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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:PEX6-PPP2R5D (FusionGDB2 ID:63978)

Fusion Gene Summary for PEX6-PPP2R5D

check button Fusion gene summary
Fusion gene informationFusion gene name: PEX6-PPP2R5D
Fusion gene ID: 63978
HgeneTgene
Gene symbol

PEX6

PPP2R5D

Gene ID

5190

5528

Gene nameperoxisomal biogenesis factor 6protein phosphatase 2 regulatory subunit B'delta
SynonymsHMLR2|PAF-2|PAF2|PBD4A|PDB4B|PXAAA1B56D|B56delta|MRD35
Cytomap

6p21.1

6p21.1

Type of geneprotein-codingprotein-coding
Descriptionperoxisome biogenesis factor 6peroxin-6peroxisomal AAA-type ATPase 1peroxisomal-type ATPase 1peroxisome assembly factor 2serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit delta isoformPP2A, B subunit, B' delta isoformPP2A, B subunit, B56 delta isoformPP2A, B subunit, PR61 delta isoformPP2A, B subunit, R5 delta isoformSerine/threonine protein phosphatase
Modification date2020031320200327
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000304611, ENST00000244546, 
ENST00000485511, ENST00000394110, 
ENST00000472118, ENST00000461010, 
Fusion gene scores* DoF score3 X 5 X 2=306 X 5 X 3=90
# samples 46
** MAII scorelog2(4/30*10)=0.415037499278844
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0		log2(6/90*10)=-0.584962500721156
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: PEX6 [Title/Abstract] AND PPP2R5D [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointPEX6(42946007)-PPP2R5D(42957349), # samples:2
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
TgenePPP2R5D

GO:0006470

protein dephosphorylation

24157919


check buttonFusion gene breakpoints across PEX6 (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 PPP2R5D (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
ChimerDB4OVTCGA-13-1505-01APEX6chr6

42946007

-PPP2R5Dchr6

42957349

+
ChimerDB4OVTCGA-13-1505PEX6chr6

42946006

-PPP2R5Dchr6

42957348

+
ChimerDB4OVTCGA-13-1505-01APEX6chr6

42946007

-PPP2R5Dchr6

42957349

+
ChimerDB4OVTCGA-13-1505-01APEX6chr6

42946271

-PPP2R5Dchr6

42957349

+


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Fusion Gene ORF analysis for PEX6-PPP2R5D

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
In-frameENST00000304611ENST00000485511PEX6chr6

