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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:PPP2R4-CRAT (FusionGDB2 ID:67627)

Fusion Gene Summary for PPP2R4-CRAT

check button Fusion gene summary
Fusion gene informationFusion gene name: PPP2R4-CRAT
Fusion gene ID: 67627
HgeneTgene
Gene symbol

PPP2R4

CRAT

Gene ID

5524

1384

Gene nameprotein phosphatase 2 phosphatase activatorcarnitine O-acetyltransferase
SynonymsPP2A|PPP2R4|PR53CAT|CAT1|NBIA8
Cytomap

9q34.11

9q34.11

Type of geneprotein-codingprotein-coding
Descriptionserine/threonine-protein phosphatase 2A activatorPP2A phosphatase activatorPP2A subunit B' isoform PR53phosphotyrosyl phosphatase activatorprotein phosphatase 2 regulatory subunit 4protein phosphatase 2A activator, regulatory subunit 4protein phosphcarnitine O-acetyltransferasecarnitine acetylase
Modification date2020032920200313
UniProtAcc.

P43155

Ensembl transtripts involved in fusion geneENST00000358994, ENST00000393370, 
ENST00000337738, ENST00000348141, 
ENST00000452489, ENST00000357197, 
ENST00000347048, ENST00000355007, 
ENST00000423100, ENST00000524946, 
ENST00000436883, ENST00000414510, 
ENST00000432124, ENST00000435305, 
ENST00000419582, ENST00000432651, 
ENST00000435132, ENST00000434095, 
ENST00000318080, ENST00000464290, 
ENST00000393384, 
Fusion gene scores* DoF score10 X 9 X 8=7204 X 3 X 4=48
# samples 124
** MAII scorelog2(12/720*10)=-2.58496250072116
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(4/48*10)=-0.263034405833794
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: PPP2R4 [Title/Abstract] AND CRAT [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointPPP2R4(131873910)-CRAT(131866585), # samples:2
Anticipated loss of major functional domain due to fusion event.PPP2R4-CRAT seems lost the major protein functional domain in Hgene partner, which is a tumor suppressor due to the frame-shifted ORF.
PPP2R4-CRAT seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
PPP2R4-CRAT seems lost the major protein functional domain in Tgene partner, which is a cell metabolism gene 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
HgenePPP2R4

GO:0032515

negative regulation of phosphoprotein phosphatase activity

16916641

HgenePPP2R4

GO:0032516

positive regulation of phosphoprotein phosphatase activity

16916641

HgenePPP2R4

GO:0035307

positive regulation of protein dephosphorylation

16916641

HgenePPP2R4

GO:0035308

negative regulation of protein dephosphorylation

16916641

HgenePPP2R4

GO:0043065

positive regulation of apoptotic process

17333320

HgenePPP2R4

GO:0043666

regulation of phosphoprotein phosphatase activity

16916641

TgeneCRAT

GO:0019254

carnitine metabolic process, CoA-linked

2351134|15099582


check buttonFusion gene breakpoints across PPP2R4 (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 CRAT (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
ChimerDB4STADTCGA-BR-8080-01APPP2R4chr9

131873910

+CRATchr9

131866585

-
ChimerDB4STADTCGA-BR-8080-01APPP2R4chr9

131873910

+CRATchr9

131865345

-
ChimerDB4STADTCGA-BR-8080-01APPP2R4chr9

131873910

-CRATchr9

131866585

-


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Fusion Gene ORF analysis for PPP2R4-CRAT

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-shiftENST00000358994ENST00000318080PPP2R4chr9

