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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:TCF7L1-GFPT1 (FusionGDB2 ID:HG83439TG2673)

Fusion Gene Summary for TCF7L1-GFPT1

check button Fusion gene summary
Fusion gene informationFusion gene name: TCF7L1-GFPT1
Fusion gene ID: hg83439tg2673
HgeneTgene
Gene symbol

TCF7L1

GFPT1

Gene ID

83439

2673

Gene nametranscription factor 7 like 1glutamine--fructose-6-phosphate transaminase 1
SynonymsTCF-3|TCF3CMS12|CMSTA1|GFA|GFAT|GFAT 1|GFAT1|GFAT1m|GFPT|GFPT1L|MSLG
Cytomap('TCF7L1')('GFPT1')

2p11.2

2p13.3

Type of geneprotein-codingprotein-coding
Descriptiontranscription factor 7-like 1HMG box transcription factor 3transcription factor 7-like 1 (T-cell specific, HMG-box)glutamine--fructose-6-phosphate aminotransferase [isomerizing] 1D-fructose-6-phosphate amidotransferase 1glucosamine--fructose-6-phosphate aminotransferase [isomerizing] 1glutamine:fructose-6-phosphate amidotransferase 1hexosephosphate aminotransferas
Modification date2020031320200313
UniProtAcc

Q9HCS4

.
Ensembl transtripts involved in fusion geneENST00000494519, ENST00000282111, 
Fusion gene scores* DoF score14 X 10 X 9=12605 X 4 X 4=80
# samples 145
** MAII scorelog2(14/1260*10)=-3.16992500144231
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(5/80*10)=-0.678071905112638
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: TCF7L1 [Title/Abstract] AND GFPT1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointTCF7L1(85361573)-GFPT1(69601245), # samples:1
Anticipated loss of major functional domain due to fusion event.TCF7L1-GFPT1 seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
TCF7L1-GFPT1 seems lost the major protein functional domain in Hgene partner, which is a transcription factor due to the frame-shifted ORF.
TCF7L1-GFPT1 seems lost the major protein functional domain in Tgene partner, which is a cell metabolism gene due to the frame-shifted ORF.
TCF7L1-GFPT1 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


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
ChimerDB4SARCTCGA-K1-A6RV-01ATCF7L1chr2

85361573

-GFPT1chr2

69601245

-


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Fusion Gene ORF analysis for TCF7L1-GFPT1

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-3CDSENST00000494519ENST00000357308TCF7L1chr2

85361573

-GFPT1chr2

69601245

-
3UTR-3CDSENST00000494519ENST00000361060TCF7L1chr2

85361573

-GFPT1chr2

69601245

-
3UTR-5UTRENST00000494519ENST00000494201TCF7L1chr2

85361573

-GFPT1chr2

69601245

-
5CDS-5UTRENST00000282111ENST00000494201TCF7L1chr2

85361573

-GFPT1chr2

69601245

-
Frame-shiftENST00000282111ENST00000357308TCF7L1chr2

85361573

-GFPT1chr2

69601245

-
Frame-shiftENST00000282111ENST00000361060TCF7L1chr2

85361573

-GFPT1chr2

69601245

-

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 TCF7L1-GFPT1


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)


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Fusion Protein Features for TCF7L1-GFPT1


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/:85361573/:69601245)
- 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
TCF7L1

Q9HCS4

.
FUNCTION: Participates in the Wnt signaling pathway. Binds to DNA and acts as a repressor in the absence of CTNNB1, and as an activator in its presence. Necessary for the terminal differentiation of epidermal cells, the formation of keratohyalin granules and the development of the barrier function of the epidermis (By similarity). Down-regulates NQO1, leading to increased mitomycin c resistance. {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 TCF7L1-GFPT1


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 TCF7L1-GFPT1


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 TCF7L1-GFPT1


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 TCF7L1-GFPT1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneTCF7L1C0040136Thyroid Neoplasm1CTD_human
HgeneTCF7L1C0151468Thyroid Gland Follicular Adenoma1CTD_human
HgeneTCF7L1C0549473Thyroid carcinoma1CTD_human
HgeneTCF7L1C0857439Pituitary hormone deficiency1GENOMICS_ENGLAND
TgeneC3552335MYASTHENIC SYNDROME, CONGENITAL, 123GENOMICS_ENGLAND;UNIPROT
TgeneC0751882Myasthenic Syndromes, Congenital2CTD_human;GENOMICS_ENGLAND
TgeneC0026848Myopathy1CTD_human
TgeneC0028754Obesity1CTD_human
TgeneC0333768Tubular aggregates1GENOMICS_ENGLAND
TgeneC0751883Congenital Myasthenic Syndromes, Postsynaptic1CTD_human
TgeneC0751884Congenital Myasthenic Syndromes, Presynaptic1CTD_human
TgeneC0751885Myasthenic Syndromes, Congenital, Slow Channel1CTD_human