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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:FLCN-NCBP2 (FusionGDB2 ID:30561) |
Fusion Gene Summary for FLCN-NCBP2 |
 Fusion gene summary |
| Fusion gene information | Fusion gene name: FLCN-NCBP2 | Fusion gene ID: 30561 | Hgene | Tgene | Gene symbol | FLCN | NCBP2 | Gene ID | 201163 | 22916 |
| Gene name | folliculin | nuclear cap binding protein subunit 2 | |
| Synonyms | BHD|DENND8B|FLCL | CBC2|CBP20|NIP1|PIG55 | |
| Cytomap | 17p11.2 | 3q29 | |
| Type of gene | protein-coding | protein-coding | |
| Description | folliculinBHD skin lesion fibrofolliculoma proteinbirt-Hogg-Dube syndrome protein | nuclear cap-binding protein subunit 220 kDa nuclear cap-binding proteinNCBP 20 kDa subunitNCBP interacting protein 1cell proliferation-inducing gene 55 proteinnuclear cap binding protein subunit 2, 20kDnuclear cap binding protein subunit 2, 20kDa | |
| Modification date | 20200327 | 20200313 | |
| UniProtAcc | Q8NFG4 | P52298 | |
| Ensembl transtripts involved in fusion gene | ENST00000285071, ENST00000389169, | ENST00000321256, ENST00000422610, ENST00000427641, ENST00000447325, ENST00000452404, ENST00000467803, | |
| Fusion gene scores | * DoF score | 5 X 5 X 3=75 | 5 X 4 X 5=100 |
| # samples | 5 | 5 | |
| ** MAII score | log2(5/75*10)=-0.584962500721156 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | log2(5/100*10)=-1 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | |
| Context | PubMed: FLCN [Title/Abstract] AND NCBP2 [Title/Abstract] AND fusion [Title/Abstract] | ||
| Most frequent breakpoint | FLCN(17122332)-NCBP2(196663953), # samples:1 | ||
| Anticipated loss of major functional domain due to fusion event. | |||
| * 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 | FLCN | GO:0000122 | negative regulation of transcription by RNA polymerase II | 20573232 |
| Hgene | FLCN | GO:0001932 | regulation of protein phosphorylation | 18663353 |
| Hgene | FLCN | GO:0030308 | negative regulation of cell growth | 20573232 |
| Hgene | FLCN | GO:0030511 | positive regulation of transforming growth factor beta receptor signaling pathway | 20573232 |
| Hgene | FLCN | GO:0045944 | positive regulation of transcription by RNA polymerase II | 20573232 |
| Hgene | FLCN | GO:1900181 | negative regulation of protein localization to nucleus | 21209915 |
| Tgene | NCBP2 | GO:0000184 | nuclear-transcribed mRNA catabolic process, nonsense-mediated decay | 11551508 |
| Tgene | NCBP2 | GO:0006446 | regulation of translational initiation | 11551508 |
| Tgene | NCBP2 | GO:0045292 | mRNA cis splicing, via spliceosome | 18426921 |
| Fusion gene breakpoints across FLCN (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 NCBP2 (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 | LIHC | TCGA-NI-A4U2 | FLCN | chr17 | 17122332 | - | NCBP2 | chr3 | 196663953 | - |
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Fusion Gene ORF analysis for FLCN-NCBP2 |
| 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-5UTR | ENST00000285071 | ENST00000321256 | FLCN | chr17 | 17122332 | - | NCBP2 | chr3 | 196663953 | - |
| 5CDS-5UTR | ENST00000285071 | ENST00000422610 | FLCN | chr17 | 17122332 | - | NCBP2 | chr3 | 196663953 | - |
| 5CDS-5UTR | ENST00000285071 | ENST00000427641 | FLCN | chr17 | 17122332 | - | NCBP2 | chr3 | 196663953 | - |
| 5CDS-5UTR | ENST00000285071 | ENST00000447325 | FLCN | chr17 | 17122332 | - | NCBP2 | chr3 | 196663953 | - |
| 5CDS-5UTR | ENST00000285071 | ENST00000452404 | FLCN | chr17 | 17122332 | - | NCBP2 | chr3 | 196663953 | - |
