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Fusion gene ID: 1607 |
FusionGeneSummary for AMFR_BBS2 |
 Fusion gene summary |
| Fusion gene information | Fusion gene name: AMFR_BBS2 | Fusion gene ID: 1607 | 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 | 20180522 | 20180523 | |
| UniProtAcc | Q9UKV5 | Q9BXC9 | |
| Ensembl transtripts involved in fusion gene | ENST00000290649, ENST00000564283, | ENST00000568104, ENST00000245157, ENST00000561951, | |
| Fusion gene scores | * DoF score | 5 X 4 X 4=80 | 4 X 4 X 4=64 |
| # samples | 5 | 5 | |
| ** MAII score | log2(5/80*10)=-0.678071905112638 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | log2(5/64*10)=-0.356143810225275 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] | ||
| 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 | AMFR | GO:0000209 | protein polyubiquitination | 17310145|19103148 |
| Hgene | AMFR | GO:0030433 | ubiquitin-dependent ERAD pathway | 11724934|17872946 |
| Hgene | AMFR | GO:0051259 | protein complex oligomerization | 17310145 |
| Hgene | AMFR | GO:0051865 | protein autoubiquitination | 24810856 |
| Hgene | AMFR | GO:0070936 | protein K48-linked ubiquitination | 12847084|24424410 |
| 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 | LD | OV | TCGA-24-1423-01A | AMFR | chr16 | 56435645 | - | BBS2 | chr16 | 56518779 | - |
| * 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 |
| In-frame | ENST00000290649 | ENST00000568104 | AMFR | chr16 | 56435645 | - | BBS2 | chr16 | 56518779 | - |
| Frame-shift | ENST00000290649 | ENST00000245157 | AMFR | chr16 | 56435645 | - | BBS2 | chr16 | 56518779 | - |
| 5CDS-intron | ENST00000290649 | ENST00000561951 | AMFR | chr16 | 56435645 | - | BBS2 | chr16 | 56518779 | - |
| intron-3CDS | ENST00000564283 | ENST00000568104 | AMFR | chr16 | 56435645 | - | BBS2 | chr16 | 56518779 | - |
| intron-3CDS | ENST00000564283 | ENST00000245157 | AMFR | chr16 | 56435645 | - | BBS2 | chr16 | 56518779 | - |
| intron-intron | ENST00000564283 | ENST00000561951 | AMFR | chr16 | 56435645 | - | BBS2 | chr16 | 56518779 | - |
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FusionProtFeatures for AMFR_BBS2 |
| Main function of each fusion partner protein. (from UniProt) |
| Hgene | Tgene |
| AMFR | BBS2 |
| E3 ubiquitin-protein ligase that mediates thepolyubiquitination of a number of proteins such as CD3D, CYP3A4,CFTR and APOB for proteasomal degradation. Component of a VCP/p97-AMFR/gp78 complex that participates in the final step ofendoplasmic reticulum-associated degradation (ERAD). The VCP/p97-AMFR/gp78 complex is involved in the sterol-accelerated ERADdegradation of HMGCR through binding to the HMGCR-INSIG complex atthe ER membrane and initiating ubiquitination of HMGCR. Theubiquitinated HMGCR is then released from the ER by the complexinto the cytosol for subsequent destruction. Also regulates ERADthrough the ubiquitination of UBL4A a component of the BAG6/BAT3complex. Also acts as a scaffold protein to assemble a complexthat couples ubiquitination, retranslocation and deglycosylation.Mediates tumor invasion and metastasis as a receptor for theGPI/autocrine motility factor. {ECO:0000269|PubMed:10456327,ECO:0000269|PubMed:11724934, ECO:0000269|PubMed:16168377,ECO:0000269|PubMed:19103148, ECO:0000269|PubMed:24424410}. | The BBSome complex is thought to function as a coatcomplex required for sorting of specific membrane proteins to theprimary cilia. The BBSome complex is required for ciliogenesis butis dispensable for centriolar satellite function. This ciliogenicfunction 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 theciliary membrane. Firstly the BBSome associates with the ciliarymembrane and binds to RAB3IP/Rabin8, the guanosyl exchange factor(GEF) for Rab8 and then the Rab8-GTP localizes to the cilium andpromotes docking and fusion of carrier vesicles to the base of theciliary membrane. The BBSome complex, together with the LTZL1,controls SMO ciliary trafficking and contributes to the sonichedgehog (SHH) pathway regulation. Required for proper BBSomecomplex 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 | Transmembrane | Helical |
