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Fusion gene ID: 20296 |
FusionGeneSummary for LRRK2_GXYLT1 |
Fusion gene summary |
Fusion gene information | Fusion gene name: LRRK2_GXYLT1 | Fusion gene ID: 20296 | Hgene | Tgene | Gene symbol | LRRK2 | GXYLT1 | Gene ID | 120892 | 283464 |
Gene name | leucine rich repeat kinase 2 | glucoside xylosyltransferase 1 | |
Synonyms | AURA17|DARDARIN|PARK8|RIPK7|ROCO2 | GLT8D3 | |
Cytomap | 12q12 | 12q12 | |
Type of gene | protein-coding | protein-coding | |
Description | leucine-rich repeat serine/threonine-protein kinase 2augmented in rheumatoid arthritis 17 | glucoside xylosyltransferase 1glycosyltransferase 8 domain containing 3glycosyltransferase 8 domain-containing protein 3 | |
Modification date | 20180523 | 20180519 | |
UniProtAcc | Q5S007 | Q4G148 | |
Ensembl transtripts involved in fusion gene | ENST00000343742, ENST00000298910, ENST00000481256, | ENST00000398675, ENST00000280876, | |
Fusion gene scores | * DoF score | 3 X 3 X 3=27 | 2 X 2 X 2=8 |
# samples | 3 | 2 | |
** MAII score | log2(3/27*10)=0.15200309344505 effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs). DoF>8 and MAII>0 | log2(2/8*10)=1.32192809488736 | |
Context | PubMed: LRRK2 [Title/Abstract] AND GXYLT1 [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 | LRRK2 | GO:0000165 | MAPK cascade | 17200152 |
Hgene | LRRK2 | GO:0000186 | activation of MAPKK activity | 19302196 |
Hgene | LRRK2 | GO:0001934 | positive regulation of protein phosphorylation | 22012985 |
Hgene | LRRK2 | GO:0006468 | protein phosphorylation | 25500533 |
Hgene | LRRK2 | GO:0010955 | negative regulation of protein processing | 21370995 |
Hgene | LRRK2 | GO:0018105 | peptidyl-serine phosphorylation | 19576176 |
Hgene | LRRK2 | GO:0018107 | peptidyl-threonine phosphorylation | 21048939 |
Hgene | LRRK2 | GO:0031398 | positive regulation of protein ubiquitination | 16352719|20173330 |
Hgene | LRRK2 | GO:0032092 | positive regulation of protein binding | 21370995 |
Hgene | LRRK2 | GO:0034260 | negative regulation of GTPase activity | 22423108 |
Hgene | LRRK2 | GO:0043068 | positive regulation of programmed cell death | 17200152 |
Hgene | LRRK2 | GO:0046039 | GTP metabolic process | 21048939 |
Hgene | LRRK2 | GO:0046777 | protein autophosphorylation | 16269541|16321986|17200152|17442267 |
Hgene | LRRK2 | GO:1902499 | positive regulation of protein autoubiquitination | 16352719 |
Hgene | LRRK2 | GO:1903125 | negative regulation of thioredoxin peroxidase activity by peptidyl-threonine phosphorylation | 21850687 |
Hgene | LRRK2 | GO:1903215 | negative regulation of protein targeting to mitochondrion | 21370995 |
Tgene | GXYLT1 | GO:0016266 | O-glycan processing | 19940119 |
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 | LGG | TCGA-DU-A5TY-01A | LRRK2 | chr12 | 40619442 | + | GXYLT1 | chr12 | 42512973 | - |
* 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 |
Frame-shift | ENST00000343742 | ENST00000398675 | LRRK2 | chr12 | 40619442 | + | GXYLT1 | chr12 | 42512973 | - |
Frame-shift | ENST00000343742 | ENST00000280876 | LRRK2 | chr12 | 40619442 | + | GXYLT1 | chr12 | 42512973 | - |
Frame-shift | ENST00000298910 | ENST00000398675 | LRRK2 | chr12 | 40619442 | + | GXYLT1 | chr12 | 42512973 | - |
Frame-shift | ENST00000298910 | ENST00000280876 | LRRK2 | chr12 | 40619442 | + | GXYLT1 | chr12 | 42512973 | - |
intron-3CDS | ENST00000481256 | ENST00000398675 | LRRK2 | chr12 | 40619442 | + | GXYLT1 | chr12 | 42512973 | - |
