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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:PDLIM5-PDC (FusionGDB2 ID:64000)

Fusion Gene Summary for PDLIM5-PDC

check button Fusion gene summary
Fusion gene informationFusion gene name: PDLIM5-PDC
Fusion gene ID: 64000
HgeneTgene
Gene symbol

PDLIM5

PDC

Gene ID

10611

25953

Gene namePDZ and LIM domain 5PNKD metallo-beta-lactamase domain containing
SynonymsENH|ENH1|L9|LIMBRP17|DYT8|FKSG19|FPD1|KIPP1184|MR-1|MR-1S|MR1|PDC|PKND1|PNKD1|R1|TAHCCP2
Cytomap

4q22.3

2q35

Type of geneprotein-codingprotein-coding
DescriptionPDZ and LIM domain protein 5enigma homologenigma-like LIM domain proteinenigma-like PDZ and LIM domains proteinprobable hydrolase PNKDPNKD, MBL domain containingbrain protein 17myofibrillogenesis regulator 1trans-activated by hepatitis C virus core protein 2
Modification date2020031320200313
UniProtAcc.

O75340

Ensembl transtripts involved in fusion geneENST00000380176, ENST00000317968, 
ENST00000437932, ENST00000514743, 
ENST00000542407, ENST00000318007, 
ENST00000359265, ENST00000380180, 
ENST00000450793, ENST00000504489, 
ENST00000508216, ENST00000512274, 
ENST00000538141, 		ENST00000391997, 
ENST00000340129, ENST00000456239, 
ENST00000497198, 
Fusion gene scores* DoF score20 X 18 X 9=32402 X 2 X 2=8
# samples 232
** MAII scorelog2(23/3240*10)=-3.81628804682761
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(2/8*10)=1.32192809488736
Context

PubMed: PDLIM5 [Title/Abstract] AND PDC [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointPDLIM5(95539258)-PDC(186430230), # 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

check buttonFusion gene breakpoints across PDLIM5 (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 PDC (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
ChiTaRS5.0N/AAF076463PDLIM5chr4

95539258

+PDCchr1

186430230

-


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Fusion Gene ORF analysis for PDLIM5-PDC

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-5UTRENST00000380176ENST00000391997PDLIM5chr4

