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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:TFEC-CHCHD3 (FusionGDB2 ID:90335)

Fusion Gene Summary for TFEC-CHCHD3

check button Fusion gene summary
Fusion gene informationFusion gene name: TFEC-CHCHD3
Fusion gene ID: 90335
HgeneTgene
Gene symbol

TFEC

CHCHD3

Gene ID

22797

54927

Gene nametranscription factor ECcoiled-coil-helix-coiled-coil-helix domain containing 3
SynonymsTCFEC|TFE-C|TFEC-L|TFECL|bHLHe34|hTFEC-LMICOS19|MINOS3|Mic19|PPP1R22
Cytomap

7q31.2

7q32.3-q33

Type of geneprotein-codingprotein-coding
Descriptiontranscription factor ECclass E basic helix-loop-helix protein 34MICOS complex subunit MIC19coiled-coil-helix-coiled-coil-helix domain-containing protein 3, mitochondrialmitochondrial contact site and cristae organizing system subunit 19mitochondrial inner membrane organizing system 3protein phosphatase 1, regulato
Modification date2020031320200327
UniProtAcc.

Q9NX63

Ensembl transtripts involved in fusion geneENST00000484212, ENST00000265440, 
ENST00000320239, ENST00000393485, 
ENST00000457268, ENST00000474337, 
ENST00000476546, ENST00000542753, 
ENST00000262570, ENST00000448878, 
Fusion gene scores* DoF score3 X 3 X 2=1822 X 24 X 8=4224
# samples 328
** MAII scorelog2(3/18*10)=0.736965594166206
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
log2(28/4224*10)=-3.91511110241349
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: TFEC [Title/Abstract] AND CHCHD3 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointTFEC(115750762)-CHCHD3(132523229), # 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
TgeneCHCHD3

GO:0000122

negative regulation of transcription by RNA polymerase II

22567091


check buttonFusion gene breakpoints across TFEC (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure

check buttonFusion gene breakpoints across CHCHD3 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure

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
ChimerDB4STADTCGA-BR-8366-01ATFECchr7

115750762

-CHCHD3chr7

132523229

-


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Fusion Gene ORF analysis for TFEC-CHCHD3

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-5UTRENST00000484212ENST00000476546TFECchr7

