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Fusion Protein:CSNK1D-VCP |
Fusion Gene and Fusion Protein Summary |
 Fusion gene summary |
| Fusion partner gene information | Fusion gene name: CSNK1D-VCP | FusionPDB ID: 19827 | FusionGDB2.0 ID: 19827 | Hgene | Tgene | Gene symbol | CSNK1D | VCP | Gene ID | 1453 | 7415 |
| Gene name | casein kinase 1 delta | valosin containing protein | |
| Synonyms | ASPS|CKI-delta|CKId|CKIdelta|FASPS2|HCKID | CDC48|TERA|p97 | |
| Cytomap | 17q25.3 | 9p13.3 | |
| Type of gene | protein-coding | protein-coding | |
| Description | casein kinase I isoform deltacasein kinase Itau-protein kinase CSNK1D | transitional endoplasmic reticulum ATPase15S Mg(2+)-ATPase p97 subunitTER ATPase | |
| Modification date | 20200313 | 20200327 | |
| UniProtAcc | P48730 Main function of 5'-partner protein: FUNCTION: Essential serine/threonine-protein kinase that regulates diverse cellular growth and survival processes including Wnt signaling, DNA repair and circadian rhythms. It can phosphorylate a large number of proteins. Casein kinases are operationally defined by their preferential utilization of acidic proteins such as caseins as substrates. Phosphorylates connexin-43/GJA1, MAP1A, SNAPIN, MAPT/TAU, TOP2A, DCK, HIF1A, EIF6, p53/TP53, DVL2, DVL3, ESR1, AIB1/NCOA3, DNMT1, PKD2, YAP1, PER1 and PER2. Central component of the circadian clock. In balance with PP1, determines the circadian period length through the regulation of the speed and rhythmicity of PER1 and PER2 phosphorylation. Controls PER1 and PER2 nuclear transport and degradation. YAP1 phosphorylation promotes its SCF(beta-TRCP) E3 ubiquitin ligase-mediated ubiquitination and subsequent degradation. DNMT1 phosphorylation reduces its DNA-binding activity. Phosphorylation of ESR1 and AIB1/NCOA3 stimulates their activity and coactivation. Phosphorylation of DVL2 and DVL3 regulates WNT3A signaling pathway that controls neurite outgrowth. EIF6 phosphorylation promotes its nuclear export. Triggers down-regulation of dopamine receptors in the forebrain. Activates DCK in vitro by phosphorylation. TOP2A phosphorylation favors DNA cleavable complex formation. May regulate the formation of the mitotic spindle apparatus in extravillous trophoblast. Modulates connexin-43/GJA1 gap junction assembly by phosphorylation. Probably involved in lymphocyte physiology. Regulates fast synaptic transmission mediated by glutamate. {ECO:0000269|PubMed:10606744, ECO:0000269|PubMed:12270943, ECO:0000269|PubMed:14761950, ECO:0000269|PubMed:16027726, ECO:0000269|PubMed:17562708, ECO:0000269|PubMed:17962809, ECO:0000269|PubMed:19043076, ECO:0000269|PubMed:19339517, ECO:0000269|PubMed:20041275, ECO:0000269|PubMed:20048001, ECO:0000269|PubMed:20407760, ECO:0000269|PubMed:20637175, ECO:0000269|PubMed:20696890, ECO:0000269|PubMed:20699359, ECO:0000269|PubMed:21084295, ECO:0000269|PubMed:21422228, ECO:0000269|PubMed:23636092}. | . | |
| Ensembl transtripts involved in fusion gene | ENST ids | ENST00000578904, ENST00000392334, ENST00000314028, ENST00000398519, | ENST00000358901, |
| Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0) | * DoF score | 17 X 16 X 13=3536 | 11 X 13 X 3=429 |
| # samples | 24 | 14 | |
| ** MAII score | log2(24/3536*10)=-3.88101196378291 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | log2(14/429*10)=-1.61555082055458 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | |
| Fusion gene context | PubMed: CSNK1D [Title/Abstract] AND VCP [Title/Abstract] AND fusion [Title/Abstract] | ||
