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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:FGD4-CNTN5 (FusionGDB2 ID:30162)

Fusion Gene Summary for FGD4-CNTN5

check button Fusion gene summary
Fusion gene informationFusion gene name: FGD4-CNTN5
Fusion gene ID: 30162
HgeneTgene
Gene symbol

FGD4

CNTN5

Gene ID

121512

53942

Gene nameFYVE, RhoGEF and PH domain containing 4contactin 5
SynonymsCMT4H|FRABP|ZFYVE6HNB-2s|NB-2
Cytomap

12p11.21

11q22.1

Type of geneprotein-codingprotein-coding
DescriptionFYVE, RhoGEF and PH domain-containing protein 4FGD1 family, member 4FGD1-related F-actin-binding proteinactin-filament binding protein frabinzinc finger FYVE domain-containing protein 6contactin-5neural adhesion moleculeneural recognition molecule NB-2
Modification date2020032820200329
UniProtAcc

Q96M96

O94779

Ensembl transtripts involved in fusion geneENST00000473513, ENST00000266482, 
ENST00000427716, ENST00000472289, 
ENST00000546442, ENST00000381025, 
ENST00000525053, ENST00000531134, 
ENST00000534526, 		ENST00000418526, 
ENST00000524871, ENST00000527185, 
ENST00000528682, ENST00000279463, 
ENST00000524560, 
Fusion gene scores* DoF score19 X 13 X 13=321118 X 15 X 12=3240
# samples 2219
** MAII scorelog2(22/3211*10)=-3.86744723620111
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(19/3240*10)=-4.09192248944104
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: FGD4 [Title/Abstract] AND CNTN5 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointFGD4(32655272)-CNTN5(99426876), # 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

check buttonFusion gene breakpoints across FGD4 (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 CNTN5 (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
ChimerDB4READTCGA-AF-6655-01AFGD4chr12

32655272

-CNTN5chr11

99426876

+
ChimerDB4READTCGA-AF-6655-01AFGD4chr12

32655272

+CNTN5chr11

99426876

+


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Fusion Gene ORF analysis for FGD4-CNTN5

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-5UTRENST00000473513ENST00000418526FGD4chr12

32655272

+CNTN5chr11

99426876

+
3UTR-5UTRENST00000473513ENST00000524871FGD4chr12

32655272

+CNTN5chr11

99426876

+
3UTR-5UTRENST00000473513ENST00000527185FGD4chr12

32655272

+CNTN5chr11

99426876

+
3UTR-5UTRENST00000473513ENST00000528682FGD4chr12

32655272

+CNTN5chr11

99426876

+
3UTR-intronENST00000473513ENST00000279463FGD4chr12

32655272

+CNTN5chr11

99426876

+
3UTR-intronENST00000473513ENST00000524560FGD4chr12

32655272

+CNTN5chr11

99426876

+
5UTR-5UTRENST00000266482ENST00000418526FGD4chr12

32655272

+CNTN5chr11

99426876

+
5UTR-5UTRENST00000266482ENST00000524871FGD4chr12

32655272

+CNTN5chr11

99426876

+
5UTR-5UTRENST00000266482ENST00000527185FGD4chr12

32655272

+CNTN5chr11

99426876

+
5UTR-5UTRENST00000266482ENST00000528682FGD4chr12

32655272

+CNTN5chr11

99426876

+
5UTR-5UTRENST00000427716ENST00000418526FGD4chr12

32655272

+CNTN5chr11

99426876

+
5UTR-5UTRENST00000427716ENST00000524871FGD4chr12

32655272

+CNTN5chr11

99426876

+
5UTR-5UTRENST00000427716ENST00000527185FGD4chr12

32655272

+CNTN5chr11

99426876

+
5UTR-5UTRENST00000427716ENST00000528682FGD4chr12

32655272

+CNTN5chr11

99426876

+
5UTR-5UTRENST00000472289ENST00000418526FGD4chr12

32655272

+CNTN5chr11

99426876

+
5UTR-5UTRENST00000472289ENST00000524871FGD4chr12

32655272

+CNTN5chr11

99426876

+
5UTR-5UTRENST00000472289ENST00000527185FGD4chr12

32655272

+CNTN5chr11

99426876

+
5UTR-5UTRENST00000472289ENST00000528682FGD4chr12

32655272

+CNTN5chr11

99426876

+
5UTR-5UTRENST00000546442ENST00000418526FGD4chr12

32655272

+CNTN5chr11

99426876

+
5UTR-5UTRENST00000546442ENST00000524871FGD4chr12

32655272

+CNTN5chr11

99426876

+
5UTR-5UTRENST00000546442ENST00000527185FGD4chr12

32655272

+CNTN5chr11

99426876

+
5UTR-5UTRENST00000546442ENST00000528682FGD4chr12

32655272

+CNTN5chr11

99426876

+
5UTR-intronENST00000266482ENST00000279463FGD4chr12

32655272

+CNTN5chr11

99426876

+
5UTR-intronENST00000266482ENST00000524560FGD4chr12

32655272

+CNTN5chr11

99426876

+
5UTR-intronENST00000427716ENST00000279463FGD4chr12

32655272

+CNTN5chr11

99426876

+
5UTR-intronENST00000427716ENST00000524560FGD4chr12

32655272

+CNTN5chr11

99426876

+
5UTR-intronENST00000472289ENST00000279463FGD4chr12

32655272

+CNTN5chr11

99426876

+
5UTR-intronENST00000472289ENST00000524560FGD4chr12

32655272

+CNTN5chr11

99426876

+
5UTR-intronENST00000546442ENST00000279463FGD4chr12

32655272

+CNTN5chr11

99426876

+
5UTR-intronENST00000546442ENST00000524560FGD4chr12

32655272

+CNTN5chr11

99426876

+
intron-5UTRENST00000381025ENST00000418526FGD4chr12

32655272

+CNTN5chr11

99426876

+
intron-5UTRENST00000381025ENST00000524871FGD4chr12

32655272

+CNTN5chr11

99426876

+
intron-5UTRENST00000381025ENST00000527185FGD4chr12

32655272

+CNTN5chr11

99426876

+
intron-5UTRENST00000381025ENST00000528682FGD4chr12

32655272

+CNTN5chr11

99426876

+
intron-5UTRENST00000525053ENST00000418526FGD4chr12

32655272

+CNTN5chr11

99426876

+
intron-5UTRENST00000525053ENST00000524871FGD4chr12

32655272

+CNTN5chr11

99426876

+
intron-5UTRENST00000525053ENST00000527185FGD4chr12

32655272

+CNTN5chr11

99426876

+
intron-5UTRENST00000525053ENST00000528682FGD4chr12

32655272

+CNTN5chr11

99426876

+
intron-5UTRENST00000531134ENST00000418526FGD4chr12

32655272

+CNTN5chr11

99426876

+
intron-5UTRENST00000531134ENST00000524871FGD4chr12

32655272

+CNTN5chr11

99426876

+
intron-5UTRENST00000531134ENST00000527185FGD4chr12

32655272

+CNTN5chr11

99426876

+
intron-5UTRENST00000531134ENST00000528682FGD4chr12

32655272

+CNTN5chr11

99426876

+
intron-5UTRENST00000534526ENST00000418526FGD4chr12

32655272

+CNTN5chr11

99426876

+
intron-5UTRENST00000534526ENST00000524871FGD4chr12

32655272

+CNTN5chr11

99426876

+
intron-5UTRENST00000534526ENST00000527185FGD4chr12

32655272

+CNTN5chr11

99426876

+
intron-5UTRENST00000534526ENST00000528682FGD4chr12

32655272

+CNTN5chr11

99426876

+
intron-intronENST00000381025ENST00000279463FGD4chr12

32655272

+CNTN5chr11

99426876

+
intron-intronENST00000381025ENST00000524560FGD4chr12

32655272

+CNTN5chr11

99426876

+
intron-intronENST00000525053ENST00000279463FGD4chr12

32655272

+CNTN5chr11

99426876

+
intron-intronENST00000525053ENST00000524560FGD4chr12

32655272

+CNTN5chr11

99426876

+
intron-intronENST00000531134ENST00000279463FGD4chr12

32655272

+CNTN5chr11

99426876

+
intron-intronENST00000531134ENST00000524560FGD4chr12

32655272

+CNTN5chr11

99426876

+
intron-intronENST00000534526ENST00000279463FGD4chr12

32655272

+CNTN5chr11

99426876

+
intron-intronENST00000534526ENST00000524560FGD4chr12

32655272

+CNTN5chr11

99426876

+

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 FGD4-CNTN5


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)
FGD4chr1232655272+CNTN5chr1199426875+2.38E-060.9999976
FGD4chr1232655272+CNTN5chr1199426875+2.38E-060.9999976

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 FGD4-CNTN5


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/:32655272/:99426876)
- 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
FGD4

Q96M96

CNTN5

O94779

FUNCTION: Activates CDC42, a member of the Ras-like family of Rho- and Rac proteins, by exchanging bound GDP for free GTP. Plays a role in regulating the actin cytoskeleton and cell shape. Activates MAPK8 (By similarity). {ECO:0000250, ECO:0000269|PubMed:15133042}.FUNCTION: Contactins mediate cell surface interactions during nervous system development. Has some neurite outgrowth-promoting activity in the cerebral cortical neurons but not in hippocampal neurons. Probably involved in neuronal activity in the auditory system (By similarity). {ECO:0000250}.

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 FGD4-CNTN5


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 FGD4-CNTN5


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 FGD4-CNTN5


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 FGD4-CNTN5


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