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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:GCNT2-LTBP4 (FusionGDB2 ID:32791)

Fusion Gene Summary for GCNT2-LTBP4

check button Fusion gene summary
Fusion gene informationFusion gene name: GCNT2-LTBP4
Fusion gene ID: 32791
HgeneTgene
Gene symbol

GCNT2

LTBP4

Gene ID

2651

8425

Gene nameglucosaminyl (N-acetyl) transferase 2 (I blood group)latent transforming growth factor beta binding protein 4
SynonymsCCAT|CTRCT13|GCNT2C|GCNT5|IGNT|II|NACGT1|NAGCT1|ULG3|bA360O19.2|bA421M1.1ARCL1C|LTBP-4|LTBP4L|LTBP4S
Cytomap

6p24.3-p24.2

19q13.2

Type of geneprotein-codingprotein-coding
DescriptionN-acetyllactosaminide beta-1,6-N-acetylglucosaminyl-transferaseI beta-1,6-N-acetylglucosaminyltransferaseIi blood groupbeta-1,6-N-acetylglucosaminyltransferase 2glucosaminyl (N-acetyl) transferase 2, I-branching enzyme (I blood group)latent-transforming growth factor beta-binding protein 4latent transforming growth factor-beta binding protein 4L
Modification date2020032920200313
UniProtAcc

Q8N0V5

Q8N2S1

Ensembl transtripts involved in fusion geneENST00000379597, ENST00000495262, 
ENST00000265012, ENST00000316170, 
ENST00000397423, ENST00000410107, 
ENST00000204005, ENST00000243562, 
ENST00000308370, ENST00000396819, 
ENST00000545697, ENST00000602240, 
Fusion gene scores* DoF score8 X 7 X 6=3365 X 7 X 4=140
# samples 97
** MAII scorelog2(9/336*10)=-1.90046432644909
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(7/140*10)=-1
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: GCNT2 [Title/Abstract] AND LTBP4 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointGCNT2(10530069)-LTBP4(41120220), # 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
TgeneLTBP4

GO:0030162

regulation of proteolysis

9660815


check buttonFusion gene breakpoints across GCNT2 (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 LTBP4 (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
ChimerDB4ESCATCGA-V5-AASXGCNT2chr6

10530069

+LTBP4chr19

41120220

+


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Fusion Gene ORF analysis for GCNT2-LTBP4

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-3UTRENST00000379597ENST00000204005GCNT2chr6

