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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:PRICKLE1-PPHLN1 (FusionGDB2 ID:68571)

Fusion Gene Summary for PRICKLE1-PPHLN1

check button Fusion gene summary
Fusion gene informationFusion gene name: PRICKLE1-PPHLN1
Fusion gene ID: 68571
HgeneTgene
Gene symbol

PRICKLE1

PPHLN1

Gene ID

144165

51535

Gene nameprickle planar cell polarity protein 1periphilin 1
SynonymsEPM1B|RILPCR|HSPC206|HSPC232
Cytomap

12q12

12q12

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 1periphilin-1CDC7 expression repressorgastric cancer antigen Ga50
Modification date2020031320200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000345127, ENST00000552200, 
ENST00000445766, ENST00000455697, 
ENST00000548696, ENST00000552240, 
ENST00000337898, ENST00000358314, 
ENST00000395568, ENST00000395580, 
ENST00000549190, ENST00000256678, 
ENST00000317560, ENST00000432191, 
ENST00000449194, ENST00000552761, 
ENST00000550535, 
Fusion gene scores* DoF score8 X 9 X 4=28812 X 11 X 8=1056
# samples 1013
** MAII scorelog2(10/288*10)=-1.52606881166759
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(13/1056*10)=-3.02202630633
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: PRICKLE1 [Title/Abstract] AND PPHLN1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointPRICKLE1(42983267)-PPHLN1(42768665), # samples:1
Anticipated loss of major functional domain due to fusion event.
* 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

TgenePPHLN1

GO:0045814

negative regulation of gene expression, epigenetic

26022416|28581500

TgenePPHLN1

GO:0090309

positive regulation of methylation-dependent chromatin silencing

28581500

TgenePPHLN1

GO:0097355

protein localization to heterochromatin

28581500


check buttonFusion gene breakpoints across PRICKLE1 (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

check buttonFusion gene breakpoints across PPHLN1 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

check button Fusion gene information from two resources (ChiTars 5.0 and ChimerDB 4.0)
* 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
ChimerDB4KIRCTCGA-BP-5202-01APRICKLE1chr12

42983267

-PPHLN1chr12

42768665

+


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Fusion Gene ORF analysis for PRICKLE1-PPHLN1

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
5UTR-3CDSENST00000345127ENST00000337898PRICKLE1chr12

