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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: 7319

FusionGeneSummary for CLCN3_SMNDC1

check button Fusion gene summary
Fusion gene informationFusion gene name: CLCN3_SMNDC1
Fusion gene ID: 7319
HgeneTgene
Gene symbol

CLCN3

SMNDC1

Gene ID

1182

10285

Gene namechloride voltage-gated channel 3survival motor neuron domain containing 1
SynonymsCLC3|ClC-3SMNR|SPF30|TDRD16C
Cytomap

4q33

10q25.2

Type of geneprotein-codingprotein-coding
DescriptionH(+)/Cl(-) exchange transporter 3chloride channel 3chloride channel protein 3chloride channel, voltage-sensitive 3chloride transporter ClC-3survival of motor neuron-related-splicing factor 3030 kDa splicing factor SMNrpSMN-related proteinsplicing factor 30, survival of motor neuron-relatedsurvival motor neuron domain-containing protein 1tudor domain containing 16C
Modification date2018052320180519
UniProtAcc

P51790

O75940

Ensembl transtripts involved in fusion geneENST00000513761, ENST00000347613, 
ENST00000360642, ENST00000504131, 
ENST00000506924, 
ENST00000369603, 
ENST00000369592, ENST00000471297, 
Fusion gene scores* DoF score8 X 7 X 4=2242 X 2 X 2=8
# samples 92
** MAII scorelog2(9/224*10)=-1.31550182572793
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(2/8*10)=1.32192809488736
Context

PubMed: CLCN3 [Title/Abstract] AND SMNDC1 [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


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
ChiTaRS3.1H05577CLCN3chr4

170634332

+SMNDC1chr10

112063316

-
* 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
Frame-shiftENST00000513761ENST00000369603CLCN3chr4

170634332

+SMNDC1chr10

112063316

-
Frame-shiftENST00000513761ENST00000369592CLCN3chr4

170634332

+SMNDC1chr10

112063316

-
5CDS-5UTRENST00000513761ENST00000471297CLCN3chr4

170634332

+SMNDC1chr10

112063316

-
Frame-shiftENST00000347613ENST00000369603CLCN3chr4

170634332

+SMNDC1chr10

112063316

-
Frame-shiftENST00000347613ENST00000369592CLCN3chr4

170634332

+SMNDC1chr10

112063316

-
5CDS-5UTRENST00000347613ENST00000471297CLCN3chr4

170634332

+SMNDC1chr10

112063316

-
Frame-shiftENST00000360642ENST00000369603CLCN3chr4

170634332

+SMNDC1chr10

112063316

-
Frame-shiftENST00000360642ENST00000369592CLCN3chr4

170634332

+SMNDC1chr10

112063316

-
5CDS-5UTRENST00000360642ENST00000471297CLCN3chr4

170634332

+SMNDC1chr10

112063316

-
Frame-shiftENST00000504131ENST00000369603CLCN3chr4

170634332

+SMNDC1chr10

112063316

-
Frame-shiftENST00000504131ENST00000369592CLCN3chr4

170634332

+SMNDC1chr10

112063316

-
5CDS-5UTRENST00000504131ENST00000471297CLCN3chr4

170634332

+SMNDC1chr10

112063316

-
intron-3CDSENST00000506924ENST00000369603CLCN3chr4

170634332

+SMNDC1chr10

112063316

-
intron-3CDSENST00000506924ENST00000369592CLCN3chr4

170634332

+SMNDC1chr10

112063316

-
intron-5UTRENST00000506924ENST00000471297CLCN3chr4

170634332

+SMNDC1chr10

112063316

-

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FusionProtFeatures for CLCN3_SMNDC1


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

P51790

SMNDC1

O75940

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}. Necessary for spliceosome assembly. Overexpressioncauses apoptosis. {ECO:0000269|PubMed:11331295,ECO:0000269|PubMed:11331595, ECO:0000269|PubMed:9817934}.

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_SMNDC1


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_SMNDC1


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_SMNDC1


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_SMNDC1


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