10530069

+LTBP4chr19

41120220

+
5CDS-3UTRENST00000379597ENST00000243562GCNT2chr6

10530069

+LTBP4chr19

41120220

+
5CDS-3UTRENST00000379597ENST00000308370GCNT2chr6

10530069

+LTBP4chr19

41120220

+
5CDS-3UTRENST00000379597ENST00000396819GCNT2chr6

10530069

+LTBP4chr19

41120220

+
5CDS-3UTRENST00000379597ENST00000545697GCNT2chr6

10530069

+LTBP4chr19

41120220

+
5CDS-3UTRENST00000379597ENST00000602240GCNT2chr6

10530069

+LTBP4chr19

41120220

+
5CDS-3UTRENST00000495262ENST00000204005GCNT2chr6

10530069

+LTBP4chr19

41120220

+
5CDS-3UTRENST00000495262ENST00000243562GCNT2chr6

10530069

+LTBP4chr19

41120220

+
5CDS-3UTRENST00000495262ENST00000308370GCNT2chr6

10530069

+LTBP4chr19

41120220

+
5CDS-3UTRENST00000495262ENST00000396819GCNT2chr6

10530069

+LTBP4chr19

41120220

+
5CDS-3UTRENST00000495262ENST00000545697GCNT2chr6

10530069

+LTBP4chr19

41120220

+
5CDS-3UTRENST00000495262ENST00000602240GCNT2chr6

10530069

+LTBP4chr19

41120220

+
intron-3UTRENST00000265012ENST00000204005GCNT2chr6

10530069

+LTBP4chr19

41120220

+
intron-3UTRENST00000265012ENST00000243562GCNT2chr6

10530069

+LTBP4chr19

41120220

+
intron-3UTRENST00000265012ENST00000308370GCNT2chr6

10530069

+LTBP4chr19

41120220

+
intron-3UTRENST00000265012ENST00000396819GCNT2chr6

10530069

+LTBP4chr19

41120220

+
intron-3UTRENST00000265012ENST00000545697GCNT2chr6

10530069

+LTBP4chr19

41120220

+
intron-3UTRENST00000265012ENST00000602240GCNT2chr6

10530069

+LTBP4chr19

41120220

+
intron-3UTRENST00000316170ENST00000204005GCNT2chr6

10530069

+LTBP4chr19

41120220

+
intron-3UTRENST00000316170ENST00000243562GCNT2chr6

10530069

+LTBP4chr19

41120220

+
intron-3UTRENST00000316170ENST00000308370GCNT2chr6

10530069

+LTBP4chr19

41120220

+
intron-3UTRENST00000316170ENST00000396819GCNT2chr6

10530069

+LTBP4chr19

41120220

+
intron-3UTRENST00000316170ENST00000545697GCNT2chr6

10530069

+LTBP4chr19

41120220

+
intron-3UTRENST00000316170ENST00000602240GCNT2chr6

10530069

+LTBP4chr19

41120220

+
intron-3UTRENST00000397423ENST00000204005GCNT2chr6

10530069

+LTBP4chr19

41120220

+
intron-3UTRENST00000397423ENST00000243562GCNT2chr6

10530069

+LTBP4chr19

41120220

+
intron-3UTRENST00000397423ENST00000308370GCNT2chr6

10530069

+LTBP4chr19

41120220

+
intron-3UTRENST00000397423ENST00000396819GCNT2chr6

10530069

+LTBP4chr19

41120220

+
intron-3UTRENST00000397423ENST00000545697GCNT2chr6

10530069

+LTBP4chr19

41120220

+
intron-3UTRENST00000397423ENST00000602240GCNT2chr6

10530069

+LTBP4chr19

41120220

+
intron-3UTRENST00000410107ENST00000204005GCNT2chr6

10530069

+LTBP4chr19

41120220

+
intron-3UTRENST00000410107ENST00000243562GCNT2chr6

10530069

+LTBP4chr19

41120220

+
intron-3UTRENST00000410107ENST00000308370GCNT2chr6

10530069

+LTBP4chr19

41120220

+
intron-3UTRENST00000410107ENST00000396819GCNT2chr6

10530069

+LTBP4chr19

41120220

+
intron-3UTRENST00000410107ENST00000545697GCNT2chr6

10530069

+LTBP4chr19

41120220

+
intron-3UTRENST00000410107ENST00000602240GCNT2chr6

10530069

+LTBP4chr19

41120220

+

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 GCNT2-LTBP4


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)
GCNT2chr610530069+LTBP4chr1941120220+0.873661340.1263386
GCNT2chr610530069+LTBP4chr1941120220+0.873661340.1263386

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.
genomic feature of top 1%

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Fusion Protein Features for GCNT2-LTBP4


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/:10530069/:41120220)
- 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
GCNT2

Q8N0V5

LTBP4

Q8N2S1

FUNCTION: Branching enzyme that converts linear into branched poly-N-acetyllactosaminoglycans. Introduces the blood group I antigen during embryonic development. It is closely associated with the development and maturation of erythroid cells. {ECO:0000269|PubMed:7579796, ECO:0000269|PubMed:8449405}.; FUNCTION: [Isoform C]: Determines the expression of the blood group I antigen in erythrocytes. {ECO:0000269|PubMed:12468428}.FUNCTION: Key regulator of transforming growth factor beta (TGFB1, TGFB2 and TGFB3) that controls TGF-beta activation by maintaining it in a latent state during storage in extracellular space. Associates specifically via disulfide bonds with the Latency-associated peptide (LAP), which is the regulatory chain of TGF-beta, and regulates integrin-dependent activation of TGF-beta. {ECO:0000250|UniProtKB:Q14766}.

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 GCNT2-LTBP4


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 GCNT2-LTBP4


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 GCNT2-LTBP4


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 GCNT2-LTBP4


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