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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: 4130

FusionGeneSummary for BGN_CLCN3

check button Fusion gene summary
Fusion gene informationFusion gene name: BGN_CLCN3
Fusion gene ID: 4130
HgeneTgene
Gene symbol

BGN

CLCN3

Gene ID

633

1182

Gene namebiglycanchloride voltage-gated channel 3
SynonymsDSPG1|MRLS|PG-S1|PGI|SEMDX|SLRR1ACLC3|ClC-3
Cytomap

Xq28

4q33

Type of geneprotein-codingprotein-coding
Descriptionbiglycanbone/cartilage proteoglycan-Idermatan sulphate proteoglycan Ismall leucine-rich protein 1AH(+)/Cl(-) exchange transporter 3chloride channel 3chloride channel protein 3chloride channel, voltage-sensitive 3chloride transporter ClC-3
Modification date2018052220180523
UniProtAcc

P21810

P51790

Ensembl transtripts involved in fusion geneENST00000331595, ENST00000480756, 
ENST00000513761, ENST00000347613, 
ENST00000360642, ENST00000504131, 
ENST00000506924, 
Fusion gene scores* DoF score15 X 7 X 11=115536 X 4 X 19=2736
# samples 1739
** MAII scorelog2(17/1155*10)=-2.76428620016572
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: BGN [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
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
TCGARVLIHCTCGA-DD-A4NB-01ABGNchrX

152775004

+CLCN3chr4

170623929

+
TCGARVPAADTCGA-IB-7654-01ABGNchrX

152775004

+CLCN3chr4

170623929

+
* 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
3UTR-intronENST00000331595ENST00000513761BGNchrX

152775004

+CLCN3chr4

170623929

+
3UTR-intronENST00000331595ENST00000347613BGNchrX

152775004

+CLCN3chr4

170623929

+
3UTR-intronENST00000331595ENST00000360642BGNchrX

152775004

+CLCN3chr4

170623929

+
3UTR-intronENST00000331595ENST00000504131BGNchrX

152775004

+CLCN3chr4

170623929

+
3UTR-intronENST00000331595ENST00000506924BGNchrX

152775004

+CLCN3chr4

170623929

+
5CDS-intronENST00000480756ENST00000513761BGNchrX

152775004

+CLCN3chr4

170623929

+
5CDS-intronENST00000480756ENST00000347613BGNchrX

152775004

+CLCN3chr4

170623929

+
5CDS-intronENST00000480756ENST00000360642BGNchrX

152775004

+CLCN3chr4

170623929

+
5CDS-intronENST00000480756ENST00000504131BGNchrX

152775004

+CLCN3chr4

170623929

+
5CDS-intronENST00000480756ENST00000506924BGNchrX

152775004

+CLCN3chr4

170623929

+

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FusionProtFeatures for BGN_CLCN3


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

P21810

CLCN3

P51790

May be involved in collagen fiber assembly.{ECO:0000250}. 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 BGN_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 BGN_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
BGNHDL3, JPH3, TGFB1, TNF, ELN, MFAP2, APP, SGCA, APOB, HSPB2CLCN3CLCN3, SLC9A3R1, PDZK1, GOPC, CFTR, LGALS3, LGALS8, LGALS9, LYPD3, HSPB1, TMEM9B, GGA1, TPCN2, TRIM25


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 BGN_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 BGN_CLCN3


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneBGNC0003873Rheumatoid Arthritis1CTD_human
HgeneBGNC0023893Liver Cirrhosis, Experimental1CTD_human
HgeneBGNC1848097Spondyloepimetaphyseal Dysplasia, X-Linked1ORPHANET;UNIPROT
TgeneCLCN3C0017638Glioma1CTD_human
TgeneCLCN3C0038356Stomach Neoplasms1CTD_human
TgeneCLCN3C2931822Nasopharyngeal carcinoma1CTD_human