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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:PLXND1-TMCC1 (FusionGDB2 ID:66596)

Fusion Gene Summary for PLXND1-TMCC1

check button Fusion gene summary
Fusion gene informationFusion gene name: PLXND1-TMCC1
Fusion gene ID: 66596
HgeneTgene
Gene symbol

PLXND1

TMCC1

Gene ID

23129

23023

Gene nameplexin D1transmembrane and coiled-coil domain family 1
SynonymsPLEXD1-
Cytomap

3q22.1

3q22.1

Type of geneprotein-codingprotein-coding
Descriptionplexin-D1transmembrane and coiled-coil domains protein 1
Modification date2020031320200313
UniProtAcc.

O94876

Ensembl transtripts involved in fusion geneENST00000393239, ENST00000324093, 
ENST00000504689, 		ENST00000329333, 
ENST00000393238, ENST00000426664, 
ENST00000432054, ENST00000515024, 
Fusion gene scores* DoF score7 X 9 X 8=5046 X 6 X 6=216
# samples 910
** MAII scorelog2(9/504*10)=-2.48542682717024
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(10/216*10)=-1.11103131238874
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: PLXND1 [Title/Abstract] AND TMCC1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointPLXND1(129324172)-TMCC1(129390107), # samples:3
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
TgeneTMCC1

GO:0016197

endosomal transport

30220460

TgeneTMCC1

GO:0090148

membrane fission

30220460

TgeneTMCC1

GO:0097750

endosome membrane tubulation

30220460


check buttonFusion gene breakpoints across PLXND1 (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 TMCC1 (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-AR-A1AI-01APLXND1chr3

129324172

-TMCC1chr3

129390107

-
ChimerDB4BRCATCGA-AR-A24Q-01APLXND1chr3

129324172

-TMCC1chr3

129390107

-
ChimerDB4HNSCTCGA-CR-5248PLXND1chr3

129324172

-TMCC1chr3

129390107

-
ChimerDB4UCECTCGA-AX-A2H4-01APLXND1chr3

129277271

-TMCC1chr3

129373946

-
ChimerKB3..PLXND1chr3

129292436

-TMCC1chr3

129370638

-
ChimerKB3..PLXND1chr3

129293178

-TMCC1chr3

129370638

-
ChimerKB3..PLXND1chr3

129293178

-TMCC1chr3

129373946

-


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Fusion Gene ORF analysis for PLXND1-TMCC1

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-3CDSENST00000393239ENST00000329333PLXND1chr3

