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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:PKP4-PDE1A (FusionGDB2 ID:65828)

Fusion Gene Summary for PKP4-PDE1A

check button Fusion gene summary
Fusion gene informationFusion gene name: PKP4-PDE1A
Fusion gene ID: 65828
HgeneTgene
Gene symbol

PKP4

PDE1A

Gene ID

8502

5136

Gene nameplakophilin 4phosphodiesterase 1A
Synonymsp0071CAM-PDE 1A|CAM-PDE-1A|HCAM-1|HCAM1|HSPDE1A
Cytomap

2q24.1

2q32.1

Type of geneprotein-codingprotein-coding
Descriptionplakophilin-4catenin 4calcium/calmodulin-dependent 3',5'-cyclic nucleotide phosphodiesterase 1A61 kDa Cam-PDEcalcium/calmodulin-stimulated cyclic nucleotide phosphodiesterasephosphodiesterase 1A, calmodulin-dependent
Modification date2020031320200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000389757, ENST00000389759, 
ENST00000495123, 		ENST00000346717, 
ENST00000351439, ENST00000358139, 
ENST00000410103, ENST00000456212, 
ENST00000482538, ENST00000331935, 
ENST00000435564, ENST00000536095, 
ENST00000409365, 
Fusion gene scores* DoF score9 X 7 X 6=3787 X 6 X 4=168
# samples 98
** MAII scorelog2(9/378*10)=-2.0703893278914
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(8/168*10)=-1.0703893278914
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: PKP4 [Title/Abstract] AND PDE1A [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointPKP4(159459616)-PDE1A(183011879), # samples:3
Anticipated loss of major functional domain due to fusion event.PKP4-PDE1A seems lost the major protein functional domain in Tgene partner, which is a cell metabolism gene due to the frame-shifted ORF.
PKP4-PDE1A 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
HgenePKP4

GO:0043547

positive regulation of GTPase activity

17115030


check buttonFusion gene breakpoints across PKP4 (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure

check buttonFusion gene breakpoints across PDE1A (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure

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
ChimerDB4OVTCGA-23-2081-01APKP4chr2

159459616

-PDE1Achr2

183011879

-
ChimerDB4OVTCGA-23-2081-01APKP4chr2

159459616

+PDE1Achr2

183011879

-
ChimerDB4OVTCGA-23-2081PKP4chr2

159459616

+PDE1Achr2

183011879

-


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Fusion Gene ORF analysis for PKP4-PDE1A

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-intronENST00000389757ENST00000346717PKP4chr2