42946007

-PPP2R5Dchr6

42957349

+
In-frameENST00000304611ENST00000394110PEX6chr6

42946007

-PPP2R5Dchr6

42957349

+
In-frameENST00000304611ENST00000472118PEX6chr6

42946007

-PPP2R5Dchr6

42957349

+
5CDS-intronENST00000304611ENST00000461010PEX6chr6

42946007

-PPP2R5Dchr6

42957349

+
In-frameENST00000244546ENST00000485511PEX6chr6

42946007

-PPP2R5Dchr6

42957349

+
In-frameENST00000244546ENST00000394110PEX6chr6

42946007

-PPP2R5Dchr6

42957349

+
In-frameENST00000244546ENST00000472118PEX6chr6

42946007

-PPP2R5Dchr6

42957349

+
5CDS-intronENST00000244546ENST00000461010PEX6chr6

42946007

-PPP2R5Dchr6

42957349

+
In-frameENST00000304611ENST00000485511PEX6chr6

42946006

-PPP2R5Dchr6

42957348

+
In-frameENST00000304611ENST00000394110PEX6chr6

42946006

-PPP2R5Dchr6

42957348

+
In-frameENST00000304611ENST00000472118PEX6chr6

42946006

-PPP2R5Dchr6

42957348

+
5CDS-intronENST00000304611ENST00000461010PEX6chr6

42946006

-PPP2R5Dchr6

42957348

+
In-frameENST00000244546ENST00000485511PEX6chr6

42946006

-PPP2R5Dchr6

42957348

+
In-frameENST00000244546ENST00000394110PEX6chr6

42946006

-PPP2R5Dchr6

42957348

+
In-frameENST00000244546ENST00000472118PEX6chr6

42946006

-PPP2R5Dchr6

42957348

+
5CDS-intronENST00000244546ENST00000461010PEX6chr6

42946006

-PPP2R5Dchr6

42957348

+
intron-3CDSENST00000304611ENST00000485511PEX6chr6

42946271

-PPP2R5Dchr6

42957349

+
intron-3CDSENST00000304611ENST00000394110PEX6chr6

42946271

-PPP2R5Dchr6

42957349

+
intron-3CDSENST00000304611ENST00000472118PEX6chr6

42946271

-PPP2R5Dchr6

42957349

+
intron-intronENST00000304611ENST00000461010PEX6chr6

42946271

-PPP2R5Dchr6

42957349

+
intron-3CDSENST00000244546ENST00000485511PEX6chr6

42946271

-PPP2R5Dchr6

42957349

+
intron-3CDSENST00000244546ENST00000394110PEX6chr6

42946271

-PPP2R5Dchr6

42957349

+
intron-3CDSENST00000244546ENST00000472118PEX6chr6

42946271

-PPP2R5Dchr6

42957349

+
intron-intronENST00000244546ENST00000461010PEX6chr6

42946271

-PPP2R5Dchr6

42957349

+

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 PEX6-PPP2R5D


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)
PEX6chr642946006-PPP2R5Dchr642957348+0.0001183950.9998816
PEX6chr642946006-PPP2R5Dchr642957348+0.0001183950.9998816
PEX6chr642946006-PPP2R5Dchr642957348+0.0001183950.9998816
PEX6chr642946006-PPP2R5Dchr642957348+0.0001183950.9998816

