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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:DFNB31-LTA (FusionGDB2 ID:HG25861TG4049)

Fusion Gene Summary for DFNB31-LTA

check button Fusion gene summary
Fusion gene informationFusion gene name: DFNB31-LTA
Fusion gene ID: hg25861tg4049
HgeneTgene
Gene symbol

DFNB31

LTA

Gene ID

25861

4049

Gene namewhirlinlymphotoxin alpha
SynonymsCIP98|DFNB31|PDZD7B|USH2D|WILT|TNFB|TNFSF1|TNLG1E
Cytomap('DFNB31')('LTA')

9q32

6p21.33

Type of geneprotein-codingprotein-coding
DescriptionwhirlinCASK-interacting protein CIP98autosomal recessive deafness type 31 proteinlymphotoxin-alphaLT-alphaTNF superfamily, member 1TNF-betatruncated lymphotoxin alphatumor necrosis factor betatumor necrosis factor ligand 1Etumor necrosis factor ligand superfamily member 1
Modification date2020032020200320
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000362057, ENST00000374057, 
ENST00000480518, ENST00000265134, 
ENST00000374059, 
Fusion gene scores* DoF score4 X 4 X 4=641 X 1 X 1=1
# samples 51
** MAII scorelog2(5/64*10)=-0.356143810225275
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(1/1*10)=3.32192809488736
Context

PubMed: DFNB31 [Title/Abstract] AND LTA [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointDFNB31(117266464)-LTA(31540511), # 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 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
ChimerDB4OVTCGA-25-1323-01ADFNB31chr9

117266464

-LTAchr6

31540511

+


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Fusion Gene ORF analysis for DFNB31-LTA

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-5UTRENST00000362057ENST00000418386DFNB31chr9