129277271

-TMCC1chr3

129373946

-
3UTR-3CDSENST00000393239ENST00000393238PLXND1chr3

129277271

-TMCC1chr3

129373946

-
3UTR-3CDSENST00000393239ENST00000426664PLXND1chr3

129277271

-TMCC1chr3

129373946

-
3UTR-3CDSENST00000393239ENST00000432054PLXND1chr3

129277271

-TMCC1chr3

129373946

-
3UTR-intronENST00000393239ENST00000515024PLXND1chr3

129277271

-TMCC1chr3

129373946

-
5CDS-5UTRENST00000324093ENST00000329333PLXND1chr3

129324172

-TMCC1chr3

129390107

-
5CDS-5UTRENST00000324093ENST00000393238PLXND1chr3

129324172

-TMCC1chr3

129390107

-
5CDS-5UTRENST00000324093ENST00000426664PLXND1chr3

129324172

-TMCC1chr3

129390107

-
5CDS-5UTRENST00000324093ENST00000432054PLXND1chr3

129324172

-TMCC1chr3

129390107

-
5CDS-5UTRENST00000393239ENST00000329333PLXND1chr3

129324172

-TMCC1chr3

129390107

-
5CDS-5UTRENST00000393239ENST00000393238PLXND1chr3

129324172

-TMCC1chr3

129390107

-
5CDS-5UTRENST00000393239ENST00000426664PLXND1chr3

129324172

-TMCC1chr3

129390107

-
5CDS-5UTRENST00000393239ENST00000432054PLXND1chr3

129324172

-TMCC1chr3

129390107

-
5CDS-intronENST00000324093ENST00000515024PLXND1chr3

129324172

-TMCC1chr3

129390107

-
5CDS-intronENST00000324093ENST00000515024PLXND1chr3

129277271

-TMCC1chr3

129373946

-
5CDS-intronENST00000324093ENST00000515024PLXND1chr3

129292436

-TMCC1chr3

129370638

-
5CDS-intronENST00000324093ENST00000515024PLXND1chr3

129293178

-TMCC1chr3

129370638

-
5CDS-intronENST00000324093ENST00000515024PLXND1chr3

129293178

-TMCC1chr3

129373946

-
5CDS-intronENST00000393239ENST00000515024PLXND1chr3

129324172

-TMCC1chr3

129390107

-
5CDS-intronENST00000393239ENST00000515024PLXND1chr3

129292436

-TMCC1chr3

129370638

-
5CDS-intronENST00000393239ENST00000515024PLXND1chr3

129293178

-TMCC1chr3

129370638

-
5CDS-intronENST00000393239ENST00000515024PLXND1chr3

129293178

-TMCC1chr3

129373946

-
Frame-shiftENST00000324093ENST00000329333PLXND1chr3

129277271

-TMCC1chr3

129373946

-
Frame-shiftENST00000324093ENST00000329333PLXND1chr3

129293178

-TMCC1chr3

129370638

-
Frame-shiftENST00000324093ENST00000329333PLXND1chr3

129293178

-TMCC1chr3

129373946

-
Frame-shiftENST00000324093ENST00000393238PLXND1chr3

129277271

-TMCC1chr3

129373946

-
Frame-shiftENST00000324093ENST00000393238PLXND1chr3

129292436

-TMCC1chr3

129370638

-
Frame-shiftENST00000324093ENST00000393238PLXND1chr3

129293178

-TMCC1chr3

129370638

-
Frame-shiftENST00000324093ENST00000393238PLXND1chr3

129293178

-TMCC1chr3

129373946

-
Frame-shiftENST00000324093ENST00000426664PLXND1chr3

129277271

-TMCC1chr3

129373946

-
Frame-shiftENST00000324093ENST00000426664PLXND1chr3

129292436

-TMCC1chr3

129370638

-
Frame-shiftENST00000324093ENST00000426664PLXND1chr3

129293178

-TMCC1chr3

129370638

-
Frame-shiftENST00000324093ENST00000426664PLXND1chr3

129293178

-TMCC1chr3

129373946

-
Frame-shiftENST00000324093ENST00000432054PLXND1chr3

129277271

-TMCC1chr3

129373946

-
Frame-shiftENST00000324093ENST00000432054PLXND1chr3

129293178

-TMCC1chr3

129370638

-
Frame-shiftENST00000324093ENST00000432054PLXND1chr3

129293178

-TMCC1chr3

129373946

-
Frame-shiftENST00000393239ENST00000329333PLXND1chr3

129292436

-TMCC1chr3

129370638

-
Frame-shiftENST00000393239ENST00000329333PLXND1chr3

129293178

-TMCC1chr3

129370638

-
Frame-shiftENST00000393239ENST00000329333PLXND1chr3

129293178

-TMCC1chr3

129373946

-
Frame-shiftENST00000393239ENST00000393238PLXND1chr3

129292436

-TMCC1chr3

129370638

-
Frame-shiftENST00000393239ENST00000393238PLXND1chr3

129293178

-TMCC1chr3

129370638

-
Frame-shiftENST00000393239ENST00000393238PLXND1chr3

129293178

-TMCC1chr3

129373946

-
Frame-shiftENST00000393239ENST00000426664PLXND1chr3

129292436

-TMCC1chr3

129370638

-
Frame-shiftENST00000393239ENST00000426664PLXND1chr3

129293178

-TMCC1chr3

129370638

-
Frame-shiftENST00000393239ENST00000426664PLXND1chr3

129293178

-TMCC1chr3

129373946

-
Frame-shiftENST00000393239ENST00000432054PLXND1chr3

129292436

-TMCC1chr3

129370638

-
Frame-shiftENST00000393239ENST00000432054PLXND1chr3

129293178

-TMCC1chr3

129370638

-
Frame-shiftENST00000393239ENST00000432054PLXND1chr3

129293178

-TMCC1chr3

129373946

-
In-frameENST00000324093ENST00000329333PLXND1chr3

129292436

-TMCC1chr3

129370638

-
In-frameENST00000324093ENST00000432054PLXND1chr3

129292436

-TMCC1chr3

129370638

-
intron-3CDSENST00000504689ENST00000329333PLXND1chr3

129277271

-TMCC1chr3

129373946

-
intron-3CDSENST00000504689ENST00000329333PLXND1chr3

129292436

-TMCC1chr3

129370638

-
intron-3CDSENST00000504689ENST00000329333PLXND1chr3

129293178

-TMCC1chr3

129370638

-
intron-3CDSENST00000504689ENST00000329333PLXND1chr3

129293178

-TMCC1chr3

129373946

-
intron-3CDSENST00000504689ENST00000393238PLXND1chr3

129277271

-TMCC1chr3

129373946

-
intron-3CDSENST00000504689ENST00000393238PLXND1chr3

129292436

-TMCC1chr3

129370638

-
intron-3CDSENST00000504689ENST00000393238PLXND1chr3

129293178

-TMCC1chr3

129370638

-
intron-3CDSENST00000504689ENST00000393238PLXND1chr3

129293178

-TMCC1chr3

129373946

-
intron-3CDSENST00000504689ENST00000426664PLXND1chr3

129277271

-TMCC1chr3

129373946

-
intron-3CDSENST00000504689ENST00000426664PLXND1chr3

129292436

-TMCC1chr3

129370638

-
intron-3CDSENST00000504689ENST00000426664PLXND1chr3

129293178

-TMCC1chr3

129370638

-
intron-3CDSENST00000504689ENST00000426664PLXND1chr3

129293178

-TMCC1chr3

129373946

-
intron-3CDSENST00000504689ENST00000432054PLXND1chr3

129277271

-TMCC1chr3

129373946

-
intron-3CDSENST00000504689ENST00000432054PLXND1chr3

129292436

-TMCC1chr3

129370638

-
intron-3CDSENST00000504689ENST00000432054PLXND1chr3

129293178

-TMCC1chr3

129370638

-
intron-3CDSENST00000504689ENST00000432054PLXND1chr3

129293178

-TMCC1chr3

129373946

-
intron-5UTRENST00000504689ENST00000329333PLXND1chr3

129324172

-TMCC1chr3

129390107

-
intron-5UTRENST00000504689ENST00000393238PLXND1chr3

129324172

-TMCC1chr3

129390107

-
intron-5UTRENST00000504689ENST00000426664PLXND1chr3

129324172

-TMCC1chr3

129390107

-
intron-5UTRENST00000504689ENST00000432054PLXND1chr3

129324172

-TMCC1chr3

129390107

-
intron-intronENST00000504689ENST00000515024PLXND1chr3

129324172

-TMCC1chr3

129390107

-
intron-intronENST00000504689ENST00000515024PLXND1chr3

129277271

-TMCC1chr3

129373946

-
intron-intronENST00000504689ENST00000515024PLXND1chr3

129292436

-TMCC1chr3

129370638

-
intron-intronENST00000504689ENST00000515024PLXND1chr3

129293178

-TMCC1chr3

129370638

-
intron-intronENST00000504689ENST00000515024PLXND1chr3

129293178

-TMCC1chr3

129373946

-

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 PLXND1-TMCC1


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 PLXND1-TMCC1


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/chr3:129324172/chr3:129390107)
- 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
.TMCC1

O94876

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: Endoplasmic reticulum membrane protein that promotes endoplasmic reticulum-associated endosome fission (PubMed:30220460). Localizes to contact sites between the endoplasmic reticulum and endosomes and acts by promoting recruitment of the endoplasmic reticulum to endosome tubules for fission (PubMed:30220460). Endosome membrane fission of early and late endosomes is essential to separate regions destined for lysosomal degradation from carriers to be recycled to the plasma membrane (PubMed:30220460). {ECO:0000269|PubMed:30220460}.

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 PLXND1-TMCC1


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 PLXND1-TMCC1


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 PLXND1-TMCC1


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 PLXND1-TMCC1


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