| 5CDS-5UTR | ENST00000285071 | ENST00000467803 | FLCN | chr17 | 17122332 | - | NCBP2 | chr3 | 196663953 | - |
| intron-5UTR | ENST00000389169 | ENST00000321256 | FLCN | chr17 | 17122332 | - | NCBP2 | chr3 | 196663953 | - |
| intron-5UTR | ENST00000389169 | ENST00000422610 | FLCN | chr17 | 17122332 | - | NCBP2 | chr3 | 196663953 | - |
| intron-5UTR | ENST00000389169 | ENST00000427641 | FLCN | chr17 | 17122332 | - | NCBP2 | chr3 | 196663953 | - |
| intron-5UTR | ENST00000389169 | ENST00000447325 | FLCN | chr17 | 17122332 | - | NCBP2 | chr3 | 196663953 | - |
| intron-5UTR | ENST00000389169 | ENST00000452404 | FLCN | chr17 | 17122332 | - | NCBP2 | chr3 | 196663953 | - |
| intron-5UTR | ENST00000389169 | ENST00000467803 | FLCN | chr17 | 17122332 | - | NCBP2 | chr3 | 196663953 | - |
| 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 FLCN-NCBP2 |
| 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) |
| 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 FLCN-NCBP2 |
| Four levels of functional features of fusion genes Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/:17122332/:196663953) - 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 |
| FLCN | NCBP2 |
| FUNCTION: GTPase-activating protein that plays a key role in the cellular response to amino acid availability through regulation of the mTORC1 signaling cascade controlling the MiT/TFE factors TFEB and TFE3 (PubMed:17028174, PubMed:18663353, PubMed:21209915, PubMed:24081491, PubMed:24095279, PubMed:31704029, PubMed:31672913). Activates mTORC1 by acting as a GTPase-activating protein: specifically stimulates GTP hydrolysis by RRAGC/RagC or RRAGD/RagD, promoting the conversion to the GDP-bound state of RRAGC/RagC or RRAGD/RagD, and thereby activating the kinase activity of mTORC1 (PubMed:24095279, PubMed:31704029, PubMed:31672913). The GTPase-activating activity is inhibited during starvation and activated in presence of nutrients (PubMed:31672913). Acts as a key component for mTORC1-dependent control of the MiT/TFE factors TFEB and TFE3, while it is not involved in mTORC1-dependent phosphorylation of canonical RPS6KB1/S6K1 and EIF4EBP1/4E-BP1 (PubMed:21209915, PubMed:24081491, PubMed:31672913). In low-amino acid conditions, the lysosomal folliculin complex (LFC) is formed on the membrane of lysosomes, which inhibits the GTPase-activating activity of FLCN, inactivates mTORC1 and maximizes nuclear translocation of TFEB and TFE3 (PubMed:31672913). Upon amino acid restimulation, RRAGA/RagA (or RRAGB/RagB) nucleotide exchange promotes disassembly of the LFC complex and liberates the GTPase-activating activity of FLCN, leading to activation of mTORC1 and subsequent cytoplasmic retention of TFEB and TFE3 (PubMed:31672913). Indirectly acts as a positive regulator of Wnt signaling by promoting mTOR-dependent cytoplasmic retention of MiT/TFE factor TFE3 (PubMed:31272105). Required for the exit of hematopoietic stem cell from pluripotency by promoting mTOR-dependent cytoplasmic retention of TFE3, thereby increasing Wnt signaling (PubMed:30733432). Acts as an inhibitor of browning of adipose tissue by regulating mTOR-dependent cytoplasmic retention of TFE3 (By similarity). In response to flow stress, regulates STK11/LKB1 accumulation and mTORC1 activation through primary cilia: may act by recruiting STK11/LKB1 to primary cilia for activation of AMPK resided at basal bodies, causing mTORC1 down-regulation (PubMed:27072130). Together with FNIP1 and/or