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Fusion Protein:CSNK1D-VCP |
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 | . | |
| 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 | |
| Context (manual curation of fusion genes in FusionPDB) | PubMed: CSNK1D [Title/Abstract] AND VCP [Title/Abstract] AND fusion [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 |
| 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 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 | STAD | TCGA-D7-A6EZ | CSNK1D | chr17 | 80213304 | - | VCP | chr9 | 35059798 | - |
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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) |
| 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 |
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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 >19827_19827_1_CSNK1D-VCP_CSNK1D_chr17_80213304_ENST00000314028_VCP_chr9_35059798_ENST00000358901_length(amino acids)=466AA_BP=225 MLGEVTSQRDGGGSFRQLKGDLGPEDPSPSAAGRGQAGPVGAGAAAAALGLSHPPRIEALGAAGRQESDGESGAVRGAEPGAGPAVAAAA APPPRVQTQEAAGRAGANRAAAAMELRVGNRYRLGRKIGSGSFGDIYLGTDIAAGEEVAIKLECVKTKHPQLHIESKIYKMMQGGVGIPT IRWCGAEGDYNVMVMELLGPSLEDLFNFCSRKFSLKTVLLLADQMARQAAPCVLFFDELDSIAKARGGNIGDGGGAADRVINQILTEMDG MSTKKNVFIIGATNRPDIIDPAILRPGRLDQLIYIPLPDEKSRVAILKANLRKSPVAKDVDLEFLAKMTNGFSGADLTEICQRACKLAIR ESIESEIRRERERQTNPSAMEVEEDDPVPEIRRDHFEEAMRFARRSVSDNDIRKYEMFAQTLQQSRGFGSFRFPSGNQGGAGPSQGSGGG -------------------------------------------------------------- >19827_19827_2_CSNK1D-VCP_CSNK1D_chr17_80213304_ENST00000398519_VCP_chr9_35059798_ENST00000358901_length(amino acids)=353AA_BP=112 MELRVGNRYRLGRKIGSGSFGDIYLGTDIAAGEEVAIKLECVKTKHPQLHIESKIYKMMQGGVGIPTIRWCGAEGDYNVMVMELLGPSLE DLFNFCSRKFSLKTVLLLADQMARQAAPCVLFFDELDSIAKARGGNIGDGGGAADRVINQILTEMDGMSTKKNVFIIGATNRPDIIDPAI LRPGRLDQLIYIPLPDEKSRVAILKANLRKSPVAKDVDLEFLAKMTNGFSGADLTEICQRACKLAIRESIESEIRRERERQTNPSAMEVE -------------------------------------------------------------- |
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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/chr17:80213304/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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| Main function of each fusion partner protein. (from UniProt) |
| Hgene | Tgene |
| CSNK1D | . |
| 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}. | 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. |
| 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 | CSNK1D | chr17:80213304 | chr9:35059798 | ENST00000314028 | - | 3 | 9 | 15_23 | 112.0 | 416.0 | Nucleotide binding | ATP |
| Hgene | CSNK1D | chr17:80213304 | chr9:35059798 | ENST00000392334 | - | 3 | 10 | 15_23 | 112.0 | 420.3333333333333 | Nucleotide binding | ATP |
| Tgene | VCP | chr17:80213304 | chr9:35059798 | ENST00000358901 | 12 | 17 | 802_806 | 565.0 | 807.0 | Motif | PIM motif |
| - 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 |
| Hgene | CSNK1D | chr17:80213304 | chr9:35059798 | ENST00000314028 | - | 3 | 9 | 9_277 | 112.0 | 416.0 | Domain | Protein kinase |
| Hgene | CSNK1D | chr17:80213304 | chr9:35059798 | ENST00000392334 | - | 3 | 10 | 9_277 | 112.0 | 420.3333333333333 | Domain | Protein kinase |
| Hgene | CSNK1D | chr17:80213304 | chr9:35059798 | ENST00000314028 | - | 3 | 9 | 278_364 | 112.0 | 416.0 | Region | Note=Centrosomal localization signal (CLS) |
| Hgene | CSNK1D | chr17:80213304 | chr9:35059798 | ENST00000314028 | - | 3 | 9 | 317_342 | 112.0 | 416.0 | Region | Autoinhibitory |
| Hgene | CSNK1D | chr17:80213304 | chr9:35059798 | ENST00000392334 | - | 3 | 10 | 278_364 | 112.0 | 420.3333333333333 | Region | Note=Centrosomal localization signal (CLS) |
| Hgene | CSNK1D | chr17:80213304 | chr9:35059798 | ENST00000392334 | - | 3 | 10 | 317_342 | 112.0 | 420.3333333333333 | Region | Autoinhibitory |
| Tgene | VCP | chr17:80213304 | chr9:35059798 | ENST00000358901 | 12 | 17 | 247_253 | 565.0 | 807.0 | Nucleotide binding | ATP 1 | |
| Tgene | VCP | chr17:80213304 | chr9:35059798 | ENST00000358901 | 12 | 17 | 521_526 | 565.0 | 807.0 | Nucleotide binding | ATP 2 |
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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 |
| CSNK1D | |
| VCP |
| - 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 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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