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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:ITM2B-TTC3 (FusionGDB2 ID:40629)

Fusion Gene Summary for ITM2B-TTC3

check button Fusion gene summary
Fusion gene informationFusion gene name: ITM2B-TTC3
Fusion gene ID: 40629
HgeneTgene
Gene symbol

ITM2B

TTC3

Gene ID

9445

7267

Gene nameintegral membrane protein 2Btetratricopeptide repeat domain 3
SynonymsABRI|BRI|BRI2|BRICD2B|E25B|E3-16|FBD|RDGCA|imBRI2DCRR1|RNF105|TPRDIII
Cytomap

13q14.2

21q22.13

Type of geneprotein-codingprotein-coding
Descriptionintegral membrane protein 2BABri/ADan amyloid peptideBRICHOS domain containing 2Bepididymis secretory sperm binding proteinimmature BRI2transmembrane protein BRIE3 ubiquitin-protein ligase TTC3RING finger protein 105RING-type E3 ubiquitin transferase TTC3TPR repeat protein 3TPR repeat protein Dtetratricopeptide repeat protein 3
Modification date2020031320200320
UniProtAcc

Q9Y287

.
Ensembl transtripts involved in fusion geneENST00000378549, ENST00000378565, 
ENST00000354749, ENST00000355666, 
ENST00000399017, ENST00000479930, 
ENST00000399010, ENST00000540756, 
Fusion gene scores* DoF score14 X 11 X 13=200219 X 18 X 9=3078
# samples 2624
** MAII scorelog2(26/2002*10)=-2.94485844580754
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(24/3078*10)=-3.68088692071969
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: ITM2B [Title/Abstract] AND TTC3 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointITM2B(48835457)-TTC3(38466305), # samples:2
TTC3(38460175)-ITM2B(48827944), # 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
HgeneITM2B

GO:0042985

negative regulation of amyloid precursor protein biosynthetic process

16027166|18524908

TgeneTTC3

GO:0006511

ubiquitin-dependent protein catabolic process

20059950

TgeneTTC3

GO:0070936

protein K48-linked ubiquitination

20059950


check buttonFusion gene breakpoints across ITM2B (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 TTC3 (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
ChimerDB4SKCMTCGA-FW-A5DX-01AITM2Bchr13

48835457

+TTC3chr21

38466305

+
ChimerDB4SKCMTCGA-FW-A5DX-01AITM2Bchr13

48835457

+TTC3chr21

38467650

+


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Fusion Gene ORF analysis for ITM2B-TTC3

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-3CDSENST00000378549ENST00000354749ITM2Bchr13

48835457

+TTC3chr21

38466305

+
3UTR-3CDSENST00000378549ENST00000354749ITM2Bchr13

48835457

+TTC3chr21

38467650

+
3UTR-3CDSENST00000378549ENST00000355666ITM2Bchr13

48835457

+TTC3chr21

38466305

+
3UTR-3CDSENST00000378549ENST00000355666ITM2Bchr13

48835457

+TTC3chr21

38467650

+
3UTR-3CDSENST00000378549ENST00000399017ITM2Bchr13

48835457

+TTC3chr21

38466305

+
3UTR-3CDSENST00000378549ENST00000399017ITM2Bchr13

48835457

+TTC3chr21

38467650

+
3UTR-3CDSENST00000378565ENST00000354749ITM2Bchr13

48835457

+TTC3chr21

38466305

+
3UTR-3CDSENST00000378565ENST00000354749ITM2Bchr13

48835457

+TTC3chr21

38467650

+
3UTR-3CDSENST00000378565ENST00000355666ITM2Bchr13

48835457

+TTC3chr21

38466305

+
3UTR-3CDSENST00000378565ENST00000355666ITM2Bchr13

48835457

+TTC3chr21

38467650

+
3UTR-3CDSENST00000378565ENST00000399017ITM2Bchr13

48835457

+TTC3chr21

38466305

+
3UTR-3CDSENST00000378565ENST00000399017ITM2Bchr13

48835457

+TTC3chr21

38467650

+
3UTR-3UTRENST00000378549ENST00000479930ITM2Bchr13

48835457

+TTC3chr21

38467650

+
3UTR-3UTRENST00000378565ENST00000479930ITM2Bchr13

48835457

+TTC3chr21

38467650

+
3UTR-intronENST00000378549ENST00000399010ITM2Bchr13

48835457

+TTC3chr21

38466305

+
3UTR-intronENST00000378549ENST00000399010ITM2Bchr13

48835457

+TTC3chr21

38467650

+
3UTR-intronENST00000378549ENST00000479930ITM2Bchr13

48835457

+TTC3chr21

38466305

+
3UTR-intronENST00000378549ENST00000540756ITM2Bchr13

48835457

+TTC3chr21

38466305

+
3UTR-intronENST00000378549ENST00000540756ITM2Bchr13

48835457

+TTC3chr21

38467650

+
3UTR-intronENST00000378565ENST00000399010ITM2Bchr13

48835457

+TTC3chr21

38466305

+
3UTR-intronENST00000378565ENST00000399010ITM2Bchr13

48835457

+TTC3chr21

38467650

+
3UTR-intronENST00000378565ENST00000479930ITM2Bchr13

48835457

+TTC3chr21

38466305

+
3UTR-intronENST00000378565ENST00000540756ITM2Bchr13

48835457

+TTC3chr21

38466305

+
3UTR-intronENST00000378565ENST00000540756ITM2Bchr13

48835457

+TTC3chr21

38467650

+

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 ITM2B-TTC3


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 ITM2B-TTC3


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/:48835457/:38466305)
- 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
ITM2B

Q9Y287

.
FUNCTION: Plays a regulatory role in the processing of the amyloid-beta A4 precursor protein (APP) and acts as an inhibitor of the amyloid-beta peptide aggregation and fibrils deposition. Plays a role in the induction of neurite outgrowth. Functions as a protease inhibitor by blocking access of secretases to APP cleavage sites.; FUNCTION: Mature BRI2 (mBRI2) functions as a modulator of the amyloid-beta A4 precursor protein (APP) processing leading to a strong reduction in the secretion of secretase-processed amyloid-beta protein 40 and amyloid-beta protein 42.; FUNCTION: Bri23 peptide prevents aggregation of APP amyloid-beta protein 42 into toxic oligomers.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}.

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 ITM2B-TTC3


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 ITM2B-TTC3


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 ITM2B-TTC3


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 ITM2B-TTC3


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