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 | Fusion Gene Summary |
| Fusion Gene ORF analysis |
| Fusion Genomic Features |
| Fusion Protein Features |
| Fusion Gene Sequence |
| Fusion Gene PPI analysis |
| Related Drugs |
| Related Diseases |
Fusion gene:CDK2AP1-KCNQ1 (FusionGDB2 ID:15273) |
Fusion Gene Summary for CDK2AP1-KCNQ1 |
 Fusion gene summary |
| Fusion gene information | Fusion gene name: CDK2AP1-KCNQ1 | Fusion gene ID: 15273 | Hgene | Tgene | Gene symbol | CDK2AP1 | KCNQ1 | Gene ID | 8099 | 3784 |
| Gene name | cyclin dependent kinase 2 associated protein 1 | potassium voltage-gated channel subfamily Q member 1 | |
| Synonyms | DOC1|DORC1|ST19|doc-1|p12DOC-1 | ATFB1|ATFB3|JLNS1|KCNA8|KCNA9|KVLQT1|Kv1.9|Kv7.1|LQT|LQT1|RWS|SQT2|WRS | |
| Cytomap | 12q24.31 | 11p15.5-p15.4 | |
| Type of gene | protein-coding | protein-coding | |
| Description | cyclin-dependent kinase 2-associated protein 1CDK2-associated protein 1Deleted in oral cancer-1deleted in oral cancer 1putative oral cancer suppressor | potassium voltage-gated channel subfamily KQT member 1IKs producing slow voltage-gated potassium channel subunit alpha KvLQT1kidney and cardiac voltage dependend K+ channelpotassium channel, voltage gated KQT-like subfamily Q, member 1potassium voltag | |
| Modification date | 20200313 | 20200313 | |
| UniProtAcc | O14519 | P51787 | |
| Ensembl transtripts involved in fusion gene | ENST00000261692, ENST00000538446, ENST00000535979, ENST00000542174, ENST00000544658, | ENST00000155840, ENST00000335475, ENST00000526095, | |
| Fusion gene scores | * DoF score | 3 X 2 X 3=18 | 10 X 10 X 5=500 |
| # samples | 3 | 12 | |
| ** MAII score | log2(3/18*10)=0.736965594166206 effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs). DoF>8 and MAII>0 | log2(12/500*10)=-2.05889368905357 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | |
| Context | PubMed: CDK2AP1 [Title/Abstract] AND KCNQ1 [Title/Abstract] AND fusion [Title/Abstract] | ||
| Most frequent breakpoint | CDK2AP1(123756111)-KCNQ1(2790074), # samples:2 | ||
| Anticipated loss of major functional domain due to fusion event. | CDK2AP1-KCNQ1 seems lost the major protein functional domain in Hgene partner, which is a tumor suppressor due to the frame-shifted ORF. CDK2AP1-KCNQ1 seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF. CDK2AP1-KCNQ1 seems lost the major protein functional domain in Tgene partner, which is a IUPHAR drug target 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 | CDK2AP1 | GO:0001934 | positive regulation of protein phosphorylation | 9506968 |
| Tgene | KCNQ1 | GO:0035690 | cellular response to drug | 9108097 |
| Tgene | KCNQ1 | GO:0060306 | regulation of membrane repolarization | 11299204 |
| Tgene | KCNQ1 | GO:0071320 | cellular response to cAMP | 11299204|16002409 |
| Tgene | KCNQ1 | GO:0071805 | potassium ion transmembrane transport | 9354802|11299204|16002409 |
| Tgene | KCNQ1 | GO:0086011 | membrane repolarization during action potential | 8900283|11299204|19646991 |
| Tgene | KCNQ1 | GO:0097623 | potassium ion export across plasma membrane | 8900283|10400998|17289006 |
| Tgene | KCNQ1 | GO:1901381 | positive regulation of potassium ion transmembrane transport | 8900283 |
| Fusion gene breakpoints across CDK2AP1 (5'-gene) * Click on the image to open the UCSC genome browser with custom track showing this image in a new window. |
| Fusion gene breakpoints across KCNQ1 (3'-gene) * Click on the image to open the UCSC genome browser with custom track showing this image in a new window. |
| 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 | OV | TCGA-20-1685-01A | CDK2AP1 | chr12 | 123756111 | - | KCNQ1 | chr11 | 2790074 | + |