115750762

-CHCHD3chr7

132523229

-
5CDS-intronENST00000484212ENST00000542753TFECchr7

115750762

-CHCHD3chr7

132523229

-
In-frameENST00000484212ENST00000262570TFECchr7

115750762

-CHCHD3chr7

132523229

-
In-frameENST00000484212ENST00000448878TFECchr7

115750762

-CHCHD3chr7

132523229

-
intron-3CDSENST00000265440ENST00000262570TFECchr7

115750762

-CHCHD3chr7

132523229

-
intron-3CDSENST00000265440ENST00000448878TFECchr7

115750762

-CHCHD3chr7

132523229

-
intron-3CDSENST00000320239ENST00000262570TFECchr7

115750762

-CHCHD3chr7

132523229

-
intron-3CDSENST00000320239ENST00000448878TFECchr7

115750762

-CHCHD3chr7

132523229

-
intron-3CDSENST00000393485ENST00000262570TFECchr7

115750762

-CHCHD3chr7

132523229

-
intron-3CDSENST00000393485ENST00000448878TFECchr7

115750762

-CHCHD3chr7

132523229

-
intron-3CDSENST00000457268ENST00000262570TFECchr7

115750762

-CHCHD3chr7

132523229

-
intron-3CDSENST00000457268ENST00000448878TFECchr7

115750762

-CHCHD3chr7

132523229

-
intron-3CDSENST00000474337ENST00000262570TFECchr7

115750762

-CHCHD3chr7

132523229

-
intron-3CDSENST00000474337ENST00000448878TFECchr7

115750762

-CHCHD3chr7

132523229

-
intron-5UTRENST00000265440ENST00000476546TFECchr7

115750762

-CHCHD3chr7

132523229

-
intron-5UTRENST00000320239ENST00000476546TFECchr7

115750762

-CHCHD3chr7

132523229

-
intron-5UTRENST00000393485ENST00000476546TFECchr7

115750762

-CHCHD3chr7

132523229

-
intron-5UTRENST00000457268ENST00000476546TFECchr7

115750762

-CHCHD3chr7

132523229

-
intron-5UTRENST00000474337ENST00000476546TFECchr7

115750762

-CHCHD3chr7

132523229

-
intron-intronENST00000265440ENST00000542753TFECchr7

115750762

-CHCHD3chr7

132523229

-
intron-intronENST00000320239ENST00000542753TFECchr7

115750762

-CHCHD3chr7

132523229

-
intron-intronENST00000393485ENST00000542753TFECchr7

115750762

-CHCHD3chr7

132523229

-
intron-intronENST00000457268ENST00000542753TFECchr7

115750762

-CHCHD3chr7

132523229

-
intron-intronENST00000474337ENST00000542753TFECchr7

115750762

-CHCHD3chr7

132523229

-

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)
ENST00000484212TFECchr7115750762-ENST00000262570CHCHD3chr7132523229-1373373175603142
ENST00000484212TFECchr7115750762-ENST00000448878CHCHD3chr7132523229-1358373175603142

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
ENST00000484212ENST00000262570TFECchr7115750762-CHCHD3chr7132523229-0.039298790.9607012
ENST00000484212ENST00000448878TFECchr7115750762-CHCHD3chr7132523229-0.0402340780.959766

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Fusion Genomic Features for TFEC-CHCHD3


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.
genomic feature

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 TFEC-CHCHD3


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/chr7:115750762/chr7:132523229)
- 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
.CHCHD3

Q9NX63

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: Component of the MICOS complex, a large protein complex of the mitochondrial inner membrane that plays crucial roles in the maintenance of crista junctions, inner membrane architecture, and formation of contact sites to the outer membrane. Has also been shown to function as a transcription factor which binds to the BAG1 promoter and represses BAG1 transcription. Plays an important role in the maintenance of the MICOS complex stability and the mitochondrial cristae morphology (PubMed:25781180). {ECO:0000269|PubMed:22567091, ECO:0000269|PubMed:25781180}.

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
TgeneCHCHD3chr7:115750762chr7:132523229ENST0000026257048180_222151228.0DomainCHCH
TgeneCHCHD3chr7:115750762chr7:132523229ENST0000026257048183_193151228.0MotifCx9C motif 1
TgeneCHCHD3chr7:115750762chr7:132523229ENST0000026257048204_214151228.0MotifCx9C motif 2

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneTFECchr7:115750762chr7:132523229ENST00000265440-18139_1920348.0DomainbHLH
HgeneTFECchr7:115750762chr7:132523229ENST00000320239-17139_1920319.0DomainbHLH
HgeneTFECchr7:115750762chr7:132523229ENST00000393485-16139_1920198.0DomainbHLH
HgeneTFECchr7:115750762chr7:132523229ENST00000457268-16139_1920281.0DomainbHLH
HgeneTFECchr7:115750762chr7:132523229ENST00000265440-181_1190348.0RegionNote=Necessary for transcriptional transactivation
HgeneTFECchr7:115750762chr7:132523229ENST00000265440-18271_3470348.0RegionNote=Necessary for transcriptional transactivation
HgeneTFECchr7:115750762chr7:132523229ENST00000320239-171_1190319.0RegionNote=Necessary for transcriptional transactivation
HgeneTFECchr7:115750762chr7:132523229ENST00000320239-17271_3470319.0RegionNote=Necessary for transcriptional transactivation
HgeneTFECchr7:115750762chr7:132523229ENST00000393485-161_1190198.0RegionNote=Necessary for transcriptional transactivation
HgeneTFECchr7:115750762chr7:132523229ENST00000393485-16271_3470198.0RegionNote=Necessary for transcriptional transactivation
HgeneTFECchr7:115750762chr7:132523229ENST00000457268-161_1190281.0RegionNote=Necessary for transcriptional transactivation
HgeneTFECchr7:115750762chr7:132523229ENST00000457268-16271_3470281.0RegionNote=Necessary for transcriptional transactivation


