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Center for Computational Systems Medicine
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FusionGeneSummary

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FusionProtFeature

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FusionGeneSequence

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FusionGenePPI

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RelatedDrugs

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RelatedDiseases

Fusion gene ID: 20296

FusionGeneSummary for LRRK2_GXYLT1

check button Fusion gene summary
Fusion gene informationFusion gene name: LRRK2_GXYLT1
Fusion gene ID: 20296
HgeneTgene
Gene symbol

LRRK2

GXYLT1

Gene ID

120892

283464

Gene nameleucine rich repeat kinase 2glucoside xylosyltransferase 1
SynonymsAURA17|DARDARIN|PARK8|RIPK7|ROCO2GLT8D3
Cytomap

12q12

12q12

Type of geneprotein-codingprotein-coding
Descriptionleucine-rich repeat serine/threonine-protein kinase 2augmented in rheumatoid arthritis 17glucoside xylosyltransferase 1glycosyltransferase 8 domain containing 3glycosyltransferase 8 domain-containing protein 3
Modification date2018052320180519
UniProtAcc

Q5S007

Q4G148

Ensembl transtripts involved in fusion geneENST00000343742, ENST00000298910, 
ENST00000481256, 
ENST00000398675, 
ENST00000280876, 
Fusion gene scores* DoF score3 X 3 X 3=272 X 2 X 2=8
# samples 32
** MAII scorelog2(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)

check button Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez
PartnerGeneGO IDGO termPubMed ID
HgeneLRRK2

GO:0000165

MAPK cascade

17200152

HgeneLRRK2

GO:0000186

activation of MAPKK activity

19302196

HgeneLRRK2

GO:0001934

positive regulation of protein phosphorylation

22012985

HgeneLRRK2

GO:0006468

protein phosphorylation

25500533

HgeneLRRK2

GO:0010955

negative regulation of protein processing

21370995

HgeneLRRK2

GO:0018105

peptidyl-serine phosphorylation

19576176

HgeneLRRK2

GO:0018107

peptidyl-threonine phosphorylation

21048939

HgeneLRRK2

GO:0031398

positive regulation of protein ubiquitination

16352719|20173330

HgeneLRRK2

GO:0032092

positive regulation of protein binding

21370995

HgeneLRRK2

GO:0034260

negative regulation of GTPase activity

22423108

HgeneLRRK2

GO:0043068

positive regulation of programmed cell death

17200152

HgeneLRRK2

GO:0046039

GTP metabolic process

21048939

HgeneLRRK2

GO:0046777

protein autophosphorylation

16269541|16321986|17200152|17442267

HgeneLRRK2

GO:1902499

positive regulation of protein autoubiquitination

16352719

HgeneLRRK2

GO:1903125

negative regulation of thioredoxin peroxidase activity by peptidyl-threonine phosphorylation

21850687

HgeneLRRK2

GO:1903215

negative regulation of protein targeting to mitochondrion

21370995

TgeneGXYLT1

GO:0016266

O-glycan processing

19940119


check button 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 typeSourceCancer typeSampleHgeneHchrHbpHstrandTgeneTchrTbpTstrand
TCGARVLGGTCGA-DU-A5TY-01ALRRK2chr12

40619442

+GXYLT1chr12

42512973

-
* LD: Li Ding group's fusion gene list
  RV: Roel Verhaak group's fusion gene list
  ChiTaRs fusion database

check button 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.
ORFHenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrand
Frame-shiftENST00000343742ENST00000398675LRRK2chr12

40619442

+GXYLT1chr12

42512973

-
Frame-shiftENST00000343742ENST00000280876LRRK2chr12

40619442

+GXYLT1chr12

42512973

-
Frame-shiftENST00000298910ENST00000398675LRRK2chr12

40619442

+GXYLT1chr12

42512973

-
Frame-shiftENST00000298910ENST00000280876LRRK2chr12

40619442

+GXYLT1chr12

42512973

-
intron-3CDSENST00000481256ENST00000398675LRRK2chr12

40619442

+GXYLT1chr12

42512973

-
intron-3CDSENST00000481256ENST00000280876LRRK2chr12

40619442

+GXYLT1chr12

42512973

-

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FusionProtFeatures for LRRK2_GXYLT1


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
LRRK2

Q5S007

GXYLT1

Q4G148

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}.

check buttonRetention 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

download page

.

* 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.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note


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FusionGeneSequence for LRRK2_GXYLT1


check button 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


check button Go to ChiPPI (Chimeric Protein-Protein interactions) to see the chimeric PPI interaction in

ChiPPI page

.

check button Protein-protein interactors with each fusion partner protein in wild-type (BIOGRID-3.4.160)
HgeneHgene's interactorsTgeneTgene's interactors
LRRK2PARK2, 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, HIF1AGXYLT1P4HB, CANX, P2RX2, OMA1, FKBP14, ASPHD2, NPTX1, VIM


check button - Retained PPIs in in-frame fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenStill interaction with


check button - Lost PPIs in in-frame fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


check button - Retained PPIs, but lost function due to frame-shift fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


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RelatedDrugs for LRRK2_GXYLT1


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.0 2018-04-02)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

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RelatedDiseases for LRRK2_GXYLT1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneLRRK2C0030567Parkinson Disease10CTD_human
HgeneLRRK2C1846862PARKINSON DISEASE 8 (disorder)10CTD_human;UNIPROT
HgeneLRRK2C0242422Parkinsonian Disorders2CTD_human
HgeneLRRK2C0007134Renal Cell Carcinoma1CTD_human
HgeneLRRK2C0014175Endometriosis1CTD_human
HgeneLRRK2C0027746Nerve Degeneration1CTD_human
HgeneLRRK2C0036341Schizophrenia1PSYGENET
HgeneLRRK2C0086132Depressive Symptoms1PSYGENET