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Fusion Protein:KCNC3-PRKDC |
Fusion Gene and Fusion Protein Summary |
 Fusion gene summary |
| Fusion partner gene information | Fusion gene name: KCNC3-PRKDC | FusionPDB ID: 41380 | FusionGDB2.0 ID: 41380 | Hgene | Tgene | Gene symbol | KCNC3 | PRKDC | Gene ID | 3748 | 5591 |
| Gene name | potassium voltage-gated channel subfamily C member 3 | protein kinase, DNA-activated, catalytic subunit | |
| Synonyms | KSHIIID|KV3.3|SCA13 | DNA-PKC|DNA-PKcs|DNAPK|DNAPKc|DNPK1|HYRC|HYRC1|IMD26|XRCC7|p350 | |
| Cytomap | 19q13.33 | 8q11.21 | |
| Type of gene | protein-coding | protein-coding | |
| Description | potassium voltage-gated channel subfamily C member 3Shaw-related voltage-gated potassium channel protein 3potassium channel, voltage gated Shaw related subfamily C, member 3potassium voltage-gated channel, Shaw-related subfamily, member 3voltage-gated | DNA-dependent protein kinase catalytic subunitDNA-PK catalytic subunithyper-radiosensitivity of murine scid mutation, complementing 1p460protein kinase, DNA-activated, catalytic polypeptide | |
| Modification date | 20200313 | 20200322 | |
| UniProtAcc | Q14003 Main function of 5'-partner protein: FUNCTION: Voltage-gated potassium channel that plays an important role in the rapid repolarization of fast-firing brain neurons. The channel opens in response to the voltage difference across the membrane, forming a potassium-selective channel through which potassium ions pass in accordance with their electrochemical gradient. The channel displays rapid activation and inactivation kinetics (PubMed:10712820, PubMed:26997484, PubMed:22289912, PubMed:23734863, PubMed:16501573, PubMed:19953606, PubMed:21479265, PubMed:25756792). It plays a role in the regulation of the frequency, shape and duration of action potentials in Purkinje cells. Required for normal survival of cerebellar neurons, probably via its role in regulating the duration and frequency of action potentials that in turn regulate the activity of voltage-gated Ca(2+) channels and cellular Ca(2+) homeostasis (By similarity). Required for normal motor function (PubMed:23734863, PubMed:16501573, PubMed:19953606, PubMed:21479265, PubMed:25756792). Plays a role in the reorganization of the cortical actin cytoskeleton and the formation of actin veil structures in neuronal growth cones via its interaction with HAX1 and the Arp2/3 complex (PubMed:26997484). {ECO:0000250|UniProtKB:Q63959, ECO:0000269|PubMed:10712820, ECO:0000269|PubMed:16501573, ECO:0000269|PubMed:19953606, ECO:0000269|PubMed:21479265, ECO:0000269|PubMed:22289912, ECO:0000269|PubMed:23734863, ECO:0000269|PubMed:25756792, ECO:0000269|PubMed:26997484}. | . | |
| Ensembl transtripts involved in fusion gene | ENST ids | ENST00000376959, ENST00000391818, ENST00000474951, ENST00000477616, | ENST00000523565, ENST00000314191, ENST00000338368, |
| Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0) | * DoF score | 5 X 4 X 5=100 | 18 X 20 X 5=1800 |
| # samples | 5 | 19 | |
| ** MAII score | log2(5/100*10)=-1 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | log2(19/1800*10)=-3.24392558288609 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | |
| Fusion gene context | PubMed: KCNC3 [Title/Abstract] AND PRKDC [Title/Abstract] AND fusion [Title/Abstract] | ||
| Fusion neoantigen context | PubMed: KCNC3 [Title/Abstract] AND PRKDC [Title/Abstract] AND neoantigen [Title/Abstract] | ||
| Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0) | KCNC3(50823850)-PRKDC(48730122), # samples:3 | ||