131873910

+CRATchr9

131866585

-
5CDS-intronENST00000358994ENST00000464290PPP2R4chr9

131873910

+CRATchr9

131866585

-
5CDS-intronENST00000358994ENST00000393384PPP2R4chr9

131873910

+CRATchr9

131866585

-
Frame-shiftENST00000393370ENST00000318080PPP2R4chr9

131873910

+CRATchr9

131866585

-
5CDS-intronENST00000393370ENST00000464290PPP2R4chr9

131873910

+CRATchr9

131866585

-
5CDS-intronENST00000393370ENST00000393384PPP2R4chr9

131873910

+CRATchr9

131866585

-
Frame-shiftENST00000337738ENST00000318080PPP2R4chr9

131873910

+CRATchr9

131866585

-
5CDS-intronENST00000337738ENST00000464290PPP2R4chr9

131873910

+CRATchr9

131866585

-
5CDS-intronENST00000337738ENST00000393384PPP2R4chr9

131873910

+CRATchr9

131866585

-
Frame-shiftENST00000348141ENST00000318080PPP2R4chr9

131873910

+CRATchr9

131866585

-
5CDS-intronENST00000348141ENST00000464290PPP2R4chr9

131873910

+CRATchr9

131866585

-
5CDS-intronENST00000348141ENST00000393384PPP2R4chr9

131873910

+CRATchr9

131866585

-
Frame-shiftENST00000452489ENST00000318080PPP2R4chr9

131873910

+CRATchr9

131866585

-
5CDS-intronENST00000452489ENST00000464290PPP2R4chr9

131873910

+CRATchr9

131866585

-
5CDS-intronENST00000452489ENST00000393384PPP2R4chr9

131873910

+CRATchr9

131866585

-
Frame-shiftENST00000357197ENST00000318080PPP2R4chr9

131873910

+CRATchr9

131866585

-
5CDS-intronENST00000357197ENST00000464290PPP2R4chr9

131873910

+CRATchr9

131866585

-
5CDS-intronENST00000357197ENST00000393384PPP2R4chr9

131873910

+CRATchr9

131866585

-
Frame-shiftENST00000347048ENST00000318080PPP2R4chr9

131873910

+CRATchr9

131866585

-
5CDS-intronENST00000347048ENST00000464290PPP2R4chr9

131873910

+CRATchr9

131866585

-
5CDS-intronENST00000347048ENST00000393384PPP2R4chr9

131873910

+CRATchr9

131866585

-
Frame-shiftENST00000355007ENST00000318080PPP2R4chr9

131873910

+CRATchr9

131866585

-
5CDS-intronENST00000355007ENST00000464290PPP2R4chr9

131873910

+CRATchr9

131866585

-
5CDS-intronENST00000355007ENST00000393384PPP2R4chr9

131873910

+CRATchr9

131866585

-
intron-3CDSENST00000423100ENST00000318080PPP2R4chr9

131873910

+CRATchr9

131866585

-
intron-intronENST00000423100ENST00000464290PPP2R4chr9

131873910

+CRATchr9

131866585

-
intron-intronENST00000423100ENST00000393384PPP2R4chr9

131873910

+CRATchr9

131866585

-
intron-3CDSENST00000524946ENST00000318080PPP2R4chr9

131873910

+CRATchr9

131866585

-
intron-intronENST00000524946ENST00000464290PPP2R4chr9

131873910

+CRATchr9

131866585

-
intron-intronENST00000524946ENST00000393384PPP2R4chr9

131873910

+CRATchr9

131866585

-
intron-3CDSENST00000436883ENST00000318080PPP2R4chr9

131873910

+CRATchr9

131866585

-
intron-intronENST00000436883ENST00000464290PPP2R4chr9

131873910

+CRATchr9

131866585

-
intron-intronENST00000436883ENST00000393384PPP2R4chr9

131873910

+CRATchr9

131866585

-
intron-3CDSENST00000414510ENST00000318080PPP2R4chr9

131873910

+CRATchr9

131866585

-
intron-intronENST00000414510ENST00000464290PPP2R4chr9

131873910

+CRATchr9

131866585

-
intron-intronENST00000414510ENST00000393384PPP2R4chr9

131873910

+CRATchr9

131866585

-
intron-3CDSENST00000432124ENST00000318080PPP2R4chr9

131873910

+CRATchr9

131866585

-
intron-intronENST00000432124ENST00000464290PPP2R4chr9

131873910

+CRATchr9

131866585

-
intron-intronENST00000432124ENST00000393384PPP2R4chr9

131873910

+CRATchr9

131866585

-
intron-3CDSENST00000435305ENST00000318080PPP2R4chr9

131873910

+CRATchr9

131866585

-
intron-intronENST00000435305ENST00000464290PPP2R4chr9

131873910

+CRATchr9

131866585

-
intron-intronENST00000435305ENST00000393384PPP2R4chr9

131873910

+CRATchr9

131866585

-
