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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:TMBIM4-NAV3 (FusionGDB2 ID:90666)

Fusion Gene Summary for TMBIM4-NAV3

check button Fusion gene summary
Fusion gene informationFusion gene name: TMBIM4-NAV3
Fusion gene ID: 90666
HgeneTgene
Gene symbol

TMBIM4

NAV3

Gene ID

51643

89795

Gene nametransmembrane BAX inhibitor motif containing 4neuron navigator 3
SynonymsCGI-119|GAAP|LFG4|S1R|ZPROPOMFIL1|STEERIN3|unc53H3
Cytomap

12q14.3

12q21.2

Type of geneprotein-codingprotein-coding
Descriptionprotein lifeguard 4Golgi anti-apoptotic proteinZ-proteintransmembrane BAX inhibitor motif-containing protein 4neuron navigator 3pore membrane and/or filament interacting like protein 1unc-53 homolog 3
Modification date2020031320200313
UniProtAcc.

Q8IVL0

Ensembl transtripts involved in fusion geneENST00000539652, ENST00000556010, 
ENST00000358230, ENST00000544599, 
ENST00000286424, ENST00000398033, 
ENST00000542724, ENST00000535812, 
ENST00000536525, ENST00000397909, 
ENST00000228327, ENST00000266692, 
ENST00000552300, ENST00000541270, 
Fusion gene scores* DoF score14 X 8 X 8=89622 X 21 X 4=1848
# samples 1820
** MAII scorelog2(18/896*10)=-2.31550182572793
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(20/1848*10)=-3.20789285164133
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: TMBIM4 [Title/Abstract] AND NAV3 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointTMBIM4(66563635)-NAV3(78520947), # samples:3
Anticipated loss of major functional domain due to fusion event.TMBIM4-NAV3 seems lost the major protein functional domain in Tgene partner, which is a essential 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
HgeneTMBIM4

GO:0050848

regulation of calcium-mediated signaling

19553469


check buttonFusion gene breakpoints across TMBIM4 (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 NAV3 (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
ChimerDB4SARCTCGA-DX-A2J0-01ATMBIM4chr12

66563635

-NAV3chr12

78520947

+
ChimerDB4SARCTCGA-DX-A2J0-01ATMBIM4chr12

66563635

-NAV3chr12

78520947

+
ChimerDB4SARCTCGA-DX-A2J0-01ATMBIM4chr12

66563635

-NAV3chr12

78520947

+


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Fusion Gene ORF analysis for TMBIM4-NAV3

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
Frame-shiftENST00000539652ENST00000536525TMBIM4chr12