| Fusion neoantigen context | PubMed: CSNK1D [Title/Abstract] AND VCP [Title/Abstract] AND neoantigen [Title/Abstract] | ||
| Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0) | CSNK1D(80213304)-VCP(35059798), # samples:1 | ||
| Anticipated loss of major functional domain due to fusion event. | CSNK1D-VCP 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. CSNK1D-VCP 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. CSNK1D-VCP 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. CSNK1D-VCP 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. CSNK1D-VCP seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF. CSNK1D-VCP seems lost the major protein functional domain in Hgene partner, which is a IUPHAR drug target due to the frame-shifted ORF. CSNK1D-VCP seems lost the major protein functional domain in Hgene partner, which is a kinase 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 |
| Hgene | CSNK1D | GO:0006468 | protein phosphorylation | 16618118 |
| Hgene | CSNK1D | GO:0018105 | peptidyl-serine phosphorylation | 25500533 |
| Hgene | CSNK1D | GO:0051225 | spindle assembly | 10826492 |
| Tgene | VCP | GO:0006302 | double-strand break repair | 10855792|22120668 |
| Tgene | VCP | GO:0006974 | cellular response to DNA damage stimulus | 16140914|22120668|23042605 |
| Tgene | VCP | GO:0016567 | protein ubiquitination | 22120668 |
| Tgene | VCP | GO:0030433 | ubiquitin-dependent ERAD pathway | 17872946 |
| Tgene | VCP | GO:0030970 | retrograde protein transport, ER to cytosol | 15215856 |
| Tgene | VCP | GO:0031334 | positive regulation of protein complex assembly | 18775313 |
| Tgene | VCP | GO:0032436 | positive regulation of proteasomal ubiquitin-dependent protein catabolic process | 9452483 |
| Tgene | VCP | GO:0036503 | ERAD pathway | 25088257 |
| Tgene | VCP | GO:0045732 | positive regulation of protein catabolic process | 11483959|18775313 |
| Tgene | VCP | GO:0090263 | positive regulation of canonical Wnt signaling pathway | 28689657 |
| Tgene | VCP | GO:1903006 | positive regulation of protein K63-linked deubiquitination | 22970133 |
| Tgene | VCP | GO:1903007 | positive regulation of Lys63-specific deubiquitinase activity | 22970133 |
| Four levels of functional features of fusion genes Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr17:80213304/chr9:35059798) - 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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| Retention analysis results 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, are available here. |
| Fusion gene breakpoints across CSNK1D (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 VCP (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 Amino Acid Sequences |
| 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) |
| ENST00000398519 | CSNK1D | chr17 | 80213304 | - | ENST00000358901 | VCP | chr9 | 35059798 | - | 2162 | 383 | 47 | 1108 | 353 |
| ENST00000314028 | CSNK1D | chr17 | 80213304 | - | ENST00000358901 | VCP | chr9 | 35059798 | - | 2465 | 686 | 11 | 1411 | 466 |
| 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 |
| ENST00000398519 | ENST00000358901 | CSNK1D | chr17 | 80213304 | - | VCP | chr9 | 35059798 | - | 0.001967584 | 0.9980324 |
| ENST00000314028 | ENST00000358901 | CSNK1D | chr17 | 80213304 | - | VCP | chr9 | 35059798 | - | 0.002295209 | 0.9977048 |
| Predicted full-length fusion amino acid sequences. For individual full-length fusion transcript sequence from FusionPDB, we ran ORFfinder and chose the longest ORF among all the predicted ones. |