| Anticipated loss of major functional domain due to fusion event. | KCNC3-PRKDC 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. KCNC3-PRKDC 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. KCNC3-PRKDC 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. KCNC3-PRKDC 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. KCNC3-PRKDC seems lost the major protein functional domain in Hgene partner, which is a IUPHAR drug target due to the frame-shifted ORF. KCNC3-PRKDC seems lost the major protein functional domain in Tgene partner, which is a epigenetic factor due to the frame-shifted ORF. KCNC3-PRKDC seems lost the major protein functional domain in Tgene partner, which is a IUPHAR drug target due to the frame-shifted ORF. KCNC3-PRKDC seems lost the major protein functional domain in Tgene 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 | KCNC3 | GO:0051262 | protein tetramerization | 23734863 |
| Tgene | PRKDC | GO:0002218 | activation of innate immune response | 28712728 |
| Tgene | PRKDC | GO:0006468 | protein phosphorylation | 26237645 |
| Tgene | PRKDC | GO:0006974 | cellular response to DNA damage stimulus | 26237645 |
| Tgene | PRKDC | GO:0018105 | peptidyl-serine phosphorylation | 15194694|19303849 |
| Tgene | PRKDC | GO:2001034 | positive regulation of double-strand break repair via nonhomologous end joining | 26237645 |
| Four levels of functional features of fusion genes Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr19:50823850/chr8:48730122) - 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 KCNC3 (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 PRKDC (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) |
| ENST00000376959 | KCNC3 | chr19 | 50823850 | - | ENST00000338368 | PRKDC | chr8 | 48730122 | - | 6248 | 2334 | 128 | 5182 | 1684 |
| ENST00000376959 | KCNC3 | chr19 | 50823850 | - | ENST00000314191 | PRKDC | chr8 | 48730122 | - | 6341 | 2334 | 128 | 5275 | 1715 |
| ENST00000477616 | KCNC3 | chr19 | 50823850 | - | ENST00000338368 | PRKDC | chr8 | 48730122 | - | 6379 | 2465 | 259 | 5313 | 1684 |
| ENST00000477616 | KCNC3 | chr19 | 50823850 | - | ENST00000314191 | PRKDC | chr8 | 48730122 | - | 6472 | 2465 | 259 | 5406 | 1715 |
| 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 |
| ENST00000376959 | ENST00000338368 | KCNC3 | chr19 | 50823850 | - | PRKDC | chr8 | 48730122 | - | 0.001336683 | 0.9986633 |
| ENST00000376959 | ENST00000314191 | KCNC3 | chr19 | 50823850 | - | PRKDC | chr8 | 48730122 | - | 0.001050846 | 0.9989492 |
| ENST00000477616 | ENST00000338368 | KCNC3 | chr19 | 50823850 | - | PRKDC | chr8 | 48730122 | - | 0.001516597 | 0.9984835 |
| ENST00000477616 | ENST00000314191 | KCNC3 | chr19 | 50823850 | - | PRKDC | chr8 | 48730122 | - | 0.001197198 | 0.9988028 |
| 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 KCNC3-PRKDC |
| +/-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 |
| KCNC3 | chr19 | 50823850 | PRKDC | chr8 | 48730122 | 2334 | 735 | TDYAPSPDGSIRKGNLSSQVPLKRLL |
| KCNC3 | chr19 | 50823850 | PRKDC | chr8 | 48730122 | 2465 | 735 | TDYAPSPDGSIRKGNLSSQVPLKRLL |
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Potential FusionNeoAntigen Information of KCNC3-PRKDC 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. |
| KCNC3-PRKDC_50823850_48730122.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) |
| KCNC3-PRKDC | chr19 | 50823850 | chr8 | 48730122 | 2334 | HLA-B07:12 | SPDGSIRKGNL | 0.9994 | 0.6677 | 5 | 16 |
| KCNC3-PRKDC | chr19 | 50823850 | chr8 | 48730122 | 2334 | HLA-B42:01 | SPDGSIRKGNL | 0.9822 | 0.6154 | 5 | 16 |
| KCNC3-PRKDC | chr19 | 50823850 | chr8 | 48730122 | 2334 | HLA-B39:10 | SPDGSIRKGNL | 0.9421 | 0.8779 | 5 | 16 |
