|
||||||
|
 | |
| |
| |
| |
| |
|
Fusion gene ID: 41558 |
FusionGeneSummary for VPS18_NTRK3 |
 Fusion gene summary |
| Fusion gene information | Fusion gene name: VPS18_NTRK3 | Fusion gene ID: 41558 | Hgene | Tgene | Gene symbol | VPS18 | NTRK3 | Gene ID | 57617 | 4916 |
| Gene name | VPS18, CORVET/HOPS core subunit | neurotrophic receptor tyrosine kinase 3 | |
| Synonyms | PEP3 | GP145-TrkC|TRKC|gp145(trkC) | |
| Cytomap | 15q15.1 | 15q25.3 | |
| Type of gene | protein-coding | protein-coding | |
| Description | vacuolar protein sorting-associated protein 18 homologhVPS18vacuolar protein sorting 18 homologvacuolar protein sorting protein 18 | NT-3 growth factor receptorETS related protein-neurotrophic receptor tyrosine kinase fusion proteinETV6-NTRK3 fusionneurotrophic tyrosine kinase, receptor, type 3tyrosine kinase receptor C | |
| Modification date | 20180523 | 20180523 | |
| UniProtAcc | Q9P253 | Q16288 | |
| Ensembl transtripts involved in fusion gene | ENST00000220509, ENST00000558474, | ENST00000394480, ENST00000557856, ENST00000357724, ENST00000355254, ENST00000360948, ENST00000542733, ENST00000558676, ENST00000317501, ENST00000558306, ENST00000540489, | |
| Fusion gene scores | * DoF score | 3 X 3 X 3=27 | 9 X 7 X 9=567 |
| # samples | 3 | 20 | |
| ** MAII score | log2(3/27*10)=0.15200309344505 effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs). DoF>8 and MAII>0 | log2(20/567*10)=-1.5033487351675 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | |
| Context | PubMed: VPS18 [Title/Abstract] AND NTRK3 [Title/Abstract] AND fusion [Title/Abstract] | ||
| Functional or gene categories assigned by FusionGDB annotation | Oncogene involved fusion gene, in-frame and retained their domain. Tumor suppressor gene involved fusion gene, in-frame but not retained their domain. Tumor suppressor gene involved fusion gene, retained protein feature but frameshift. DDR (DNA damage repair) gene involved fusion gene, in-frame but not retained their domain. Kinase involved fusion gene, inframe and retained kinase domain. | ||
| * 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 | VPS18 | GO:0007032 | endosome organization | 18799622 |
| Hgene | VPS18 | GO:0007040 | lysosome organization | 18799622 |
| Tgene | NTRK3 | GO:0000187 | activation of MAPK activity | 23027130 |
| Tgene | NTRK3 | GO:0001933 | negative regulation of protein phosphorylation | 23027130 |
| Tgene | NTRK3 | GO:0007169 | transmembrane receptor protein tyrosine kinase signaling pathway | 23027130 |
| Tgene | NTRK3 | GO:0008284 | positive regulation of cell proliferation | 23027130 |
| Tgene | NTRK3 | GO:0010628 | positive regulation of gene expression | 23027130 |
| Tgene | NTRK3 | GO:0030335 | positive regulation of cell migration | 23027130 |
| Tgene | NTRK3 | GO:0032148 | activation of protein kinase B activity | 23027130 |
| Tgene | NTRK3 | GO:0033138 | positive regulation of peptidyl-serine phosphorylation | 23027130 |
| Tgene | NTRK3 | GO:0050927 | positive regulation of positive chemotaxis | 23027130 |
| Tgene | NTRK3 | GO:0090630 | activation of GTPase activity | 23027130 |
| Tgene | NTRK3 | GO:2000251 | positive regulation of actin cytoskeleton reorganization | 23027130 |
| 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 |
| TCGA | RV | COAD | TCGA-A6-2674-01A | VPS18 | chr15 | 41193212 | + | NTRK3 | chr15 | 88423659 | - |
| * 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 |
| In-frame | ENST00000220509 | ENST00000394480 | VPS18 | chr15 | 41193212 | + | NTRK3 | chr15 | 88423659 | - |
| In-frame | ENST00000220509 | ENST00000557856 | VPS18 | chr15 | 41193212 | + | NTRK3 | chr15 | 88423659 | - |
| In-frame | ENST00000220509 | ENST00000357724 | VPS18 | chr15 | 41193212 | + | NTRK3 | chr15 | 88423659 | - |
| In-frame | ENST00000220509 | ENST00000355254 | VPS18 | chr15 | 41193212 | + | NTRK3 | chr15 | 88423659 | - |
| In-frame | ENST00000220509 | ENST00000360948 | VPS18 | chr15 | 41193212 | + | NTRK3 | chr15 | 88423659 | - |
| 5CDS-intron | ENST00000220509 | ENST00000542733 | VPS18 | chr15 | 41193212 | + | NTRK3 | chr15 | 88423659 | - |
| 5CDS-intron | ENST00000220509 | ENST00000558676 | VPS18 | chr15 | 41193212 | + | NTRK3 | chr15 | 88423659 | - |
| 5CDS-intron | ENST00000220509 | ENST00000317501 | VPS18 | chr15 | 41193212 | + | NTRK3 | chr15 | 88423659 | - |
| 5CDS-intron | ENST00000220509 | ENST00000558306 | VPS18 | chr15 | 41193212 | + | NTRK3 | chr15 | 88423659 | - |
| 5CDS-intron | ENST00000220509 | ENST00000540489 | VPS18 | chr15 | 41193212 | + | NTRK3 | chr15 | 88423659 | - |
| intron-3CDS | ENST00000558474 | ENST00000394480 | VPS18 | chr15 | 41193212 | + | NTRK3 | chr15 | 88423659 | - |
| intron-3CDS | ENST00000558474 | ENST00000557856 | VPS18 | chr15 | 41193212 | + | NTRK3 | chr15 | 88423659 | - |
| intron-3CDS | ENST00000558474 | ENST00000357724 | VPS18 | chr15 | 41193212 | + | NTRK3 | chr15 | 88423659 | - |
| intron-3CDS | ENST00000558474 | ENST00000355254 | VPS18 | chr15 | 41193212 | + | NTRK3 | chr15 | 88423659 | - |
| intron-3CDS | ENST00000558474 | ENST00000360948 | VPS18 | chr15 | 41193212 | + | NTRK3 | chr15 | 88423659 | - |
| intron-intron | ENST00000558474 | ENST00000542733 | VPS18 | chr15 | 41193212 | + | NTRK3 | chr15 | 88423659 | - |
| intron-intron | ENST00000558474 | ENST00000558676 | VPS18 | chr15 | 41193212 | + | NTRK3 | chr15 | 88423659 | - |
| intron-intron | ENST00000558474 | ENST00000317501 | VPS18 | chr15 | 41193212 | + | NTRK3 | chr15 | 88423659 | - |
| intron-intron | ENST00000558474 | ENST00000558306 | VPS18 | chr15 | 41193212 | + | NTRK3 | chr15 | 88423659 | - |
| intron-intron | ENST00000558474 | ENST00000540489 | VPS18 | chr15 | 41193212 | + | NTRK3 | chr15 | 88423659 | - |
Top |
FusionProtFeatures for VPS18_NTRK3 |
| Main function of each fusion partner protein. (from UniProt) |
| Hgene | Tgene |
| VPS18 | NTRK3 |