intron-3CDSENST00000419582ENST00000318080PPP2R4chr9

131873910

+CRATchr9

131866585

-
intron-intronENST00000419582ENST00000464290PPP2R4chr9

131873910

+CRATchr9

131866585

-
intron-intronENST00000419582ENST00000393384PPP2R4chr9

131873910

+CRATchr9

131866585

-
intron-3CDSENST00000432651ENST00000318080PPP2R4chr9

131873910

+CRATchr9

131866585

-
intron-intronENST00000432651ENST00000464290PPP2R4chr9

131873910

+CRATchr9

131866585

-
intron-intronENST00000432651ENST00000393384PPP2R4chr9

131873910

+CRATchr9

131866585

-
intron-3CDSENST00000435132ENST00000318080PPP2R4chr9

131873910

+CRATchr9

131866585

-
intron-intronENST00000435132ENST00000464290PPP2R4chr9

131873910

+CRATchr9

131866585

-
intron-intronENST00000435132ENST00000393384PPP2R4chr9

131873910

+CRATchr9

131866585

-
intron-3CDSENST00000434095ENST00000318080PPP2R4chr9

131873910

+CRATchr9

131866585

-
intron-intronENST00000434095ENST00000464290PPP2R4chr9

131873910

+CRATchr9

131866585

-
intron-intronENST00000434095ENST00000393384PPP2R4chr9

131873910

+CRATchr9

131866585

-
Frame-shiftENST00000358994ENST00000318080PPP2R4chr9

131873910

+CRATchr9

131865345

-
5CDS-5UTRENST00000358994ENST00000464290PPP2R4chr9

131873910

+CRATchr9

131865345

-
5CDS-intronENST00000358994ENST00000393384PPP2R4chr9

131873910

+CRATchr9

131865345

-
Frame-shiftENST00000393370ENST00000318080PPP2R4chr9

131873910

+CRATchr9

131865345

-
5CDS-5UTRENST00000393370ENST00000464290PPP2R4chr9

131873910

+CRATchr9

131865345

-
5CDS-intronENST00000393370ENST00000393384PPP2R4chr9

131873910

+CRATchr9

131865345

-
Frame-shiftENST00000337738ENST00000318080PPP2R4chr9

131873910

+CRATchr9

131865345

-
5CDS-5UTRENST00000337738ENST00000464290PPP2R4chr9

131873910

+CRATchr9

131865345

-
5CDS-intronENST00000337738ENST00000393384PPP2R4chr9

131873910

+CRATchr9

131865345

-
Frame-shiftENST00000348141ENST00000318080PPP2R4chr9

131873910

+CRATchr9

131865345

-
5CDS-5UTRENST00000348141ENST00000464290PPP2R4chr9

131873910

+CRATchr9

131865345

-
5CDS-intronENST00000348141ENST00000393384PPP2R4chr9

131873910

+CRATchr9

131865345

-
Frame-shiftENST00000452489ENST00000318080PPP2R4chr9

131873910

+CRATchr9

131865345

-
5CDS-5UTRENST00000452489ENST00000464290PPP2R4chr9

131873910

+CRATchr9

131865345

-
5CDS-intronENST00000452489ENST00000393384PPP2R4chr9

131873910

+CRATchr9

131865345

-
Frame-shiftENST00000357197ENST00000318080PPP2R4chr9

131873910

+CRATchr9

131865345

-
5CDS-5UTRENST00000357197ENST00000464290PPP2R4chr9

131873910

+CRATchr9

131865345

-
5CDS-intronENST00000357197ENST00000393384PPP2R4chr9

131873910

+CRATchr9

131865345

-
Frame-shiftENST00000347048ENST00000318080PPP2R4chr9

131873910

+CRATchr9

131865345

-
5CDS-5UTRENST00000347048ENST00000464290PPP2R4chr9

131873910

+CRATchr9

131865345

-
5CDS-intronENST00000347048ENST00000393384PPP2R4chr9

131873910

+CRATchr9

131865345

-
Frame-shiftENST00000355007ENST00000318080PPP2R4chr9

131873910

+CRATchr9

131865345

-
5CDS-5UTRENST00000355007ENST00000464290PPP2R4chr9

131873910

+CRATchr9

131865345

-
5CDS-intronENST00000355007ENST00000393384PPP2R4chr9

131873910

+CRATchr9

131865345

-
intron-3CDSENST00000423100ENST00000318080PPP2R4chr9

131873910

+CRATchr9

131865345

-
intron-5UTRENST00000423100ENST00000464290PPP2R4chr9

131873910

+CRATchr9

131865345

-
intron-intronENST00000423100ENST00000393384PPP2R4chr9

131873910

+CRATchr9

131865345

-
intron-3CDSENST00000524946ENST00000318080PPP2R4chr9

131873910

+CRATchr9

131865345

-
intron-5UTRENST00000524946ENST00000464290PPP2R4chr9

131873910

+CRATchr9

131865345

-
intron-intronENST00000524946ENST00000393384PPP2R4chr9

131873910

+CRATchr9

131865345

-