Get the fusion protein sequences from here. |
| Fusion protein sequence information is available in the fasta format. >FusionGDB ID_FusionGDB isoform ID_FGname_Hgene_Hchr_Hbp_Henst_Tgene_Tchr_Tbp_Tenst_length(fusion AA) seq_BP |
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Fusion Protein Breakpoint Sequences for CSNK1D-VCP |
| +/-13 AA sequence from the breakpoints of the fusion protein sequences. |
| Hgene | Hchr | Hbp | Tgene | Tchr | Tbp | Length(fusion protein) | BP in fusion protein | Peptide |
| CSNK1D | chr17 | 80213304 | VCP | chr9 | 35059798 | 383 | 112 | FSLKTVLLLADQMARQAAPCVLFFDE |
| CSNK1D | chr17 | 80213304 | VCP | chr9 | 35059798 | 686 | 225 | FSLKTVLLLADQMARQAAPCVLFFDE |
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Potential FusionNeoAntigen Information of CSNK1D-VCP in HLA I |
| Multiple sequence alignments of the potential FusionNeoAntigens per fusion breakpoints. If the MSA is empty, then it means that there were predicted fusion neoantigens in this fusion breakpoint, but those predicted fusion neoantigens were not across the breakpoint, which is not fusion-specific. |
| CSNK1D-VCP_80213304_35059798.msa |
| Potential FusionNeoAntigen Information * We used NetMHCpan v4.1 (%rank<0.5) and deepHLApan v1.1 (immunogenic score>0.5) |
| Fusion gene | Hchr | Hbp | Tgene | Tchr | Tbp | HLA I | FusionNeoAntigen peptide | Binding score | Immunogenic score | Neoantigen start (at BP 13) | Neoantigen end (at BP 13) |
| CSNK1D-VCP | chr17 | 80213304 | chr9 | 35059798 | 686 | HLA-B08:09 | DQMARQAA | 0.9954 | 0.9279 | 10 | 18 |
| CSNK1D-VCP | chr17 | 80213304 | chr9 | 35059798 | 686 | HLA-B78:01 | MARQAAPCV | 0.9174 | 0.8676 | 12 | 21 |
| CSNK1D-VCP | chr17 | 80213304 | chr9 | 35059798 | 686 | HLA-A02:03 | LLADQMARQA | 0.995 | 0.9253 | 7 | 17 |
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Potential FusionNeoAntigen Information of CSNK1D-VCP in HLA II |
| Multiple sequence alignments of the potential FusionNeoAntigens per fusion breakpoints. If the MSA is empty, then it means that there were predicted fusion neoantigens in this fusion breakpoint, but those predicted fusion neoantigens were not across the breakpoint, which is not fusion-specific. |
| Potential FusionNeoAntigen Information * We used NetMHCIIpan v4.1 (%rank<0.5). |
| Fusion gene | Hchr | Hbp | Tgene | Tchr | Tbp | HLA II | FusionNeoAntigen peptide | Neoantigen start (at BP 13) | Neoantigen end (at BP 13) |
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Fusion breakpoint peptide structures of CSNK1D-VCP |
| 3D structures of the fusion breakpoint peptide of 14AA sequence that have potential fusion neoantigens * The minimum length of the amino acid sequence in RoseTTAFold is 14AA. Here, we predicted the 14AA fusion protein breakpoint sequence not the fusion neoantigen peptide, which is shorter than 14 AA. |
| File name | BPseq | Hgene | Tgene | Hchr | Hbp | Tchr | Tbp | AAlen |
| 5237 | LLLADQMARQAAPC | CSNK1D | VCP | chr17 | 80213304 | chr9 | 35059798 | 686 |
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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of CSNK1D-VCP |
| Virtual screening between 25 HLAs (from PDB) and FusionNeoAntigens * We used Glide to predict the interaction between HLAs and neoantigens. |
| HLA allele | PDB ID | File name | BPseq | Docking score | Glide score |
| HLA-B14:02 | 3BVN | 5237 | LLLADQMARQAAPC | -7.9962 | -8.1096 |
| HLA-B14:02 | 3BVN | 5237 | LLLADQMARQAAPC | -5.70842 | -6.74372 |
