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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: 28651

FusionGeneSummary for PRICKLE1_LRIG3

check button Fusion gene summary
Fusion gene informationFusion gene name: PRICKLE1_LRIG3
Fusion gene ID: 28651
HgeneTgene
Gene symbol

PRICKLE1

LRIG3

Gene ID

144165

121227

Gene nameprickle planar cell polarity protein 1leucine rich repeats and immunoglobulin like domains 3
SynonymsEPM1B|RILPLIG3
Cytomap

12q12

12q14.1

Type of geneprotein-codingprotein-coding
Descriptionprickle-like protein 1REST (RE-1 silencing transcription factor)/NRSF (neuron-restrictive silencer factor)-interacting LIM domain proteinREST/NRSF interacting LIM domain proteinREST/NRSF-interacting LIM domain protein 1prickle homolog 1prickle-like 1leucine-rich repeats and immunoglobulin-like domains protein 3LIG-3
Modification date2018052220180523
UniProtAcc

Q96MT3

Q6UXM1

Ensembl transtripts involved in fusion geneENST00000455697, ENST00000445766, 
ENST00000548696, ENST00000345127, 
ENST00000552240, ENST00000552200, 
ENST00000379141, ENST00000320743, 
Fusion gene scores* DoF score3 X 2 X 3=183 X 2 X 2=12
# samples 33
** MAII scorelog2(3/18*10)=0.736965594166206
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
log2(3/12*10)=1.32192809488736
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context

PubMed: PRICKLE1 [Title/Abstract] AND LRIG3 [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
HgenePRICKLE1

GO:0006606

protein import into nucleus

21199191

HgenePRICKLE1

GO:0031398

positive regulation of protein ubiquitination

17030191

HgenePRICKLE1

GO:0032436

positive regulation of proteasomal ubiquitin-dependent protein catabolic process

17030191

HgenePRICKLE1

GO:0045892

negative regulation of transcription, DNA-templated

17030191

HgenePRICKLE1

GO:0090090

negative regulation of canonical Wnt signaling pathway

17030191

HgenePRICKLE1

GO:2000691

negative regulation of cardiac muscle cell myoblast differentiation

21199191


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
TCGARVSARCTCGA-DX-A7EI-01APRICKLE1chr12

42983267

-LRIG3chr12

59284578

-
* 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
intron-3CDSENST00000455697ENST00000379141PRICKLE1chr12

42983267

-LRIG3chr12

59284578

-
intron-3CDSENST00000455697ENST00000320743PRICKLE1chr12

42983267

-LRIG3chr12

59284578

-
intron-3CDSENST00000445766ENST00000379141PRICKLE1chr12

42983267

-LRIG3chr12

59284578

-
intron-3CDSENST00000445766ENST00000320743PRICKLE1chr12

42983267

-LRIG3chr12

59284578

-
intron-3CDSENST00000548696ENST00000379141PRICKLE1chr12

42983267

-LRIG3chr12

59284578

-
intron-3CDSENST00000548696ENST00000320743PRICKLE1chr12

42983267

-LRIG3chr12

59284578

-
5UTR-3CDSENST00000345127ENST00000379141PRICKLE1chr12

42983267

-LRIG3chr12

59284578

-
5UTR-3CDSENST00000345127ENST00000320743PRICKLE1chr12

42983267

-LRIG3chr12

59284578

-
intron-3CDSENST00000552240ENST00000379141PRICKLE1chr12

42983267

-LRIG3chr12

59284578

-
intron-3CDSENST00000552240ENST00000320743PRICKLE1chr12

42983267

-LRIG3chr12

59284578

-
5UTR-3CDSENST00000552200ENST00000379141PRICKLE1chr12

42983267

-LRIG3chr12

59284578

-
5UTR-3CDSENST00000552200ENST00000320743PRICKLE1chr12

42983267

-LRIG3chr12

59284578

-

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FusionProtFeatures for PRICKLE1_LRIG3


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
PRICKLE1

Q96MT3

LRIG3

Q6UXM1

Involved in the planar cell polarity pathway thatcontrols convergent extension during gastrulation and neural tubeclosure. Convergent extension is a complex morphogenetic processduring which cells elongate, move mediolaterally, and intercalatebetween neighboring cells, leading to convergence toward themediolateral axis and extension along the anteroposterior axis.Necessary for nuclear localization of REST. May serve as nuclearreceptor. {ECO:0000269|PubMed:21901791}. May play a role in craniofacial and inner earmorphogenesis during embryonic development. May act within theotic vesicle epithelium to control formation of the lateralsemicircular canal in the inner ear, possibly by restricting theexpression of NTN1 (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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FusionGeneSequence for PRICKLE1_LRIG3


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 PRICKLE1_LRIG3


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
PRICKLE1DVL3, UTP14C, PRPF31, RASSF10, USP9X, EGFRLRIG3CAND1, TAZ, TNFSF13B, PVRIG, GINM1, LPAR6, PTPRK, PTGER3, GAL3ST1, LRIG1, LRRN2, TMPRSS3


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 PRICKLE1_LRIG3


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 PRICKLE1_LRIG3


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgenePRICKLE1C2676254Prickle1-Related Progressive Myoclonus Epilepsy with Ataxia1CTD_human;UNIPROT