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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:PPP6R3-CPT1A (FusionGDB2 ID:67869)

Fusion Gene Summary for PPP6R3-CPT1A

check button Fusion gene summary
Fusion gene informationFusion gene name: PPP6R3-CPT1A
Fusion gene ID: 67869
HgeneTgene
Gene symbol

PPP6R3

CPT1A

Gene ID

55291

1374

Gene nameprotein phosphatase 6 regulatory subunit 3carnitine palmitoyltransferase 1A
SynonymsC11orf23|PP6R3|SAP190|SAPL|SAPLa|SAPS3CPT1|CPT1-L|L-CPT1
Cytomap

11q13.2

11q13.3

Type of geneprotein-codingprotein-coding
Descriptionserine/threonine-protein phosphatase 6 regulatory subunit 3SAPS domain family, member 3sporulation-induced transcript 4-associated protein SAPLcarnitine O-palmitoyltransferase 1, liver isoformCPT ICPTI-Lcarnitine O-palmitoyltransferase I, liver isoformcarnitine palmitoyltransferase 1A (liver)carnitine palmitoyltransferase I, liver
Modification date2020031320200315
UniProtAcc.

P50416

Ensembl transtripts involved in fusion geneENST00000393799, ENST00000530427, 
ENST00000393800, ENST00000534534, 
ENST00000524845, ENST00000265637, 
ENST00000524904, ENST00000393801, 
ENST00000265636, ENST00000529710, 
ENST00000527403, 		ENST00000540367, 
ENST00000376618, ENST00000265641, 
ENST00000539743, ENST00000537756, 
ENST00000538994, 
Fusion gene scores* DoF score34 X 21 X 15=1071012 X 9 X 8=864
# samples 4315
** MAII scorelog2(43/10710*10)=-4.63847801004816
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(15/864*10)=-2.52606881166759
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: PPP6R3 [Title/Abstract] AND CPT1A [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointPPP6R3(68228295)-CPT1A(68580044), # 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
HgenePPP6R3

GO:0043666

regulation of phosphoprotein phosphatase activity

16716191

TgeneCPT1A

GO:0001676

long-chain fatty acid metabolic process

11350182

TgeneCPT1A

GO:0009437

carnitine metabolic process

11350182


check buttonFusion gene breakpoints across PPP6R3 (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 CPT1A (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-D7-A4Z0-01APPP6R3chr11

68228295

+CPT1Achr11

68580044

-


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Fusion Gene ORF analysis for PPP6R3-CPT1A

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-3CDSENST00000393799ENST00000540367PPP6R3chr11