42983267

-PPHLN1chr12

42768665

+
5UTR-3CDSENST00000345127ENST00000358314PRICKLE1chr12

42983267

-PPHLN1chr12

42768665

+
5UTR-3CDSENST00000345127ENST00000395568PRICKLE1chr12

42983267

-PPHLN1chr12

42768665

+
5UTR-3CDSENST00000345127ENST00000395580PRICKLE1chr12

42983267

-PPHLN1chr12

42768665

+
5UTR-3CDSENST00000345127ENST00000549190PRICKLE1chr12

42983267

-PPHLN1chr12

42768665

+
5UTR-3CDSENST00000552200ENST00000337898PRICKLE1chr12

42983267

-PPHLN1chr12

42768665

+
5UTR-3CDSENST00000552200ENST00000358314PRICKLE1chr12

42983267

-PPHLN1chr12

42768665

+
5UTR-3CDSENST00000552200ENST00000395568PRICKLE1chr12

42983267

-PPHLN1chr12

42768665

+
5UTR-3CDSENST00000552200ENST00000395580PRICKLE1chr12

42983267

-PPHLN1chr12

42768665

+
5UTR-3CDSENST00000552200ENST00000549190PRICKLE1chr12

42983267

-PPHLN1chr12

42768665

+
5UTR-5UTRENST00000345127ENST00000256678PRICKLE1chr12

42983267

-PPHLN1chr12

42768665

+
5UTR-5UTRENST00000345127ENST00000317560PRICKLE1chr12

42983267

-PPHLN1chr12

42768665

+
5UTR-5UTRENST00000345127ENST00000432191PRICKLE1chr12

42983267

-PPHLN1chr12

42768665

+
5UTR-5UTRENST00000345127ENST00000449194PRICKLE1chr12

42983267

-PPHLN1chr12

42768665

+
5UTR-5UTRENST00000345127ENST00000552761PRICKLE1chr12

42983267

-PPHLN1chr12

42768665

+
5UTR-5UTRENST00000552200ENST00000256678PRICKLE1chr12

42983267

-PPHLN1chr12

42768665

+
5UTR-5UTRENST00000552200ENST00000317560PRICKLE1chr12

42983267

-PPHLN1chr12

42768665

+
5UTR-5UTRENST00000552200ENST00000432191PRICKLE1chr12

42983267

-PPHLN1chr12

42768665

+
5UTR-5UTRENST00000552200ENST00000449194PRICKLE1chr12

42983267

-PPHLN1chr12

42768665

+
5UTR-5UTRENST00000552200ENST00000552761PRICKLE1chr12

42983267

-PPHLN1chr12

42768665

+
5UTR-intronENST00000345127ENST00000550535PRICKLE1chr12

42983267

-PPHLN1chr12

42768665

+
5UTR-intronENST00000552200ENST00000550535PRICKLE1chr12

42983267

-PPHLN1chr12

42768665

+
intron-3CDSENST00000445766ENST00000337898PRICKLE1chr12

42983267

-PPHLN1chr12

42768665

+
intron-3CDSENST00000445766ENST00000358314PRICKLE1chr12

42983267

-PPHLN1chr12

42768665

+
intron-3CDSENST00000445766ENST00000395568PRICKLE1chr12

42983267

-PPHLN1chr12

42768665

+
intron-3CDSENST00000445766ENST00000395580PRICKLE1chr12

42983267

-PPHLN1chr12

42768665

+
intron-3CDSENST00000445766ENST00000549190PRICKLE1chr12

42983267

-PPHLN1chr12

42768665

+
intron-3CDSENST00000455697ENST00000337898PRICKLE1chr12

42983267

-PPHLN1chr12

42768665

+
intron-3CDSENST00000455697ENST00000358314PRICKLE1chr12

42983267

-PPHLN1chr12

42768665

+
intron-3CDSENST00000455697ENST00000395568PRICKLE1chr12

42983267

-PPHLN1chr12

42768665

+
intron-3CDSENST00000455697ENST00000395580PRICKLE1chr12

42983267

-PPHLN1chr12

42768665

+
intron-3CDSENST00000455697ENST00000549190PRICKLE1chr12

42983267

-PPHLN1chr12

42768665

+
intron-3CDSENST00000548696ENST00000337898PRICKLE1chr12

42983267

-PPHLN1chr12

42768665

+
intron-3CDSENST00000548696ENST00000358314PRICKLE1chr12

42983267

-PPHLN1chr12

42768665

+
intron-3CDSENST00000548696ENST00000395568PRICKLE1chr12

42983267

-PPHLN1chr12

42768665

+
intron-3CDSENST00000548696ENST00000395580PRICKLE1chr12

42983267

-PPHLN1chr12

42768665

+
intron-3CDSENST00000548696ENST00000549190PRICKLE1chr12

42983267

-PPHLN1chr12

42768665

+
intron-3CDSENST00000552240ENST00000337898PRICKLE1chr12

42983267

-PPHLN1chr12

42768665

+
intron-3CDSENST00000552240ENST00000358314PRICKLE1chr12

42983267

-PPHLN1chr12

42768665

+
intron-3CDSENST00000552240ENST00000395568PRICKLE1chr12

42983267

-PPHLN1chr12

42768665

+
intron-3CDSENST00000552240ENST00000395580PRICKLE1chr12

42983267

-PPHLN1chr12

42768665

+
intron-3CDSENST00000552240ENST00000549190PRICKLE1chr12