intron-3CDSENST00000436883ENST00000318080PPP2R4chr9

131873910

+CRATchr9

131865345

-
intron-5UTRENST00000436883ENST00000464290PPP2R4chr9

131873910

+CRATchr9

131865345

-
intron-intronENST00000436883ENST00000393384PPP2R4chr9

131873910

+CRATchr9

131865345

-
intron-3CDSENST00000414510ENST00000318080PPP2R4chr9

131873910

+CRATchr9

131865345

-
intron-5UTRENST00000414510ENST00000464290PPP2R4chr9

131873910

+CRATchr9

131865345

-
intron-intronENST00000414510ENST00000393384PPP2R4chr9

131873910

+CRATchr9

131865345

-
intron-3CDSENST00000432124ENST00000318080PPP2R4chr9

131873910

+CRATchr9

131865345

-
intron-5UTRENST00000432124ENST00000464290PPP2R4chr9

131873910

+CRATchr9

131865345

-
intron-intronENST00000432124ENST00000393384PPP2R4chr9

131873910

+CRATchr9

131865345

-
intron-3CDSENST00000435305ENST00000318080PPP2R4chr9

131873910

+CRATchr9

131865345

-
intron-5UTRENST00000435305ENST00000464290PPP2R4chr9

131873910

+CRATchr9

131865345

-
intron-intronENST00000435305ENST00000393384PPP2R4chr9

131873910

+CRATchr9

131865345

-
intron-3CDSENST00000419582ENST00000318080PPP2R4chr9

131873910

+CRATchr9

131865345

-
intron-5UTRENST00000419582ENST00000464290PPP2R4chr9

131873910

+CRATchr9

131865345

-
intron-intronENST00000419582ENST00000393384PPP2R4chr9

131873910

+CRATchr9

131865345

-
intron-3CDSENST00000432651ENST00000318080PPP2R4chr9

131873910

+CRATchr9

131865345

-
intron-5UTRENST00000432651ENST00000464290PPP2R4chr9

131873910

+CRATchr9

131865345

-
intron-intronENST00000432651ENST00000393384PPP2R4chr9

131873910

+CRATchr9

131865345

-
intron-3CDSENST00000435132ENST00000318080PPP2R4chr9

131873910

+CRATchr9

131865345

-
intron-5UTRENST00000435132ENST00000464290PPP2R4chr9

131873910

+CRATchr9

131865345

-
intron-intronENST00000435132ENST00000393384PPP2R4chr9

131873910

+CRATchr9

131865345

-
intron-3CDSENST00000434095ENST00000318080PPP2R4chr9

131873910

+CRATchr9

131865345

-
intron-5UTRENST00000434095ENST00000464290PPP2R4chr9

131873910

+CRATchr9

131865345

-
intron-intronENST00000434095ENST00000393384PPP2R4chr9

131873910

+CRATchr9

131865345

-

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 PPP2R4-CRAT


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.

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 PPP2R4-CRAT


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
.CRAT

P43155

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: Catalyzes the reversible transfer of acyl groups from carnitine to coenzyme A (CoA) and regulates the acyl-CoA/CoA ratio. Also plays a crucial role in the transport of fatty acids for beta-oxidation (PubMed:15099582, PubMed:29395073). Responsible for the synthesis of short- and branched-chain acylcarnitines (PubMed:23485643). Active towards some branched-chain amino acid oxidation pathway (BCAAO) intermediates (PubMed:23485643). Trans-2-enoyl-CoAs and 2-methylacyl-CoAs are poor substrates (PubMed:23485643). {ECO:0000269|PubMed:15099582, ECO:0000269|PubMed:23485643, ECO:0000269|PubMed:29395073}.

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 PPP2R4-CRAT


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 PPP2R4-CRAT


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 PPP2R4-CRAT


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status
TgeneCRATP43155DB00583LevocarnitineSmall moleculeApproved|Investigational
TgeneCRATP43155DB00583LevocarnitineSmall moleculeApproved|Investigational

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Related Diseases for PPP2R4-CRAT


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneCRATC4693587NEURODEGENERATION WITH BRAIN IRON ACCUMULATION 81GENOMICS_ENGLAND;UNIPROT