD_human;GENOMICS_ENGLAND