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Fusion gene ID: 41603 |
FusionGeneSummary for VPS39_VPS39 |
 Fusion gene summary |
| Fusion gene information | Fusion gene name: VPS39_VPS39 | Fusion gene ID: 41603 | Hgene | Tgene | Gene symbol | VPS39 | VPS39 | Gene ID | 23339 | 23339 |
| Gene name | VPS39, HOPS complex subunit | VPS39, HOPS complex subunit | |
| Synonyms | TLP|VAM6|hVam6p | TLP|VAM6|hVam6p | |
| Cytomap | 15q15.1 | 15q15.1 | |
| Type of gene | protein-coding | protein-coding | |
| Description | vam6/Vps39-like proteinTRAP1-like proteinvacuolar protein sorting 39 homolog | vam6/Vps39-like proteinTRAP1-like proteinvacuolar protein sorting 39 homolog | |
| Modification date | 20180523 | 20180523 | |
| UniProtAcc | Q96JC1 | Q96JC1 | |
| Ensembl transtripts involved in fusion gene | ENST00000318006, ENST00000348544, ENST00000568357, | ENST00000318006, ENST00000348544, ENST00000568357, | |
| Fusion gene scores | * DoF score | 4 X 3 X 3=36 | 6 X 6 X 4=144 |
| # samples | 4 | 6 | |
| ** MAII score | log2(4/36*10)=0.15200309344505 effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs). DoF>8 and MAII>0 | log2(6/144*10)=-1.26303440583379 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | |
| Context | PubMed: VPS39 [Title/Abstract] AND VPS39 [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 | VPS39 | GO:0034058 | endosomal vesicle fusion | 23167963 |
| Hgene | VPS39 | GO:1902774 | late endosome to lysosome transport | 23167963 |
| Tgene | VPS39 | GO:0034058 | endosomal vesicle fusion | 23167963 |
| Tgene | VPS39 | GO:1902774 | late endosome to lysosome transport | 23167963 |
| 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 | BE816198 | VPS39 | chr15 | 42451747 | + | VPS39 | chr15 | 42451502 | - |
| * 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 |
| intron-3UTR | ENST00000318006 | ENST00000318006 | VPS39 | chr15 | 42451747 | + | VPS39 | chr15 | 42451502 | - |
| intron-intron | ENST00000318006 | ENST00000348544 | VPS39 | chr15 | 42451747 | + | VPS39 | chr15 | 42451502 | - |
| intron-intron | ENST00000318006 | ENST00000568357 | VPS39 | chr15 | 42451747 | + | VPS39 | chr15 | 42451502 | - |
| intron-3UTR | ENST00000348544 | ENST00000318006 | VPS39 | chr15 | 42451747 | + | VPS39 | chr15 | 42451502 | - |
| intron-intron | ENST00000348544 | ENST00000348544 | VPS39 | chr15 | 42451747 | + | VPS39 | chr15 | 42451502 | - |
| intron-intron | ENST00000348544 | ENST00000568357 | VPS39 | chr15 | 42451747 | + | VPS39 | chr15 | 42451502 | - |
| intron-3UTR | ENST00000568357 | ENST00000318006 | VPS39 | chr15 | 42451747 | + | VPS39 | chr15 | 42451502 | - |
| intron-intron | ENST00000568357 | ENST00000348544 | VPS39 | chr15 | 42451747 | + | VPS39 | chr15 | 42451502 | - |
| intron-intron | ENST00000568357 | ENST00000568357 | VPS39 | chr15 | 42451747 | + | VPS39 | chr15 | 42451502 | - |
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FusionProtFeatures for VPS39_VPS39 |
| Main function of each fusion partner protein. (from UniProt) |
| Hgene | Tgene |
| VPS39 | VPS39 |
| Regulator of TGF-beta/activin signaling, inhibitingSMAD3- and activating SMAD2-dependent transcription. Acts byinterfering with SMAD3/SMAD4 complex formation, this would lead toinhibition of SMAD3-dependent transcription and relieve SMAD3inhibition of SMAD2-dependent promoters, thus increasing SMAD2-dependent transcription. Does not affect TGF-beta-induced SMAD2 orSMAD3 phosphorylation, nor SMAD2/SMAD4 complex formation.{ECO:0000269|PubMed:12941698}. Plays a role in vesicle-mediated protein trafficking tolysosomal compartments including the endocytic membrane transportand autophagic pathways. Believed to act in part as a component ofthe putative HOPS endosomal tethering complex which is proposed tobe involved in the Rab5-to-Rab7 endosome conversion probablyimplicating MON1A/B, and via binding SNAREs and SNARE complexes tomediate tethering and docking events during SNARE-mediatedmembrane fusion. The HOPS complex is proposed to be recruited toRab7 on the late endosomal membrane and to regulate lateendocytic, phagocytic and autophagic traffic towards lysosomes(PubMed:23351085). Involved in homotypic vesicle fusions betweenlate endosomes and in heterotypic fusions between late endosomesand lysosomes (PubMed:11448994, PubMed:23351085, PubMed:23167963).Required for fusion of endosomes and autophagosomes with lysosomes(PubMed:25783203). {ECO:0000269|PubMed:11448994,ECO:0000269|PubMed:23167963, ECO:0000269|PubMed:25783203,ECO:0000305|PubMed:23351085}. | Regulator of TGF-beta/activin signaling, inhibitingSMAD3- and activating SMAD2-dependent transcription. Acts byinterfering with SMAD3/SMAD4 complex formation, this would lead toinhibition of SMAD3-dependent transcription and relieve SMAD3inhibition of SMAD2-dependent promoters, thus increasing SMAD2-dependent transcription. Does not affect TGF-beta-induced SMAD2 orSMAD3 phosphorylation, nor SMAD2/SMAD4 complex formation.{ECO:0000269|PubMed:12941698}. Plays a role in vesicle-mediated protein trafficking tolysosomal compartments including the endocytic membrane transportand autophagic pathways. Believed to act in part as a component ofthe putative HOPS endosomal tethering complex which is proposed tobe involved in the Rab5-to-Rab7 endosome conversion probablyimplicating MON1A/B, and via binding SNAREs and SNARE complexes tomediate tethering and docking events during SNARE-mediatedmembrane fusion. The HOPS complex is proposed to be recruited toRab7 on the late endosomal membrane and to regulate lateendocytic, phagocytic and autophagic traffic towards lysosomes(PubMed:23351085). Involved in homotypic vesicle fusions betweenlate endosomes and in heterotypic fusions between late endosomesand lysosomes (PubMed:11448994, PubMed:23351085, PubMed:23167963).Required for fusion of endosomes and autophagosomes with lysosomes(PubMed:25783203). {ECO:0000269|PubMed:11448994,ECO:0000269|PubMed:23167963, ECO:0000269|PubMed:25783203,ECO:0000305|PubMed:23351085}. |
| 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 VPS39_VPS39 |
| 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 VPS39_VPS39 |
| 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 VPS39_VPS39 |
| 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 VPS39_VPS39 |
| Diseases associated with fusion partners. (DisGeNet 4.0) |
| Partner | Gene | Disease ID | Disease name | # pubmeds | Source |
| Hgene | VPS39 | C0036341 | Schizophrenia | 1 | CTD_human |
| Hgene | VPS39 | C1458155 | Mammary Neoplasms | 1 | CTD_human |
| Tgene | VPS39 | C0036341 | Schizophrenia | 1 | CTD_human |
| Tgene | VPS39 | C1458155 | Mammary Neoplasms | 1 | CTD_human |
Copyright 2018-Present -The University of Texas Health Science Center at Houston (UTHealth)
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