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Fusion gene ID: 2218 |
FusionGeneSummary for APOE_CLCN3 |
 Fusion gene summary |
| Fusion gene information | Fusion gene name: APOE_CLCN3 | Fusion gene ID: 2218 | Hgene | Tgene | Gene symbol | APOE | CLCN3 | Gene ID | 348 | 1182 |
| Gene name | apolipoprotein E | chloride voltage-gated channel 3 | |
| Synonyms | AD2|APO-E|ApoE4|LDLCQ5|LPG | CLC3|ClC-3 | |
| Cytomap | 19q13.32 | 4q33 | |
| Type of gene | protein-coding | protein-coding | |
| Description | apolipoprotein Eapolipoprotein E3 | H(+)/Cl(-) exchange transporter 3chloride channel 3chloride channel protein 3chloride channel, voltage-sensitive 3chloride transporter ClC-3 | |
| Modification date | 20180527 | 20180523 | |
| UniProtAcc | P02649 | P51790 | |
| Ensembl transtripts involved in fusion gene | ENST00000252486, | ENST00000513761, ENST00000347613, ENST00000360642, ENST00000504131, ENST00000506924, | |
| Fusion gene scores | * DoF score | 9 X 4 X 4=144 | 36 X 4 X 19=2736 |
| # samples | 10 | 39 | |
| ** MAII score | log2(10/144*10)=-0.526068811667588 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | log2(39/2736*10)=-2.81052220113629 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | |
| Context | PubMed: APOE [Title/Abstract] AND CLCN3 [Title/Abstract] AND fusion [Title/Abstract] | ||
| Functional or gene categories assigned by FusionGDB annotation | |||
| * 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 | APOE | GO:0001937 | negative regulation of endothelial cell proliferation | 9685360 |
| Hgene | APOE | GO:0006641 | triglyceride metabolic process | 9649566 |
| Hgene | APOE | GO:0006898 | receptor-mediated endocytosis | 1917954 |
| Hgene | APOE | GO:0007186 | G-protein coupled receptor signaling pathway | 16443932 |
| Hgene | APOE | GO:0007263 | nitric oxide mediated signal transduction | 8995232 |
| Hgene | APOE | GO:0008203 | cholesterol metabolic process | 9649566 |
| Hgene | APOE | GO:0010544 | negative regulation of platelet activation | 8995232 |
| Hgene | APOE | GO:0010873 | positive regulation of cholesterol esterification | 15654758 |
| Hgene | APOE | GO:0010875 | positive regulation of cholesterol efflux | 12042316|14754908 |
| Hgene | APOE | GO:0010976 | positive regulation of neuron projection development | 7592957|23845000 |
| Hgene | APOE | GO:0010977 | negative regulation of neuron projection development | 7592957 |
| Hgene | APOE | GO:0015909 | long-chain fatty acid transport | 24345162 |
| Hgene | APOE | GO:0017038 | protein import | 24446231 |
| Hgene | APOE | GO:0019934 | cGMP-mediated signaling | 8995232 |
| Hgene | APOE | GO:0030195 | negative regulation of blood coagulation | 8995232 |
| Hgene | APOE | GO:0030828 | positive regulation of cGMP biosynthetic process | 8995232 |
| Hgene | APOE | GO:0032462 | regulation of protein homooligomerization | 25207746 |
| Hgene | APOE | GO:0032489 | regulation of Cdc42 protein signal transduction | 16443932 |
| Hgene | APOE | GO:0032805 | positive regulation of low-density lipoprotein particle receptor catabolic process | 15950758 |
| Hgene | APOE | GO:0033344 | cholesterol efflux | 11162594|16443932 |
| Hgene | APOE | GO:0033700 | phospholipid efflux | 11162594 |
| Hgene | APOE | GO:0034372 | very-low-density lipoprotein particle remodeling | 15654758 |