FNIP2, regulates autophagy: following phosphorylation by ULK1, interacts with GABARAP and promotes autophagy (PubMed:25126726). Required for starvation-induced perinuclear clustering of lysosomes by promoting association of RILP with its effector RAB34 (PubMed:27113757). {ECO:0000250|UniProtKB:Q8QZS3, ECO:0000269|PubMed:17028174, ECO:0000269|PubMed:18663353, ECO:0000269|PubMed:21209915, ECO:0000269|PubMed:24081491, ECO:0000269|PubMed:24095279, ECO:0000269|PubMed:25126726, ECO:0000269|PubMed:27072130, ECO:0000269|PubMed:27113757, ECO:0000269|PubMed:30733432, ECO:0000269|PubMed:31272105, ECO:0000269|PubMed:31672913, ECO:0000269|PubMed:31704029}. | FUNCTION: Component of the cap-binding complex (CBC), which binds co-transcriptionally to the 5' cap of pre-mRNAs and is involved in various processes such as pre-mRNA splicing, translation regulation, nonsense-mediated mRNA decay, RNA-mediated gene silencing (RNAi) by microRNAs (miRNAs) and mRNA export. The CBC complex is involved in mRNA export from the nucleus via its interaction with ALYREF/THOC4/ALY, leading to the recruitment of the mRNA export machinery to the 5' end of mRNA and to mRNA export in a 5' to 3' direction through the nuclear pore. The CBC complex is also involved in mediating U snRNA and intronless mRNAs export from the nucleus. The CBC complex is essential for a pioneer round of mRNA translation, before steady state translation when the CBC complex is replaced by cytoplasmic cap-binding protein eIF4E. The pioneer round of mRNA translation mediated by the CBC complex plays a central role in nonsense-mediated mRNA decay (NMD), NMD only taking place in mRNAs bound to the CBC complex, but not on eIF4E-bound mRNAs. The CBC complex enhances NMD in mRNAs containing at least one exon-junction complex (EJC) via its interaction with UPF1, promoting the interaction between UPF1 and UPF2. The CBC complex is also involved in 'failsafe' NMD, which is independent of the EJC complex, while it does not participate in Staufen-mediated mRNA decay (SMD). During cell proliferation, the CBC complex is also involved in microRNAs (miRNAs) biogenesis via its interaction with SRRT/ARS2, thereby being required for miRNA-mediated RNA interference. The CBC complex also acts as a negative regulator of PARN, thereby acting as an inhibitor of mRNA deadenylation. In the CBC complex, NCBP2/CBP20 recognizes and binds capped RNAs (m7GpppG-capped RNA) but requires NCBP1/CBP80 to stabilize the movement of its N-terminal loop and lock the CBC into a high affinity cap-binding state with the cap structure. The conventional cap-binding complex with NCBP2 binds both small nuclear RNA (snRNA) and messenger (mRNA) and is involved in their export from the nucleus (PubMed:26382858). {ECO:0000269|PubMed:11551508, ECO:0000269|PubMed:15361857, ECO:0000269|PubMed:17190602, ECO:0000269|PubMed:17363367, ECO:0000269|PubMed:17873884, ECO:0000269|PubMed:18369367, ECO:0000269|PubMed:19632182, ECO:0000269|PubMed:26382858}. |
| 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 FLCN-NCBP2 |
| 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 FLCN-NCBP2 |
| 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 FLCN-NCBP2 |
| 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 |
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Related Diseases for FLCN-NCBP2 |
| Diseases associated with fusion partners. (DisGeNet 4.0) |
| Partner | Gene | Disease ID | Disease name | # pubmeds | Source |
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