intron-3CDS | ENST00000481256 | ENST00000280876 | LRRK2 | chr12 | 40619442 | + | GXYLT1 | chr12 | 42512973 | - |
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FusionProtFeatures for LRRK2_GXYLT1 |
Main function of each fusion partner protein. (from UniProt) |
Hgene | Tgene |
LRRK2 | GXYLT1 |
Positively regulates autophagy through a calcium-dependent activation of the CaMKK/AMPK signaling pathway. Theprocess involves activation of nicotinic acid adenine dinucleotidephosphate (NAADP) receptors, increase in lysosomal pH, and calciumrelease from lysosomes. Together with RAB29, plays a role in theretrograde trafficking pathway for recycling proteins, such asmannose 6 phosphate receptor (M6PR), between lysosomes and theGolgi apparatus in a retromer-dependent manner. Regulates neuronalprocess morphology in the intact central nervous system (CNS).Plays a role in synaptic vesicle trafficking. PhosphorylatesPRDX3. Has GTPase activity. May play a role in the phosphorylationof proteins central to Parkinson disease.{ECO:0000269|PubMed:17114044, ECO:0000269|PubMed:18230735,ECO:0000269|PubMed:20949042, ECO:0000269|PubMed:21850687,ECO:0000269|PubMed:22012985, ECO:0000269|PubMed:23395371,ECO:0000269|PubMed:24687852}. | Glycosyltransferase which elongates the O-linked glucoseattached to EGF-like repeats in the extracellular domain of Notchproteins by catalyzing the addition of xylose.{ECO:0000269|PubMed:19940119}. |
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 LRRK2_GXYLT1 |
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 LRRK2_GXYLT1 |
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 |
LRRK2 | PARK2, SNCA, STUB1, HSP90AA1, TUBA1C, TUBB, RPS8, RPL23, YWHAZ, YWHAQ, YWHAE, YWHAB, YWHAH, CDC37, HSP90AB1, YWHAG, SH3GL2, SH3GL1, SH3GL3, LRRK2, MBP, TAOK3, RIPK2, PRKCZ, STK3, STK24, STK25, TRAF2, AGO2, AGO1, MDN1, CLTC, VIM, SCFD1, PRKDC, AKAP8, HSPD1, DNM1L, ARFGAP1, MAP1B, TUBA1A, HSPA8, MAPT, EIF4EBP1, MAP2K3, EEF1A1, DYNC1H1, HMMR, HSPA4, DNAJA1, ARHGEF7, CDC42, ACTBL2, ACTB, ACTG1, ACTA2, ACTG2, ACTR2, ACTR3, ARPC1B, ARPC2, ARPC4, ARPC5, CAPZA1, CAPZA2, CAPZB, TMOD3, TPM1, TPM3, TPM2, LIMA1, DBN1, RAI14, PLEC, MYO1B, MYO1C, MYO1D, MYO1F, MYL12B, MYL9, MYL6, PPP1R12A, MPRIP, CALM1, CALM2, CALM3, GNAI2, GNA12, GNA13, MPC2, ATP5L, EFHD2, HIST1H3A, H3F3A, MAP2K6, MAP2K4, MAP2K7, TRADD, FADD, RIPK1, CASP8, RAC1, RHOA, AKT1, LRP6, LRRK1, DAPK1, RAB5B, STRBP, BAG5, PTPN23, L3MBTL3, RALYL, DVL2, DVL3, DVL1, IQGAP1, CSE1L, TNPO1, PPP2R1A, PSMD11, NRON, NFATC2, BAX, EPRS, SRPK1, HSPA9, ATRX, TK1, CHD1L, C17orf53, HERC2, NEURL4, RAB5A, RAB7A, RAB11A, RAB11B, ITCH, TP53, SQSTM1, WSB1, LINC01139, HIF1A | GXYLT1 | P4HB, CANX, P2RX2, OMA1, FKBP14, ASPHD2, NPTX1, VIM |
- 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 LRRK2_GXYLT1 |
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 LRRK2_GXYLT1 |
Diseases associated with fusion partners. (DisGeNet 4.0) |
Partner | Gene | Disease ID | Disease name | # pubmeds | Source |
Hgene | LRRK2 | C0030567 | Parkinson Disease | 10 | CTD_human |
Hgene | LRRK2 | C1846862 | PARKINSON DISEASE 8 (disorder) | 10 | CTD_human;UNIPROT |
Hgene | LRRK2 | C0242422 | Parkinsonian Disorders | 2 | CTD_human |
Hgene | LRRK2 | C0007134 | Renal Cell Carcinoma | 1 | CTD_human |
Hgene | LRRK2 | C0014175 | Endometriosis | 1 | CTD_human |
Hgene | LRRK2 | C0027746 | Nerve Degeneration | 1 | CTD_human |
Hgene | LRRK2 | C0036341 | Schizophrenia | 1 | PSYGENET |
Hgene | LRRK2 | C0086132 | Depressive Symptoms | 1 | PSYGENET |