159459616

+PDE1Achr2

183011879

-
5CDS-intronENST00000389757ENST00000351439PKP4chr2

159459616

+PDE1Achr2

183011879

-
5CDS-intronENST00000389757ENST00000358139PKP4chr2

159459616

+PDE1Achr2

183011879

-
5CDS-intronENST00000389757ENST00000410103PKP4chr2

159459616

+PDE1Achr2

183011879

-
5CDS-intronENST00000389757ENST00000456212PKP4chr2

159459616

+PDE1Achr2

183011879

-
5CDS-intronENST00000389757ENST00000482538PKP4chr2

159459616

+PDE1Achr2

183011879

-
5CDS-intronENST00000389759ENST00000346717PKP4chr2

159459616

+PDE1Achr2

183011879

-
5CDS-intronENST00000389759ENST00000351439PKP4chr2

159459616

+PDE1Achr2

183011879

-
5CDS-intronENST00000389759ENST00000358139PKP4chr2

159459616

+PDE1Achr2

183011879

-
5CDS-intronENST00000389759ENST00000410103PKP4chr2

159459616

+PDE1Achr2

183011879

-
5CDS-intronENST00000389759ENST00000456212PKP4chr2

159459616

+PDE1Achr2

183011879

-
5CDS-intronENST00000389759ENST00000482538PKP4chr2

159459616

+PDE1Achr2

183011879

-
Frame-shiftENST00000389757ENST00000331935PKP4chr2

159459616

+PDE1Achr2

183011879

-
Frame-shiftENST00000389757ENST00000435564PKP4chr2

159459616

+PDE1Achr2

183011879

-
Frame-shiftENST00000389757ENST00000536095PKP4chr2

159459616

+PDE1Achr2

183011879

-
Frame-shiftENST00000389759ENST00000331935PKP4chr2

159459616

+PDE1Achr2

183011879

-
Frame-shiftENST00000389759ENST00000435564PKP4chr2

159459616

+PDE1Achr2

183011879

-
Frame-shiftENST00000389759ENST00000536095PKP4chr2

159459616

+PDE1Achr2

183011879

-
In-frameENST00000389757ENST00000409365PKP4chr2

159459616

+PDE1Achr2

183011879

-
In-frameENST00000389759ENST00000409365PKP4chr2

159459616

+PDE1Achr2

183011879

-
intron-3CDSENST00000495123ENST00000331935PKP4chr2

159459616

+PDE1Achr2

183011879

-
intron-3CDSENST00000495123ENST00000409365PKP4chr2

159459616

+PDE1Achr2

183011879

-
intron-3CDSENST00000495123ENST00000435564PKP4chr2

159459616

+PDE1Achr2

183011879

-
intron-3CDSENST00000495123ENST00000536095PKP4chr2

159459616

+PDE1Achr2

183011879

-
intron-intronENST00000495123ENST00000346717PKP4chr2

159459616

+PDE1Achr2

183011879

-
intron-intronENST00000495123ENST00000351439PKP4chr2

159459616

+PDE1Achr2

183011879

-
intron-intronENST00000495123ENST00000358139PKP4chr2

159459616

+PDE1Achr2

183011879

-
intron-intronENST00000495123ENST00000410103PKP4chr2

159459616

+PDE1Achr2

183011879

-
intron-intronENST00000495123ENST00000456212PKP4chr2

159459616

+PDE1Achr2

183011879

-
intron-intronENST00000495123ENST00000482538PKP4chr2

159459616

+PDE1Achr2

183011879

-

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)
ENST00000389757PKP4chr2159459616+ENST00000409365PDE1Achr2183011879-52240586478130
ENST00000389759PKP4chr2159459616+ENST00000409365PDE1Achr2183011879-50939273465130

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
ENST00000389757ENST00000409365PKP4chr2159459616+PDE1Achr2183011879-0.0084674530.9915325
ENST00000389759ENST00000409365PKP4chr2159459616+PDE1Achr2183011879-0.0070157010.9929843

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Fusion Genomic Features for PKP4-PDE1A


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)

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.
genomic feature

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.

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Fusion Protein Features for PKP4-PDE1A


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/chr2:159459616/chr2:183011879)
- 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
HgenePKP4chr2:159459616chr2:183011879ENST00000389757+42136_70931150.0Coiled coilOntology_term=ECO:0000255
HgenePKP4chr2:159459616chr2:183011879ENST00000389759+42236_70931193.0Coiled coilOntology_term=ECO:0000255
TgenePDE1Achr2:159459616chr2:183011879ENST00000351439014142_5220520.0DomainPDEase
TgenePDE1Achr2:159459616chr2:183011879ENST00000358139014142_5220536.0DomainPDEase
TgenePDE1Achr2:159459616chr2:183011879ENST00000410103015142_5220536.0DomainPDEase
TgenePDE1Achr2:159459616chr2:183011879ENST00000456212013142_5220553.0DomainPDEase
TgenePDE1Achr2:159459616chr2:183011879ENST0000035143901424_440520.0RegionCalmodulin-binding
TgenePDE1Achr2:159459616chr2:183011879ENST0000035813901424_440536.0RegionCalmodulin-binding
TgenePDE1Achr2:159459616chr2:183011879ENST0000041010301524_440536.0RegionCalmodulin-binding
TgenePDE1Achr2:159459616chr2:183011879ENST0000045621201324_440553.0RegionCalmodulin-binding

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgenePKP4chr2:159459616chr2:183011879ENST00000389757+421788_794931150.0Compositional biasNote=Poly-Lys
HgenePKP4chr2:159459616chr2:183011879ENST00000389759+422788_794931193.0Compositional biasNote=Poly-Lys
HgenePKP4chr2:159459616chr2:183011879ENST00000389757+421415_455931150.0RepeatNote=ARM 1
HgenePKP4chr2:159459616chr2:183011879ENST00000389757+421518_557931150.0RepeatNote=ARM 2
HgenePKP4chr2:159459616chr2:183011879ENST00000389757+421560_599931150.0RepeatNote=ARM 3
HgenePKP4chr2:159459616chr2:183011879ENST00000389757+421604_644931150.0RepeatNote=ARM 4
HgenePKP4chr2:159459616chr2:183011879ENST00000389757+421660_702931150.0RepeatNote=ARM 5
HgenePKP4chr2:159459616chr2:183011879ENST00000389757+421706_751931150.0RepeatNote=ARM 6
HgenePKP4chr2:159459616chr2:183011879ENST00000389757+421815_855931150.0RepeatNote=ARM 7
HgenePKP4chr2:159459616chr2:183011879ENST00000389757+421862_901931150.0RepeatNote=ARM 8
HgenePKP4chr2:159459616chr2:183011879ENST00000389757+421950_993931150.0RepeatNote=ARM 9
HgenePKP4chr2:159459616chr2:183011879ENST00000389759+422415_455931193.0RepeatNote=ARM 1
HgenePKP4chr2:159459616chr2:183011879ENST00000389759+422518_557931193.0RepeatNote=ARM 2
HgenePKP4chr2:159459616chr2:183011879ENST00000389759+422560_599931193.0RepeatNote=ARM 3
HgenePKP4chr2:159459616chr2:183011879ENST00000389759+422604_644931193.0RepeatNote=ARM 4
HgenePKP4chr2:159459616chr2:183011879ENST00000389759+422660_702931193.0RepeatNote=ARM 5
HgenePKP4chr2:159459616chr2:183011879ENST00000389759+422706_751931193.0RepeatNote=ARM 6
HgenePKP4chr2:159459616chr2:183011879ENST00000389759+422815_855931193.0RepeatNote=ARM 7
HgenePKP4chr2:159459616chr2:183011879ENST00000389759+422862_901931193.0RepeatNote=ARM 8
HgenePKP4chr2:159459616chr2:183011879ENST00000389759+422950_993931193.0RepeatNote=ARM 9
TgenePDE1Achr2:159459616chr2:183011879ENST000003319351214142_522521546.0DomainPDEase
TgenePDE1Achr2:159459616chr2:183011879ENST000003467171114142_522487589.6666666666666DomainPDEase
TgenePDE1Achr2:159459616chr2:183011879ENST000004093651214142_522505530.0DomainPDEase
TgenePDE1Achr2:159459616chr2:183011879ENST000004355641215142_5225211447.3333333333333DomainPDEase
TgenePDE1Achr2:159459616chr2:183011879ENST00000331935121424_44521546.0RegionCalmodulin-binding
TgenePDE1Achr2:159459616chr2:183011879ENST00000346717111424_44487589.6666666666666RegionCalmodulin-binding
TgenePDE1Achr2:159459616chr2:183011879ENST00000409365121424_44505530.0RegionCalmodulin-binding
TgenePDE1Achr2:159459616chr2:183011879ENST00000435564121524_445211447.3333333333333RegionCalmodulin-binding