| ChimerDB4 | OV | TCGA-20-1685-01A | CDK2AP1 | chr12 | 123756111 | - | KCNQ1 | chr11 | 2790074 | + |
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Fusion Gene ORF analysis for CDK2AP1-KCNQ1 |
| 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 |
| Frame-shift | ENST00000261692 | ENST00000155840 | CDK2AP1 | chr12 | 123756111 | - | KCNQ1 | chr11 | 2790074 | + |
| Frame-shift | ENST00000261692 | ENST00000335475 | CDK2AP1 | chr12 | 123756111 | - | KCNQ1 | chr11 | 2790074 | + |
| 5CDS-intron | ENST00000261692 | ENST00000526095 | CDK2AP1 | chr12 | 123756111 | - | KCNQ1 | chr11 | 2790074 | + |
| intron-3CDS | ENST00000538446 | ENST00000155840 | CDK2AP1 | chr12 | 123756111 | - | KCNQ1 | chr11 | 2790074 | + |
| intron-3CDS | ENST00000538446 | ENST00000335475 | CDK2AP1 | chr12 | 123756111 | - | KCNQ1 | chr11 | 2790074 | + |
| intron-intron | ENST00000538446 | ENST00000526095 | CDK2AP1 | chr12 | 123756111 | - | KCNQ1 | chr11 | 2790074 | + |
| intron-3CDS | ENST00000535979 | ENST00000155840 | CDK2AP1 | chr12 | 123756111 | - | KCNQ1 | chr11 | 2790074 | + |
| intron-3CDS | ENST00000535979 | ENST00000335475 | CDK2AP1 | chr12 | 123756111 | - | KCNQ1 | chr11 | 2790074 | + |
| intron-intron | ENST00000535979 | ENST00000526095 | CDK2AP1 | chr12 | 123756111 | - | KCNQ1 | chr11 | 2790074 | + |
| intron-3CDS | ENST00000542174 | ENST00000155840 | CDK2AP1 | chr12 | 123756111 | - | KCNQ1 | chr11 | 2790074 | + |
| intron-3CDS | ENST00000542174 | ENST00000335475 | CDK2AP1 | chr12 | 123756111 | - | KCNQ1 | chr11 | 2790074 | + |
| intron-intron | ENST00000542174 | ENST00000526095 | CDK2AP1 | chr12 | 123756111 | - | KCNQ1 | chr11 | 2790074 | + |
| intron-3CDS | ENST00000544658 | ENST00000155840 | CDK2AP1 | chr12 | 123756111 | - | KCNQ1 | chr11 | 2790074 | + |
| intron-3CDS | ENST00000544658 | ENST00000335475 | CDK2AP1 | chr12 | 123756111 | - | KCNQ1 | chr11 | 2790074 | + |
| intron-intron | ENST00000544658 | ENST00000526095 | CDK2AP1 | chr12 | 123756111 | - | KCNQ1 | chr11 | 2790074 | + |
| ORFfinder result based on the fusion transcript sequence of in-frame fusion genes. |
| 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) |
| 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 |
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Fusion Genomic Features for CDK2AP1-KCNQ1 |
| FusionAI prediction of the potential fusion gene breakpoint based on the pre-mature RNA sequence context (+/- 5kb of individual partner genes, total 20kb length sequence). FusionAI is a fusion gene breakpoint classifier based on convolutional neural network by comparing the fusion positive and negative sequence context of ~ 20K fusion gene data. From here, we can have the relative potentency of the 20K genomic sequence how individual sequnce will be likely used as the gene fusion breakpoints. |
| Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand | 1-p | p (fusion gene breakpoint) |
| CDK2AP1 | chr12 | 123756110 | - | KCNQ1 | chr11 | 2790073 | + | 1.18E-05 | 0.9999882 |
| CDK2AP1 | chr12 | 123756110 | - | KCNQ1 | chr11 | 2790073 | + | 1.18E-05 | 0.9999882 |
| Distribution of 44 human genomic features loci across 20kb length fusion breakpoint regions. We integrated a total of 44 different types of human genomic feature loci information across five big categories including virus integration sites, repeats, structural variants, chromatin states, and gene expression regulation. More details are in help page. |
| Distribution of 44 human genomic features loci across 20kb length fusion breakpoint regions that are ovelapped with the top 1% feature importance score regions. More details are in help page. |
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Fusion Protein Features for CDK2AP1-KCNQ1 |