| Hgene | AMFR | chr16:56435645 | chr16:56518779 | ENST00000290649 | - | 8 | 14 | 145_165 | 361 | 644 | Transmembrane | Helical |
| Hgene | AMFR | chr16:56435645 | chr16:56518779 | ENST00000290649 | - | 8 | 14 | 186_206 | 361 | 644 | Transmembrane | Helical |
| Hgene | AMFR | chr16:56435645 | chr16:56518779 | ENST00000290649 | - | 8 | 14 | 215_235 | 361 | 644 | Transmembrane | Helical |
| Hgene | AMFR | chr16:56435645 | chr16:56518779 | ENST00000290649 | - | 8 | 14 | 276_296 | 361 | 644 | Transmembrane | Helical |
| Hgene | AMFR | chr16:56435645 | chr16:56518779 | ENST00000290649 | - | 8 | 14 | 82_102 | 361 | 644 | 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 | Domain | CUE |
| Hgene | >AMFR | chr16:56435645 | chr16:56518779 | ENST00000290649 | - | 8 | 14 | 622_640 | 361 | 644 | Region | VCP/p97-interacting motif (VIM) |
| Hgene | >AMFR | chr16:56435645 | chr16:56518779 | ENST00000290649 | - | 8 | 14 | 429_449 | 361 | 644 | Transmembrane | Helical |
| Hgene | >AMFR | chr16:56435645 | chr16:56518779 | ENST00000290649 | - | 8 | 14 | 341_379 | 361 | 644 | Zinc finger | RING-type |
| Tgene | BBS2 | chr16:56435645 | chr16:56518779 | ENST00000245157 | - | 15 | 17 | 325_369 | 686 | 722 | Coiled coil | Ontology_term=ECO:0000255 |
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FusionGeneSequence for AMFR_BBS2 |
| 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 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 |
| AMFR | UBE2G2, VCP, CYP3A4, FAF2, CFTR, DERL1, DERL2, DERL3, RNF5, HSPD1, UFD1L, RPL5, SVIP, CD3D, VIMP, UBE2D1, UBE2D2, UBE2D3, UBE2D4, UBE2N, UBE2T, UBE2W, INSIG1, UBC, HERPUD1, KPNB1, SYVN1, HTT, UBXN7, FAF1, UBXN1, PDIA2, UBE2G1, INSIG2, SOD1, ATXN3, HMGCR, ERLIN2, ERLIN1, CYP2E1, TMUB1, HSPA5, HSP90B1, HSPA4, CANX, CSE1L, TIMM50, HAX1, RHOT1, TCP1, TRIM28, AIFM1, CCDC47, EEF1A1, ATP2A2, SEC61B, SRPRB, CRMP1, TOM1L1, ELAVL1, ITPR1, CD82, AMFR, SARAF, UBXN4, BAG6, UBL4A, GET4, NPLOC4, MDC1, AUP1, ADRB2, ADRA1D, YOD1, MAVS, GPI, DHFR, TRIM25, DGAT2, PMP22, UBE2K, PSMB4, PSMA7, PSMA1, PSMA2, PSMB1, PSMA3, PSMA4, MYH10, PSMB2, PSMB7, PSMD3, PSMB6, PSMB3, PSMD6, PSMA5, OSBPL8, PSME4, PSMB5, PSMA6, PSMD14, PSMC2, MYH9, BRI3BP, UBAC2, USP13, HTR3E, NTRK1, SEL1L, OS9, MGRN1, KCNC4, ATG9A, SLC17A2, ZNRF4, FAM189B, HSD17B3, SLC13A2, GLRA2, SLC45A2, CIDEC, PRNP, HSPA1L | BBS2 | PSME3, ALDOB, BHMT, EEF1A1, EPAS1, EXOC7, FHOD1, HSCB, KRT18, PAX2, GLIS2, MDFI, RBPMS, ENDOV, LZTFL1, LPCAT1, THBS3, BBS5, BBS7, BBS1, NME3, TRIM44, GUCY1B3, BBS9, PCK2, TTC8, BBS4, RBFOX1, CLUAP1 |
| - 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 AMFR_BBS2 |
| 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 |
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RelatedDiseases for AMFR_BBS2 |
| Diseases associated with fusion partners. (DisGeNet 4.0) |
| Partner | Gene | Disease ID | Disease name | # pubmeds | Source |
| Hgene | AMFR | C0002395 | Alzheimer's Disease | 1 | CTD_human |
| Hgene | AMFR | C0005695 | Bladder Neoplasm | 1 | CTD_human |
| Tgene | BBS2 | C2936863 | Bardet-Biedl syndrome 2 (disorder) | 9 | UNIPROT |
| Tgene | BBS2 | C4225281 | RETINITIS PIGMENTOSA 74 | 1 | UNIPROT |
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