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Fusion Gene Sequence for TFEC-CHCHD3


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.
>90335_90335_1_TFEC-CHCHD3_TFEC_chr7_115750762_ENST00000484212_CHCHD3_chr7_132523229_ENST00000262570_length(transcript)=1373nt_BP=373nt
GAAAAAGAGGAGAAGTGGGAGTAAACAGAAAGATAATGCTTATGGTACATACAAAACAAATGGAGAGATTGAGTCTCACGGATTCTTCGC
CTGAGCCACCAGCAAAGAGTCCTATCAATGATTTAGTTCCCTAGAGAAAATCAGAAAGTAAAAGTGAGAAGAAAAGAAGAGAAATATGTT
ACAAGCTTTAACTGGACTTCAATTTCAGCTGAAAGAACAATTAGGAGAAAAGGAGAGAAGACTTCAAATCAGCCAGGAAATCAGTGCCCA
TAGAACAGAGTTCCACATGCAGTTTTCATACAAACCAGTGTTGCATAGACTTGTCCCAGCAAGACCACAAATTTATTCAAGTCAATTACC
ATCCTTTACCAGGAGCTCAGAGTTCTACAGAGTCACCACTGAACAATATCAGAAAGCTGCTGAAGAGGTGGAAGCAAAGTTCAAGCGATA
TGAGTCTCATCCAGTCTGTGCTGATCTGCAGGCCAAAATTCTTCAGTGTTACCGTGAGAACACCCACCAGACCCTCAAATGCTCCGCTCT
GGCCACCCAGTATATGCACTGTGTCAATCATGCCAAACAGAGCATGCTTGAGAAGGGAGGATAAAAACTTTCAGAATGAGCAAAACACCA
TCAACGTTAATTCCAGAGATGGAACATTTTTTTTCCTAGTGAGAAAACAACCCATTTGAAGAGAAGACCACTAATGAGAAGACCACTAAA
GAGAGACATCAAGAATGGATTCAGCAGAATCATTTCACGTTTTGAACAGCAGCAGTTTGAAGGGCCAAAGCCTTGATCAGGGATCAGTCA
TTAAAGGACACTCTTGAGTATTAGTAAACCCTCTTATGATGATTAAAAGAGAAGGGCAGCCCTCTCCACCTTTTGGTACTTTCTATTCAA
CTTGCACTGACCATAAAATGTTTCTCTTCTGAACAAGCCCCATCATTTGGTGAACCTCCACCCTAACAAAGTAGGATGGGGTTGGGGGCT
AAATTAATTGGAGTGGGGCGAGGAGAGAGCCAGAAAACATAGATCCGAGGGCAGCAGTGCTGGGTGGAGAGAGCCAGAAAACAGATCTGG
AGGCAGCAGTGCTGGATGGAATTGTCTAGGCTGTGGCATGTTGGTTTTGTCTTTCTTTTCTCCTTTGATTATGTAAGAGCTATTTCATTA
TAACTTATTATGGTGATTATACAGGCAAGAAGACAAAAAGGAGAGAAAATGTACCTCTTCTACTGGAATAATGTTTATGATTACAAGTGA
GATAAGGTATTTTTATCAATATGAAGGCAACCTTGGCTGATAAAACCTCTATAGTGAATACTCACATCTTTACTTCACTCACTATCAATA

>90335_90335_1_TFEC-CHCHD3_TFEC_chr7_115750762_ENST00000484212_CHCHD3_chr7_132523229_ENST00000262570_length(amino acids)=142AA_BP=66
MLQALTGLQFQLKEQLGEKERRLQISQEISAHRTEFHMQFSYKPVLHRLVPARPQIYSSQLPSFTRSSEFYRVTTEQYQKAAEEVEAKFK