117266464

-LTAchr6

31540511

+
5CDS-5UTRENST00000362057ENST00000454783DFNB31chr9

117266464

-LTAchr6

31540511

+
5CDS-5UTRENST00000374057ENST00000418386DFNB31chr9

117266464

-LTAchr6

31540511

+
5CDS-5UTRENST00000374057ENST00000454783DFNB31chr9

117266464

-LTAchr6

31540511

+
5CDS-intronENST00000362057ENST00000383303DFNB31chr9

117266464

-LTAchr6

31540511

+
5CDS-intronENST00000362057ENST00000383304DFNB31chr9

117266464

-LTAchr6

31540511

+
5CDS-intronENST00000362057ENST00000383499DFNB31chr9

117266464

-LTAchr6

31540511

+
5CDS-intronENST00000362057ENST00000400272DFNB31chr9

117266464

-LTAchr6

31540511

+
5CDS-intronENST00000362057ENST00000412851DFNB31chr9

117266464

-LTAchr6

31540511

+
5CDS-intronENST00000362057ENST00000426845DFNB31chr9

117266464

-LTAchr6

31540511

+
5CDS-intronENST00000362057ENST00000432632DFNB31chr9

117266464

-LTAchr6

31540511

+
5CDS-intronENST00000362057ENST00000436519DFNB31chr9

117266464

-LTAchr6

31540511

+
5CDS-intronENST00000362057ENST00000441939DFNB31chr9

117266464

-LTAchr6

31540511

+
5CDS-intronENST00000362057ENST00000448630DFNB31chr9

117266464

-LTAchr6

31540511

+
5CDS-intronENST00000362057ENST00000454550DFNB31chr9

117266464

-LTAchr6

31540511

+
5CDS-intronENST00000362057ENST00000456789DFNB31chr9

117266464

-LTAchr6

31540511

+
5CDS-intronENST00000362057ENST00000549694DFNB31chr9

117266464

-LTAchr6

31540511

+
5CDS-intronENST00000362057ENST00000549761DFNB31chr9

117266464

-LTAchr6

31540511

+
5CDS-intronENST00000362057ENST00000550394DFNB31chr9

117266464

-LTAchr6

31540511

+
5CDS-intronENST00000362057ENST00000550546DFNB31chr9

117266464

-LTAchr6

31540511

+
5CDS-intronENST00000362057ENST00000550792DFNB31chr9

117266464

-LTAchr6

31540511

+
5CDS-intronENST00000362057ENST00000552271DFNB31chr9

117266464

-LTAchr6

31540511

+
5CDS-intronENST00000374057ENST00000383303DFNB31chr9

117266464

-LTAchr6

31540511

+
5CDS-intronENST00000374057ENST00000383304DFNB31chr9

117266464

-LTAchr6

31540511

+
5CDS-intronENST00000374057ENST00000383499DFNB31chr9

117266464

-LTAchr6

31540511

+
5CDS-intronENST00000374057ENST00000400272DFNB31chr9

117266464

-LTAchr6

31540511

+
5CDS-intronENST00000374057ENST00000412851DFNB31chr9

117266464

-LTAchr6

31540511

+
5CDS-intronENST00000374057ENST00000426845DFNB31chr9

117266464

-LTAchr6

31540511

+
5CDS-intronENST00000374057ENST00000432632DFNB31chr9

117266464

-LTAchr6

31540511

+
5CDS-intronENST00000374057ENST00000436519DFNB31chr9

117266464

-LTAchr6

31540511

+
5CDS-intronENST00000374057ENST00000441939DFNB31chr9

117266464

-LTAchr6

31540511

+
5CDS-intronENST00000374057ENST00000448630DFNB31chr9

117266464

-LTAchr6

31540511

+
5CDS-intronENST00000374057ENST00000454550DFNB31chr9

117266464

-LTAchr6

31540511

+
5CDS-intronENST00000374057ENST00000456789DFNB31chr9

117266464

-LTAchr6

31540511

+
5CDS-intronENST00000374057ENST00000549694DFNB31chr9

117266464

-LTAchr6

31540511

+
5CDS-intronENST00000374057ENST00000549761DFNB31chr9

117266464

-LTAchr6

31540511

+
5CDS-intronENST00000374057ENST00000550394DFNB31chr9

117266464

-LTAchr6

31540511

+
5CDS-intronENST00000374057ENST00000550546DFNB31chr9

117266464

-LTAchr6

31540511

+
5CDS-intronENST00000374057ENST00000550792DFNB31chr9

117266464

-LTAchr6

31540511

+
5CDS-intronENST00000374057ENST00000552271DFNB31chr9

117266464

-LTAchr6

31540511

+
5UTR-5UTRENST00000480518ENST00000418386DFNB31chr9

117266464

-LTAchr6

31540511

+
5UTR-5UTRENST00000480518ENST00000454783DFNB31chr9

117266464

-LTAchr6

31540511

+
5UTR-intronENST00000480518ENST00000383303DFNB31chr9

117266464

-LTAchr6

31540511

+
5UTR-intronENST00000480518ENST00000383304DFNB31chr9

117266464

-LTAchr6

31540511

+
5UTR-intronENST00000480518ENST00000383499DFNB31chr9

117266464

-LTAchr6

31540511

+
5UTR-intronENST00000480518ENST00000400272DFNB31chr9

117266464

-LTAchr6

31540511

+
5UTR-intronENST00000480518ENST00000412851DFNB31chr9

117266464

-LTAchr6

31540511

+
5UTR-intronENST00000480518ENST00000426845DFNB31chr9

117266464

-LTAchr6

31540511

+
5UTR-intronENST00000480518ENST00000432632DFNB31chr9

117266464

-LTAchr6

31540511

+
5UTR-intronENST00000480518ENST00000436519DFNB31chr9

117266464

-LTAchr6

31540511

+
5UTR-intronENST00000480518ENST00000441939DFNB31chr9

117266464

-LTAchr6

31540511

+
5UTR-intronENST00000480518ENST00000448630DFNB31chr9

117266464

-LTAchr6

31540511

+
5UTR-intronENST00000480518ENST00000454550DFNB31chr9

117266464

-LTAchr6

31540511

+
5UTR-intronENST00000480518ENST00000456789DFNB31chr9

117266464

-LTAchr6

31540511

+
5UTR-intronENST00000480518ENST00000549694DFNB31chr9

117266464

-LTAchr6

31540511

+
5UTR-intronENST00000480518ENST00000549761DFNB31chr9

117266464

-LTAchr6

31540511

+
5UTR-intronENST00000480518ENST00000550394DFNB31chr9

117266464

-LTAchr6

31540511

+
5UTR-intronENST00000480518ENST00000550546DFNB31chr9

117266464

-LTAchr6

31540511

+
5UTR-intronENST00000480518ENST00000550792DFNB31chr9

117266464

-LTAchr6

31540511

+
