|
||||||
|
 | 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:AMFR-BBS2 (FusionGDB2 ID:4213) |
Fusion Gene Summary for AMFR-BBS2 |
 Fusion gene summary |
| Fusion gene information | Fusion gene name: AMFR-BBS2 | Fusion gene ID: 4213 | Hgene | Tgene | Gene symbol | AMFR | BBS2 | Gene ID | 267 | 583 |
| Gene name | autocrine motility factor receptor | Bardet-Biedl syndrome 2 | |
| Synonyms | GP78|RNF45 | BBS|RP74 | |
| Cytomap | 16q13 | 16q13 | |
| Type of gene | protein-coding | protein-coding | |
| Description | E3 ubiquitin-protein ligase AMFRRING finger protein 45RING-type E3 ubiquitin transferase AMFR | Bardet-Biedl syndrome 2 protein | |
| Modification date | 20200327 | 20200313 | |
| UniProtAcc | Q9UKV5 | Q9BXC9 | |
| Ensembl transtripts involved in fusion gene | ENST00000290649, ENST00000564283, | ENST00000561951, ENST00000245157, ENST00000568104, | |
| Fusion gene scores | * DoF score | 7 X 5 X 5=175 | 5 X 5 X 5=125 |
| # samples | 8 | 7 | |
| ** MAII score | log2(8/175*10)=-1.12928301694497 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | log2(7/125*10)=-0.836501267717121 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | |
| Context | PubMed: AMFR [Title/Abstract] AND BBS2 [Title/Abstract] AND fusion [Title/Abstract] | ||
| Most frequent breakpoint | AMFR(56435645)-BBS2(56518779), # samples:2 | ||
| Anticipated loss of major functional domain due to fusion event. | AMFR-BBS2 seems lost the major protein functional domain in Hgene partner, which is a essential gene 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 | AMFR | GO:0000209 | protein polyubiquitination | 17310145|19103148 |
| Hgene | AMFR | GO:0030433 | ubiquitin-dependent ERAD pathway | 11724934|17872946 |
| Hgene | AMFR | GO:0051865 | protein autoubiquitination | 24810856 |
| Hgene | AMFR | GO:0070936 | protein K48-linked ubiquitination | 12847084|24424410 |
| Fusion gene breakpoints across AMFR (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 BBS2 (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-24-1423-01A | AMFR | chr16 | 56435645 | - | BBS2 | chr16 | 56518779 | - |
Top |
Fusion Gene ORF analysis for AMFR-BBS2 |
| 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 | ENST00000290649 | ENST00000561951 | AMFR | chr16 | 56435645 | - | BBS2 | chr16 | 56518779 | - |
| Frame-shift | ENST00000290649 | ENST00000245157 | AMFR | chr16 | 56435645 | - | BBS2 | chr16 | 56518779 | - |
| In-frame | ENST00000290649 | ENST00000568104 | AMFR | chr16 | 56435645 | - | BBS2 | chr16 | 56518779 | - |
| intron-3CDS | ENST00000564283 | ENST00000245157 | AMFR | chr16 | 56435645 | - | BBS2 | chr16 | 56518779 | - |
| intron-3CDS | ENST00000564283 | ENST00000568104 | AMFR | chr16 | 56435645 | - | BBS2 | chr16 | 56518779 | - |
| intron-intron | ENST00000564283 | ENST00000561951 | AMFR | chr16 | 56435645 | - | BBS2 | chr16 | 56518779 | - |
| 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 |
Top |
Fusion Genomic Features for AMFR-BBS2 |
| 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. |
Top |
Fusion Protein Features for AMFR-BBS2 |
| Four levels of functional features of fusion genes Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr16:56435645/chr16:56518779) - 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. |
 |
| Main function of each fusion partner protein. (from UniProt) |
| Hgene | Tgene |
| AMFR | BBS2 |
| FUNCTION: E3 ubiquitin-protein ligase that mediates the polyubiquitination of lysine and cysteine residues on target proteins, such as CD3D, CYP3A4, CFTR, INSIG1, SOAT2/ACAT2 and APOB for proteasomal degradation (PubMed:10456327, PubMed:11724934, PubMed:12670940, PubMed:19103148, PubMed:24424410, PubMed:28604676). Component of a VCP/p97-AMFR/gp78 complex that participates in the final step of endoplasmic reticulum-associated degradation (ERAD) (PubMed:10456327, PubMed:11724934, PubMed:19103148, PubMed:24424410). The VCP/p97-AMFR/gp78 complex is involved in the sterol-accelerated ERAD degradation of HMGCR through binding to the HMGCR-INSIG1 complex at the ER membrane (PubMed:16168377, PubMed:22143767). In addition, interaction of AMFR with AUP1 facilitates interaction of AMFR with ubiquitin-conjugating enzyme UBE2G2 and ubiquitin ligase RNF139, leading to sterol-induced HMGCR ubiquitination (PubMed:23223569). The ubiquitinated HMGCR is then released from the ER into the cytosol for subsequent destruction (PubMed:16168377, PubMed:22143767, PubMed:23223569). In addition to ubiquitination on lysine residues, catalyzes ubiquitination on cysteine residues: together with