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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:PLD3-ACTN4 (FusionGDB2 ID:66090)

Fusion Gene Summary for PLD3-ACTN4

check button Fusion gene summary
Fusion gene informationFusion gene name: PLD3-ACTN4
Fusion gene ID: 66090
HgeneTgene
Gene symbol

PLD3

ACTN4

Gene ID

23646

81

Gene namephospholipase D family member 3actinin alpha 4
SynonymsAD19|HU-K4|HUK4|SCA46ACTININ-4|FSGS|FSGS1
Cytomap

19q13.2

19q13.2

Type of geneprotein-codingprotein-coding
Descriptionphospholipase D3choline phosphatase 3hindIII K4L homologphosphatidylcholine-hydrolyzing phospholipase D3alpha-actinin-4focal segmental glomerulosclerosis 1non-muscle alpha-actinin 4
Modification date2020032920200327
UniProtAcc.

O43707

Ensembl transtripts involved in fusion geneENST00000594085, ENST00000409419, 
ENST00000409587, ENST00000409735, 
ENST00000356508, ENST00000409281, 
ENST00000252699, ENST00000390009, 
ENST00000424234, ENST00000497637, 
Fusion gene scores* DoF score16 X 15 X 8=192027 X 38 X 12=12312
# samples 2048
** MAII scorelog2(20/1920*10)=-3.26303440583379
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(48/12312*10)=-4.68088692071969
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: PLD3 [Title/Abstract] AND ACTN4 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointPLD3(40854675)-ACTN4(39198757), # 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
HgenePLD3

GO:0014902

myotube differentiation

22428023

TgeneACTN4

GO:0033209

tumor necrosis factor-mediated signaling pathway

25411248

TgeneACTN4

GO:0035357

peroxisome proliferator activated receptor signaling pathway

22351778

TgeneACTN4

GO:0048384

retinoic acid receptor signaling pathway

22351778

TgeneACTN4

GO:0051272

positive regulation of cellular component movement

9508771


check buttonFusion gene breakpoints across PLD3 (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 ACTN4 (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
ChimerDB4BRCATCGA-EW-A1PH-01APLD3chr19

40854675

+ACTN4chr19

39198757

+
ChimerDB4BRCATCGA-EW-A1PHPLD3chr19

40854675

+ACTN4chr19

39198756

+


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Fusion Gene ORF analysis for PLD3-ACTN4

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
3UTR-3CDSENST00000594085ENST00000252699PLD3chr19