| Go to FGviewer for the breakpoints of :-: - FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels. |
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| Main function of each fusion partner protein. (from UniProt) |
| Hgene | Tgene |
| CDK2AP1 | KCNQ1 |
| FUNCTION: specific inhibitor of the cell-cycle kinase CDK2. {ECO:0000250}. | FUNCTION: Potassium channel that plays an important role in a number of tissues, including heart, inner ear, stomach and colon (PubMed:10646604, PubMed:25441029). Associates with KCNE beta subunits that modulates current kinetics (PubMed:9312006, PubMed:9108097, PubMed:8900283, PubMed:10646604, PubMed:11101505, PubMed:19687231). Induces a voltage-dependent current by rapidly activating and slowly deactivating potassium-selective outward current (PubMed:9312006, PubMed:9108097, PubMed:8900283, PubMed:10646604, PubMed:11101505, PubMed:25441029). Promotes also a delayed voltage activated potassium current showing outward rectification characteristic (By similarity). During beta-adrenergic receptor stimulation participates in cardiac repolarization by associating with KCNE1 to form the I(Ks) cardiac potassium current that increases the amplitude and slows down the activation kinetics of outward potassium current I(Ks) (By similarity) (PubMed:9312006, PubMed:9108097, PubMed:8900283, PubMed:10646604, PubMed:11101505). Muscarinic agonist oxotremorine-M strongly suppresses KCNQ1/KCNE1 current (PubMed:10713961). When associated with KCNE3, forms the potassium channel that is important for cyclic AMP-stimulated intestinal secretion of chloride ions (PubMed:10646604). This interaction with KCNE3 is reduced by 17beta-estradiol, resulting in the reduction of currents (By similarity). During conditions of increased substrate load, maintains the driving force for proximal tubular and intestinal sodium ions absorption, gastric acid secretion, and cAMP-induced jejunal chloride ions secretion (By similarity). Allows the provision of potassium ions to the luminal membrane of the secretory canaliculus in the resting state as well as during stimulated acid secretion (By similarity). When associated with KCNE2, forms a heterooligomer complex leading to currents with an apparently instantaneous activation, a rapid deactivation process and a linear current-voltage relationship and decreases the amplitude of the outward current (PubMed:11101505). When associated with KCNE4, inhibits voltage-gated potassium channel activity (PubMed:19687231). When associated with KCNE5, this complex only conducts current upon strong and continued depolarization (PubMed:12324418). Also forms a heterotetramer with KCNQ5; has a voltage-gated potassium channel activity (PubMed:24855057). Binds with phosphatidylinositol 4,5-bisphosphate (PubMed:25037568). {ECO:0000250|UniProtKB:P97414, ECO:0000250|UniProtKB:Q9Z0N7, ECO:0000269|PubMed:10646604, ECO:0000269|PubMed:10713961, ECO:0000269|PubMed:11101505, ECO:0000269|PubMed:12324418, ECO:0000269|PubMed:19687231, ECO:0000269|PubMed:24855057, ECO:0000269|PubMed:25037568, ECO:0000269|PubMed:8900283, ECO:0000269|PubMed:9108097, ECO:0000269|PubMed:9312006}.; FUNCTION: [Isoform 2]: Non-functional alone but modulatory when coexpressed with the full-length isoform 1. {ECO:0000269|PubMed:9305853}. |
| 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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Fusion Gene Sequence for CDK2AP1-KCNQ1 |
| For in-frame fusion transcripts, we provide the fusion transcript sequences and fusion amino acid sequences. To have fusion amino acid sequence, we ran ORFfinder and chose the longest ORF among the all predicted ones. |