INSIG1, mediates polyubiquitination of SOAT2/ACAT2 at 'Cys-277', leading to its degradation when the lipid levels are low (PubMed:28604676). Catalyzes ubiquitination and subsequent degradation of INSIG1 when cells are depleted of sterols (PubMed:17043353). Mediates polyubiquitination of INSIG2 at 'Cys-215' in some tissues, leading to its degradation (PubMed:31953408). Also regulates ERAD through the ubiquitination of UBL4A a component of the BAG6/BAT3 complex (PubMed:21636303). Also acts as a scaffold protein to assemble a complex that couples ubiquitination, retranslocation and deglycosylation (PubMed:21636303). Mediates tumor invasion and metastasis as a receptor for the GPI/autocrine motility factor (PubMed:10456327). In association with LMBR1L and UBAC2, negatively regulates the canonical Wnt signaling pathway in the lymphocytes by promoting the ubiquitin-mediated degradation of CTNNB1 and Wnt receptors FZD6 and LRP6 (PubMed:31073040). {ECO:0000269|PubMed:10456327, ECO:0000269|PubMed:11724934, ECO:0000269|PubMed:12670940, ECO:0000269|PubMed:16168377, ECO:0000269|PubMed:17043353, ECO:0000269|PubMed:19103148, ECO:0000269|PubMed:21636303, ECO:0000269|PubMed:22143767, ECO:0000269|PubMed:23223569, ECO:0000269|PubMed:24424410, ECO:0000269|PubMed:28604676, ECO:0000269|PubMed:31073040, ECO:0000269|PubMed:31953408}. | FUNCTION: The BBSome complex is thought to function as a coat complex required for sorting of specific membrane proteins to the primary cilia. The BBSome complex is required for ciliogenesis but is dispensable for centriolar satellite function. This ciliogenic function is mediated in part by the Rab8 GDP/GTP exchange factor, which localizes to the basal body and contacts the BBSome. Rab8(GTP) enters the primary cilium and promotes extension of the ciliary membrane. Firstly the BBSome associates with the ciliary membrane and binds to RAB3IP/Rabin8, the guanosyl exchange factor (GEF) for Rab8 and then the Rab8-GTP localizes to the cilium and promotes docking and fusion of carrier vesicles to the base of the ciliary membrane. The BBSome complex, together with the LTZL1, controls SMO ciliary trafficking and contributes to the sonic hedgehog (SHH) pathway regulation. Required for proper BBSome complex assembly and its ciliary localization. {ECO:0000269|PubMed:17574030, ECO:0000269|PubMed:22072986}. |
| 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 |
| Hgene | AMFR | chr16:56435645 | chr16:56518779 | ENST00000290649 | - | 8 | 14 | 122_142 | 361 | 644.0 | Transmembrane | Helical |
| Hgene | AMFR | chr16:56435645 | chr16:56518779 | ENST00000290649 | - | 8 | 14 | 145_165 | 361 | 644.0 | Transmembrane | Helical |
| Hgene | AMFR | chr16:56435645 | chr16:56518779 | ENST00000290649 | - | 8 | 14 | 186_206 | 361 | 644.0 | Transmembrane | Helical |
| Hgene | AMFR | chr16:56435645 | chr16:56518779 | ENST00000290649 | - | 8 | 14 | 215_235 | 361 | 644.0 | Transmembrane | Helical |
| Hgene | AMFR | chr16:56435645 | chr16:56518779 | ENST00000290649 | - | 8 | 14 | 276_296 | 361 | 644.0 | Transmembrane | Helical |
| Hgene | AMFR | chr16:56435645 | chr16:56518779 | ENST00000290649 | - | 8 | 14 | 82_102 | 361 | 644.0 | Transmembrane | Helical |
| - 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 |
| Hgene | AMFR | chr16:56435645 | chr16:56518779 | ENST00000290649 | - | 8 | 14 | 456_498 | 361 | 644.0 | Domain | CUE |
| Hgene | AMFR | chr16:56435645 | chr16:56518779 | ENST00000290649 | - | 8 | 14 | 622_640 | 361 | 644.0 | Region | VCP/p97-interacting motif (VIM) |
| Hgene | AMFR | chr16:56435645 | chr16:56518779 | ENST00000290649 | - | 8 | 14 | 429_449 | 361 | 644.0 | Transmembrane | Helical |
| Hgene | AMFR | chr16:56435645 | chr16:56518779 | ENST00000290649 | - | 8 | 14 | 341_379 | 361 | 644.0 | Zinc finger | RING-type |
| Tgene | BBS2 | chr16:56435645 | chr16:56518779 | ENST00000245157 | 15 | 17 | 325_369 | 686 | 722.0 | Coiled coil | Ontology_term=ECO:0000255 |
Top |
Fusion Gene Sequence for AMFR-BBS2 |
| 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. |
Top |
Fusion Gene PPI Analysis for AMFR-BBS2 |
| 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 |
Top |
Related Drugs for AMFR-BBS2 |
| 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 |
Top |
Related Diseases for AMFR-BBS2 |
| Diseases associated with fusion partners. (DisGeNet 4.0) |
| Partner | Gene | Disease ID | Disease name | # pubmeds | Source |
Copyright 2021-Present -The University of Texas Health Science Center at Houston (UTHealth)
Web File Viewing | Emergency Information |Campus Carry|Site Policies