66563635

-NAV3chr12

78520947

+
Frame-shiftENST00000539652ENST00000397909TMBIM4chr12

66563635

-NAV3chr12

78520947

+
Frame-shiftENST00000539652ENST00000228327TMBIM4chr12

66563635

-NAV3chr12

78520947

+
5CDS-intronENST00000539652ENST00000266692TMBIM4chr12

66563635

-NAV3chr12

78520947

+
5CDS-intronENST00000539652ENST00000552300TMBIM4chr12

66563635

-NAV3chr12

78520947

+
5CDS-intronENST00000539652ENST00000541270TMBIM4chr12

66563635

-NAV3chr12

78520947

+
Frame-shiftENST00000556010ENST00000536525TMBIM4chr12

66563635

-NAV3chr12

78520947

+
Frame-shiftENST00000556010ENST00000397909TMBIM4chr12

66563635

-NAV3chr12

78520947

+
Frame-shiftENST00000556010ENST00000228327TMBIM4chr12

66563635

-NAV3chr12

78520947

+
5CDS-intronENST00000556010ENST00000266692TMBIM4chr12

66563635

-NAV3chr12

78520947

+
5CDS-intronENST00000556010ENST00000552300TMBIM4chr12

66563635

-NAV3chr12

78520947

+
5CDS-intronENST00000556010ENST00000541270TMBIM4chr12

66563635

-NAV3chr12

78520947

+
Frame-shiftENST00000358230ENST00000536525TMBIM4chr12

66563635

-NAV3chr12

78520947

+
Frame-shiftENST00000358230ENST00000397909TMBIM4chr12

66563635

-NAV3chr12

78520947

+
Frame-shiftENST00000358230ENST00000228327TMBIM4chr12

66563635

-NAV3chr12

78520947

+
5CDS-intronENST00000358230ENST00000266692TMBIM4chr12

66563635

-NAV3chr12

78520947

+
5CDS-intronENST00000358230ENST00000552300TMBIM4chr12

66563635

-NAV3chr12

78520947

+
5CDS-intronENST00000358230ENST00000541270TMBIM4chr12

66563635

-NAV3chr12

78520947

+
intron-3CDSENST00000544599ENST00000536525TMBIM4chr12

66563635

-NAV3chr12

78520947

+
intron-3CDSENST00000544599ENST00000397909TMBIM4chr12

66563635

-NAV3chr12

78520947

+
intron-3CDSENST00000544599ENST00000228327TMBIM4chr12

66563635

-NAV3chr12

78520947

+
intron-intronENST00000544599ENST00000266692TMBIM4chr12

66563635

-NAV3chr12

78520947

+
intron-intronENST00000544599ENST00000552300TMBIM4chr12

66563635

-NAV3chr12

78520947

+
intron-intronENST00000544599ENST00000541270TMBIM4chr12

66563635

-NAV3chr12

78520947

+
Frame-shiftENST00000286424ENST00000536525TMBIM4chr12

66563635

-NAV3chr12

78520947

+
Frame-shiftENST00000286424ENST00000397909TMBIM4chr12

66563635

-NAV3chr12

78520947

+
Frame-shiftENST00000286424ENST00000228327TMBIM4chr12

66563635

-NAV3chr12

78520947

+
5CDS-intronENST00000286424ENST00000266692TMBIM4chr12

66563635

-NAV3chr12

78520947

+
5CDS-intronENST00000286424ENST00000552300TMBIM4chr12

66563635

-NAV3chr12

78520947

+
5CDS-intronENST00000286424ENST00000541270TMBIM4chr12

66563635

-NAV3chr12

78520947

+
Frame-shiftENST00000398033ENST00000536525TMBIM4chr12

66563635

-NAV3chr12

78520947

+
Frame-shiftENST00000398033ENST00000397909TMBIM4chr12

66563635

-NAV3chr12

78520947

+
Frame-shiftENST00000398033ENST00000228327TMBIM4chr12

66563635

-NAV3chr12

78520947

+
5CDS-intronENST00000398033ENST00000266692TMBIM4chr12

66563635

-NAV3chr12

78520947

+
5CDS-intronENST00000398033ENST00000552300TMBIM4chr12

66563635

-NAV3chr12

78520947

+
5CDS-intronENST00000398033ENST00000541270TMBIM4chr12

66563635

-NAV3chr12

78520947

+
Frame-shiftENST00000542724ENST00000536525TMBIM4chr12

66563635

-NAV3chr12

78520947

+
Frame-shiftENST00000542724ENST00000397909TMBIM4chr12

66563635

-NAV3chr12

78520947

+
Frame-shiftENST00000542724ENST00000228327TMBIM4chr12

66563635

-NAV3chr12

78520947

+
5CDS-intronENST00000542724ENST00000266692TMBIM4chr12

66563635

-NAV3chr12

78520947

+
5CDS-intronENST00000542724ENST00000552300TMBIM4chr12

66563635

-NAV3chr12

78520947

+
5CDS-intronENST00000542724ENST00000541270TMBIM4chr12

66563635

-NAV3chr12

78520947

+
5UTR-3CDSENST00000535812ENST00000536525TMBIM4chr12

66563635

-NAV3chr12

78520947

+
5UTR-3CDSENST00000535812ENST00000397909TMBIM4chr12

66563635

-NAV3chr12

78520947

+
5UTR-3CDSENST00000535812ENST00000228327TMBIM4chr12

66563635

-NAV3chr12

78520947

+
5UTR-intronENST00000535812ENST00000266692TMBIM4chr12

66563635

-NAV3chr12

78520947

+
5UTR-intronENST00000535812ENST00000552300TMBIM4chr12

66563635

-NAV3chr12

78520947

+
5UTR-intronENST00000535812ENST00000541270TMBIM4chr12

66563635

-NAV3chr12

78520947

+

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 TMBIM4-NAV3


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)
TMBIM4chr1266563634-NAV3chr1278520946+1.35E-060.9999987
TMBIM4chr1266563634-NAV3chr1278520946+1.35E-060.9999987

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 TMBIM4-NAV3


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
.NAV3

Q8IVL0

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.FUNCTION: May regulate IL2 production by T-cells. May be involved in neuron regeneration. {ECO:0000269|PubMed:16166283}.

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 TMBIM4-NAV3


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 TMBIM4-NAV3


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 TMBIM4-NAV3


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 TMBIM4-NAV3


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneTMBIM4C0010093Corpus Luteum Cyst1CTD_human
HgeneTMBIM4C0029927Ovarian Cysts1CTD_human
TgeneNAV3C0007134Renal Cell Carcinoma1CTD_human
TgeneNAV3C0027412Opioid-Related Disorders1CTD_human
TgeneNAV3C0029095Opioid abuse1CTD_human
TgeneNAV3C0279702Conventional (Clear Cell) Renal Cell Carcinoma1CTD_human
TgeneNAV3C0524661Narcotic Abuse1CTD_human
TgeneNAV3C0524662Opiate Addiction1CTD_human
TgeneNAV3C1266042Chromophobe Renal Cell Carcinoma1CTD_human
TgeneNAV3C1266043Sarcomatoid Renal Cell Carcinoma1CTD_human
TgeneNAV3C1266044Collecting Duct Carcinoma of the Kidney1CTD_human
TgeneNAV3C1306837Papillary Renal Cell Carcinoma1CTD_human
TgeneNAV3C1527402Narcotic Dependence1CTD_human
TgeneNAV3C4551628Opiate Abuse1CTD_human