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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:PDE6B-PPP2R2D (FusionGDB2 ID:63373)

Fusion Gene Summary for PDE6B-PPP2R2D

check button Fusion gene summary
Fusion gene informationFusion gene name: PDE6B-PPP2R2D
Fusion gene ID: 63373
HgeneTgene
Gene symbol

PDE6B

PPP2R2D

Gene ID

5158

55844

Gene namephosphodiesterase 6Bprotein phosphatase 2 regulatory subunit Bdelta
SynonymsCSNB3|CSNBAD2|GMP-PDEbeta|PDEB|RP40|rd1B55D|B55delta|MDS026
Cytomap

4p16.3

10q26.3

Type of geneprotein-codingprotein-coding
Descriptionrod cGMP-specific 3',5'-cyclic phosphodiesterase subunit betaGMP-PDE betaphosphodiesterase 6B, cGMP-specific, rod, betarod cGMP-phosphodiesterase beta-subunitserine/threonine-protein phosphatase 2A 55 kDa regulatory subunit B delta isoformPP2A subunit B isoform B55-deltaPP2A subunit B isoform PR55-deltaPP2A subunit B isoform R2-deltaPP2A subunit B isoform deltaprotein phosphatase 2 regulatory subunit B, d
Modification date2020032820200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000255622, ENST00000496514, 
ENST00000429163, 		ENST00000422256, 
ENST00000470416, 
Fusion gene scores* DoF score1 X 1 X 1=16 X 7 X 3=126
# samples 27
** MAII scorelog2(2/1*10)=4.32192809488736log2(7/126*10)=-0.84799690655495
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: PDE6B [Title/Abstract] AND PPP2R2D [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointPDE6B(619882)-PPP2R2D(133747960), # samples:7
Anticipated loss of major functional domain due to fusion event.PDE6B-PPP2R2D seems lost the major protein functional domain in Hgene partner, which is a cell metabolism gene due to the frame-shifted ORF.
PDE6B-PPP2R2D seems lost the major protein functional domain in Hgene 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

check buttonFusion gene breakpoints across PDE6B (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 PPP2R2D (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
ChimerDB4Non-CancerTCGA-BH-A1ET-11BPDE6Bchr4

619882

+PPP2R2Dchr10

133753533

+
ChimerDB4Non-CancerTCGA-A7-A0CH-11APDE6Bchr4

619882

+PPP2R2Dchr10

133753533

+
ChimerDB4Non-CancerTCGA-BH-A0B8-11APDE6Bchr4

619882

+PPP2R2Dchr10

133747960

+
ChimerDB4Non-CancerTCGA-A6-2685-11APDE6Bchr4

619882

+PPP2R2Dchr10

133747960

+
ChimerDB4Non-CancerTCGA-KN-8437-11APDE6Bchr4

619882

+PPP2R2Dchr10

133753533

+
ChimerDB4Non-CancerERR188157PDE6Bchr4

619882

+PPP2R2Dchr10

133747960

+
ChimerDB4Non-CancerERR188117PDE6Bchr4

619882

+PPP2R2Dchr10

133747960

+
ChimerDB4Non-CancerERR188057PDE6Bchr4

619882

+PPP2R2Dchr10

133753533

+
ChimerDB4Non-CancerERR188310PDE6Bchr4

619882

+PPP2R2Dchr10

133753533

+
ChimerDB4Non-CancerERR188412PDE6Bchr4

619882

+PPP2R2Dchr10

133747960

+
ChimerDB4Non-CancerERR188029PDE6Bchr4

619882

+PPP2R2Dchr10

133747960

+
ChimerDB4Non-CancerERR188212PDE6Bchr4

619882

+PPP2R2Dchr10

133747960

+
ChimerDB4Non-CancerERR188085PDE6Bchr4

619882

+PPP2R2Dchr10

133753533

+


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Fusion Gene ORF analysis for PDE6B-PPP2R2D

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-shiftENST00000255622ENST00000422256PDE6Bchr4

