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Center for Computational Systems Medicine
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FusionGeneSummary

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FusionProtFeature

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FusionGeneSequence

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FusionGenePPI

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RelatedDrugs

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RelatedDiseases

Fusion gene ID: 7315

FusionGeneSummary for CLCN3_CLCN3

check button Fusion gene summary
Fusion gene informationFusion gene name: CLCN3_CLCN3
Fusion gene ID: 7315
HgeneTgene
Gene symbol

CLCN3

CLCN3

Gene ID

1182

1182

Gene namechloride voltage-gated channel 3chloride voltage-gated channel 3
SynonymsCLC3|ClC-3CLC3|ClC-3
Cytomap

4q33

4q33

Type of geneprotein-codingprotein-coding
DescriptionH(+)/Cl(-) exchange transporter 3chloride channel 3chloride channel protein 3chloride channel, voltage-sensitive 3chloride transporter ClC-3H(+)/Cl(-) exchange transporter 3chloride channel 3chloride channel protein 3chloride channel, voltage-sensitive 3chloride transporter ClC-3
Modification date2018052320180523
UniProtAcc

P51790

P51790

Ensembl transtripts involved in fusion geneENST00000513761, ENST00000347613, 
ENST00000360642, ENST00000504131, 
ENST00000506924, 		ENST00000513761, 
ENST00000347613, ENST00000360642, 
ENST00000504131, ENST00000506924, 
Fusion gene scores* DoF score8 X 7 X 4=22436 X 4 X 19=2736
# samples 939
** MAII scorelog2(9/224*10)=-1.31550182572793
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(39/2736*10)=-2.81052220113629
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: CLCN3 [Title/Abstract] AND CLCN3 [Title/Abstract] AND fusion [Title/Abstract]

Functional or gene categories assigned by FusionGDB annotation
* 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
HgeneCLCN3

GO:1902476

chloride transmembrane transport

11274166

TgeneCLCN3

GO:1902476

chloride transmembrane transport

11274166


check button Fusion gene information from three resources
(ChiTars (NAR, 2018), tumorfusions (NAR, 2018), Gao et al. (Cell, 2018))
* 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.
Data typeSourceCancer typeSampleHgeneHchrHbpHstrandTgeneTchrTbpTstrand
ChiTaRS3.1X78520CLCN3chr4

170541744

-CLCN3chr4

170541799

+
ChiTaRS3.1AA525427CLCN3chr4

170642963

+CLCN3chr4

170642842

-
* LD: Li Ding group's fusion gene list
  RV: Roel Verhaak group's fusion gene list
  ChiTaRs fusion database

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
5UTR-5UTRENST00000513761ENST00000513761CLCN3chr4

