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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:GLI3-GLI3 (FusionGDB2 ID:33158)

Fusion Gene Summary for GLI3-GLI3

check button Fusion gene summary
Fusion gene informationFusion gene name: GLI3-GLI3
Fusion gene ID: 33158
HgeneTgene
Gene symbol

GLI3

GLI3

Gene ID

2737

2737

Gene nameGLI family zinc finger 3GLI family zinc finger 3
SynonymsACLS|GCPS|GLI3-190|GLI3FL|PAP-A|PAPA|PAPA1|PAPB|PHS|PPDIVACLS|GCPS|GLI3-190|GLI3FL|PAP-A|PAPA|PAPA1|PAPB|PHS|PPDIV
Cytomap

7p14.1

7p14.1

Type of geneprotein-codingprotein-coding
Descriptiontranscriptional activator GLI3GLI-Kruppel family member GLI3glioma-associated oncogene family zinc finger 3oncogene GLI3zinc finger protein GLI3transcriptional activator GLI3GLI-Kruppel family member GLI3glioma-associated oncogene family zinc finger 3oncogene GLI3zinc finger protein GLI3
Modification date2020031320200313
UniProtAcc.

P10071

Ensembl transtripts involved in fusion geneENST00000395925, ENST00000479210, 
ENST00000437480, 		ENST00000395925, 
ENST00000479210, ENST00000437480, 
Fusion gene scores* DoF score11 X 11 X 8=9687 X 7 X 5=245
# samples 148
** MAII scorelog2(14/968*10)=-2.78958022032963
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(8/245*10)=-1.61470984411521
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: GLI3 [Title/Abstract] AND GLI3 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointGLI3(42034993)-GLI3(42035984), # samples:1
GLI3(42063066)-GLI3(42088295), # samples:1
GLI3(42048577)-GLI3(42050811), # 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
HgeneGLI3

GO:0000122

negative regulation of transcription by RNA polymerase II

10693759|12435627|19084012

HgeneGLI3

GO:0045892

negative regulation of transcription, DNA-templated

12435627|16254602|19084012

HgeneGLI3

GO:0045944

positive regulation of transcription by RNA polymerase II

17000779

HgeneGLI3

GO:0090090

negative regulation of canonical Wnt signaling pathway

17331723

TgeneGLI3

GO:0000122

negative regulation of transcription by RNA polymerase II

10693759|12435627|19084012

TgeneGLI3

GO:0045892

negative regulation of transcription, DNA-templated

12435627|16254602|19084012

TgeneGLI3

GO:0045944

positive regulation of transcription by RNA polymerase II

17000779

TgeneGLI3

GO:0090090

negative regulation of canonical Wnt signaling pathway

17331723


check buttonFusion gene breakpoints across GLI3 (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 GLI3 (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
ChiTaRS5.0N/ADW437787GLI3chr7

42034993

-GLI3chr7

42035984

-
ChiTaRS5.0N/AAA077306GLI3chr7

42063066

-GLI3chr7

42088295

-
ChiTaRS5.0N/AFN160636GLI3chr7

42048577

-GLI3chr7

42050811

-


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Fusion Gene ORF analysis for GLI3-GLI3

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
intron-intronENST00000395925ENST00000395925GLI3chr7