--------------------------------------------------------------
>90335_90335_2_TFEC-CHCHD3_TFEC_chr7_115750762_ENST00000484212_CHCHD3_chr7_132523229_ENST00000448878_length(transcript)=1358nt_BP=373nt
GAAAAAGAGGAGAAGTGGGAGTAAACAGAAAGATAATGCTTATGGTACATACAAAACAAATGGAGAGATTGAGTCTCACGGATTCTTCGC
CTGAGCCACCAGCAAAGAGTCCTATCAATGATTTAGTTCCCTAGAGAAAATCAGAAAGTAAAAGTGAGAAGAAAAGAAGAGAAATATGTT
ACAAGCTTTAACTGGACTTCAATTTCAGCTGAAAGAACAATTAGGAGAAAAGGAGAGAAGACTTCAAATCAGCCAGGAAATCAGTGCCCA
TAGAACAGAGTTCCACATGCAGTTTTCATACAAACCAGTGTTGCATAGACTTGTCCCAGCAAGACCACAAATTTATTCAAGTCAATTACC
ATCCTTTACCAGGAGCTCAGAGTTCTACAGAGTCACCACTGAACAATATCAGAAAGCTGCTGAAGAGGTGGAAGCAAAGTTCAAGCGATA
TGAGTCTCATCCAGTCTGTGCTGATCTGCAGGCCAAAATTCTTCAGTGTTACCGTGAGAACACCCACCAGACCCTCAAATGCTCCGCTCT
GGCCACCCAGTATATGCACTGTGTCAATCATGCCAAACAGAGCATGCTTGAGAAGGGAGGATAAAAACTTTCAGAATGAGCAAAACACCA
TCAACGTTAATTCCAGAGATGGAACATTTTTTTTCCTAGTGAGAAAACAACCCATTTGAAGAGAAGACCACTAATGAGAAGACCACTAAA
GAGAGACATCAAGAATGGATTCAGCAGAATCATTTCACGTTTTGAACAGCAGCAGTTTGAAGGGCCAAAGCCTTGATCAGGGATCAGTCA
TTAAAGGACACTCTTGAGTATTAGTAAACCCTCTTATGATGATTAAAAGAGAAGGGCAGCCCTCTCCACCTTTTGGTACTTTCTATTCAA
CTTGCACTGACCATAAAATGTTTCTCTTCTGAACAAGCCCCATCATTTGGTGAACCTCCACCCTAACAAAGTAGGATGGGGTTGGGGGCT
AAATTAATTGGAGTGGGGCGAGGAGAGAGCCAGAAAACATAGATCCGAGGGCAGCAGTGCTGGGTGGAGAGAGCCAGAAAACAGATCTGG
AGGCAGCAGTGCTGGATGGAATTGTCTAGGCTGTGGCATGTTGGTTTTGTCTTTCTTTTCTCCTTTGATTATGTAAGAGCTATTTCATTA
TAACTTATTATGGTGATTATACAGGCAAGAAGACAAAAAGGAGAGAAAATGTACCTCTTCTACTGGAATAATGTTTATGATTACAAGTGA
GATAAGGTATTTTTATCAATATGAAGGCAACCTTGGCTGATAAAACCTCTATAGTGAATACTCACATCTTTACTTCACTCACTATCAATA

>90335_90335_2_TFEC-CHCHD3_TFEC_chr7_115750762_ENST00000484212_CHCHD3_chr7_132523229_ENST00000448878_length(amino acids)=142AA_BP=66
MLQALTGLQFQLKEQLGEKERRLQISQEISAHRTEFHMQFSYKPVLHRLVPARPQIYSSQLPSFTRSSEFYRVTTEQYQKAAEEVEAKFK

--------------------------------------------------------------

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Fusion Gene PPI Analysis for TFEC-CHCHD3


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 TFEC-CHCHD3


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 TFEC-CHCHD3


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