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 PEX6-PPP2R5D


check button Go to

FGviewer for the breakpoints of chr6:42946007-chr6:42957349

.
- 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
TgenePPP2R5Dchr6:42946006chr6:42957348ENST00000394110016523_5309.0571.0MotifSH3-binding%3B class I
TgenePPP2R5Dchr6:42946006chr6:42957348ENST00000394110016548_5659.0571.0MotifNuclear localization signal
TgenePPP2R5Dchr6:42946006chr6:42957348ENST00000461010014523_5300497.0MotifSH3-binding%3B class I
TgenePPP2R5Dchr6:42946006chr6:42957348ENST00000461010014548_5650497.0MotifNuclear localization signal
TgenePPP2R5Dchr6:42946006chr6:42957348ENST00000485511016523_5309.0603.0MotifSH3-binding%3B class I
TgenePPP2R5Dchr6:42946006chr6:42957348ENST00000485511016548_5659.0603.0MotifNuclear localization signal
TgenePPP2R5Dchr6:42946007chr6:42957349ENST00000394110016523_5309.0571.0MotifSH3-binding%3B class I
TgenePPP2R5Dchr6:42946007chr6:42957349ENST00000394110016548_5659.0571.0MotifNuclear localization signal
TgenePPP2R5Dchr6:42946007chr6:42957349ENST00000461010014523_5300497.0MotifSH3-binding%3B class I
TgenePPP2R5Dchr6:42946007chr6:42957349ENST00000461010014548_5650497.0MotifNuclear localization signal
TgenePPP2R5Dchr6:42946007chr6:42957349ENST00000485511016523_5309.0603.0MotifSH3-binding%3B class I
TgenePPP2R5Dchr6:42946007chr6:42957349ENST00000485511016548_5659.0603.0MotifNuclear localization signal
TgenePPP2R5Dchr6:42946006chr6:42957348ENST0000039411001637_529.0571.0RegionNote=8 X 2 AA approximate tandem repeats of Q-P
TgenePPP2R5Dchr6:42946006chr6:42957348ENST0000046101001437_520497.0RegionNote=8 X 2 AA approximate tandem repeats of Q-P
TgenePPP2R5Dchr6:42946006chr6:42957348ENST0000048551101637_529.0603.0RegionNote=8 X 2 AA approximate tandem repeats of Q-P
TgenePPP2R5Dchr6:42946007chr6:42957349ENST0000039411001637_529.0571.0RegionNote=8 X 2 AA approximate tandem repeats of Q-P
TgenePPP2R5Dchr6:42946007chr6:42957349ENST0000046101001437_520497.0RegionNote=8 X 2 AA approximate tandem repeats of Q-P
TgenePPP2R5Dchr6:42946007chr6:42957349ENST0000048551101637_529.0603.0RegionNote=8 X 2 AA approximate tandem repeats of Q-P
TgenePPP2R5Dchr6:42946006chr6:42957348ENST0000039411001637_389.0571.0RepeatNote=1
TgenePPP2R5Dchr6:42946006chr6:42957348ENST0000039411001639_409.0571.0RepeatNote=2
TgenePPP2R5Dchr6:42946006chr6:42957348ENST0000039411001641_429.0571.0RepeatNote=3
TgenePPP2R5Dchr6:42946006chr6:42957348ENST0000039411001643_449.0571.0RepeatNote=4
TgenePPP2R5Dchr6:42946006chr6:42957348ENST0000039411001645_469.0571.0RepeatNote=5
TgenePPP2R5Dchr6:42946006chr6:42957348ENST0000039411001647_489.0571.0RepeatNote=6%3B approximate
TgenePPP2R5Dchr6:42946006chr6:42957348ENST0000039411001649_509.0571.0RepeatNote=7%3B approximate
TgenePPP2R5Dchr6:42946006chr6:42957348ENST0000039411001651_529.0571.0RepeatNote=8
TgenePPP2R5Dchr6:42946006chr6:42957348ENST0000046101001437_380497.0RepeatNote=1
TgenePPP2R5Dchr6:42946006chr6:42957348ENST0000046101001439_400497.0RepeatNote=2
TgenePPP2R5Dchr6:42946006chr6:42957348ENST0000046101001441_420497.0RepeatNote=3
TgenePPP2R5Dchr6:42946006chr6:42957348ENST0000046101001443_440497.0RepeatNote=4
TgenePPP2R5Dchr6:42946006chr6:42957348ENST0000046101001445_460497.0RepeatNote=5
TgenePPP2R5Dchr6:42946006chr6:42957348ENST0000046101001447_480497.0RepeatNote=6%3B approximate
TgenePPP2R5Dchr6:42946006chr6:42957348ENST0000046101001449_500497.0RepeatNote=7%3B approximate
TgenePPP2R5Dchr6:42946006chr6:42957348ENST0000046101001451_520497.0RepeatNote=8
TgenePPP2R5Dchr6:42946006chr6:42957348ENST0000048551101637_389.0603.0RepeatNote=1
TgenePPP2R5Dchr6:42946006chr6:42957348ENST0000048551101639_409.0603.0RepeatNote=2
TgenePPP2R5Dchr6:42946006chr6:42957348ENST0000048551101641_429.0603.0RepeatNote=3
TgenePPP2R5Dchr6:42946006chr6:42957348ENST0000048551101643_449.0603.0RepeatNote=4
TgenePPP2R5Dchr6:42946006chr6:42957348ENST0000048551101645_469.0603.0RepeatNote=5
TgenePPP2R5Dchr6:42946006chr6:42957348ENST0000048551101647_489.0603.0RepeatNote=6%3B approximate
TgenePPP2R5Dchr6:42946006chr6:42957348ENST0000048551101649_509.0603.0RepeatNote=7%3B approximate
TgenePPP2R5Dchr6:42946006chr6:42957348ENST0000048551101651_529.0603.0RepeatNote=8
TgenePPP2R5Dchr6:42946007chr6:42957349ENST0000039411001637_389.0571.0RepeatNote=1
TgenePPP2R5Dchr6:42946007chr6:42957349ENST0000039411001639_409.0571.0RepeatNote=2
TgenePPP2R5Dchr6:42946007chr6:42957349ENST0000039411001641_429.0571.0RepeatNote=3
TgenePPP2R5Dchr6:42946007chr6:42957349ENST0000039411001643_449.0571.0RepeatNote=4
TgenePPP2R5Dchr6:42946007chr6:42957349ENST0000039411001645_469.0571.0RepeatNote=5
TgenePPP2R5Dchr6:42946007chr6:42957349ENST0000039411001647_489.0571.0RepeatNote=6%3B approximate
TgenePPP2R5Dchr6:42946007chr6:42957349ENST0000039411001649_509.0571.0RepeatNote=7%3B approximate
TgenePPP2R5Dchr6:42946007chr6:42957349ENST0000039411001651_529.0571.0RepeatNote=8
TgenePPP2R5Dchr6:42946007chr6:42957349ENST0000046101001437_380497.0RepeatNote=1
TgenePPP2R5Dchr6:42946007chr6:42957349ENST0000046101001439_400497.0RepeatNote=2
TgenePPP2R5Dchr6:42946007chr6:42957349ENST0000046101001441_420497.0RepeatNote=3
TgenePPP2R5Dchr6:42946007chr6:42957349ENST0000046101001443_440497.0RepeatNote=4
TgenePPP2R5Dchr6:42946007chr6:42957349ENST0000046101001445_460497.0RepeatNote=5
TgenePPP2R5Dchr6:42946007chr6:42957349ENST0000046101001447_480497.0RepeatNote=6%3B approximate
TgenePPP2R5Dchr6:42946007chr6:42957349ENST0000046101001449_500497.0RepeatNote=7%3B approximate
TgenePPP2R5Dchr6:42946007chr6:42957349ENST0000046101001451_520497.0RepeatNote=8
TgenePPP2R5Dchr6:42946007chr6:42957349ENST0000048551101637_389.0603.0RepeatNote=1
TgenePPP2R5Dchr6:42946007chr6:42957349ENST0000048551101639_409.0603.0RepeatNote=2
TgenePPP2R5Dchr6:42946007chr6:42957349ENST0000048551101641_429.0603.0RepeatNote=3
TgenePPP2R5Dchr6:42946007chr6:42957349ENST0000048551101643_449.0603.0RepeatNote=4
TgenePPP2R5Dchr6:42946007chr6:42957349ENST0000048551101645_469.0603.0RepeatNote=5
TgenePPP2R5Dchr6:42946007chr6:42957349ENST0000048551101647_489.0603.0RepeatNote=6%3B approximate
TgenePPP2R5Dchr6:42946007chr6:42957349ENST0000048551101649_509.0603.0RepeatNote=7%3B approximate
TgenePPP2R5Dchr6:42946007chr6:42957349ENST0000048551101651_529.0603.0RepeatNote=8

