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Fusion Protein:VPS53-CHTOP |
Fusion Protein Summary |
 Fusion gene summary |
| Fusion partner gene information | Fusion gene name: VPS53-CHTOP | FusionPDB ID: 98477 | FusionGDB2.0 ID: 98477 | Hgene | Tgene | Gene symbol | VPS53 | CHTOP | Gene ID | 55275 | 26097 |
| Gene name | VPS53 subunit of GARP complex | chromatin target of PRMT1 | |
| Synonyms | HCCS1|PCH2E|hVps53L|pp13624 | C10orf77|C1orf77|FL-SRAG|FOP|SRAG|SRAG-3|SRAG-5|pp7704 | |
| Cytomap | 17p13.3 | 1q21.3 | |
| Type of gene | protein-coding | protein-coding | |
| Description | vacuolar protein sorting-associated protein 53 homologVPS53, GARP complex subunit | chromatin target of PRMT1 proteinfriend of PRMT1 proteinsmall protein rich in arginine and glycine | |
| Modification date | 20200313 | 20200313 | |
| UniProtAcc | . | Q9Y3Y2 | |
| Ensembl transtripts involved in fusion gene | ENST ids | ENST00000291074, ENST00000401468, ENST00000437048, ENST00000446250, ENST00000571805, ENST00000576149, ENST00000574029, | ENST00000368686, ENST00000368687, ENST00000368690, ENST00000403433, ENST00000495554, ENST00000368694, |
| Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0) | * DoF score | 18 X 15 X 14=3780 | 5 X 7 X 5=175 |
| # samples | 24 | 8 | |
| ** MAII score | log2(24/3780*10)=-3.97727992349992 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | log2(8/175*10)=-1.12928301694497 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | |
| Context (manual curation of fusion genes in FusionPDB) | PubMed: VPS53 [Title/Abstract] AND CHTOP [Title/Abstract] AND fusion [Title/Abstract] | ||
| Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0) | VPS53(456620)-CHTOP(153614719), # samples:1 | ||
| Anticipated loss of major functional domain due to fusion event. | VPS53-CHTOP seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF. VPS53-CHTOP seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame ORF. VPS53-CHTOP seems lost the major protein functional domain in Hgene partner, which is a tumor suppressor due to the frame-shifted ORF. VPS53-CHTOP seems lost the major protein functional domain in Tgene partner, which is a epigenetic factor due to the frame-shifted ORF. VPS53-CHTOP seems lost the major protein functional domain in Tgene partner, which is a essential gene due to the frame-shifted ORF. | ||
| * 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 | CHTOP | GO:0006406 | mRNA export from nucleus | 23299939 |
| Tgene | CHTOP | GO:0032781 | positive regulation of ATPase activity | 23299939 |
| Tgene | CHTOP | GO:0051096 | positive regulation of helicase activity | 23299939 |
| Fusion gene breakpoints across VPS53 (5'-gene) * Click on the image to open the UCSC genome browser with custom track showing this image in a new window. |
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| Fusion gene breakpoints across CHTOP (3'-gene) * Click on the image to open the UCSC genome browser with custom track showing this image in a new window. |
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Fusion Gene Sample Information |
| Fusion gene information from FusionGDB2.0. |
| Fusion gene information from two resources (ChiTars 5.0 and ChimerDB 4.0) * 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. |
| Source | Disease | Sample | Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand |
| ChimerDB4 | Non-Cancer | ERR315330 | VPS53 | chr17 | 456620 | - | CHTOP | chr1 | 153614719 | + |
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Fusion ORF Analysis |
| Fusion information from ORFfinder translation from full-length transcript sequence from FusionPDB. |