68228295

+CPT1Achr11

68580044

-
5UTR-3CDSENST00000393799ENST00000376618PPP6R3chr11

68228295

+CPT1Achr11

68580044

-
5UTR-3CDSENST00000393799ENST00000265641PPP6R3chr11

68228295

+CPT1Achr11

68580044

-
5UTR-3CDSENST00000393799ENST00000539743PPP6R3chr11

68228295

+CPT1Achr11

68580044

-
5UTR-intronENST00000393799ENST00000537756PPP6R3chr11

68228295

+CPT1Achr11

68580044

-
5UTR-intronENST00000393799ENST00000538994PPP6R3chr11

68228295

+CPT1Achr11

68580044

-
3UTR-3CDSENST00000530427ENST00000540367PPP6R3chr11

68228295

+CPT1Achr11

68580044

-
3UTR-3CDSENST00000530427ENST00000376618PPP6R3chr11

68228295

+CPT1Achr11

68580044

-
3UTR-3CDSENST00000530427ENST00000265641PPP6R3chr11

68228295

+CPT1Achr11

68580044

-
3UTR-3CDSENST00000530427ENST00000539743PPP6R3chr11

68228295

+CPT1Achr11

68580044

-
3UTR-intronENST00000530427ENST00000537756PPP6R3chr11

68228295

+CPT1Achr11

68580044

-
3UTR-intronENST00000530427ENST00000538994PPP6R3chr11

68228295

+CPT1Achr11

68580044

-
5UTR-3CDSENST00000393800ENST00000540367PPP6R3chr11

68228295

+CPT1Achr11

68580044

-
5UTR-3CDSENST00000393800ENST00000376618PPP6R3chr11

68228295

+CPT1Achr11

68580044

-
5UTR-3CDSENST00000393800ENST00000265641PPP6R3chr11

68228295

+CPT1Achr11

68580044

-
5UTR-3CDSENST00000393800ENST00000539743PPP6R3chr11

68228295

+CPT1Achr11

68580044

-
5UTR-intronENST00000393800ENST00000537756PPP6R3chr11

68228295

+CPT1Achr11

68580044

-
5UTR-intronENST00000393800ENST00000538994PPP6R3chr11

68228295

+CPT1Achr11

68580044

-
5UTR-3CDSENST00000534534ENST00000540367PPP6R3chr11

68228295

+CPT1Achr11

68580044

-
5UTR-3CDSENST00000534534ENST00000376618PPP6R3chr11

68228295

+CPT1Achr11

68580044

-
5UTR-3CDSENST00000534534ENST00000265641PPP6R3chr11

68228295

+CPT1Achr11

68580044

-
5UTR-3CDSENST00000534534ENST00000539743PPP6R3chr11

68228295

+CPT1Achr11

68580044

-
5UTR-intronENST00000534534ENST00000537756PPP6R3chr11

68228295

+CPT1Achr11

68580044

-
5UTR-intronENST00000534534ENST00000538994PPP6R3chr11

68228295

+CPT1Achr11

68580044

-
5UTR-3CDSENST00000524845ENST00000540367PPP6R3chr11

68228295

+CPT1Achr11

68580044

-
5UTR-3CDSENST00000524845ENST00000376618PPP6R3chr11

68228295

+CPT1Achr11

68580044

-
5UTR-3CDSENST00000524845ENST00000265641PPP6R3chr11

68228295

+CPT1Achr11

68580044

-
5UTR-3CDSENST00000524845ENST00000539743PPP6R3chr11

68228295

+CPT1Achr11

68580044

-
5UTR-intronENST00000524845ENST00000537756PPP6R3chr11

68228295

+CPT1Achr11

68580044

-
5UTR-intronENST00000524845ENST00000538994PPP6R3chr11

68228295

+CPT1Achr11

68580044

-
5UTR-3CDSENST00000265637ENST00000540367PPP6R3chr11

68228295

+CPT1Achr11

68580044

-
5UTR-3CDSENST00000265637ENST00000376618PPP6R3chr11

68228295

+CPT1Achr11

68580044

-
5UTR-3CDSENST00000265637ENST00000265641PPP6R3chr11

68228295

+CPT1Achr11

68580044

-
5UTR-3CDSENST00000265637ENST00000539743PPP6R3chr11

68228295

+CPT1Achr11

68580044

-
5UTR-intronENST00000265637ENST00000537756PPP6R3chr11

68228295

+CPT1Achr11

68580044

-
5UTR-intronENST00000265637ENST00000538994PPP6R3chr11

68228295

+CPT1Achr11

68580044

-
5UTR-3CDSENST00000524904ENST00000540367PPP6R3chr11

68228295

+CPT1Achr11

68580044

-
5UTR-3CDSENST00000524904ENST00000376618PPP6R3chr11

68228295

+CPT1Achr11

68580044

-
5UTR-3CDSENST00000524904ENST00000265641PPP6R3chr11

68228295

+CPT1Achr11

68580044

-
5UTR-3CDSENST00000524904ENST00000539743PPP6R3chr11

68228295

+CPT1Achr11

68580044

-
5UTR-intronENST00000524904ENST00000537756PPP6R3chr11

68228295

+CPT1Achr11

68580044

-
5UTR-intronENST00000524904ENST00000538994PPP6R3chr11

68228295

+CPT1Achr11

68580044

-
5UTR-3CDSENST00000393801ENST00000540367PPP6R3chr11

68228295

+CPT1Achr11

68580044

-
5UTR-3CDSENST00000393801ENST00000376618PPP6R3chr11

68228295

+CPT1Achr11

68580044

-
5UTR-3CDSENST00000393801ENST00000265641PPP6R3chr11

68228295

+CPT1Achr11

68580044

-
5UTR-3CDSENST00000393801ENST00000539743PPP6R3chr11

68228295

+CPT1Achr11

68580044

-
5UTR-intronENST00000393801ENST00000537756PPP6R3chr11

68228295

+CPT1Achr11

68580044

-
