FusionGDB Logo

Home

Download

Statistics

Examples

Help

Contact
Center for Computational Systems Medicine
leaf

Fusion Gene Summary

leaf

Fusion Gene ORF analysis

leaf

Fusion Genomic Features

leaf

Fusion Protein Features

leaf

Fusion Gene Sequence

leaf

Fusion Gene PPI analysis

leaf

Related Drugs

leaf

Related Diseases

Fusion gene:CLIC6-ITSN1 (FusionGDB2 ID:17139)

Fusion Gene Summary for CLIC6-ITSN1

check button Fusion gene summary
Fusion gene informationFusion gene name: CLIC6-ITSN1
Fusion gene ID: 17139
HgeneTgene
Gene symbol

CLIC6

ITSN1

Gene ID

54102

6453

Gene namechloride intracellular channel 6intersectin 1
SynonymsCLIC1LITSN|SH3D1A|SH3P17
Cytomap

21q22.12

21q22.11

Type of geneprotein-codingprotein-coding
Descriptionchloride intracellular channel protein 6chloride channel form Aparchorinintersectin-1SH3 domain-containing protein 1ASrc homology 3 domain-containing proteinhuman intersectin-SH3 domain-containing protein SH3P17intersectin 1 (SH3 domain protein)intersectin 1 short form variant 3intersectin 1 short form variant, 11inter
Modification date2020031320200313
UniProtAcc

Q96NY7

Q15811

Ensembl transtripts involved in fusion geneENST00000349499, ENST00000360731, 
ENST00000399326, ENST00000379960, 
ENST00000381285, ENST00000381291, 
ENST00000381318, ENST00000399338, 
ENST00000399349, ENST00000399352, 
ENST00000399353, ENST00000399355, 
ENST00000399367, ENST00000437442, 
ENST00000488166, 
Fusion gene scores* DoF score5 X 5 X 2=5019 X 21 X 7=2793
# samples 522
** MAII scorelog2(5/50*10)=0log2(22/2793*10)=-3.66624014475529
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: CLIC6 [Title/Abstract] AND ITSN1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointCLIC6(36043061)-ITSN1(35254547), # samples:2
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 CLIC6 (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 ITSN1 (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
ChimerDB4LUADTCGA-55-7913-01BCLIC6chr21

36043061

-ITSN1chr21

35254547

+
ChimerDB4LUADTCGA-55-7913-01BCLIC6chr21

36043061

+ITSN1chr21

35254547

+


Top

Fusion Gene ORF analysis for CLIC6-ITSN1

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-3UTRENST00000349499ENST00000399326CLIC6chr21