95539258

+PDCchr1

186430230

-
3UTR-intronENST00000380176ENST00000340129PDLIM5chr4

95539258

+PDCchr1

186430230

-
3UTR-intronENST00000380176ENST00000456239PDLIM5chr4

95539258

+PDCchr1

186430230

-
3UTR-intronENST00000380176ENST00000497198PDLIM5chr4

95539258

+PDCchr1

186430230

-
5CDS-5UTRENST00000317968ENST00000391997PDLIM5chr4

95539258

+PDCchr1

186430230

-
5CDS-5UTRENST00000437932ENST00000391997PDLIM5chr4

95539258

+PDCchr1

186430230

-
5CDS-5UTRENST00000514743ENST00000391997PDLIM5chr4

95539258

+PDCchr1

186430230

-
5CDS-5UTRENST00000542407ENST00000391997PDLIM5chr4

95539258

+PDCchr1

186430230

-
5CDS-intronENST00000317968ENST00000340129PDLIM5chr4

95539258

+PDCchr1

186430230

-
5CDS-intronENST00000317968ENST00000456239PDLIM5chr4

95539258

+PDCchr1

186430230

-
5CDS-intronENST00000317968ENST00000497198PDLIM5chr4

95539258

+PDCchr1

186430230

-
5CDS-intronENST00000437932ENST00000340129PDLIM5chr4

95539258

+PDCchr1

186430230

-
5CDS-intronENST00000437932ENST00000456239PDLIM5chr4

95539258

+PDCchr1

186430230

-
5CDS-intronENST00000437932ENST00000497198PDLIM5chr4

95539258

+PDCchr1

186430230

-
5CDS-intronENST00000514743ENST00000340129PDLIM5chr4

95539258

+PDCchr1

186430230

-
5CDS-intronENST00000514743ENST00000456239PDLIM5chr4

95539258

+PDCchr1

186430230

-
5CDS-intronENST00000514743ENST00000497198PDLIM5chr4

95539258

+PDCchr1

186430230

-
5CDS-intronENST00000542407ENST00000340129PDLIM5chr4

95539258

+PDCchr1

186430230

-
5CDS-intronENST00000542407ENST00000456239PDLIM5chr4

95539258

+PDCchr1

186430230

-
5CDS-intronENST00000542407ENST00000497198PDLIM5chr4

95539258

+PDCchr1

186430230

-
intron-5UTRENST00000318007ENST00000391997PDLIM5chr4

95539258

+PDCchr1

186430230

-
intron-5UTRENST00000359265ENST00000391997PDLIM5chr4

95539258

+PDCchr1

186430230

-
intron-5UTRENST00000380180ENST00000391997PDLIM5chr4

95539258

+PDCchr1

186430230

-
intron-5UTRENST00000450793ENST00000391997PDLIM5chr4

95539258

+PDCchr1

186430230

-
intron-5UTRENST00000504489ENST00000391997PDLIM5chr4

95539258

+PDCchr1

186430230

-
intron-5UTRENST00000508216ENST00000391997PDLIM5chr4

95539258

+PDCchr1

186430230

-
intron-5UTRENST00000512274ENST00000391997PDLIM5chr4

95539258

+PDCchr1

186430230

-
intron-5UTRENST00000538141ENST00000391997PDLIM5chr4

95539258

+PDCchr1

186430230

-
intron-intronENST00000318007ENST00000340129PDLIM5chr4

95539258

+PDCchr1

186430230

-
intron-intronENST00000318007ENST00000456239PDLIM5chr4

95539258

+PDCchr1

186430230

-
intron-intronENST00000318007ENST00000497198PDLIM5chr4

95539258

+PDCchr1

186430230

-
intron-intronENST00000359265ENST00000340129PDLIM5chr4

95539258

+PDCchr1

186430230

-
intron-intronENST00000359265ENST00000456239PDLIM5chr4

95539258

+PDCchr1

186430230

-
intron-intronENST00000359265ENST00000497198PDLIM5chr4

95539258

+PDCchr1

186430230

-
intron-intronENST00000380180ENST00000340129PDLIM5chr4

95539258

+PDCchr1

186430230

-
intron-intronENST00000380180ENST00000456239PDLIM5chr4

95539258

+PDCchr1

186430230

-
intron-intronENST00000380180ENST00000497198PDLIM5chr4

95539258

+PDCchr1

186430230

-
intron-intronENST00000450793ENST00000340129PDLIM5chr4

95539258

+PDCchr1

186430230

-
intron-intronENST00000450793ENST00000456239PDLIM5chr4

95539258

+PDCchr1

186430230

-
intron-intronENST00000450793ENST00000497198PDLIM5chr4

95539258

+PDCchr1

186430230

-
intron-intronENST00000504489ENST00000340129PDLIM5chr4

95539258

+PDCchr1

186430230

-
intron-intronENST00000504489ENST00000456239PDLIM5chr4

95539258

+PDCchr1

186430230

-
intron-intronENST00000504489ENST00000497198PDLIM5chr4

95539258

+PDCchr1

186430230

-
intron-intronENST00000508216ENST00000340129PDLIM5chr4

95539258

+PDCchr1

186430230

-
intron-intronENST00000508216ENST00000456239PDLIM5chr4

95539258

+PDCchr1

186430230

-
intron-intronENST00000508216ENST00000497198PDLIM5chr4

95539258

+PDCchr1

186430230

-
intron-intronENST00000512274ENST00000340129PDLIM5chr4

95539258

+PDCchr1

186430230

-
intron-intronENST00000512274ENST00000456239PDLIM5chr4

95539258

+PDCchr1

186430230

-
intron-intronENST00000512274ENST00000497198PDLIM5chr4

95539258

+PDCchr1

186430230

-
intron-intronENST00000538141ENST00000340129PDLIM5chr4

95539258

+PDCchr1

186430230

-
intron-intronENST00000538141ENST00000456239PDLIM5chr4

95539258

+PDCchr1

186430230

-
intron-intronENST00000538141ENST00000497198PDLIM5chr4

95539258

+PDCchr1

186430230

-

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 PDLIM5-PDC


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 PDLIM5-PDC


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/:95539258/:186430230)
- 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
.PDC

O75340

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: Calcium sensor that plays a key role in processes such as endoplasmic reticulum (ER)-Golgi vesicular transport, endosomal biogenesis or membrane repair. Acts as an adapter that bridges unrelated proteins or stabilizes weak protein-protein complexes in response to calcium: calcium-binding triggers exposure of apolar surface, promoting interaction with different sets of proteins thanks to 3 different hydrophobic pockets, leading to translocation to membranes (PubMed:20691033, PubMed:25667979). Involved in ER-Golgi transport by promoting the association between PDCD6IP and TSG101, thereby bridging together the ESCRT-III and ESCRT-I complexes (PubMed:19520058). Together with PEF1, acts as calcium-dependent adapter for the BCR(KLHL12) complex, a complex involved in ER-Golgi transport by regulating the size of COPII coats (PubMed:27716508). In response to cytosolic calcium increase, the heterodimer formed with PEF1 interacts with, and bridges together the BCR(KLHL12) complex and SEC31 (SEC31A or SEC31B), promoting monoubiquitination of SEC31 and subsequent collagen export, which is required for neural crest specification (PubMed:27716508). Involved in the regulation of the distribution and function of MCOLN1 in the endosomal pathway (PubMed:19864416). Promotes localization and polymerization of TFG at endoplasmic reticulum exit site (PubMed:27813252). Required for T-cell receptor-, Fas-, and glucocorticoid-induced apoptosis (By similarity). May mediate Ca(2+)-regulated signals along the death pathway: interaction with DAPK1 can accelerate apoptotic cell death by increasing caspase-3 activity (PubMed:16132846). Its role in apoptosis may however be indirect, as suggested by knockout experiments (By similarity). May inhibit KDR/VEGFR2-dependent angiogenesis; the function involves inhibition of VEGF-induced phosphorylation of the Akt signaling pathway (PubMed:21893193). In case of infection by HIV-1 virus, indirectly inhibits HIV-1 production by affecting viral Gag expression and distribution (PubMed:27784779). {ECO:0000250|UniProtKB:P12815, ECO:0000269|PubMed:16132846, ECO:0000269|PubMed:19520058, ECO:0000269|PubMed:19864416, ECO:0000269|PubMed:20691033, ECO:0000269|PubMed:21893193, ECO:0000269|PubMed:25667979, ECO:0000269|PubMed:27716508, ECO:0000269|PubMed:27784779, ECO:0000269|PubMed:27813252}.; FUNCTION: [Isoform 2]: Has a lower Ca(2+) affinity than isoform 1 (By similarity). {ECO:0000250|UniProtKB:P12815}.

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 PDLIM5-PDC


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 PDLIM5-PDC


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 PDLIM5-PDC


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 PDLIM5-PDC


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