| Henst | Tenst | Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand | Seq length (transcript) | BP loci (transcript) | Predicted start (transcript) | Predicted stop (transcript) | Seq length (amino acids) |
| ENST00000446250 | VPS53 | chr17 | 456620 | - | ENST00000368694 | CHTOP | chr1 | 153614719 | + | 3597 | 2032 | 839 | 2038 | 399 |
| DeepORF prediction of the coding potential based on the fusion transcript sequence of in-frame fusion genes. DeepORF is a coding potential classifier based on convolutional neural network by comparing the real Ribo-seq data. If the no-coding score < 0.5 and coding score > 0.5, then the in-frame fusion transcript is predicted as being likely translated. |
| Henst | Tenst | Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand | No-coding score | Coding score |
| ENST00000446250 | ENST00000368694 | VPS53 | chr17 | 456620 | - | CHTOP | chr1 | 153614719 | + | 0.001001846 | 0.9989981 |
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Fusion Amino Acid Sequences |
| For individual full-length fusion transcript sequence from FusionPDB, we ran ORFfinder and chose the longest ORF among the all predicted ones. |
| >FusionGDB ID_FusionGDB isoform ID_FGname_Hgene_Hchr_Hbp_Henst_Tgene_Tchr_Tbp_Tenst_length(fusion AA) seq_BP >98477_98477_1_VPS53-CHTOP_VPS53_chr17_456620_ENST00000446250_CHTOP_chr1_153614719_ENST00000368694_length(amino acids)=399AA_BP= MFSLIVKAAQTELGQQILADFEEAFPSQGTKRPGGPSNVLRDACLVANILDPRIKQEIIKKFIKQHLSEYLVLFQENQDVAWLDKIDRRY AWIKRQLVDYEEKYGRMFPREWCMAERIAVEFCHVTRAELAKIMRTRAKEIEVKLLLFAIQRTTNFEGFLAKRFSGCTLTDGTLKKLESP PPSTNPFLEDEPTPEMEELATEKGDLDQPKKPKAPDNPFHGIVSKCFEPHLYVYIESQDKNLGELIDRFVADFKAQGPPKPNTDEGGAVL PSCADLFVYYKKCMVQCSQLSTGEPMIALTTIFQKYLREYAWKILSGNLPKTTTSSGGLTISSLLKEKEGSEVAKFTLEELCLICNILST -------------------------------------------------------------- |
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Fusion Protein Functional Features |
| Four levels of functional features of fusion genes Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr17:456620/chr1:153614719) - FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels. - How to search 1. Put your fusion gene symbol. 2. Press the tab key until there will be shown the breakpoint information filled. 4. Go down and press 'Search' tab twice. 4. Go down to have the hyperlink of the search result. 5. Click the hyperlink. 6. See the FGviewer result for your fusion gene. |
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| Main function of each fusion partner protein. (from UniProt) |
| Hgene | Tgene |
| . | CHTOP |
| FUNCTION: Might normally function as a transcriptional repressor. EWS-fusion-proteins (EFPS) may play a role in the tumorigenic process. They may disturb gene expression by mimicking, or interfering with the normal function of CTD-POLII within the transcription initiation complex. They may also contribute to an aberrant activation of the fusion protein target genes. | FUNCTION: Plays an important role in the ligand-dependent activation of estrogen receptor target genes (PubMed:19858291). May play a role in the silencing of fetal globin genes (PubMed:20688955). Recruits the 5FMC complex to ZNF148, leading to desumoylation of ZNF148 and subsequent transactivation of ZNF148 target genes (By similarity). Plays an important role in the tumorigenicity of glioblastoma cells. Binds to 5-hydroxymethylcytosine (5hmC) and associates with the methylosome complex containing PRMT1, PRMT5, MEP50 and ERH. The CHTOP-methylosome complex associated with 5hmC is recruited to selective sites on the chromosome, where it methylates H4R3 and activates the transcription of genes involved in glioblastomagenesis (PubMed:25284789). {ECO:0000250|UniProtKB:Q9CY57, ECO:0000269|PubMed:19858291, ECO:0000269|PubMed:20688955, ECO:0000269|PubMed:25284789}.; FUNCTION: Required for effective mRNA nuclear export and is a component of the TREX complex which is thought to couple mRNA transcription, processing and nuclear export, and specifically associates with spliced mRNA and not with unspliced pre-mRNA. TREX is recruited to spliced mRNAs by a transcription-independent mechanism, binds to mRNA upstream of the exon-junction complex (EJC) and is recruited in a splicing- and cap-dependent manner to a region near the 5' end of the mRNA where it functions in mRNA export to the cytoplasm via the TAP/NFX1 pathway. The TREX complex is essential for the export of Kaposi's sarcoma-associated herpesvirus (KSHV) intronless mRNAs and infectious virus production. Stimulates DDX39B ATPase and helicase activities. In cooperation with ALYREF/THOC4 enhances NXF1 RNA binding activity (PubMed:23299939). {ECO:0000269|PubMed:23299939}. |
| 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. |
| - 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 |
| Hgene | VPS53 | chr17:456620 | chr1:153614719 | ENST00000291074 | - | 15 | 18 | 97_138 | 566.6666666666666 | 671.0 | Coiled coil | Ontology_term=ECO:0000255 |
| Hgene | VPS53 | chr17:456620 | chr1:153614719 | ENST00000437048 | - | 16 | 22 | 97_138 | 595.6666666666666 | 833.0 | Coiled coil | Ontology_term=ECO:0000255 |
| Hgene | VPS53 | chr17:456620 | chr1:153614719 | ENST00000571805 | - | 16 | 19 | 97_138 | 595.6666666666666 | 700.0 | Coiled coil | Ontology_term=ECO:0000255 |
| Tgene | CHTOP | chr17:456620 | chr1:153614719 | ENST00000368690 | 1 | 4 | 87_208 | 73.0 | 203.0 | Compositional bias | Note=Arg/Gly-rich | |
| Tgene | CHTOP | chr17:456620 | chr1:153614719 | ENST00000368694 | 2 | 6 | 87_208 | 73.0 | 249.0 | Compositional bias | Note=Arg/Gly-rich | |
| Tgene | CHTOP | chr17:456620 | chr1:153614719 | ENST00000403433 | 2 | 5 | 87_208 | 73.0 | 203.0 | Compositional bias | Note=Arg/Gly-rich | |
| Tgene | CHTOP | chr17:456620 | chr1:153614719 | ENST00000368690 | 1 | 4 | 194_203 | 73.0 | 203.0 | Motif | GAR motif%3B involved in 5hmC binding | |
| Tgene | CHTOP | chr17:456620 | chr1:153614719 | ENST00000368694 | 2 | 6 | 194_203 | 73.0 | 249.0 | Motif | GAR motif%3B involved in 5hmC binding | |
| Tgene | CHTOP | chr17:456620 | chr1:153614719 | ENST00000403433 | 2 | 5 | 194_203 | 73.0 | 203.0 | Motif | GAR motif%3B involved in 5hmC binding |
| - 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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Fusion Protein-Protein Interaction |
| 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 from validated records (BIOGRID-3.4.160) |
| Gene | PPI interactors |
| Protein-protein interactors based on sequence similarity (STRING) |
| Gene | STRING network |
| VPS53 | |
| CHTOP |
| - Retained interactions in fusion protein (protein functional feature from UniProt). |
| Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Still interaction with |
| - Lost interactions due to fusion (protein functional feature from UniProt). |
| Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Interaction lost with |
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Related Drugs to VPS53-CHTOP |
| Drugs used for this fusion-positive patient. (Manual curation of PubMed, 04-30-2022 + MyCancerGenome) |
| Hgene | Tgene | Drug | Source | PMID |
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Related Diseases to VPS53-CHTOP |
| Diseases that have this fusion gene. (Manual curation of PubMed, 04-30-2022 + MyCancerGenome) |
| Hgene | Tgene | Disease | Source | PMID |
| Diseases associated with fusion partners. (DisGeNet 4.0) |
| Partner | Gene | Disease ID | Disease name | # pubmeds | Source |
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