36043061

+ITSN1chr21

35254547

+
5CDS-3UTRENST00000360731ENST00000399326CLIC6chr21

36043061

+ITSN1chr21

35254547

+
5CDS-intronENST00000349499ENST00000379960CLIC6chr21

36043061

+ITSN1chr21

35254547

+
5CDS-intronENST00000349499ENST00000381285CLIC6chr21

36043061

+ITSN1chr21

35254547

+
5CDS-intronENST00000349499ENST00000381291CLIC6chr21

36043061

+ITSN1chr21

35254547

+
5CDS-intronENST00000349499ENST00000381318CLIC6chr21

36043061

+ITSN1chr21

35254547

+
5CDS-intronENST00000349499ENST00000399338CLIC6chr21

36043061

+ITSN1chr21

35254547

+
5CDS-intronENST00000349499ENST00000399349CLIC6chr21

36043061

+ITSN1chr21

35254547

+
5CDS-intronENST00000349499ENST00000399352CLIC6chr21

36043061

+ITSN1chr21

35254547

+
5CDS-intronENST00000349499ENST00000399353CLIC6chr21

36043061

+ITSN1chr21

35254547

+
5CDS-intronENST00000349499ENST00000399355CLIC6chr21

36043061

+ITSN1chr21

35254547

+
5CDS-intronENST00000349499ENST00000399367CLIC6chr21

36043061

+ITSN1chr21

35254547

+
5CDS-intronENST00000349499ENST00000437442CLIC6chr21

36043061

+ITSN1chr21

35254547

+
5CDS-intronENST00000349499ENST00000488166CLIC6chr21

36043061

+ITSN1chr21

35254547

+
5CDS-intronENST00000360731ENST00000379960CLIC6chr21

36043061

+ITSN1chr21

35254547

+
5CDS-intronENST00000360731ENST00000381285CLIC6chr21

36043061

+ITSN1chr21

35254547

+
5CDS-intronENST00000360731ENST00000381291CLIC6chr21

36043061

+ITSN1chr21

35254547

+
5CDS-intronENST00000360731ENST00000381318CLIC6chr21

36043061

+ITSN1chr21

35254547

+
5CDS-intronENST00000360731ENST00000399338CLIC6chr21

36043061

+ITSN1chr21

35254547

+
5CDS-intronENST00000360731ENST00000399349CLIC6chr21

36043061

+ITSN1chr21

35254547

+
5CDS-intronENST00000360731ENST00000399352CLIC6chr21

36043061

+ITSN1chr21

35254547

+
5CDS-intronENST00000360731ENST00000399353CLIC6chr21

36043061

+ITSN1chr21

35254547

+
5CDS-intronENST00000360731ENST00000399355CLIC6chr21

36043061

+ITSN1chr21

35254547

+
5CDS-intronENST00000360731ENST00000399367CLIC6chr21

36043061

+ITSN1chr21

35254547

+
5CDS-intronENST00000360731ENST00000437442CLIC6chr21

36043061

+ITSN1chr21

35254547

+
5CDS-intronENST00000360731ENST00000488166CLIC6chr21

36043061

+ITSN1chr21

35254547

+

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

Top

Fusion Genomic Features for CLIC6-ITSN1


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)
CLIC6chr2136043061+ITSN1chr2135254546+1.79E-070.99999976
CLIC6chr2136043061+ITSN1chr2135254546+1.79E-070.99999976

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%

Top

Fusion Protein Features for CLIC6-ITSN1


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/:36043061/:35254547)
- 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
CLIC6

Q96NY7

ITSN1

Q15811

FUNCTION: May insert into membranes and form chloride ion channels. May play a critical role in water-secreting cells, possibly through the regulation of chloride ion transport (By similarity). {ECO:0000250}.FUNCTION: Adapter protein that provides a link between the endocytic membrane traffic and the actin assembly machinery (PubMed:11584276, PubMed:29887380). Acts as guanine nucleotide exchange factor (GEF) for CDC42, and thereby stimulates actin nucleation mediated by WASL and the ARP2/3 complex (PubMed:11584276). Plays a role in the assembly and maturation of clathrin-coated vesicles (By similarity). Recruits FCHSD2 to clathrin-coated pits (PubMed:29887380). Involved in endocytosis of activated EGFR, and probably also other growth factor receptors (By similarity). Involved in endocytosis of integrin beta-1 (ITGB1) and transferrin receptor (TFR); internalization of ITGB1 as DAB2-dependent cargo but not TFR may involve association with DAB2 (PubMed:22648170). Promotes ubiquitination and subsequent degradation of EGFR, and thereby contributes to the down-regulation of EGFR-dependent signaling pathways. In chromaffin cells, required for normal exocytosis of catecholamines. Required for rapid replenishment of release-ready synaptic vesicles at presynaptic active zones (By similarity). Inhibits ARHGAP31 activity toward RAC1 (PubMed:11744688). {ECO:0000250|UniProtKB:Q9WVE9, ECO:0000250|UniProtKB:Q9Z0R4, ECO:0000269|PubMed:11584276, ECO:0000269|PubMed:11744688, ECO:0000269|PubMed:22648170, ECO:0000269|PubMed:29887380}.; FUNCTION: [Isoform 1]: Plays a role in synaptic vesicle endocytosis in brain neurons. {ECO:0000250|UniProtKB:Q9Z0R4}.

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


Top

Fusion Gene Sequence for CLIC6-ITSN1


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.

Top

Fusion Gene PPI Analysis for CLIC6-ITSN1


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


Top

Related Drugs for CLIC6-ITSN1


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

Top

Related Diseases for CLIC6-ITSN1


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