| Hgene | APOE | GO:0034380 | high-density lipoprotein particle assembly | 17305370 |
| Hgene | APOE | GO:0034384 | high-density lipoprotein particle clearance | 210175 |
| Hgene | APOE | GO:0034447 | very-low-density lipoprotein particle clearance | 1917954 |
| Hgene | APOE | GO:0042632 | cholesterol homeostasis | 9649566 |
| Hgene | APOE | GO:0042982 | amyloid precursor protein metabolic process | 21593558 |
| Hgene | APOE | GO:0043407 | negative regulation of MAP kinase activity | 9685360 |
| Hgene | APOE | GO:0043537 | negative regulation of blood vessel endothelial cell migration | 9685360 |
| Hgene | APOE | GO:0043691 | reverse cholesterol transport | 8127890 |
| Hgene | APOE | GO:0045541 | negative regulation of cholesterol biosynthetic process | 1917954 |
| Hgene | APOE | GO:0045807 | positive regulation of endocytosis | 7683668|8300609 |
| Hgene | APOE | GO:0046889 | positive regulation of lipid biosynthetic process | 12042316 |
| Hgene | APOE | GO:0051000 | positive regulation of nitric-oxide synthase activity | 8995232 |
| Hgene | APOE | GO:0051044 | positive regulation of membrane protein ectodomain proteolysis | 15950758 |
| Hgene | APOE | GO:0055089 | fatty acid homeostasis | 24345162 |
| Hgene | APOE | GO:0060999 | positive regulation of dendritic spine development | 24328732 |
| Hgene | APOE | GO:0090090 | negative regulation of canonical Wnt signaling pathway | 16805831 |
| Hgene | APOE | GO:0097113 | AMPA glutamate receptor clustering | 24328732 |
| Hgene | APOE | GO:0097114 | NMDA glutamate receptor clustering | 24328732 |
| Hgene | APOE | GO:1900221 | regulation of amyloid-beta clearance | 24446231 |
| Hgene | APOE | GO:1900272 | negative regulation of long-term synaptic potentiation | 16273551 |
| Hgene | APOE | GO:1901215 | negative regulation of neuron death | 24259049 |
| Hgene | APOE | GO:1901628 | positive regulation of postsynaptic membrane organization | 24259049 |
| Hgene | APOE | GO:1901630 | negative regulation of presynaptic membrane organization | 24259049 |
| Hgene | APOE | GO:1902430 | negative regulation of amyloid-beta formation | 24154541 |
| Hgene | APOE | GO:1902952 | positive regulation of dendritic spine maintenance | 24328732 |
| Hgene | APOE | GO:1902995 | positive regulation of phospholipid efflux | 12042316 |
| Hgene | APOE | GO:1903002 | positive regulation of lipid transport across blood brain barrier | 24345162 |
| Hgene | APOE | GO:1905855 | positive regulation of heparan sulfate binding | 7683668 |
| Hgene | APOE | GO:1905860 | positive regulation of heparan sulfate proteoglycan binding | 8300609 |
| Hgene | APOE | GO:1905890 | regulation of cellular response to very-low-density lipoprotein particle stimulus | 7592957 |
| Hgene | APOE | GO:1905906 | regulation of amyloid fibril formation | 25207746 |
| Tgene | CLCN3 | GO:1902476 | chloride transmembrane transport | 11274166 |
| Fusion gene information from three resources (ChiTars (NAR, 2018), tumorfusions (NAR, 2018), Gao et al. (Cell, 2018)) * 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. |
| Data type | Source | Cancer type | Sample | Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand |
| TCGA | RV | ACC | TCGA-OR-A5K9-01A | APOE | chr19 | 45412650 | + | CLCN3 | chr4 | 170623929 | + |