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Fusion Gene Sequence for PKP4-PDE1A


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.
>65828_65828_1_PKP4-PDE1A_PKP4_chr2_159459616_ENST00000389757_PDE1A_chr2_183011879_ENST00000409365_length(transcript)=522nt_BP=405nt
GGGGCGGGCAGCCGCGCCGCCGCGGCACTTTTTTAATTTTTTCGGGTGCCGCAGCGGCGACCCCTCGGCGCCGATGTCCCTGATCCCTGG
AGCGACGACGGCCGCTGCCTAAGCTGGAAAGAGGAATGCCAGCTCCTGAGCAGGCCTCATTGGTGGAGGAGGGGCAACCACAGACCCGCC
AGGAAGCTGCCTCCACTGGCCCAGGCATGGAACCCGAGACCACAGCCACCACTATTCTAGCATCCGTGAAGGAGCAGGAGCTTCAGTTTC
AGCGACTCACCCGAGAACTGGAAGTGGAAAGGCAGATTGTTGCCAGTCAGCTAGAAAGATGTAGGCTTGGAGCAGAATCACCAAGCATCG
CCAGCACCAGCTCAACTGAGAAGTCATTTCCTTGGAGATCAACAGGTGAATCTGATCTTCATAAGAACTCAGAAGACTTAGTAAATGCTG

>65828_65828_1_PKP4-PDE1A_PKP4_chr2_159459616_ENST00000389757_PDE1A_chr2_183011879_ENST00000409365_length(amino acids)=130AA_BP=106
MERRRPLPKLERGMPAPEQASLVEEGQPQTRQEAASTGPGMEPETTATTILASVKEQELQFQRLTRELEVERQIVASQLERCRLGAESPS

--------------------------------------------------------------
>65828_65828_2_PKP4-PDE1A_PKP4_chr2_159459616_ENST00000389759_PDE1A_chr2_183011879_ENST00000409365_length(transcript)=509nt_BP=392nt
GCGCCGCCGCGGCACTTTTTTAATTTTTTCGGGTGCCGCAGCGGCGACCCCTCGGCGCCGATGTCCCTGATCCCTGGAGCGACGACGGCC
GCTGCCTAAGCTGGAAAGAGGAATGCCAGCTCCTGAGCAGGCCTCATTGGTGGAGGAGGGGCAACCACAGACCCGCCAGGAAGCTGCCTC
CACTGGCCCAGGCATGGAACCCGAGACCACAGCCACCACTATTCTAGCATCCGTGAAGGAGCAGGAGCTTCAGTTTCAGCGACTCACCCG
AGAACTGGAAGTGGAAAGGCAGATTGTTGCCAGTCAGCTAGAAAGATGTAGGCTTGGAGCAGAATCACCAAGCATCGCCAGCACCAGCTC
AACTGAGAAGTCATTTCCTTGGAGATCAACAGGTGAATCTGATCTTCATAAGAACTCAGAAGACTTAGTAAATGCTGAAGAAAAACATGA

>65828_65828_2_PKP4-PDE1A_PKP4_chr2_159459616_ENST00000389759_PDE1A_chr2_183011879_ENST00000409365_length(amino acids)=130AA_BP=106
MERRRPLPKLERGMPAPEQASLVEEGQPQTRQEAASTGPGMEPETTATTILASVKEQELQFQRLTRELEVERQIVASQLERCRLGAESPS

--------------------------------------------------------------

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Fusion Gene PPI Analysis for PKP4-PDE1A


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 PKP4-PDE1A


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 PKP4-PDE1A


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