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Fusion Gene PPI Analysis for CDK2AP1-KCNQ1 |
| 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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Related Drugs for CDK2AP1-KCNQ1 |
| Drugs targeting genes involved in this fusion gene. (DrugBank Version 5.1.8 2021-05-08) |
| Partner | Gene | UniProtAcc | DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
| Tgene | KCNQ1 | P51787 | DB04855 | Dronedarone | Inhibitor | Small molecule | Approved |
| Tgene | KCNQ1 | P51787 | DB04855 | Dronedarone | Inhibitor | Small molecule | Approved |
| Tgene | KCNQ1 | P51787 | DB04855 | Dronedarone | Inhibitor | Small molecule | Approved |
| Tgene | KCNQ1 | P51787 | DB04855 | Dronedarone | Inhibitor | Small molecule | Approved |
| Tgene | KCNQ1 | P51787 | DB11633 | Isavuconazole | Inhibitor | Small molecule | Approved|Investigational |
| Tgene | KCNQ1 | P51787 | DB11633 | Isavuconazole | Inhibitor | Small molecule | Approved|Investigational |
| Tgene | KCNQ1 | P51787 | DB11633 | Isavuconazole | Inhibitor | Small molecule | Approved|Investigational |
| Tgene | KCNQ1 | P51787 | DB11633 | Isavuconazole | Inhibitor | Small molecule | Approved|Investigational |
| Tgene | KCNQ1 | P51787 | DB01244 | Bepridil | Inhibitor | Small molecule | Approved|Withdrawn |
| Tgene | KCNQ1 | P51787 | DB01244 | Bepridil | Inhibitor | Small molecule | Approved|Withdrawn |
| Tgene | KCNQ1 | P51787 | DB01244 | Bepridil | Inhibitor | Small molecule | Approved|Withdrawn |
| Tgene | KCNQ1 | P51787 | DB01244 | Bepridil | Inhibitor | Small molecule | Approved|Withdrawn |
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Related Diseases for CDK2AP1-KCNQ1 |
| Diseases associated with fusion partners. (DisGeNet 4.0) |
| Partner | Gene | Disease ID | Disease name | # pubmeds | Source |
| Tgene | KCNQ1 | C4551647 | Long QT Syndrome 1 | 44 | CTD_human;GENOMICS_ENGLAND;UNIPROT |
| Tgene | KCNQ1 | C0022387 | Jervell-Lange Nielsen Syndrome | 10 | CLINGEN;CTD_human;ORPHANET |
| Tgene | KCNQ1 | C4551509 | Jervell And Lange-Nielsen Syndrome 1 | 9 | CTD_human;GENOMICS_ENGLAND;UNIPROT |
| Tgene | KCNQ1 | C0023976 | Long QT Syndrome | 7 | CTD_human;GENOMICS_ENGLAND |
| Tgene | KCNQ1 | C0011860 | Diabetes Mellitus, Non-Insulin-Dependent | 3 | CTD_human |
| Tgene | KCNQ1 | C1837014 | Atrial Fibrillation, Familial, 3 | 3 | CTD_human;GENOMICS_ENGLAND;UNIPROT |
| Tgene | KCNQ1 | C1865019 | SHORT QT SYNDROME 2 (disorder) | 3 | CTD_human;GENOMICS_ENGLAND;UNIPROT |
| Tgene | KCNQ1 | C1843687 | ATRIAL FIBRILLATION, FAMILIAL, 1 (disorder) | 2 | ORPHANET |
| Tgene | KCNQ1 | C1865020 | Short QT Syndrome 1 | 2 | ORPHANET |
| Tgene | KCNQ1 | C0001418 | Adenocarcinoma | 1 | CTD_human |
| Tgene | KCNQ1 | C0007194 | Hypertrophic Cardiomyopathy | 1 | CLINGEN;GENOMICS_ENGLAND |
| Tgene | KCNQ1 | C0018781 | Noise-induced hearing loss | 1 | CTD_human |
| Tgene | KCNQ1 | C0021841 | Intestinal Neoplasms | 1 | CTD_human |
| Tgene | KCNQ1 | C0035828 | Romano-Ward Syndrome | 1 | ORPHANET |
| Tgene | KCNQ1 | C0205641 | Adenocarcinoma, Basal Cell | 1 | CTD_human |
| Tgene | KCNQ1 | C0205642 | Adenocarcinoma, Oxyphilic | 1 | CTD_human |
| Tgene | KCNQ1 | C0205643 | Carcinoma, Cribriform | 1 | CTD_human |
| Tgene | KCNQ1 | C0205644 | Carcinoma, Granular Cell | 1 | CTD_human |
| Tgene | KCNQ1 | C0205645 | Adenocarcinoma, Tubular | 1 | CTD_human |
| Tgene | KCNQ1 | C0340493 | Paroxysmal familial ventricular fibrillation | 1 | GENOMICS_ENGLAND |
| Tgene | KCNQ1 | C0346627 | Intestinal Cancer | 1 | CTD_human |
| Tgene | KCNQ1 | C0857439 | Pituitary hormone deficiency | 1 | GENOMICS_ENGLAND |
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