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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:CLCN5-CTNND2 (FusionGDB2 ID:HG1184TG1501)

Fusion Gene Summary for CLCN5-CTNND2

check button Fusion gene summary
Fusion gene informationFusion gene name: CLCN5-CTNND2
Fusion gene ID: hg1184tg1501
HgeneTgene
Gene symbol

CLCN5

CTNND2

Gene ID

1184

1501

Gene namechloride voltage-gated channel 5catenin delta 2
SynonymsCLC5|CLCK2|ClC-5|DENTS|NPHL1|NPHL2|XLRH|XRN|hCIC-K2GT24|NPRAP
Cytomap('CLCN5')('CTNND2')

Xp11.23

5p15.2

Type of geneprotein-codingprotein-coding
DescriptionH(+)/Cl(-) exchange transporter 5chloride channel, voltage-sensitive 5chloride transporter ClC-5voltage-gated chloride ion channel CLCN5catenin delta-2T-cell delta-catenincatenin (cadherin-associated protein), delta 2 (neural plakophilin-related arm-repeat protein)neurojungin
Modification date2020031320200320
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000376088, ENST00000376091, 
ENST00000482218, ENST00000307367, 
ENST00000376108, 
Fusion gene scores* DoF score6 X 4 X 4=9616 X 9 X 9=1296
# samples 617
** MAII scorelog2(6/96*10)=-0.678071905112638
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(17/1296*10)=-2.93045906674692
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: CLCN5 [Title/Abstract] AND CTNND2 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointCLCN5(49689924)-CTNND2(11082958), # samples:1
Anticipated loss of major functional domain due to fusion event.CLCN5-CTNND2 seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
CLCN5-CTNND2 seems lost the major protein functional domain in Hgene partner, which is a IUPHAR drug target due to the frame-shifted ORF.
CLCN5-CTNND2 seems lost the major protein functional domain in Tgene partner, which is a CGC due to the frame-shifted ORF.
CLCN5-CTNND2 seems lost the major protein functional domain in Tgene partner, which is a essential gene 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


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
ChimerDB4GBMTCGA-06-0882-01ACLCN5chrX

49689924

+CTNND2chr5

11082958

-


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Fusion Gene ORF analysis for CLCN5-CTNND2

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-5UTRENST00000376088ENST00000495388CLCN5chrX

