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Fusion gene ID: 7319 |
FusionGeneSummary for CLCN3_SMNDC1 |
 Fusion gene summary |
| Fusion gene information | Fusion gene name: CLCN3_SMNDC1 | Fusion gene ID: 7319 | Hgene | Tgene | Gene symbol | CLCN3 | SMNDC1 | Gene ID | 1182 | 10285 |
| Gene name | chloride voltage-gated channel 3 | survival motor neuron domain containing 1 | |
| Synonyms | CLC3|ClC-3 | SMNR|SPF30|TDRD16C | |
| Cytomap | 4q33 | 10q25.2 | |
| Type of gene | protein-coding | protein-coding | |
| Description | H(+)/Cl(-) exchange transporter 3chloride channel 3chloride channel protein 3chloride channel, voltage-sensitive 3chloride transporter ClC-3 | survival 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 date | 20180523 | 20180519 | |
| UniProtAcc | P51790 | O75940 | |
| Ensembl transtripts involved in fusion gene | ENST00000513761, ENST00000347613, ENST00000360642, ENST00000504131, ENST00000506924, | ENST00000369603, ENST00000369592, ENST00000471297, | |
| Fusion gene scores | * DoF score | 8 X 7 X 4=224 | 2 X 2 X 2=8 |
| # samples | 9 | 2 | |
| ** MAII score | log2(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) |
| Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
| Partner | Gene | GO ID | GO term | PubMed ID |
| Hgene | CLCN3 | GO:1902476 | chloride transmembrane transport | 11274166 |
| 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 type | Source | Cancer type | Sample | Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand |
| ChiTaRS3.1 | H05577 | CLCN3 | chr4 | 170634332 | + | SMNDC1 | chr10 | 112063316 | - |
| * LD: Li Ding group's fusion gene list RV: Roel Verhaak group's fusion gene list ChiTaRs fusion database |
| 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. |
| ORF | Henst | Tenst | Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand |
| Frame-shift | ENST00000513761 | ENST00000369603 | CLCN3 | chr4 | 170634332 | + | SMNDC1 | chr10 | 112063316 | - |
| Frame-shift | ENST00000513761 | ENST00000369592 | CLCN3 | chr4 | 170634332 | + | SMNDC1 | chr10 | 112063316 | - |
| 5CDS-5UTR | ENST00000513761 | ENST00000471297 | CLCN3 | chr4 | 170634332 | + | SMNDC1 | chr10 | 112063316 | - |
| Frame-shift | ENST00000347613 | ENST00000369603 | CLCN3 | chr4 | 170634332 | + | SMNDC1 | chr10 | 112063316 | - |
| Frame-shift | ENST00000347613 | ENST00000369592 | CLCN3 | chr4 | 170634332 | + | SMNDC1 | chr10 | 112063316 | - |
| 5CDS-5UTR | ENST00000347613 | ENST00000471297 | CLCN3 | chr4 | 170634332 | + | SMNDC1 | chr10 | 112063316 | - |
| Frame-shift | ENST00000360642 | ENST00000369603 | CLCN3 | chr4 | 170634332 | + | SMNDC1 | chr10 | 112063316 | - |
| Frame-shift | ENST00000360642 | ENST00000369592 | CLCN3 | chr4 | 170634332 | + | SMNDC1 | chr10 | 112063316 | - |
| 5CDS-5UTR | ENST00000360642 | ENST00000471297 | CLCN3 | chr4 | 170634332 | + | SMNDC1 | chr10 | 112063316 | - |
| Frame-shift | ENST00000504131 | ENST00000369603 | CLCN3 | chr4 | 170634332 | + | SMNDC1 | chr10 | 112063316 | - |
| Frame-shift | ENST00000504131 | ENST00000369592 | CLCN3 | chr4 | 170634332 | + | SMNDC1 | chr10 | 112063316 | - |
| 5CDS-5UTR | ENST00000504131 | ENST00000471297 | CLCN3 | chr4 | 170634332 | + | SMNDC1 | chr10 | 112063316 | - |
| intron-3CDS | ENST00000506924 | ENST00000369603 | CLCN3 | chr4 | 170634332 | + | SMNDC1 | chr10 | 112063316 | - |
| intron-3CDS | ENST00000506924 | ENST00000369592 | CLCN3 | chr4 | 170634332 | + | SMNDC1 | chr10 | 112063316 | - |
| intron-5UTR | ENST00000506924 | ENST00000471297 | CLCN3 | chr4 | 170634332 | + | SMNDC1 | chr10 | 112063316 | - |
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FusionProtFeatures for CLCN3_SMNDC1 |
| Main function of each fusion partner protein. (from UniProt) |
| Hgene | Tgene |
| CLCN3 | SMNDC1 |
| 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}. |
| Retention 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 . * 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. |
| Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Protein feature | Protein feature note |
| - In-frame and not-retained protein feature among the 13 regional features. |
| Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Protein feature | Protein feature note |
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FusionGeneSequence for CLCN3_SMNDC1 |
| 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 |
| Go to ChiPPI (Chimeric Protein-Protein interactions) to see the chimeric PPI interaction in . |
| Protein-protein interactors with each fusion partner protein in wild-type (BIOGRID-3.4.160) |
| Hgene | Hgene's interactors | Tgene | Tgene's interactors |
| - Retained PPIs in in-frame fusion. |
| Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Still interaction with |
| - Lost PPIs in in-frame fusion. |
| Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Interaction lost with |
| - Retained PPIs, but lost function due to frame-shift fusion. |
| Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Interaction lost with |
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RelatedDrugs for CLCN3_SMNDC1 |
| Drugs targeting genes involved in this fusion gene. (DrugBank Version 5.1.0 2018-04-02) |
| Partner | Gene | UniProtAcc | DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
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RelatedDiseases for CLCN3_SMNDC1 |
| Diseases associated with fusion partners. (DisGeNet 4.0) |
| Partner | Gene | Disease ID | Disease name | # pubmeds | Source |
| Hgene | CLCN3 | C0017638 | Glioma | 1 | CTD_human |
| Hgene | CLCN3 | C0038356 | Stomach Neoplasms | 1 | CTD_human |
| Hgene | CLCN3 | C2931822 | Nasopharyngeal carcinoma | 1 | CTD_human |
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