5UTR-intronENST00000480518ENST00000552271DFNB31chr9

117266464

-LTAchr6

31540511

+
intron-5UTRENST00000265134ENST00000418386DFNB31chr9

117266464

-LTAchr6

31540511

+
intron-5UTRENST00000265134ENST00000454783DFNB31chr9

117266464

-LTAchr6

31540511

+
intron-5UTRENST00000374059ENST00000418386DFNB31chr9

117266464

-LTAchr6

31540511

+
intron-5UTRENST00000374059ENST00000454783DFNB31chr9

117266464

-LTAchr6

31540511

+
intron-intronENST00000265134ENST00000383303DFNB31chr9

117266464

-LTAchr6

31540511

+
intron-intronENST00000265134ENST00000383304DFNB31chr9

117266464

-LTAchr6

31540511

+
intron-intronENST00000265134ENST00000383499DFNB31chr9

117266464

-LTAchr6

31540511

+
intron-intronENST00000265134ENST00000400272DFNB31chr9

117266464

-LTAchr6

31540511

+
intron-intronENST00000265134ENST00000412851DFNB31chr9

117266464

-LTAchr6

31540511

+
intron-intronENST00000265134ENST00000426845DFNB31chr9

117266464

-LTAchr6

31540511

+
intron-intronENST00000265134ENST00000432632DFNB31chr9

117266464

-LTAchr6

31540511

+
intron-intronENST00000265134ENST00000436519DFNB31chr9

117266464

-LTAchr6

31540511

+
intron-intronENST00000265134ENST00000441939DFNB31chr9

117266464

-LTAchr6

31540511

+
intron-intronENST00000265134ENST00000448630DFNB31chr9

117266464

-LTAchr6

31540511

+
intron-intronENST00000265134ENST00000454550DFNB31chr9

117266464

-LTAchr6

31540511

+
intron-intronENST00000265134ENST00000456789DFNB31chr9

117266464

-LTAchr6

31540511

+
intron-intronENST00000265134ENST00000549694DFNB31chr9

117266464

-LTAchr6

31540511

+
intron-intronENST00000265134ENST00000549761DFNB31chr9

117266464

-LTAchr6

31540511

+
intron-intronENST00000265134ENST00000550394DFNB31chr9

117266464

-LTAchr6

31540511

+
intron-intronENST00000265134ENST00000550546DFNB31chr9

117266464

-LTAchr6

31540511

+
intron-intronENST00000265134ENST00000550792DFNB31chr9

117266464

-LTAchr6

31540511

+
intron-intronENST00000265134ENST00000552271DFNB31chr9

117266464

-LTAchr6

31540511

+
intron-intronENST00000374059ENST00000383303DFNB31chr9

117266464

-LTAchr6

31540511

+
intron-intronENST00000374059ENST00000383304DFNB31chr9

117266464

-LTAchr6

31540511

+
intron-intronENST00000374059ENST00000383499DFNB31chr9

117266464

-LTAchr6

31540511

+
intron-intronENST00000374059ENST00000400272DFNB31chr9

117266464

-LTAchr6

31540511

+
intron-intronENST00000374059ENST00000412851DFNB31chr9

117266464

-LTAchr6

31540511

+
intron-intronENST00000374059ENST00000426845DFNB31chr9

117266464

-LTAchr6

31540511

+
intron-intronENST00000374059ENST00000432632DFNB31chr9

117266464

-LTAchr6

31540511

+
intron-intronENST00000374059ENST00000436519DFNB31chr9

117266464

-LTAchr6

31540511

+
intron-intronENST00000374059ENST00000441939DFNB31chr9

117266464

-LTAchr6

31540511

+
intron-intronENST00000374059ENST00000448630DFNB31chr9

117266464

-LTAchr6

31540511

+
intron-intronENST00000374059ENST00000454550DFNB31chr9

117266464

-LTAchr6

31540511

+
intron-intronENST00000374059ENST00000456789DFNB31chr9

117266464

-LTAchr6

31540511

+
intron-intronENST00000374059ENST00000549694DFNB31chr9

117266464

-LTAchr6

31540511

+
intron-intronENST00000374059ENST00000549761DFNB31chr9

117266464

-LTAchr6

31540511

+
intron-intronENST00000374059ENST00000550394DFNB31chr9

117266464

-LTAchr6

31540511

+
intron-intronENST00000374059ENST00000550546DFNB31chr9

117266464

-LTAchr6

31540511

+
intron-intronENST00000374059ENST00000550792DFNB31chr9

117266464

-LTAchr6

31540511

+
intron-intronENST00000374059ENST00000552271DFNB31chr9

117266464

-LTAchr6

31540511

+

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 DFNB31-LTA


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)
DFNB31chr9117266463-LTAchr631540510+4.57E-091
DFNB31chr9117266463-LTAchr631540510+4.57E-091


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 DFNB31-LTA


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/:117266464/:31540511)
- 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


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Fusion Gene Sequence for DFNB31-LTA


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 DFNB31-LTA


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 DFNB31-LTA


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 DFNB31-LTA


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneC0027051Myocardial Infarction2CTD_human
TgeneC0003872Arthritis, Psoriatic1CTD_human
TgeneC0010054Coronary Arteriosclerosis1CTD_human
TgeneC0019147Hepatic Coma1CTD_human
TgeneC0019151Hepatic Encephalopathy1CTD_human
TgeneC0023343Leprosy1CTD_human
TgeneC0034189Pyemia1CTD_human
TgeneC0036341Schizophrenia1PSYGENET
TgeneC0036690Septicemia1CTD_human
TgeneC0243026Sepsis1CTD_human
TgeneC0279626Squamous cell carcinoma of esophagus1CTD_human
TgeneC0345967Malignant mesothelioma1CTD_human
TgeneC0751197Fulminant Hepatic Failure with Cerebral Edema1CTD_human
TgeneC0751198Hepatic Stupor1CTD_human
TgeneC1719672Severe Sepsis1CTD_human
TgeneC1956346Coronary Artery Disease1CTD_human