49689924

+CTNND2chr5

11082958

-
5CDS-5UTRENST00000376091ENST00000495388CLCN5chrX

49689924

+CTNND2chr5

11082958

-
5CDS-5UTRENST00000482218ENST00000495388CLCN5chrX

49689924

+CTNND2chr5

11082958

-
Frame-shiftENST00000376088ENST00000304623CLCN5chrX

49689924

+CTNND2chr5

11082958

-
Frame-shiftENST00000376088ENST00000359640CLCN5chrX

49689924

+CTNND2chr5

11082958

-
Frame-shiftENST00000376088ENST00000458100CLCN5chrX

49689924

+CTNND2chr5

11082958

-
Frame-shiftENST00000376088ENST00000503622CLCN5chrX

49689924

+CTNND2chr5

11082958

-
Frame-shiftENST00000376088ENST00000511377CLCN5chrX

49689924

+CTNND2chr5

11082958

-
Frame-shiftENST00000376091ENST00000304623CLCN5chrX

49689924

+CTNND2chr5

11082958

-
Frame-shiftENST00000376091ENST00000359640CLCN5chrX

49689924

+CTNND2chr5

11082958

-
Frame-shiftENST00000376091ENST00000458100CLCN5chrX

49689924

+CTNND2chr5

11082958

-
Frame-shiftENST00000376091ENST00000503622CLCN5chrX

49689924

+CTNND2chr5

11082958

-
Frame-shiftENST00000376091ENST00000511377CLCN5chrX

49689924

+CTNND2chr5

11082958

-
Frame-shiftENST00000482218ENST00000304623CLCN5chrX

49689924

+CTNND2chr5

11082958

-
Frame-shiftENST00000482218ENST00000359640CLCN5chrX

49689924

+CTNND2chr5

11082958

-
Frame-shiftENST00000482218ENST00000458100CLCN5chrX

49689924

+CTNND2chr5

11082958

-
Frame-shiftENST00000482218ENST00000503622CLCN5chrX

49689924

+CTNND2chr5

11082958

-
Frame-shiftENST00000482218ENST00000511377CLCN5chrX

49689924

+CTNND2chr5

11082958

-
intron-3CDSENST00000307367ENST00000304623CLCN5chrX

49689924

+CTNND2chr5

11082958

-
intron-3CDSENST00000307367ENST00000359640CLCN5chrX

49689924

+CTNND2chr5

11082958

-
intron-3CDSENST00000307367ENST00000458100CLCN5chrX

49689924

+CTNND2chr5

11082958

-
intron-3CDSENST00000307367ENST00000503622CLCN5chrX

49689924

+CTNND2chr5

11082958

-
intron-3CDSENST00000307367ENST00000511377CLCN5chrX

49689924

+CTNND2chr5

11082958

-
intron-3CDSENST00000376108ENST00000304623CLCN5chrX

49689924

+CTNND2chr5

11082958

-
intron-3CDSENST00000376108ENST00000359640CLCN5chrX

49689924

+CTNND2chr5

11082958

-
intron-3CDSENST00000376108ENST00000458100CLCN5chrX

49689924

+CTNND2chr5

11082958

-
intron-3CDSENST00000376108ENST00000503622CLCN5chrX

49689924

+CTNND2chr5

11082958

-
intron-3CDSENST00000376108ENST00000511377CLCN5chrX

49689924

+CTNND2chr5

11082958

-
intron-5UTRENST00000307367ENST00000495388CLCN5chrX

49689924

+CTNND2chr5

11082958

-
intron-5UTRENST00000376108ENST00000495388CLCN5chrX

49689924

+CTNND2chr5

11082958

-

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 CLCN5-CTNND2


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)


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Fusion Protein Features for CLCN5-CTNND2


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/:49689924/:11082958)
- 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
..
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: 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 CLCN5-CTNND2


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 CLCN5-CTNND2


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 CLCN5-CTNND2


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 CLCN5-CTNND2


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneCLCN5C1848336Dent disease 116CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
HgeneCLCN5C0403720X-linked recessive nephrolithiasis with renal failure4CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
HgeneCLCN5C0878681Dent's disease4CTD_human;GENOMICS_ENGLAND
HgeneCLCN5C1839874Low Molecular Weight Proteinuria with Hypercalciuria and Nephrocalcinosis4CTD_human;GENOMICS_ENGLAND;UNIPROT
HgeneCLCN5C1845168Hypophosphatemic Rickets, X-Linked Recessive4CTD_human;GENOMICS_ENGLAND;UNIPROT
HgeneCLCN5C0017638Glioma1CTD_human
HgeneCLCN5C0018021Goiter1CTD_human
HgeneCLCN5C0033687Proteinuria1CTD_human
HgeneCLCN5C0259783mixed gliomas1CTD_human
HgeneCLCN5C0555198Malignant Glioma1CTD_human
TgeneC0007621Neoplastic Cell Transformation1CTD_human
TgeneC0017636Glioblastoma1CTD_human
TgeneC0036341Schizophrenia1PSYGENET
TgeneC0041696Unipolar Depression1PSYGENET
TgeneC0334588Giant Cell Glioblastoma1CTD_human
TgeneC1269683Major Depressive Disorder1PSYGENET
TgeneC1621958Glioblastoma Multiforme1CTD_human
TgeneC1832841EPILEPSY, FAMILIAL ADULT MYOCLONIC, 11ORPHANET
TgeneC3495676Anorectal Malformations1GENOMICS_ENGLAND