5UTR-intronENST00000393801ENST00000538994PPP6R3chr11

68228295

+CPT1Achr11

68580044

-
5UTR-3CDSENST00000265636ENST00000540367PPP6R3chr11

68228295

+CPT1Achr11

68580044

-
5UTR-3CDSENST00000265636ENST00000376618PPP6R3chr11

68228295

+CPT1Achr11

68580044

-
5UTR-3CDSENST00000265636ENST00000265641PPP6R3chr11

68228295

+CPT1Achr11

68580044

-
5UTR-3CDSENST00000265636ENST00000539743PPP6R3chr11

68228295

+CPT1Achr11

68580044

-
5UTR-intronENST00000265636ENST00000537756PPP6R3chr11

68228295

+CPT1Achr11

68580044

-
5UTR-intronENST00000265636ENST00000538994PPP6R3chr11

68228295

+CPT1Achr11

68580044

-
5UTR-3CDSENST00000529710ENST00000540367PPP6R3chr11

68228295

+CPT1Achr11

68580044

-
5UTR-3CDSENST00000529710ENST00000376618PPP6R3chr11

68228295

+CPT1Achr11

68580044

-
5UTR-3CDSENST00000529710ENST00000265641PPP6R3chr11

68228295

+CPT1Achr11

68580044

-
5UTR-3CDSENST00000529710ENST00000539743PPP6R3chr11

68228295

+CPT1Achr11

68580044

-
5UTR-intronENST00000529710ENST00000537756PPP6R3chr11

68228295

+CPT1Achr11

68580044

-
5UTR-intronENST00000529710ENST00000538994PPP6R3chr11

68228295

+CPT1Achr11

68580044

-
intron-3CDSENST00000527403ENST00000540367PPP6R3chr11

68228295

+CPT1Achr11

68580044

-
intron-3CDSENST00000527403ENST00000376618PPP6R3chr11

68228295

+CPT1Achr11

68580044

-
intron-3CDSENST00000527403ENST00000265641PPP6R3chr11

68228295

+CPT1Achr11

68580044

-
intron-3CDSENST00000527403ENST00000539743PPP6R3chr11

68228295

+CPT1Achr11

68580044

-
intron-intronENST00000527403ENST00000537756PPP6R3chr11

68228295

+CPT1Achr11

68580044

-
intron-intronENST00000527403ENST00000538994PPP6R3chr11

68228295

+CPT1Achr11

68580044

-

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 PPP6R3-CPT1A


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 PPP6R3-CPT1A


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
.CPT1A

P50416

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 transfer of the acyl group of long-chain fatty acid-CoA conjugates onto carnitine, an essential step for the mitochondrial uptake of long-chain fatty acids and their subsequent beta-oxidation in the mitochondrion (PubMed:9691089, PubMed:11350182, PubMed:14517221). Plays an important role in hepatic triglyceride metabolism (By similarity). {ECO:0000250|UniProtKB:P32198, ECO:0000269|PubMed:11350182, ECO:0000269|PubMed:14517221, ECO:0000269|PubMed:9691089}.

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 PPP6R3-CPT1A


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 PPP6R3-CPT1A


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 PPP6R3-CPT1A


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status
TgeneCPT1AP50416DB01016GlyburideInhibitorSmall moleculeApproved
TgeneCPT1AP50416DB01016GlyburideInhibitorSmall moleculeApproved
TgeneCPT1AP50416DB00583LevocarnitineActivatorSmall moleculeApproved|Investigational
TgeneCPT1AP50416DB00583LevocarnitineActivatorSmall moleculeApproved|Investigational
TgeneCPT1AP50416DB01074PerhexilineInhibitorSmall moleculeApproved|Investigational
TgeneCPT1AP50416DB01074PerhexilineInhibitorSmall moleculeApproved|Investigational

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Related Diseases for PPP6R3-CPT1A


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneCPT1AC1829703Carnitine palmitoyl transferase 1A deficiency13CLINGEN;CTD_human;GENOMICS_ENGLAND;UNIPROT
TgeneCPT1AC0002152Alloxan Diabetes1CTD_human
TgeneCPT1AC0006142Malignant neoplasm of breast1CTD_human
TgeneCPT1AC0011849Diabetes Mellitus1CTD_human
TgeneCPT1AC0011853Diabetes Mellitus, Experimental1CTD_human
TgeneCPT1AC0011860Diabetes Mellitus, Non-Insulin-Dependent1CTD_human
TgeneCPT1AC0022661Kidney Failure, Chronic1CTD_human
TgeneCPT1AC0038433Streptozotocin Diabetes1CTD_human
TgeneCPT1AC0400966Non-alcoholic Fatty Liver Disease1CTD_human
TgeneCPT1AC0678222Breast Carcinoma1CTD_human
TgeneCPT1AC1257931Mammary Neoplasms, Human1CTD_human
TgeneCPT1AC1458155Mammary Neoplasms1CTD_human
TgeneCPT1AC3241937Nonalcoholic Steatohepatitis1CTD_human
TgeneCPT1AC4704874Mammary Carcinoma, Human1CTD_human