619882

+PPP2R2Dchr10

133753533

+
5CDS-intronENST00000255622ENST00000470416PDE6Bchr4

619882

+PPP2R2Dchr10

133753533

+
Frame-shiftENST00000496514ENST00000422256PDE6Bchr4

619882

+PPP2R2Dchr10

133753533

+
5CDS-intronENST00000496514ENST00000470416PDE6Bchr4

619882

+PPP2R2Dchr10

133753533

+
intron-3CDSENST00000429163ENST00000422256PDE6Bchr4

619882

+PPP2R2Dchr10

133753533

+
intron-intronENST00000429163ENST00000470416PDE6Bchr4

619882

+PPP2R2Dchr10

133753533

+
5CDS-intronENST00000255622ENST00000422256PDE6Bchr4

619882

+PPP2R2Dchr10

133747960

+
5CDS-intronENST00000255622ENST00000470416PDE6Bchr4

619882

+PPP2R2Dchr10

133747960

+
5CDS-intronENST00000496514ENST00000422256PDE6Bchr4

619882

+PPP2R2Dchr10

133747960

+
5CDS-intronENST00000496514ENST00000470416PDE6Bchr4

619882

+PPP2R2Dchr10

133747960

+
intron-intronENST00000429163ENST00000422256PDE6Bchr4

619882

+PPP2R2Dchr10

133747960

+
intron-intronENST00000429163ENST00000470416PDE6Bchr4

619882

+PPP2R2Dchr10

133747960

+

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 PDE6B-PPP2R2D


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)
PDE6Bchr4619883+PPP2R2Dchr10133753532+0.0073638520.99263614
PDE6Bchr4619883+PPP2R2Dchr10133753532+0.0073638520.99263614

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.

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Fusion Protein Features for PDE6B-PPP2R2D


check button Go to

FGviewer for the breakpoints of :-:

.
- FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels.
FGviewer

check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
..
FUNCTION: Might normally function as a transcriptional repressor. EWS-fusion-proteins (EFPS) may play a role in the tumorigenic process. They may disturb gene expression by mimicking, or interfering with the normal function of CTD-POLII within the transcription initiation complex. They may also contribute to an aberrant activation of the fusion protein target genes.FUNCTION: Might normally function as a transcriptional repressor. EWS-fusion-proteins (EFPS) may play a role in the tumorigenic process. They may disturb gene expression by mimicking, or interfering with the normal function of CTD-POLII within the transcription initiation complex. They may also contribute to an aberrant activation of the fusion protein target genes.

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 PDE6B-PPP2R2D


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 PDE6B-PPP2R2D


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 PDE6B-PPP2R2D


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 PDE6B-PPP2R2D


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgenePDE6BC3151107RETINITIS PIGMENTOSA 40 (disorder)7CTD_human;GENOMICS_ENGLAND;UNIPROT
HgenePDE6BC0035304Retinal Degeneration4CTD_human
HgenePDE6BC0035334Retinitis Pigmentosa1CTD_human;GENOMICS_ENGLAND
HgenePDE6BC0339535Night blindness, congenital stationary1CTD_human;GENOMICS_ENGLAND;ORPHANET
HgenePDE6BC1848172NIGHT BLINDNESS, CONGENITAL STATIONARY, TYPE 2A1CTD_human
HgenePDE6BC1850362NIGHT BLINDNESS, CONGENITAL STATIONARY, TYPE 1B1CTD_human
HgenePDE6BC1864877NIGHT BLINDNESS, CONGENITAL STATIONARY, TYPE 2B (disorder)1CTD_human
HgenePDE6BC1876182NIGHT BLINDNESS, CONGENITAL STATIONARY, AUTOSOMAL DOMINANT 21CTD_human;GENOMICS_ENGLAND;UNIPROT
HgenePDE6BC3495587Night Blindness, Congenital Stationary, Type 1A1CTD_human
HgenePDE6BC3501847Night blindness, congenital stationary, type 11CTD_human
HgenePDE6BC3711543X-Linked Csnb1CTD_human
HgenePDE6BC4041558Cone-rod synaptic disorder, congenital nonprogressive1CTD_human