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Fusion gene ID: 19936 |
FusionGeneSummary for LNX1_GABRB1 |
 Fusion gene summary |
| Fusion gene information | Fusion gene name: LNX1_GABRB1 | Fusion gene ID: 19936 | Hgene | Tgene | Gene symbol | LNX1 | GABRB1 | Gene ID | 84708 | 2560 |
| Gene name | ligand of numb-protein X 1 | gamma-aminobutyric acid type A receptor beta1 subunit | |
| Synonyms | LNX|MPDZ|PDZRN2 | EIEE45 | |
| Cytomap | 4q12 | 4p12 | |
| Type of gene | protein-coding | protein-coding | |
| Description | E3 ubiquitin-protein ligase LNXPDZ domain-containing ring finger protein 2RING-type E3 ubiquitin transferase LNXligand of numb-protein X 1, E3 ubiquitin protein ligasemulti-PDZ-domain-containing protein, E3 ubiquitin-protein ligase LNXnumb-binding pr | gamma-aminobutyric acid receptor subunit beta-1gamma-aminobutyric acid (GABA) A receptor, beta 1 | |
| Modification date | 20180522 | 20180523 | |
| UniProtAcc | Q8TBB1 | P18505 | |
| Ensembl transtripts involved in fusion gene | ENST00000306888, ENST00000263925, ENST00000504605, | ENST00000295454, ENST00000538619, ENST00000509366, | |
| Fusion gene scores | * DoF score | 5 X 3 X 4=60 | 5 X 2 X 4=40 |
| # samples | 5 | 5 | |
| ** MAII score | log2(5/60*10)=-0.263034405833794 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | log2(5/40*10)=0.321928094887362 effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs). DoF>8 and MAII>0 | |
| Context | PubMed: LNX1 [Title/Abstract] AND GABRB1 [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 |
| Tgene | GABRB1 | GO:1902476 | chloride transmembrane transport | 9039914 |
| 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 | BRCA | TCGA-A8-A09A-01A | LNX1 | chr4 | 54439790 | - | GABRB1 | chr4 | 47322144 | + |
| * 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 |
| intron-3CDS | ENST00000306888 | ENST00000295454 | LNX1 | chr4 | 54439790 | - | GABRB1 | chr4 | 47322144 | + |
| intron-3CDS | ENST00000306888 | ENST00000538619 | LNX1 | chr4 | 54439790 | - | GABRB1 | chr4 | 47322144 | + |
| intron-intron | ENST00000306888 | ENST00000509366 | LNX1 | chr4 | 54439790 | - | GABRB1 | chr4 | 47322144 | + |
| Frame-shift | ENST00000263925 | ENST00000295454 | LNX1 | chr4 | 54439790 | - | GABRB1 | chr4 | 47322144 | + |
| Frame-shift | ENST00000263925 | ENST00000538619 | LNX1 | chr4 | 54439790 | - | GABRB1 | chr4 | 47322144 | + |
| 5CDS-intron | ENST00000263925 | ENST00000509366 | LNX1 | chr4 | 54439790 | - | GABRB1 | chr4 | 47322144 | + |
| intron-3CDS | ENST00000504605 | ENST00000295454 | LNX1 | chr4 | 54439790 | - | GABRB1 | chr4 | 47322144 | + |
| intron-3CDS | ENST00000504605 | ENST00000538619 | LNX1 | chr4 | 54439790 | - | GABRB1 | chr4 | 47322144 | + |
| intron-intron | ENST00000504605 | ENST00000509366 | LNX1 | chr4 | 54439790 | - | GABRB1 | chr4 | 47322144 | + |
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FusionProtFeatures for LNX1_GABRB1 |
| Main function of each fusion partner protein. (from UniProt) |
| Hgene | Tgene |
| LNX1 | GABRB1 |