40854675

+ACTN4chr19

39198757

+
3UTR-3CDSENST00000594085ENST00000252699PLD3chr19

40854675

+ACTN4chr19

39198756

+
3UTR-intronENST00000594085ENST00000390009PLD3chr19

40854675

+ACTN4chr19

39198757

+
3UTR-intronENST00000594085ENST00000390009PLD3chr19

40854675

+ACTN4chr19

39198756

+
3UTR-intronENST00000594085ENST00000424234PLD3chr19

40854675

+ACTN4chr19

39198757

+
3UTR-intronENST00000594085ENST00000424234PLD3chr19

40854675

+ACTN4chr19

39198756

+
3UTR-intronENST00000594085ENST00000497637PLD3chr19

40854675

+ACTN4chr19

39198757

+
3UTR-intronENST00000594085ENST00000497637PLD3chr19

40854675

+ACTN4chr19

39198756

+
5UTR-3CDSENST00000409419ENST00000252699PLD3chr19

40854675

+ACTN4chr19

39198757

+
5UTR-3CDSENST00000409419ENST00000252699PLD3chr19

40854675

+ACTN4chr19

39198756

+
5UTR-3CDSENST00000409587ENST00000252699PLD3chr19

40854675

+ACTN4chr19

39198757

+
5UTR-3CDSENST00000409587ENST00000252699PLD3chr19

40854675

+ACTN4chr19

39198756

+
5UTR-3CDSENST00000409735ENST00000252699PLD3chr19

40854675

+ACTN4chr19

39198757

+
5UTR-3CDSENST00000409735ENST00000252699PLD3chr19

40854675

+ACTN4chr19

39198756

+
5UTR-intronENST00000409419ENST00000390009PLD3chr19

40854675

+ACTN4chr19

39198757

+
5UTR-intronENST00000409419ENST00000390009PLD3chr19

40854675

+ACTN4chr19

39198756

+
5UTR-intronENST00000409419ENST00000424234PLD3chr19

40854675

+ACTN4chr19

39198757

+
5UTR-intronENST00000409419ENST00000424234PLD3chr19

40854675

+ACTN4chr19

39198756

+
5UTR-intronENST00000409419ENST00000497637PLD3chr19

40854675

+ACTN4chr19

39198757

+
5UTR-intronENST00000409419ENST00000497637PLD3chr19

40854675

+ACTN4chr19

39198756

+
5UTR-intronENST00000409587ENST00000390009PLD3chr19

40854675

+ACTN4chr19

39198757

+
5UTR-intronENST00000409587ENST00000390009PLD3chr19

40854675

+ACTN4chr19

39198756

+
5UTR-intronENST00000409587ENST00000424234PLD3chr19

40854675

+ACTN4chr19

39198757

+
5UTR-intronENST00000409587ENST00000424234PLD3chr19

40854675

+ACTN4chr19

39198756

+
5UTR-intronENST00000409587ENST00000497637PLD3chr19

40854675

+ACTN4chr19

39198757

+
5UTR-intronENST00000409587ENST00000497637PLD3chr19

40854675

+ACTN4chr19

39198756

+
5UTR-intronENST00000409735ENST00000390009PLD3chr19

40854675

+ACTN4chr19

39198757

+
5UTR-intronENST00000409735ENST00000390009PLD3chr19

40854675

+ACTN4chr19

39198756

+
5UTR-intronENST00000409735ENST00000424234PLD3chr19

40854675

+ACTN4chr19

39198757

+
5UTR-intronENST00000409735ENST00000424234PLD3chr19

40854675

+ACTN4chr19

39198756

+
5UTR-intronENST00000409735ENST00000497637PLD3chr19

40854675

+ACTN4chr19

39198757

+
5UTR-intronENST00000409735ENST00000497637PLD3chr19

40854675

+ACTN4chr19

39198756

+
intron-3CDSENST00000356508ENST00000252699PLD3chr19

40854675

+ACTN4chr19

39198757

+
intron-3CDSENST00000356508ENST00000252699PLD3chr19

40854675

+ACTN4chr19

39198756

+
intron-3CDSENST00000409281ENST00000252699PLD3chr19

40854675

+ACTN4chr19

39198757

+
intron-3CDSENST00000409281ENST00000252699PLD3chr19

40854675

+ACTN4chr19

39198756

+
intron-intronENST00000356508ENST00000390009PLD3chr19

40854675

+ACTN4chr19

39198757

+
intron-intronENST00000356508ENST00000390009PLD3chr19

40854675

+ACTN4chr19

39198756

+
intron-intronENST00000356508ENST00000424234PLD3chr19

40854675

+ACTN4chr19

39198757

+
intron-intronENST00000356508ENST00000424234PLD3chr19

40854675

+ACTN4chr19

39198756

+
intron-intronENST00000356508ENST00000497637PLD3chr19

40854675

+ACTN4chr19

39198757

+
intron-intronENST00000356508ENST00000497637PLD3chr19

40854675

+ACTN4chr19

39198756

+
intron-intronENST00000409281ENST00000390009PLD3chr19

40854675

+ACTN4chr19

39198757

+
intron-intronENST00000409281ENST00000390009PLD3chr19

40854675

+ACTN4chr19

39198756

+
intron-intronENST00000409281ENST00000424234PLD3chr19

40854675

+ACTN4chr19

39198757

+
intron-intronENST00000409281ENST00000424234PLD3chr19

40854675

+ACTN4chr19

39198756

+
intron-intronENST00000409281ENST00000497637PLD3chr19

40854675

+ACTN4chr19

39198757

+
intron-intronENST00000409281ENST00000497637PLD3chr19

40854675

+ACTN4chr19

39198756

+

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 PLD3-ACTN4


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)
PLD3chr1940854675+ACTN4chr1939198756+0.000128940.999871
PLD3chr1940854675+ACTN4chr1939198756+0.000128940.999871
PLD3chr1940854675+ACTN4chr1939198756+0.000128940.999871
PLD3chr1940854675+ACTN4chr1939198756+0.000128940.999871

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.
genomic feature of top 1%

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Fusion Protein Features for PLD3-ACTN4


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/:40854675/:39198757)
- 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
.ACTN4

O43707

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: F-actin cross-linking protein which is thought to anchor actin to a variety of intracellular structures. This is a bundling protein (Probable). Probably involved in vesicular trafficking via its association with the CART complex. The CART complex is necessary for efficient transferrin receptor recycling but not for EGFR degradation (PubMed:15772161). Involved in tight junction assembly in epithelial cells probably through interaction with MICALL2. Links MICALL2 to the actin cytoskeleton and recruits it to the tight junctions (By similarity). May also function as a transcriptional coactivator, stimulating transcription mediated by the nuclear hormone receptors PPARG and RARA (PubMed:22351778). {ECO:0000250|UniProtKB:P57780, ECO:0000269|PubMed:15772161, ECO:0000269|PubMed:22351778, ECO:0000305|PubMed:9508771}.

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 PLD3-ACTN4


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 PLD3-ACTN4


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 PLD3-ACTN4


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 PLD3-ACTN4


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