Fusion Gene Studies
in Kim Lab

FusionBase FusionGDB FusionGDB2 FusionPDB FusionNeoAntigen FusionAI FusionNW FGviewer Publication Contact
FusionGDB Logo

Home

Download

Statistics

Examples

Help

Contact

Center for Computational Systems Medicine
leaf

Fusion Gene Summary

leaf

Fusion Gene ORF analysis

leaf

Fusion Genomic Features

leaf

Fusion Protein Features

leaf

Fusion Gene Sequence

leaf

Fusion Gene PPI analysis

leaf

Related Drugs

leaf

Related Diseases

Fusion gene:ITSN2-HADHA (FusionGDB2 ID:HG50618TG3030)

Fusion Gene Summary for ITSN2-HADHA

check button Fusion gene summary
Fusion gene informationFusion gene name: ITSN2-HADHA
Fusion gene ID: hg50618tg3030
HgeneTgene
Gene symbol

ITSN2

HADHA

Gene ID

50618

3030

Gene nameintersectin 2hydroxyacyl-CoA dehydrogenase trifunctional multienzyme complex subunit alpha
SynonymsPRO2015|SH3D1B|SH3P18|SWA|SWAPECHA|GBP|HADH|LCEH|LCHAD|MTPA|TP-ALPHA
Cytomap('ITSN2')('HADHA')

2p23.3

2p23.3

Type of geneprotein-codingprotein-coding
Descriptionintersectin-2SH3 domain-containing protein 1BSH3P18-like WASP-associated proteintrifunctional enzyme subunit alpha, mitochondrial3-ketoacyl-Coenzyme A (CoA) thiolase, alpha subunit3-oxoacyl-CoA thiolase78 kDa gastrin-binding proteingastrin-binding proteinhydroxyacyl-CoA dehydrogenase/3-ketoacyl-CoA thiolase/enoyl-CoA hydratase (
Modification date2020031320200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000355123, ENST00000361999, 
ENST00000406921, ENST00000407704, 
Fusion gene scores* DoF score13 X 16 X 6=12487 X 6 X 7=294
# samples 189
** MAII scorelog2(18/1248*10)=-2.79354912253257
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(9/294*10)=-1.70781924850669
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: ITSN2 [Title/Abstract] AND HADHA [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointITSN2(24493540)-HADHA(26438044), # samples:1
Anticipated loss of major functional domain due to fusion event.ITSN2-HADHA seems lost the major protein functional domain in Tgene partner, which is a cell metabolism gene due to the frame-shifted ORF.
* 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
HgeneITSN2

GO:1903861

positive regulation of dendrite extension

23999003

TgeneHADHA

GO:0035965

cardiolipin acyl-chain remodeling

23152787



check button Fusion gene information
* 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-A2-A04U-01AITSN2chr2

24493540

-HADHAchr2

26438044

-


Top

Fusion Gene ORF analysis for ITSN2-HADHA

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
5CDS-intronENST00000355123ENST00000461025ITSN2chr2

24493540

-HADHAchr2

26438044

-
5CDS-intronENST00000361999ENST00000461025ITSN2chr2

24493540

-HADHAchr2

26438044

-
5CDS-intronENST00000406921ENST00000461025ITSN2chr2

24493540

-HADHAchr2

26438044

-
Frame-shiftENST00000355123ENST00000380649ITSN2chr2

24493540

-HADHAchr2

26438044

-
Frame-shiftENST00000355123ENST00000457468ITSN2chr2

24493540

-HADHAchr2

26438044

-
Frame-shiftENST00000361999ENST00000380649ITSN2chr2

24493540

-HADHAchr2

26438044

-
Frame-shiftENST00000361999ENST00000457468ITSN2chr2

24493540

-HADHAchr2

26438044

-
Frame-shiftENST00000406921ENST00000380649ITSN2chr2

24493540

-HADHAchr2

26438044

-
Frame-shiftENST00000406921ENST00000457468ITSN2chr2

24493540

-HADHAchr2

26438044

-
intron-3CDSENST00000407704ENST00000380649ITSN2chr2

24493540

-HADHAchr2

26438044

-
intron-3CDSENST00000407704ENST00000457468ITSN2chr2

24493540

-HADHAchr2

26438044

-
intron-intronENST00000407704ENST00000461025ITSN2chr2

24493540

-HADHAchr2

26438044

-

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

Top

Fusion Genomic Features for ITSN2-HADHA


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)


Top

Fusion Protein Features for ITSN2-HADHA


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/:24493540/:26438044)
- 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
..
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: 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


Top

Fusion Gene Sequence for ITSN2-HADHA


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.

Top

Fusion Gene PPI Analysis for ITSN2-HADHA


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


Top

Related Drugs for ITSN2-HADHA


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

Top

Related Diseases for ITSN2-HADHA


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneITSN2C0006142Malignant neoplasm of breast1CTD_human
HgeneITSN2C0027643Neoplasm Recurrence, Local1CTD_human
HgeneITSN2C0033578Prostatic Neoplasms1CTD_human
HgeneITSN2C0086981Sicca Syndrome1CTD_human
HgeneITSN2C0376358Malignant neoplasm of prostate1CTD_human
HgeneITSN2C0678222Breast Carcinoma1CTD_human
HgeneITSN2C1257931Mammary Neoplasms, Human1CTD_human
HgeneITSN2C1458155Mammary Neoplasms1CTD_human
HgeneITSN2C1527336Sjogren's Syndrome1CTD_human
HgeneITSN2C4704874Mammary Carcinoma, Human1CTD_human
TgeneC3711645Long chain 3-hydroxyacyl-CoA dehydrogenase deficiency9CLINGEN;CTD_human;GENOMICS_ENGLAND;UNIPROT
TgeneC1969443Trifunctional Protein Deficiency With Myopathy And Neuropathy3CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
TgeneC0019193Hepatitis, Toxic1CTD_human
TgeneC0029408Degenerative polyarthritis1CTD_human
TgeneC0086743Osteoarthrosis Deformans1CTD_human
TgeneC0151744Myocardial Ischemia1CTD_human
TgeneC0369183Erythrocyte Mean Corpuscular Hemoglobin Test1GENOMICS_ENGLAND
TgeneC0860207Drug-Induced Liver Disease1CTD_human
TgeneC1261502Finding of Mean Corpuscular Hemoglobin1GENOMICS_ENGLAND
TgeneC1262760Hepatitis, Drug-Induced1CTD_human
TgeneC1455728Acute fatty liver of pregnancy1ORPHANET
TgeneC3658290Drug-Induced Acute Liver Injury1CTD_human
TgeneC4277682Chemical and Drug Induced Liver Injury1CTD_human
TgeneC4279912Chemically-Induced Liver Toxicity1CTD_human