| E3 ubiquitin-protein ligase that mediates ubiquitinationand subsequent proteasomal degradation of NUMB. E3 ubiquitinligases accept ubiquitin from an E2 ubiquitin-conjugating enzymein the form of a thioester and then directly transfers theubiquitin to targeted substrates. Mediates ubiquitination ofisoform p66 and isoform p72 of NUMB, but not that of isoform p71or isoform p65. {ECO:0000250|UniProtKB:O70263}. Isoform 2 provides an endocytic scaffold for IGSF5/JAM4.{ECO:0000250|UniProtKB:O70263}. | Component of the heteropentameric receptor for GABA, themajor inhibitory neurotransmitter in the vertebrate brain.Functions also as histamine receptor and mediates cellularresponses to histamine. Functions as receptor for diazepines andvarious anesthetics, such as pentobarbital; these are bound at aseparate allosteric effector binding site. Functions as ligand-gated chloride channel. {ECO:0000269|PubMed:26950270}. |
| 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 LNX1_GABRB1 |
| 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 LNX1_GABRB1 |
| 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 |
| LNX1 | MAGEA11, DCTD, LDOC1, CUTC, CALCOCO2, SRSF1, NADK, ENOX1, RBMX, RPIA, TRAF2, KHDRBS3, CCDC85B, PAFAH1B3, KLHL12, TRIP13, TIFA, CEP72, RABAC1, PCBD1, KRTAP4-12, NAGK, KCTD13, MAGEB18, AIMP2, APIP, KCTD17, DDX17, FHL3, TRIM23, NECAB2, SAT1, TSC22D4, ZBTB43, AKIRIN2, KXD1, KRT15, DVL3, EHMT2, PAICS, RAD54B, FBP1, ZBTB8A, NUMB, RHOC, CD8A, SRC, AMMECR1L, AURKB, AURKC, FAM212B, CAMK2N2, DAPK1, DEPTOR, EBF4, EPHB3, KIAA1598, MRPS24, MUSTN1, NKD2, PLEKHG5, PPID, RASL11B, SCLT1, SNCB, ZADH2, WWP1, SAPCD1, TMEM14C, WAC, STX5, PAK6, PBK, TYK2, KCNA4, PRKCA, SDK1, INSC, NRCAM, ABCB1, KALRN, CLDN17, GPR142, EXOC8, DOCK9, LRRC3B, GRIN1, ARHGAP6, LNX2, SSTR3, ADRA1D, SLC6A15, LGR6, TYRO3, CITED1, CGN, PTGIR, SLC6A5, HUNK, GIPR, ARVCF, CTNND2, PKP4, GAS2L2, CLDN1, TSC2, GJD4, TNFRSF18, CLDN2, ILF3, CTSO, VRK2, WNT8A, STRN, ARHGEF16, PQBP1, CDC42EP4, ORMDL3, BPIFA1, ABR, JOSD1, NUP37, BCR, HTR2B, PKDREJ, PDZRN3, PDZRN4, CXADR, ABCA1, SNW1, COIL, UBE2D2, APP, HSP90AA1, NACAP1, PRPH, IL3RA, ULK2, SUV39H1, SUV39H2, IGSF5, SPHKAP, CTBP1, ACAT2, ALDOC, BLVRA, CA8, CDA, CIRBP, CLK2, DAB1, GDI1, GRB2, HSBP1, PKM, PPIA, MAPK9, PTS, RAD51D, RBMY1A1, DPF2, SNRPF, TPM4, VCP, EIF4H, NCK2, SSNA1, RFPL3, NEK6, RUVBL2, MTUS2, ISCU, DNPEP, OSBP2, NME7, OSGIN1, ZNF593, MEMO1, ZNF581, PRR13, ROPN1, ZCCHC10, FBXL12, FAM118A, TRMT12, GOLPH3L, POMGNT1, ZFP64, NXT2, TRIM39, LGALS14, AGTRAP, TRIM54, HOMEZ, LSM2, PBLD, ROBO3, AIDA, MTMR9, HMBOX1, SNRNP25, CCDC102B, THAP7, APOL4, TSSK3, KRTAP9-2, ATRIP, DCUN1D5, LNX1, KRTAP4-2, MVB12B, ATPAF2, ACY3, CCDC114, CCDC101, C1QTNF1, MRFAP1L1, CIB3, METTL21A, FAM9B, KCTD6, TBCEL, FAM124A, ALKBH3, CPNE2, LCLAT1, NUDT14, CATSPERD, KCTD1, RUFY4, STAC2, NOTCH2NL, JAK3, PTPN11, SH2D2A, SOCS6, LRFN4, NXF2B | GABRB1 | UBQLN1, CUL1, NOD1, NEUROD4, HSPA8 |
| - 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 LNX1_GABRB1 |
| 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 |
| Tgene | GABRB1 | P18505 | DB00546 | Adinazolam | Gamma-aminobutyric acid receptor subunit beta-1 | small molecule | approved |
| Tgene | GABRB1 | P18505 | DB00842 | Oxazepam | Gamma-aminobutyric acid receptor subunit beta-1 | small molecule | approved |