170541744

-CLCN3chr4

170541799

+
5UTR-5UTRENST00000513761ENST00000347613CLCN3chr4

170541744

-CLCN3chr4

170541799

+
5UTR-5UTRENST00000513761ENST00000360642CLCN3chr4

170541744

-CLCN3chr4

170541799

+
5UTR-intronENST00000513761ENST00000504131CLCN3chr4

170541744

-CLCN3chr4

170541799

+
5UTR-intronENST00000513761ENST00000506924CLCN3chr4

170541744

-CLCN3chr4

170541799

+
5UTR-5UTRENST00000347613ENST00000513761CLCN3chr4

170541744

-CLCN3chr4

170541799

+
5UTR-5UTRENST00000347613ENST00000347613CLCN3chr4

170541744

-CLCN3chr4

170541799

+
5UTR-5UTRENST00000347613ENST00000360642CLCN3chr4

170541744

-CLCN3chr4

170541799

+
5UTR-intronENST00000347613ENST00000504131CLCN3chr4

170541744

-CLCN3chr4

170541799

+
5UTR-intronENST00000347613ENST00000506924CLCN3chr4

170541744

-CLCN3chr4

170541799

+
5UTR-5UTRENST00000360642ENST00000513761CLCN3chr4

170541744

-CLCN3chr4

170541799

+
5UTR-5UTRENST00000360642ENST00000347613CLCN3chr4

170541744

-CLCN3chr4

170541799

+
5UTR-5UTRENST00000360642ENST00000360642CLCN3chr4

170541744

-CLCN3chr4

170541799

+
5UTR-intronENST00000360642ENST00000504131CLCN3chr4

170541744

-CLCN3chr4

170541799

+
5UTR-intronENST00000360642ENST00000506924CLCN3chr4

170541744

-CLCN3chr4

170541799

+
intron-5UTRENST00000504131ENST00000513761CLCN3chr4

170541744

-CLCN3chr4

170541799

+
intron-5UTRENST00000504131ENST00000347613CLCN3chr4

170541744

-CLCN3chr4

170541799

+
intron-5UTRENST00000504131ENST00000360642CLCN3chr4

170541744

-CLCN3chr4

170541799

+
intron-intronENST00000504131ENST00000504131CLCN3chr4

170541744

-CLCN3chr4

170541799

+
intron-intronENST00000504131ENST00000506924CLCN3chr4

170541744

-CLCN3chr4

170541799

+
intron-5UTRENST00000506924ENST00000513761CLCN3chr4

170541744

-CLCN3chr4

170541799

+
intron-5UTRENST00000506924ENST00000347613CLCN3chr4

170541744

-CLCN3chr4

170541799

+
intron-5UTRENST00000506924ENST00000360642CLCN3chr4

170541744

-CLCN3chr4

170541799

+
intron-intronENST00000506924ENST00000504131CLCN3chr4

170541744

-CLCN3chr4

170541799

+
intron-intronENST00000506924ENST00000506924CLCN3chr4

170541744

-CLCN3chr4

170541799

+
3UTR-3UTRENST00000513761ENST00000513761CLCN3chr4

170642963

+CLCN3chr4

170642842

-
3UTR-intronENST00000513761ENST00000347613CLCN3chr4

170642963

+CLCN3chr4

170642842

-
3UTR-intronENST00000513761ENST00000360642CLCN3chr4

170642963

+CLCN3chr4

170642842

-
3UTR-intronENST00000513761ENST00000504131CLCN3chr4

170642963

+CLCN3chr4

170642842

-
3UTR-intronENST00000513761ENST00000506924CLCN3chr4

170642963

+CLCN3chr4

170642842

-
intron-3UTRENST00000347613ENST00000513761CLCN3chr4

170642963

+CLCN3chr4

170642842

-
intron-intronENST00000347613ENST00000347613CLCN3chr4

170642963

+CLCN3chr4

170642842

-
intron-intronENST00000347613ENST00000360642CLCN3chr4

170642963

+CLCN3chr4

170642842

-
intron-intronENST00000347613ENST00000504131CLCN3chr4

170642963

+CLCN3chr4

170642842

-
intron-intronENST00000347613ENST00000506924CLCN3chr4

170642963

+CLCN3chr4

170642842

-
intron-3UTRENST00000360642ENST00000513761CLCN3chr4

170642963

+CLCN3chr4

170642842

-
intron-intronENST00000360642ENST00000347613CLCN3chr4

170642963

+CLCN3chr4

170642842

-
intron-intronENST00000360642ENST00000360642CLCN3chr4

170642963

+CLCN3chr4

170642842

-
intron-intronENST00000360642ENST00000504131CLCN3chr4

170642963

+CLCN3chr4

170642842

-
intron-intronENST00000360642ENST00000506924CLCN3chr4

170642963

+CLCN3chr4

170642842

-
intron-3UTRENST00000504131ENST00000513761CLCN3chr4

170642963

+CLCN3chr4

170642842

-
intron-intronENST00000504131ENST00000347613CLCN3chr4

170642963

+CLCN3chr4

170642842

-
intron-intronENST00000504131ENST00000360642CLCN3chr4

170642963

+CLCN3chr4

170642842

-
intron-intronENST00000504131ENST00000504131CLCN3chr4

170642963

+CLCN3chr4

170642842

-
intron-intronENST00000504131ENST00000506924CLCN3chr4

170642963

+CLCN3chr4

170642842

-
intron-3UTRENST00000506924ENST00000513761CLCN3chr4

170642963

+CLCN3chr4

170642842

-
intron-intronENST00000506924ENST00000347613CLCN3chr4

170642963

+CLCN3chr4

170642842

-
intron-intronENST00000506924ENST00000360642CLCN3chr4

170642963

+CLCN3chr4

170642842

-
intron-intronENST00000506924ENST00000504131CLCN3chr4

170642963

+CLCN3chr4

170642842

-
intron-intronENST00000506924ENST00000506924CLCN3chr4

170642963

+CLCN3chr4

170642842

-

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FusionProtFeatures for CLCN3_CLCN3


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
CLCN3

P51790

CLCN3

P51790

Mediates the exchange of chloride ions against protons.Functions as antiporter and contributes to the acidification ofthe endosome and synaptic vesicle lumen, and may thereby affectvesicle trafficking and exocytosis. May play an important role inneuronal cell function through regulation of membrane excitabilityby protein kinase C. It could help neuronal cells to establishshort-term memory. {ECO:0000269|PubMed:11967229}. Mediates the exchange of chloride ions against protons.Functions as antiporter and contributes to the acidification ofthe endosome and synaptic vesicle lumen, and may thereby affectvesicle trafficking and exocytosis. May play an important role inneuronal cell function through regulation of membrane excitabilityby protein kinase C. It could help neuronal cells to establishshort-term memory. {ECO:0000269|PubMed:11967229}.

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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FusionGeneSequence for CLCN3_CLCN3


check button For in-frame fusion transcripts, we provide the fusion transcript sequences and fusion amino acid sequences.
(nt: nucleotides, aa: amino acids)

* Fusion amino acid sequences.

* Fusion transcript sequences (only coding sequence (CDS) region).

* Fusion transcript sequences (Full-length transcript).

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FusionGenePPI for CLCN3_CLCN3


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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RelatedDrugs for CLCN3_CLCN3


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.0 2018-04-02)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

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RelatedDiseases for CLCN3_CLCN3


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneCLCN3C0017638Glioma1CTD_human
HgeneCLCN3C0038356Stomach Neoplasms1CTD_human
HgeneCLCN3C2931822Nasopharyngeal carcinoma1CTD_human
TgeneCLCN3C0017638Glioma1CTD_human
TgeneCLCN3C0038356Stomach Neoplasms1CTD_human
TgeneCLCN3C2931822Nasopharyngeal carcinoma1CTD_human