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Center for Computational Systems Medicine
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Fusion Gene Summary

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Fusion Gene ORF analysis

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Fusion Genomic Features

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Fusion Protein Features

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Fusion Gene Sequence

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Fusion Gene PPI analysis

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Related Drugs

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Related Diseases

Fusion gene:LGR5-PTPRR (FusionGDB2 ID:HG8549TG5801)

Fusion Gene Summary for LGR5-PTPRR

check button Fusion gene summary
Fusion gene informationFusion gene name: LGR5-PTPRR
Fusion gene ID: hg8549tg5801
HgeneTgene
Gene symbol

LGR5

PTPRR

Gene ID

8549

5801

Gene nameleucine rich repeat containing G protein-coupled receptor 5protein tyrosine phosphatase receptor type R
SynonymsFEX|GPR49|GPR67|GRP49|HG38EC-PTP|PCPTP1|PTP-SL|PTPBR7|PTPRQ
Cytomap('LGR5')('PTPRR')

12q21.1

12q15

Type of geneprotein-codingprotein-coding
Descriptionleucine-rich repeat-containing G-protein coupled receptor 5G-protein coupled receptor 49G-protein coupled receptor 67G-protein coupled receptor HG38orphan G protein-coupled receptor HG38receptor-type tyrosine-protein phosphatase RCh-1 PTPaseNC-PTPCOM1R-PTP-Rch-1PTPaseprotein tyrosine phosphatase Cr1PTPaseprotein-tyrosine phosphatase NC-PTPCOM1protein-tyrosine phosphatase PCPTP1
Modification date2020032920200313
UniProtAcc

O75473

.
Ensembl transtripts involved in fusion geneENST00000266674, ENST00000536515, 
ENST00000540815, 
Fusion gene scores* DoF score5 X 3 X 2=3038 X 16 X 13=7904
# samples 542
** MAII scorelog2(5/30*10)=0.736965594166206
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
log2(42/7904*10)=-4.23412171391856
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: LGR5 [Title/Abstract] AND PTPRR [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointLGR5(71898465)-PTPRR(71286757), # samples:3
Anticipated loss of major functional domain due to fusion event.LGR5-PTPRR seems lost the major protein functional domain in Hgene partner, which is a IUPHAR drug target due to the frame-shifted ORF.
LGR5-PTPRR seems lost the major protein functional domain in Tgene partner, which is a IUPHAR drug target 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)

check button Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez
PartnerGeneGO IDGO termPubMed ID
HgeneLGR5

GO:0090263

positive regulation of canonical Wnt signaling pathway

21693646|22815884



check button Fusion gene information
* 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.
SourceDiseaseSampleHgeneHchrHbpHstrandTgeneTchrTbpTstrand
ChimerDB4BLCATCGA-ZF-AA4U-01ALGR5chr12

71898465

-PTPRRchr12

71286757

-
ChimerDB4BLCATCGA-ZF-AA4U-01ALGR5chr12

71898465

+PTPRRchr12

71286757

-


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Fusion Gene ORF analysis for LGR5-PTPRR

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
5CDS-intronENST00000266674ENST00000342084LGR5chr12