| Tgene | GABRB1 | P18505 | DB00898 | Ethanol | Gamma-aminobutyric acid receptor subunit beta-1 | small molecule | approved |
| Tgene | GABRB1 | P18505 | DB01587 | Ketazolam | Gamma-aminobutyric acid receptor subunit beta-1 | small molecule | approved |
| Tgene | GABRB1 | P18505 | DB01594 | Cinolazepam | Gamma-aminobutyric acid receptor subunit beta-1 | small molecule | approved |
| Tgene | GABRB1 | P18505 | DB01595 | Nitrazepam | Gamma-aminobutyric acid receptor subunit beta-1 | small molecule | approved |
| Tgene | GABRB1 | P18505 | DB00683 | Midazolam | Gamma-aminobutyric acid receptor subunit beta-1 | small molecule | approved|illicit |
| Tgene | GABRB1 | P18505 | DB01215 | Estazolam | Gamma-aminobutyric acid receptor subunit beta-1 | small molecule | approved|illicit |
| Tgene | GABRB1 | P18505 | DB01559 | Clotiazepam | Gamma-aminobutyric acid receptor subunit beta-1 | small molecule | approved|illicit |
| Tgene | GABRB1 | P18505 | DB01567 | Fludiazepam | Gamma-aminobutyric acid receptor subunit beta-1 | small molecule | approved|illicit |
| Tgene | GABRB1 | P18505 | DB01588 | Prazepam | Gamma-aminobutyric acid receptor subunit beta-1 | small molecule | approved|illicit |
| Tgene | GABRB1 | P18505 | DB01589 | Quazepam | Gamma-aminobutyric acid receptor subunit beta-1 | small molecule | approved|illicit |
| Tgene | GABRB1 | P18505 | DB00690 | Flurazepam | Gamma-aminobutyric acid receptor subunit beta-1 | small molecule | approved|illicit|investigational |
| Tgene | GABRB1 | P18505 | DB01558 | Bromazepam | Gamma-aminobutyric acid receptor subunit beta-1 | small molecule | approved|illicit|investigational |
| Tgene | GABRB1 | P18505 | DB00829 | Diazepam | Gamma-aminobutyric acid receptor subunit beta-1 | small molecule | approved|illicit|investigational|vet_approved |
| Tgene | GABRB1 | P18505 | DB00801 | Halazepam | Gamma-aminobutyric acid receptor subunit beta-1 | small molecule | approved|illicit|withdrawn |
| Tgene | GABRB1 | P18505 | DB00231 | Temazepam | Gamma-aminobutyric acid receptor subunit beta-1 | small molecule | approved|investigational |
| Tgene | GABRB1 | P18505 | DB00897 | Triazolam | Gamma-aminobutyric acid receptor subunit beta-1 | small molecule | approved|investigational |
| Tgene | GABRB1 | P18505 | DB00431 | Lindane | Gamma-aminobutyric acid receptor subunit beta-1 | small molecule | approved|withdrawn |
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RelatedDiseases for LNX1_GABRB1 |
| Diseases associated with fusion partners. (DisGeNet 4.0) |
| Partner | Gene | Disease ID | Disease name | # pubmeds | Source |
| Tgene | GABRB1 | C0001973 | Alcoholic Intoxication, Chronic | 5 | PSYGENET |
| Tgene | GABRB1 | C0004352 | Autistic Disorder | 2 | CTD_human |
| Tgene | GABRB1 | C0005586 | Bipolar Disorder | 2 | PSYGENET |
| Tgene | GABRB1 | C0036341 | Schizophrenia | 2 | PSYGENET |
| Tgene | GABRB1 | C0019151 | Hepatic Encephalopathy | 1 | CTD_human |
| Tgene | GABRB1 | C0035222 | Respiratory Distress Syndrome, Adult | 1 | CTD_human |
| Tgene | GABRB1 | C0270496 | Schizoaffective disorder, bipolar type | 1 | PSYGENET |
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