| * LD: Li Ding group's fusion gene list RV: Roel Verhaak group's fusion gene list ChiTaRs fusion database |
| 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 |
| 5CDS-intron | ENST00000252486 | ENST00000513761 | APOE | chr19 | 45412650 | + | CLCN3 | chr4 | 170623929 | + |
| 5CDS-intron | ENST00000252486 | ENST00000347613 | APOE | chr19 | 45412650 | + | CLCN3 | chr4 | 170623929 | + |
| 5CDS-intron | ENST00000252486 | ENST00000360642 | APOE | chr19 | 45412650 | + | CLCN3 | chr4 | 170623929 | + |
| 5CDS-intron | ENST00000252486 | ENST00000504131 | APOE | chr19 | 45412650 | + | CLCN3 | chr4 | 170623929 | + |
| 5CDS-intron | ENST00000252486 | ENST00000506924 | APOE | chr19 | 45412650 | + | CLCN3 | chr4 | 170623929 | + |
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FusionProtFeatures for APOE_CLCN3 |
| Main function of each fusion partner protein. (from UniProt) |
| Hgene | Tgene |
| APOE | CLCN3 |
| Mediates the binding, internalization, and catabolism oflipoprotein particles. It can serve as a ligand for the LDL (apoB/E) receptor and for the specific apo-E receptor (chylomicronremnant) of hepatic tissues. {ECO:0000303|PubMed:3283935}. | Mediates the exchange of chloride ions against protons.Functions as antiporter and contributes to the acidification ofthe endosome and synaptic vesicle lumen, and may thereby affectvesicle trafficking and exocytosis. May play an important role inneuronal cell function through regulation of membrane excitabilityby protein kinase C. It could help neuronal cells to establishshort-term memory. {ECO:0000269|PubMed:11967229}. |
| 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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FusionGeneSequence for APOE_CLCN3 |
| For in-frame fusion transcripts, we provide the fusion transcript sequences and fusion amino acid sequences. (nt: nucleotides, aa: amino acids) |
| * Fusion amino acid sequences. |
| * Fusion transcript sequences (only coding sequence (CDS) region). |
| * Fusion transcript sequences (Full-length transcript). |
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FusionGenePPI for APOE_CLCN3 |
| 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 |
| APOE | LRP8, PLTP, LRP2, A2M, MAPT, NEFM, LRP1, CSNK2A1, GCDH, PDCD4, CDC37, CYP2C8, ECSIT, IFIT3, LOXL4, MAST1, PSEN1, RNF32, APOE, C19orf52, CYP2C18, ELAVL1, FARSA, FBXL12, IFIT5, LONP1, NOS3, PRAM1, PRDX2, RHEB, ST13, ACTG1, ANKH, EPN2, FOXG1, FXYD7, HTRA1, IQSEC1, MID1IP1, PCMT1, PLEKHA6, RPL4, TYRO3, ZNF558, ALB, LCAT, ARFGAP1, HLA-DPA1, VDAC1, MMRN1, MMP3, MANSC1, C9, VDAC3, MMP10, IFNA8 | CLCN3 | CLCN3, SLC9A3R1, PDZK1, GOPC, CFTR, LGALS3, LGALS8, LGALS9, LYPD3, HSPB1, TMEM9B, GGA1, TPCN2, TRIM25 |
| - 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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RelatedDrugs for APOE_CLCN3 |
| Drugs targeting genes involved in this fusion gene. (DrugBank Version 5.1.0 2018-04-02) |
| Partner | Gene | UniProtAcc | DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
| Hgene | APOE | P02649 | DB00062 | Human Serum Albumin | Apolipoprotein E | biotech | approved |
| Hgene | APOE | P02649 | DB01593 | Zinc | Apolipoprotein E | small molecule | approved|investigational |
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RelatedDiseases for APOE_CLCN3 |