| HLA-B52:01 | 3W39 | 5237 | LLLADQMARQAAPC | -6.83737 | -6.95077 |
| HLA-B52:01 | 3W39 | 5237 | LLLADQMARQAAPC | -4.4836 | -5.5189 |
| HLA-A11:01 | 4UQ2 | 5237 | LLLADQMARQAAPC | -10.0067 | -10.1201 |
| HLA-A11:01 | 4UQ2 | 5237 | LLLADQMARQAAPC | -9.03915 | -10.0745 |
| HLA-A24:02 | 5HGA | 5237 | LLLADQMARQAAPC | -6.56204 | -6.67544 |
| HLA-A24:02 | 5HGA | 5237 | LLLADQMARQAAPC | -5.42271 | -6.45801 |
| HLA-B44:05 | 3DX8 | 5237 | LLLADQMARQAAPC | -7.85648 | -8.89178 |
| HLA-B44:05 | 3DX8 | 5237 | LLLADQMARQAAPC | -5.3978 | -5.5112 |
| HLA-A02:01 | 6TDR | 5237 | LLLADQMARQAAPC | -3.37154 | -4.40684 |
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Vaccine Design for the FusionNeoAntigens of CSNK1D-VCP |
| mRNA and peptide sequences of FusionNeoAntigens that have potential interaction with HLA-Is. |
| Fusion gene | Hchr | Hbp | Tchr | Tbp | Start in +/-13AA | End in +/-13AA | FusionNeoAntigen peptide sequence | FusionNeoAntigen RNA sequence |
| CSNK1D-VCP | chr17 | 80213304 | chr9 | 35059798 | 10 | 18 | DQMARQAA | GACCAAATGGCCCGCCAAGCTGCC |
| CSNK1D-VCP | chr17 | 80213304 | chr9 | 35059798 | 12 | 21 | MARQAAPCV | ATGGCCCGCCAAGCTGCCCCCTGTGTG |
| CSNK1D-VCP | chr17 | 80213304 | chr9 | 35059798 | 7 | 17 | LLADQMARQA | CTGCTTGCTGACCAAATGGCCCGCCAAGCT |
| mRNA and peptide sequences of FusionNeoAntigens that have potential interaction with HLA-IIs. |
| Fusion gene | Hchr | Hbp | Tchr | Tbp | Start in +/-13AA | End in +/-13AA | FusionNeoAntigen peptide | FusionNEoAntigen RNA sequence |
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Information of the samples that have these potential fusion neoantigens of CSNK1D-VCP |
| These samples were reported as having these fusion breakpoints. For individual breakpoints, we checked the open reading frames considering multiple gene isoforms and chose the in-frame fusion genes only. Then, we made fusion protein sequences and predicted the fusion neoantigens. These fusion-positive samples may have these potential fusion neoantigens. |
| Cancer type | Fusion gene | Hchr | Hbp | Henst | Tchr | Tbp | Tenst | Sample |
| STAD | CSNK1D-VCP | chr17 | 80213304 | ENST00000314028 | chr9 | 35059798 | ENST00000358901 | TCGA-D7-A6EZ |
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Potential target of CAR-T therapy development for CSNK1D-VCP |
| Predicted 3D structure. We used RoseTTAFold. |
| 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, to provide the retention of the transmembrane domain, we only show the protein feature retention information of those transmembrane features * Minus value of BPloci means that the break point is located before the CDS. |
| - In-frame and retained 'Transmembrane'. |
| Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Protein feature | Protein feature note |
| Subcellular localization prediction of the transmembrane domain retained fusion proteins * We used DeepLoc 1.0. The order of the X-axis of the barplot is as follows: Entry_ID, Localization, Type, Nucleus, Cytoplasm, Extracellular, Mitochondrion, Cell_membrane, Endoplasmic_reticulum, Plastid, Golgi.apparatus, Lysosome.Vacuole, Peroxisome. Y-axis is the output score of DeepLoc. Clicking the image will open a new tab with a large image. |
| Hgene | Hchr | Hbp | Henst | Tgene | Tchr | Tbp | Tenst | DeepLoc result |
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Related Drugs to CSNK1D-VCP |
| 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 CSNK1D-VCP |
| 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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