42983267

-PPHLN1chr12

42768665

+
intron-5UTRENST00000445766ENST00000256678PRICKLE1chr12

42983267

-PPHLN1chr12

42768665

+
intron-5UTRENST00000445766ENST00000317560PRICKLE1chr12

42983267

-PPHLN1chr12

42768665

+
intron-5UTRENST00000445766ENST00000432191PRICKLE1chr12

42983267

-PPHLN1chr12

42768665

+
intron-5UTRENST00000445766ENST00000449194PRICKLE1chr12

42983267

-PPHLN1chr12

42768665

+
intron-5UTRENST00000445766ENST00000552761PRICKLE1chr12

42983267

-PPHLN1chr12

42768665

+
intron-5UTRENST00000455697ENST00000256678PRICKLE1chr12

42983267

-PPHLN1chr12

42768665

+
intron-5UTRENST00000455697ENST00000317560PRICKLE1chr12

42983267

-PPHLN1chr12

42768665

+
intron-5UTRENST00000455697ENST00000432191PRICKLE1chr12

42983267

-PPHLN1chr12

42768665

+
intron-5UTRENST00000455697ENST00000449194PRICKLE1chr12

42983267

-PPHLN1chr12

42768665

+
intron-5UTRENST00000455697ENST00000552761PRICKLE1chr12

42983267

-PPHLN1chr12

42768665

+
intron-5UTRENST00000548696ENST00000256678PRICKLE1chr12

42983267

-PPHLN1chr12

42768665

+
intron-5UTRENST00000548696ENST00000317560PRICKLE1chr12

42983267

-PPHLN1chr12

42768665

+
intron-5UTRENST00000548696ENST00000432191PRICKLE1chr12

42983267

-PPHLN1chr12

42768665

+
intron-5UTRENST00000548696ENST00000449194PRICKLE1chr12

42983267

-PPHLN1chr12

42768665

+
intron-5UTRENST00000548696ENST00000552761PRICKLE1chr12

42983267

-PPHLN1chr12

42768665

+
intron-5UTRENST00000552240ENST00000256678PRICKLE1chr12

42983267

-PPHLN1chr12

42768665

+
intron-5UTRENST00000552240ENST00000317560PRICKLE1chr12

42983267

-PPHLN1chr12

42768665

+
intron-5UTRENST00000552240ENST00000432191PRICKLE1chr12

42983267

-PPHLN1chr12

42768665

+
intron-5UTRENST00000552240ENST00000449194PRICKLE1chr12

42983267

-PPHLN1chr12

42768665

+
intron-5UTRENST00000552240ENST00000552761PRICKLE1chr12

42983267

-PPHLN1chr12

42768665

+
intron-intronENST00000445766ENST00000550535PRICKLE1chr12

42983267

-PPHLN1chr12

42768665

+
intron-intronENST00000455697ENST00000550535PRICKLE1chr12

42983267

-PPHLN1chr12

42768665

+
intron-intronENST00000548696ENST00000550535PRICKLE1chr12

42983267

-PPHLN1chr12

42768665

+
intron-intronENST00000552240ENST00000550535PRICKLE1chr12

42983267

-PPHLN1chr12

42768665

+

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 PRICKLE1-PPHLN1


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)
PRICKLE1chr1242983266-PPHLN1chr1242768664+1.28E-050.99998724
PRICKLE1chr1242983266-PPHLN1chr1242768664+1.28E-050.99998724

check buttonDistribution of 44 human genomic features loci across 20kb length fusion breakpoint regions. We integrated a total of 44 different types of human genomic feature loci information across five big categories including virus integration sites, repeats, structural variants, chromatin states, and gene expression regulation. More details are in help page.

check buttonDistribution of 44 human genomic features loci across 20kb length fusion breakpoint regions that are ovelapped with the top 1% feature importance score regions. More details are in help page.
genomic feature of top 1%

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Fusion Protein Features for PRICKLE1-PPHLN1


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/:42983267/:42768665)
- 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
..
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}.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 PRICKLE1-PPHLN1


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 PRICKLE1-PPHLN1


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 PRICKLE1-PPHLN1


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 PRICKLE1-PPHLN1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource