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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-TTC39B (FusionGDB2 ID:30088)

Fusion Gene Summary for FGD4-TTC39B

check button Fusion gene summary
Fusion gene informationFusion gene name: FGD4-TTC39B
Fusion gene ID: 30088
HgeneTgene
Gene symbol

FGD4

TTC39B

Gene ID

121512

158219

Gene nameFYVE, RhoGEF and PH domain containing 4tetratricopeptide repeat domain 39B
SynonymsCMT4H|FRABP|ZFYVE6C9orf52
Cytomap

12p11.21

9p22.3

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 6tetratricopeptide repeat protein 39BTPR repeat protein 39B
Modification date2020032820200313
UniProtAcc

Q96M96

.
Ensembl transtripts involved in fusion geneENST00000534526, ENST00000531134, 
ENST00000427716, ENST00000266482, 
ENST00000546442, ENST00000525053, 
ENST00000381025, ENST00000472289, 
ENST00000473513, 		ENST00000512701, 
ENST00000355694, ENST00000380850, 
ENST00000297615, ENST00000507285, 
ENST00000507993, ENST00000541445, 
ENST00000582994, 
Fusion gene scores* DoF score19 X 13 X 13=32116 X 6 X 3=108
# samples 226
** MAII scorelog2(22/3211*10)=-3.86744723620111
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(6/108*10)=-0.84799690655495
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: FGD4 [Title/Abstract] AND TTC39B [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointFGD4(32655272)-TTC39B(15226012), # 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 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 TTC39B (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/ADB443222FGD4chr12

32655272

+TTC39Bchr9

15226012

-


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Fusion Gene ORF analysis for FGD4-TTC39B

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
intron-3CDSENST00000534526ENST00000512701FGD4chr12

32655272

+TTC39Bchr9

15226012

-
intron-3CDSENST00000534526ENST00000355694FGD4chr12

32655272

+TTC39Bchr9

15226012

-
intron-3CDSENST00000534526ENST00000380850FGD4chr12

32655272

+TTC39Bchr9

15226012

-
intron-intronENST00000534526ENST00000297615FGD4chr12

32655272

+TTC39Bchr9

15226012

-
intron-5UTRENST00000534526ENST00000507285FGD4chr12

32655272

+TTC39Bchr9

15226012

-
intron-intronENST00000534526ENST00000507993FGD4chr12

32655272

+TTC39Bchr9

15226012

-
intron-intronENST00000534526ENST00000541445FGD4chr12

32655272

+TTC39Bchr9

15226012

-
intron-5UTRENST00000534526ENST00000582994FGD4chr12

32655272

+TTC39Bchr9

15226012

-
intron-3CDSENST00000531134ENST00000512701FGD4chr12

32655272

+TTC39Bchr9

15226012

-
intron-3CDSENST00000531134ENST00000355694FGD4chr12

32655272

+TTC39Bchr9

15226012

-
intron-3CDSENST00000531134ENST00000380850FGD4chr12

32655272

+TTC39Bchr9

15226012

-
intron-intronENST00000531134ENST00000297615FGD4chr12

32655272

+TTC39Bchr9

15226012

-
intron-5UTRENST00000531134ENST00000507285FGD4chr12

32655272

+TTC39Bchr9

15226012

-
intron-intronENST00000531134ENST00000507993FGD4chr12

32655272

+TTC39Bchr9

15226012

-
intron-intronENST00000531134ENST00000541445FGD4chr12

32655272

+TTC39Bchr9

15226012

-
intron-5UTRENST00000531134ENST00000582994FGD4chr12

32655272

+TTC39Bchr9

15226012

-
5UTR-3CDSENST00000427716ENST00000512701FGD4chr12

32655272

+TTC39Bchr9

15226012

-
5UTR-3CDSENST00000427716ENST00000355694FGD4chr12

32655272

+TTC39Bchr9

15226012

-
5UTR-3CDSENST00000427716ENST00000380850FGD4chr12

32655272

+TTC39Bchr9

15226012

-
5UTR-intronENST00000427716ENST00000297615FGD4chr12

32655272

+TTC39Bchr9

15226012

-
5UTR-5UTRENST00000427716ENST00000507285FGD4chr12

32655272

+TTC39Bchr9

15226012

-
5UTR-intronENST00000427716ENST00000507993FGD4chr12

32655272

+TTC39Bchr9

15226012

-
5UTR-intronENST00000427716ENST00000541445FGD4chr12

32655272

+TTC39Bchr9

15226012

-
5UTR-5UTRENST00000427716ENST00000582994FGD4chr12

32655272

+TTC39Bchr9

15226012

-
5UTR-3CDSENST00000266482ENST00000512701FGD4chr12

32655272

+TTC39Bchr9

15226012

-
5UTR-3CDSENST00000266482ENST00000355694FGD4chr12

32655272

+TTC39Bchr9

15226012

-
5UTR-3CDSENST00000266482ENST00000380850FGD4chr12

32655272

+TTC39Bchr9

15226012

-
5UTR-intronENST00000266482ENST00000297615FGD4chr12

32655272

+TTC39Bchr9

15226012

-
5UTR-5UTRENST00000266482ENST00000507285FGD4chr12

32655272

+TTC39Bchr9

15226012

-
5UTR-intronENST00000266482ENST00000507993FGD4chr12

32655272

+TTC39Bchr9

15226012

-
5UTR-intronENST00000266482ENST00000541445FGD4chr12

32655272

+TTC39Bchr9

15226012

-
5UTR-5UTRENST00000266482ENST00000582994FGD4chr12

32655272

+TTC39Bchr9

15226012

-
5UTR-3CDSENST00000546442ENST00000512701FGD4chr12

32655272

+TTC39Bchr9

15226012

-
5UTR-3CDSENST00000546442ENST00000355694FGD4chr12

32655272

+TTC39Bchr9

15226012

-
5UTR-3CDSENST00000546442ENST00000380850FGD4chr12

32655272

+TTC39Bchr9

15226012

-
5UTR-intronENST00000546442ENST00000297615FGD4chr12

32655272

+TTC39Bchr9

15226012

-
5UTR-5UTRENST00000546442ENST00000507285FGD4chr12

32655272

+TTC39Bchr9

15226012

-
5UTR-intronENST00000546442ENST00000507993FGD4chr12

32655272

+TTC39Bchr9

15226012

-
5UTR-intronENST00000546442ENST00000541445FGD4chr12

32655272

+TTC39Bchr9

15226012

-
5UTR-5UTRENST00000546442ENST00000582994FGD4chr12

32655272

+TTC39Bchr9

15226012

-
intron-3CDSENST00000525053ENST00000512701FGD4chr12

32655272

+TTC39Bchr9

15226012

-
intron-3CDSENST00000525053ENST00000355694FGD4chr12

32655272

+TTC39Bchr9

15226012

-
intron-3CDSENST00000525053ENST00000380850FGD4chr12

32655272

+TTC39Bchr9

15226012

-
intron-intronENST00000525053ENST00000297615FGD4chr12

32655272

+TTC39Bchr9

15226012

-
intron-5UTRENST00000525053ENST00000507285FGD4chr12

32655272

+TTC39Bchr9

15226012

-
intron-intronENST00000525053ENST00000507993FGD4chr12

32655272

+TTC39Bchr9

15226012

-
intron-intronENST00000525053ENST00000541445FGD4chr12

32655272

+TTC39Bchr9

15226012

-
intron-5UTRENST00000525053ENST00000582994FGD4chr12

32655272

+TTC39Bchr9

15226012

-
intron-3CDSENST00000381025ENST00000512701FGD4chr12

32655272

+TTC39Bchr9

15226012

-
intron-3CDSENST00000381025ENST00000355694FGD4chr12

32655272

+TTC39Bchr9

15226012

-
intron-3CDSENST00000381025ENST00000380850FGD4chr12

32655272

+TTC39Bchr9

15226012

-
intron-intronENST00000381025ENST00000297615FGD4chr12

32655272

+TTC39Bchr9

15226012

-
intron-5UTRENST00000381025ENST00000507285FGD4chr12

32655272

+TTC39Bchr9

15226012

-
intron-intronENST00000381025ENST00000507993FGD4chr12

32655272

+TTC39Bchr9

15226012

-
intron-intronENST00000381025ENST00000541445FGD4chr12

32655272

+TTC39Bchr9

15226012

-
intron-5UTRENST00000381025ENST00000582994FGD4chr12

32655272

+TTC39Bchr9

15226012

-
5UTR-3CDSENST00000472289ENST00000512701FGD4chr12

32655272

+TTC39Bchr9

15226012

-
5UTR-3CDSENST00000472289ENST00000355694FGD4chr12

32655272

+TTC39Bchr9

15226012

-
5UTR-3CDSENST00000472289ENST00000380850FGD4chr12

32655272

+TTC39Bchr9

15226012

-
5UTR-intronENST00000472289ENST00000297615FGD4chr12

32655272

+TTC39Bchr9

15226012

-
5UTR-5UTRENST00000472289ENST00000507285FGD4chr12

32655272

+TTC39Bchr9

15226012

-
5UTR-intronENST00000472289ENST00000507993FGD4chr12

32655272

+TTC39Bchr9

15226012

-
5UTR-intronENST00000472289ENST00000541445FGD4chr12

32655272

+TTC39Bchr9

15226012

-
5UTR-5UTRENST00000472289ENST00000582994FGD4chr12

32655272

+TTC39Bchr9

15226012

-
3UTR-3CDSENST00000473513ENST00000512701FGD4chr12

32655272

+TTC39Bchr9

15226012

-
3UTR-3CDSENST00000473513ENST00000355694FGD4chr12

32655272

+TTC39Bchr9

15226012

-
3UTR-3CDSENST00000473513ENST00000380850FGD4chr12

32655272

+TTC39Bchr9

15226012

-
3UTR-intronENST00000473513ENST00000297615FGD4chr12

32655272

+TTC39Bchr9

15226012

-
3UTR-5UTRENST00000473513ENST00000507285FGD4chr12

32655272

+TTC39Bchr9

15226012

-
3UTR-intronENST00000473513ENST00000507993FGD4chr12

32655272

+TTC39Bchr9

15226012

-
3UTR-intronENST00000473513ENST00000541445FGD4chr12

32655272

+TTC39Bchr9

15226012

-
3UTR-5UTRENST00000473513ENST00000582994FGD4chr12

32655272

+TTC39Bchr9

15226012

-

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-TTC39B


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 FGD4-TTC39B


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
FGD4

Q96M96

.
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: 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.

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-TTC39B


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-TTC39B


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-TTC39B


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-TTC39B


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneFGD4C1836336CHARCOT-MARIE-TOOTH DISEASE, TYPE 4H3CTD_human;GENOMICS_ENGLAND;UNIPROT