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Fusion gene ID: 41547 |
FusionGeneSummary for VPS13C_RAPGEF1 |
 Fusion gene summary |
| Fusion gene information | Fusion gene name: VPS13C_RAPGEF1 | Fusion gene ID: 41547 | Hgene | Tgene | Gene symbol | VPS13C | RAPGEF1 | Gene ID | 54832 | 2889 |
| Gene name | vacuolar protein sorting 13 homolog C | Rap guanine nucleotide exchange factor 1 | |
| Synonyms | PARK23 | C3G|GRF2 | |
| Cytomap | 15q22.2 | 9q34.13 | |
| Type of gene | protein-coding | protein-coding | |
| Description | vacuolar protein sorting-associated protein 13C | rap guanine nucleotide exchange factor 1CRK SH3-binding GNRPRap guanine nucleotide exchange factor (GEF) 1guanine nucleotide-releasing factor 2 (specific for crk proto-oncogene) | |
| Modification date | 20180523 | 20180522 | |
| UniProtAcc | Q709C8 | Q13905 | |
| Ensembl transtripts involved in fusion gene | ENST00000249837, ENST00000261517, ENST00000395896, ENST00000395898, ENST00000558919, | ENST00000372189, ENST00000372195, ENST00000372190, ENST00000481260, | |
| Fusion gene scores | * DoF score | 13 X 13 X 7=1183 | 4 X 4 X 1=16 |
| # samples | 13 | 4 | |
| ** MAII score | log2(13/1183*10)=-3.18586654531133 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | log2(4/16*10)=1.32192809488736 effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs). DoF>8 and MAII>0 | |
| Context | PubMed: VPS13C [Title/Abstract] AND RAPGEF1 [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 |
| Tgene | RAPGEF1 | GO:0038180 | nerve growth factor signaling pathway | 17724123 |
| Tgene | RAPGEF1 | GO:0043547 | positive regulation of GTPase activity | 10548487 |
| Tgene | RAPGEF1 | GO:0071320 | cellular response to cAMP | 21840392 |
| Tgene | RAPGEF1 | GO:1990090 | cellular response to nerve growth factor stimulus | 17724123 |
| 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 | DA122668 | VPS13C | chr15 | 62336412 | - | RAPGEF1 | chr9 | 134501428 | - |
| * 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 | ENST00000249837 | ENST00000372189 | VPS13C | chr15 | 62336412 | - | RAPGEF1 | chr9 | 134501428 | - |
| Frame-shift | ENST00000249837 | ENST00000372195 | VPS13C | chr15 | 62336412 | - | RAPGEF1 | chr9 | 134501428 | - |
| Frame-shift | ENST00000249837 | ENST00000372190 | VPS13C | chr15 | 62336412 | - | RAPGEF1 | chr9 | 134501428 | - |
| 5CDS-intron | ENST00000249837 | ENST00000481260 | VPS13C | chr15 | 62336412 | - | RAPGEF1 | chr9 | 134501428 | - |
| Frame-shift | ENST00000261517 | ENST00000372189 | VPS13C | chr15 | 62336412 | - | RAPGEF1 | chr9 | 134501428 | - |
| Frame-shift | ENST00000261517 | ENST00000372195 | VPS13C | chr15 | 62336412 | - | RAPGEF1 | chr9 | 134501428 | - |
| Frame-shift | ENST00000261517 | ENST00000372190 | VPS13C | chr15 | 62336412 | - | RAPGEF1 | chr9 | 134501428 | - |
| 5CDS-intron | ENST00000261517 | ENST00000481260 | VPS13C | chr15 | 62336412 | - | RAPGEF1 | chr9 | 134501428 | - |
| Frame-shift | ENST00000395896 | ENST00000372189 | VPS13C | chr15 | 62336412 | - | RAPGEF1 | chr9 | 134501428 | - |
| Frame-shift | ENST00000395896 | ENST00000372195 | VPS13C | chr15 | 62336412 | - | RAPGEF1 | chr9 | 134501428 | - |
| Frame-shift | ENST00000395896 | ENST00000372190 | VPS13C | chr15 | 62336412 | - | RAPGEF1 | chr9 | 134501428 | - |
| 5CDS-intron | ENST00000395896 | ENST00000481260 | VPS13C | chr15 | 62336412 | - | RAPGEF1 | chr9 | 134501428 | - |
| Frame-shift | ENST00000395898 | ENST00000372189 | VPS13C | chr15 | 62336412 | - | RAPGEF1 | chr9 | 134501428 | - |
| Frame-shift | ENST00000395898 | ENST00000372195 | VPS13C | chr15 | 62336412 | - | RAPGEF1 | chr9 | 134501428 | - |
| Frame-shift | ENST00000395898 | ENST00000372190 | VPS13C | chr15 | 62336412 | - | RAPGEF1 | chr9 | 134501428 | - |
| 5CDS-intron | ENST00000395898 | ENST00000481260 | VPS13C | chr15 | 62336412 | - | RAPGEF1 | chr9 | 134501428 | - |
| intron-3CDS | ENST00000558919 | ENST00000372189 | VPS13C | chr15 | 62336412 | - | RAPGEF1 | chr9 | 134501428 | - |
| intron-3CDS | ENST00000558919 | ENST00000372195 | VPS13C | chr15 | 62336412 | - | RAPGEF1 | chr9 | 134501428 | - |
| intron-3CDS | ENST00000558919 | ENST00000372190 | VPS13C | chr15 | 62336412 | - | RAPGEF1 | chr9 | 134501428 | - |
| intron-intron | ENST00000558919 | ENST00000481260 | VPS13C | chr15 | 62336412 | - | RAPGEF1 | chr9 | 134501428 | - |
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FusionProtFeatures for VPS13C_RAPGEF1 |
| Main function of each fusion partner protein. (from UniProt) |
| Hgene | Tgene |
| VPS13C | RAPGEF1 |
| Necessary for proper mitochondrial function andmaintenance of mitochondrial transmembrane potential. Involved inthe regulation of PINK1/PRKN-mediated mitophagy in response tomitochondrial depolarization. {ECO:0000269|PubMed:26942284}. | Guanine nucleotide-releasing protein that binds to SH3domain of CRK and GRB2/ASH. Transduces signals from CRK toactivate RAS. Plays a role in the establishment of basalendothelial barrier function. Plays a role in nerve growth factor(NGF)-induced sustained activation of Rap1 and neurite outgrowth.{ECO:0000269|PubMed:17724123, ECO:0000269|PubMed:21840392,ECO:0000269|PubMed:7806500}. |
| 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 VPS13C_RAPGEF1 |
| 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 VPS13C_RAPGEF1 |
| 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 VPS13C_RAPGEF1 |
| 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 VPS13C_RAPGEF1 |
| Diseases associated with fusion partners. (DisGeNet 4.0) |
| Partner | Gene | Disease ID | Disease name | # pubmeds | Source |
| Hgene | VPS13C | C4225186 | PARKINSON DISEASE 23, AUTOSOMAL RECESSIVE EARLY-ONSET | 1 | UNIPROT |
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