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgenePEX6chr6:42946006chr6:42957348ENST00000304611-117470_477294.0981.0Nucleotide bindingATP
HgenePEX6chr6:42946006chr6:42957348ENST00000304611-117744_751294.0981.0Nucleotide bindingATP
HgenePEX6chr6:42946007chr6:42957349ENST00000304611-117470_477294.0981.0Nucleotide bindingATP
HgenePEX6chr6:42946007chr6:42957349ENST00000304611-117744_751294.0981.0Nucleotide bindingATP


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Fusion Gene Sequence for PEX6-PPP2R5D


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 PEX6-PPP2R5D


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 PEX6-PPP2R5D


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 PEX6-PPP2R5D


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgenePEX6C3553936PEROXISOME BIOGENESIS DISORDER 4A (ZELLWEGER)10CTD_human;GENOMICS_ENGLAND;UNIPROT
HgenePEX6C3553937PEROXISOME BIOGENESIS DISORDER 4B5CTD_human;GENOMICS_ENGLAND
HgenePEX6C4225267HEIMLER SYNDROME 24GENOMICS_ENGLAND;UNIPROT
HgenePEX6C1832200Peroxisome biogenesis disorders3CTD_human;GENOMICS_ENGLAND
HgenePEX6C0043459Zellweger Syndrome2CTD_human;GENOMICS_ENGLAND
HgenePEX6C0751594Zellweger-Like Syndrome2CTD_human
HgenePEX6C3658299Zellweger Spectrum2CTD_human
HgenePEX6C0020796Profound Mental Retardation1CTD_human
HgenePEX6C0025363Mental Retardation, Psychosocial1CTD_human
HgenePEX6C0917816Mental deficiency1CTD_human
HgenePEX6C1849094SPINOCEREBELLAR ATAXIA, AUTOSOMAL RECESSIVE 31ORPHANET
HgenePEX6C1856186Deafness enamel hypoplasia nail defects1CTD_human;ORPHANET
HgenePEX6C3714756Intellectual Disability1CTD_human
TgenePPP2R5DC4225354MENTAL RETARDATION, AUTOSOMAL DOMINANT 353CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
TgenePPP2R5DC1535926Neurodevelopmental Disorders1CTD_human
TgenePPP2R5DC3714756Intellectual Disability1GENOMICS_ENGLAND