| KCNC3-PRKDC | chr19 | 50823850 | chr8 | 48730122 | 2334 | HLA-B67:01 | SPDGSIRKGNL | 0.9275 | 0.753 | 5 | 16 |
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Potential FusionNeoAntigen Information of KCNC3-PRKDC 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 KCNC3-PRKDC |
| 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 |
| 6538 | PDGSIRKGNLSSQV | KCNC3 | PRKDC | chr19 | 50823850 | chr8 | 48730122 | 2334 |
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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of KCNC3-PRKDC |
| 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 | 6538 | PDGSIRKGNLSSQV | -7.15543 | -7.26883 |
| HLA-B14:02 | 3BVN | 6538 | PDGSIRKGNLSSQV | -4.77435 | -5.80965 |
| HLA-B52:01 | 3W39 | 6538 | PDGSIRKGNLSSQV | -6.80875 | -6.92215 |
| HLA-B52:01 | 3W39 | 6538 | PDGSIRKGNLSSQV | -4.20386 | -5.23916 |
| HLA-A11:01 | 4UQ2 | 6538 | PDGSIRKGNLSSQV | -7.5194 | -8.5547 |
| HLA-A11:01 | 4UQ2 | 6538 | PDGSIRKGNLSSQV | -6.9601 | -7.0735 |
| HLA-A24:02 | 5HGA | 6538 | PDGSIRKGNLSSQV | -7.52403 | -7.63743 |
| HLA-A24:02 | 5HGA | 6538 | PDGSIRKGNLSSQV | -5.82433 | -6.85963 |
| HLA-B27:05 | 6PYJ | 6538 | PDGSIRKGNLSSQV | -3.28285 | -4.31815 |
| HLA-B44:05 | 3DX8 | 6538 | PDGSIRKGNLSSQV | -5.91172 | -6.94702 |
| HLA-B44:05 | 3DX8 | 6538 | PDGSIRKGNLSSQV | -4.24346 | -4.35686 |
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Vaccine Design for the FusionNeoAntigens of KCNC3-PRKDC |
| 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 |
| KCNC3-PRKDC | chr19 | 50823850 | chr8 | 48730122 | 5 | 16 | SPDGSIRKGNL | CCCCTGATGGCTCCATCCGAAAAGGCAATTTAT |
| 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 KCNC3-PRKDC |
| 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 |
| CESC | KCNC3-PRKDC | chr19 | 50823850 | ENST00000376959 | chr8 | 48730122 | ENST00000314191 | TCGA-VS-A8EI-01A |
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Potential target of CAR-T therapy development for KCNC3-PRKDC |
| 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 |
| Hgene | KCNC3 | chr19:50823850 | chr8:48730122 | ENST00000477616 | - | 3 | 5 | 291_309 | 723 | 237.33333333333334 | Transmembrane | Helical%3B Name%3DSegment S1 |
| Hgene | KCNC3 | chr19:50823850 | chr8:48730122 | ENST00000477616 | - | 3 | 5 | 351_370 | 723 | 237.33333333333334 | Transmembrane | Helical%3B Name%3DSegment S2 |
| Hgene | KCNC3 | chr19:50823850 | chr8:48730122 | ENST00000477616 | - | 3 | 5 | 380_398 | 723 | 237.33333333333334 | Transmembrane | Helical%3B Name%3DSegment S3 |
| Hgene | KCNC3 | chr19:50823850 | chr8:48730122 | ENST00000477616 | - | 3 | 5 | 412_434 | 723 | 237.33333333333334 | Transmembrane | Helical%3B Voltage-sensor%3B Name%3DSegment S4 |
| Hgene | KCNC3 | chr19:50823850 | chr8:48730122 | ENST00000477616 | - | 3 | 5 | 448_469 | 723 | 237.33333333333334 | Transmembrane | Helical%3B Name%3DSegment S5 |
| Hgene | KCNC3 | chr19:50823850 | chr8:48730122 | ENST00000477616 | - | 3 | 5 | 518_539 | 723 | 237.33333333333334 | Transmembrane | Helical%3B Name%3DSegment S6 |
| 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 |
| KCNC3 | chr19 | 50823850 | ENST00000376959 | PRKDC | chr8 | 48730122 | ENST00000314191 |  |
| KCNC3 | chr19 | 50823850 | ENST00000376959 | PRKDC | chr8 | 48730122 | ENST00000338368 |  |
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Related Drugs to KCNC3-PRKDC |
| 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 KCNC3-PRKDC |
| 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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