71898465

+PTPRRchr12

71286757

-
5CDS-intronENST00000266674ENST00000378778LGR5chr12

71898465

+PTPRRchr12

71286757

-
5CDS-intronENST00000266674ENST00000440835LGR5chr12

71898465

+PTPRRchr12

71286757

-
5CDS-intronENST00000266674ENST00000537619LGR5chr12

71898465

+PTPRRchr12

71286757

-
5CDS-intronENST00000266674ENST00000549308LGR5chr12

71898465

+PTPRRchr12

71286757

-
5CDS-intronENST00000536515ENST00000342084LGR5chr12

71898465

+PTPRRchr12

71286757

-
5CDS-intronENST00000536515ENST00000378778LGR5chr12

71898465

+PTPRRchr12

71286757

-
5CDS-intronENST00000536515ENST00000440835LGR5chr12

71898465

+PTPRRchr12

71286757

-
5CDS-intronENST00000536515ENST00000537619LGR5chr12

71898465

+PTPRRchr12

71286757

-
5CDS-intronENST00000536515ENST00000549308LGR5chr12

71898465

+PTPRRchr12

71286757

-
5CDS-intronENST00000540815ENST00000342084LGR5chr12

71898465

+PTPRRchr12

71286757

-
5CDS-intronENST00000540815ENST00000378778LGR5chr12

71898465

+PTPRRchr12

71286757

-
5CDS-intronENST00000540815ENST00000440835LGR5chr12

71898465

+PTPRRchr12

71286757

-
5CDS-intronENST00000540815ENST00000537619LGR5chr12

71898465

+PTPRRchr12

71286757

-
5CDS-intronENST00000540815ENST00000549308LGR5chr12

71898465

+PTPRRchr12

71286757

-
Frame-shiftENST00000266674ENST00000283228LGR5chr12

71898465

+PTPRRchr12

71286757

-
Frame-shiftENST00000536515ENST00000283228LGR5chr12

71898465

+PTPRRchr12

71286757

-
Frame-shiftENST00000540815ENST00000283228LGR5chr12

71898465

+PTPRRchr12

71286757

-

check buttonORFfinder result based on the fusion transcript sequence of in-frame fusion genes.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandSeq length
(transcript)
BP loci
(transcript)
Predicted start
(transcript)
Predicted stop
(transcript)
Seq length
(amino acids)

check buttonDeepORF 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.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandNo-coding scoreCoding score

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Fusion Genomic Features for LGR5-PTPRR


check buttonFusionAI 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.
HgeneHchrHbpHstrandTgeneTchrTbpTstrand1-pp (fusion gene breakpoint)


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Fusion Protein Features for LGR5-PTPRR


check button Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/:71898465/:71286757)
- 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.
FGviewer

check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
LGR5

O75473

.
FUNCTION: Receptor for R-spondins that potentiates the canonical Wnt signaling pathway and acts as a stem cell marker of the intestinal epithelium and the hair follicle. Upon binding to R-spondins (RSPO1, RSPO2, RSPO3 or RSPO4), associates with phosphorylated LRP6 and frizzled receptors that are activated by extracellular Wnt receptors, triggering the canonical Wnt signaling pathway to increase expression of target genes. In contrast to classical G-protein coupled receptors, does not activate heterotrimeric G-proteins to transduce the signal. Involved in the development and/or maintenance of the adult intestinal stem cells during postembryonic development. {ECO:0000269|PubMed:21693646, ECO:0000269|PubMed:21727895, ECO:0000269|PubMed:21909076, ECO:0000269|PubMed:22815884, ECO:0000269|PubMed:23809763}.FUNCTION: Transcriptional activator which is required for calcium-dependent dendritic growth and branching in cortical neurons. Recruits CREB-binding protein (CREBBP) to nuclear bodies. Component of the CREST-BRG1 complex, a multiprotein complex that regulates promoter activation by orchestrating a calcium-dependent release of a repressor complex and a recruitment of an activator complex. In resting neurons, transcription of the c-FOS promoter is inhibited by BRG1-dependent recruitment of a phospho-RB1-HDAC1 repressor complex. Upon calcium influx, RB1 is dephosphorylated by calcineurin, which leads to release of the repressor complex. At the same time, there is increased recruitment of CREBBP to the promoter by a CREST-dependent mechanism, which leads to transcriptional activation. The CREST-BRG1 complex also binds to the NR2B promoter, and activity-dependent induction of NR2B expression involves a release of HDAC1 and recruitment of CREBBP (By similarity). {ECO:0000250}.

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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Fusion Gene Sequence for LGR5-PTPRR


check button 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.

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Fusion Gene PPI Analysis for LGR5-PTPRR


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


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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Related Drugs for LGR5-PTPRR


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

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Related Diseases for LGR5-PTPRR


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneLGR5C0007102Malignant tumor of colon1CTD_human
HgeneLGR5C0009375Colonic Neoplasms1CTD_human
HgeneLGR5C0009402Colorectal Carcinoma1CTD_human
HgeneLGR5C0009404Colorectal Neoplasms1CTD_human
TgeneC0041696Unipolar Depression1PSYGENET
TgeneC1269683Major Depressive Disorder1PSYGENET