| Diseases associated with fusion partners. (DisGeNet 4.0) |
| Partner | Gene | Disease ID | Disease name | # pubmeds | Source |
| Hgene | APOE | C0004153 | Atherosclerosis | 25 | CTD_human;HPO |
| Hgene | APOE | C0011206 | Delirium | 5 | PSYGENET |
| Hgene | APOE | C2936350 | Plaque, Atherosclerotic | 5 | CTD_human |
| Hgene | APOE | C0001973 | Alcoholic Intoxication, Chronic | 4 | PSYGENET |
| Hgene | APOE | C0002395 | Alzheimer's Disease | 4 | CTD_human;HPO |
| Hgene | APOE | C0020443 | Hypercholesterolemia | 4 | CTD_human;HPO |
| Hgene | APOE | C0020473 | Hyperlipidemia | 4 | CTD_human |
| Hgene | APOE | C0020479 | Hyperlipoproteinemia Type III | 3 | CTD_human;ORPHANET |
| Hgene | APOE | C2673196 | LIPOPROTEIN GLOMERULOPATHY | 3 | CTD_human;ORPHANET;UNIPROT |
| Hgene | APOE | C0003850 | Arteriosclerosis | 2 | CTD_human |
| Hgene | APOE | C0005586 | Bipolar Disorder | 2 | PSYGENET |
| Hgene | APOE | C0020538 | Hypertensive disease | 2 | CTD_human |
| Hgene | APOE | C0024121 | Lung Neoplasms | 2 | CTD_human |
| Hgene | APOE | C0000786 | Spontaneous abortion | 1 | CTD_human |
| Hgene | APOE | C0001418 | Adenocarcinoma | 1 | CTD_human |
| Hgene | APOE | C0002726 | Amyloidosis | 1 | CTD_human |
| Hgene | APOE | C0007222 | Cardiovascular Diseases | 1 | CTD_human |
| Hgene | APOE | C0007273 | Carotid Artery Diseases | 1 | CTD_human |
| Hgene | APOE | C0007282 | Carotid Stenosis | 1 | CTD_human |
| Hgene | APOE | C0009241 | Cognition Disorders | 1 | CTD_human |
| Hgene | APOE | C0010068 | Coronary heart disease | 1 | CTD_human |
| Hgene | APOE | C0013990 | Pathological accumulation of air in tissues | 1 | CTD_human |
| Hgene | APOE | C0019202 | Hepatolenticular Degeneration | 1 | CTD_human |
| Hgene | APOE | C0020445 | Hypercholesterolemia, Familial | 1 | CTD_human;HPO |
| Hgene | APOE | C0025427 | Mercury Poisoning | 1 | CTD_human |
| Hgene | APOE | C0026769 | Multiple Sclerosis | 1 | CTD_human |
| Hgene | APOE | C0027051 | Myocardial Infarction | 1 | CTD_human |
| Hgene | APOE | C0027746 | Nerve Degeneration | 1 | CTD_human |
| Hgene | APOE | C0028754 | Obesity | 1 | CTD_human;HPO |
| Hgene | APOE | C0033687 | Proteinuria | 1 | CTD_human;HPO |
| Hgene | APOE | C0033860 | Psoriasis | 1 | CTD_human |
| Hgene | APOE | C0036341 | Schizophrenia | 1 | CTD_human |
| Hgene | APOE | C0036489 | Sea-Blue Histiocyte Syndrome | 1 | CTD_human;HPO;ORPHANET |
| Hgene | APOE | C0036572 | Seizures | 1 | CTD_human |
| Hgene | APOE | C0038002 | Splenomegaly | 1 | CTD_human;HPO |
| Hgene | APOE | C0085220 | Cerebral Amyloid Angiopathy | 1 | CTD_human;HPO |
| Hgene | APOE | C0085762 | Alcohol abuse | 1 | PSYGENET |
| Hgene | APOE | C0242339 | Dyslipidemias | 1 | CTD_human |
| Hgene | APOE | C0242383 | Age related macular degeneration | 1 | CTD_human |
| Hgene | APOE | C0751967 | Multiple Sclerosis, Relapsing-Remitting | 1 | CTD_human |
| Hgene | APOE | C1384666 | hearing impairment | 1 | CTD_human |
| Hgene | APOE | C1565489 | Renal Insufficiency | 1 | CTD_human;HPO |
| Hgene | APOE | C4277682 | Chemical and Drug Induced Liver Injury | 1 | CTD_human |
| Tgene | CLCN3 | C0017638 | Glioma | 1 | CTD_human |
| Tgene | CLCN3 | C0038356 | Stomach Neoplasms | 1 | CTD_human |
| Tgene | CLCN3 | C2931822 | Nasopharyngeal carcinoma | 1 | CTD_human |
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