42034993

-GLI3chr7

42035984

-
intron-intronENST00000395925ENST00000479210GLI3chr7

42034993

-GLI3chr7

42035984

-
intron-intronENST00000395925ENST00000437480GLI3chr7

42034993

-GLI3chr7

42035984

-
intron-intronENST00000479210ENST00000395925GLI3chr7

42034993

-GLI3chr7

42035984

-
intron-intronENST00000479210ENST00000479210GLI3chr7

42034993

-GLI3chr7

42035984

-
intron-intronENST00000479210ENST00000437480GLI3chr7

42034993

-GLI3chr7

42035984

-
intron-intronENST00000437480ENST00000395925GLI3chr7

42034993

-GLI3chr7

42035984

-
intron-intronENST00000437480ENST00000479210GLI3chr7

42034993

-GLI3chr7

42035984

-
intron-intronENST00000437480ENST00000437480GLI3chr7

42034993

-GLI3chr7

42035984

-
In-frameENST00000395925ENST00000395925GLI3chr7

42063066

-GLI3chr7

42088295

-
5CDS-5UTRENST00000395925ENST00000479210GLI3chr7

42063066

-GLI3chr7

42088295

-
5CDS-intronENST00000395925ENST00000437480GLI3chr7

42063066

-GLI3chr7

42088295

-
5UTR-3CDSENST00000479210ENST00000395925GLI3chr7

42063066

-GLI3chr7

42088295

-
5UTR-5UTRENST00000479210ENST00000479210GLI3chr7

42063066

-GLI3chr7

42088295

-
5UTR-intronENST00000479210ENST00000437480GLI3chr7

42063066

-GLI3chr7

42088295

-
intron-3CDSENST00000437480ENST00000395925GLI3chr7

42063066

-GLI3chr7

42088295

-
intron-5UTRENST00000437480ENST00000479210GLI3chr7

42063066

-GLI3chr7

42088295

-
intron-intronENST00000437480ENST00000437480GLI3chr7

42063066

-GLI3chr7

42088295

-
intron-intronENST00000395925ENST00000395925GLI3chr7

42048577

-GLI3chr7

42050811

-
intron-intronENST00000395925ENST00000479210GLI3chr7

42048577

-GLI3chr7

42050811

-
intron-intronENST00000395925ENST00000437480GLI3chr7

42048577

-GLI3chr7

42050811

-
intron-intronENST00000479210ENST00000395925GLI3chr7

42048577

-GLI3chr7

42050811

-
intron-intronENST00000479210ENST00000479210GLI3chr7

42048577

-GLI3chr7

42050811

-
intron-intronENST00000479210ENST00000437480GLI3chr7

42048577

-GLI3chr7

42050811

-
intron-intronENST00000437480ENST00000395925GLI3chr7

42048577

-GLI3chr7

42050811

-
intron-intronENST00000437480ENST00000479210GLI3chr7

42048577

-GLI3chr7

42050811

-
intron-intronENST00000437480ENST00000437480GLI3chr7

42048577

-GLI3chr7

42050811

-

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 GLI3-GLI3


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.

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 GLI3-GLI3


check button Go to

FGviewer for the breakpoints of chr7:42063066-chr7:42088295

.
- 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
.GLI3

P10071

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: Has a dual function as a transcriptional activator and a repressor of the sonic hedgehog (Shh) pathway, and plays a role in limb development. The full-length GLI3 form (GLI3FL) after phosphorylation and nuclear translocation, acts as an activator (GLI3A) while GLI3R, its C-terminally truncated form, acts as a repressor. A proper balance between the GLI3 activator and the repressor GLI3R, rather than the repressor gradient itself or the activator/repressor ratio gradient, specifies limb digit number and identity. In concert with TRPS1, plays a role in regulating the size of the zone of distal chondrocytes, in restricting the zone of PTHLH expression in distal cells and in activating chondrocyte proliferation. Binds to the minimal GLI-consensus sequence 5'-GGGTGGTC-3'. {ECO:0000269|PubMed:10693759, ECO:0000269|PubMed:11238441, ECO:0000269|PubMed:17764085}.

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
TgeneGLI3chr7:42063066chr7:42088295ENST000003959253151492_1512157.666666666666661581.0Compositional biasNote=Asp/Glu-rich (acidic)
TgeneGLI3chr7:42063066chr7:42088295ENST00000395925315480_505157.666666666666661581.0Zinc fingerC2H2-type 1
TgeneGLI3chr7:42063066chr7:42088295ENST00000395925315513_540157.666666666666661581.0Zinc fingerC2H2-type 2
TgeneGLI3chr7:42063066chr7:42088295ENST00000395925315546_570157.666666666666661581.0Zinc fingerC2H2-type 3
TgeneGLI3chr7:42063066chr7:42088295ENST00000395925315576_601157.666666666666661581.0Zinc fingerC2H2-type 4
TgeneGLI3chr7:42063066chr7:42088295ENST00000395925315607_632157.666666666666661581.0Zinc fingerC2H2-type 5

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneGLI3chr7:42063066chr7:42088295ENST00000395925-10151492_1512499.01581.0Compositional biasNote=Asp/Glu-rich (acidic)
HgeneGLI3chr7:42063066chr7:42088295ENST00000395925-1015480_505499.01581.0Zinc fingerC2H2-type 1
HgeneGLI3chr7:42063066chr7:42088295ENST00000395925-1015513_540499.01581.0Zinc fingerC2H2-type 2
HgeneGLI3chr7:42063066chr7:42088295ENST00000395925-1015546_570499.01581.0Zinc fingerC2H2-type 3
HgeneGLI3chr7:42063066chr7:42088295ENST00000395925-1015576_601499.01581.0Zinc fingerC2H2-type 4
HgeneGLI3chr7:42063066chr7:42088295ENST00000395925-1015607_632499.01581.0Zinc fingerC2H2-type 5


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Fusion Gene Sequence for GLI3-GLI3


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 GLI3-GLI3


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 GLI3-GLI3


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 GLI3-GLI3


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneGLI3C0265306Greig cephalopolysyndactyly syndrome13CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
HgeneGLI3C0265220Pallister-Hall syndrome6CTD_human;GENOMICS_ENGLAND
HgeneGLI3C0152427Polydactyly2CTD_human;GENOMICS_ENGLAND
HgeneGLI3C0796147Acrocallosal Syndrome2ORPHANET
HgeneGLI3C1868111Polydactyly, preaxial 42CTD_human;GENOMICS_ENGLAND;ORPHANET
HgeneGLI3C1868120POSTAXIAL POLYDACTYLY, TYPE B2CTD_human;ORPHANET
HgeneGLI3C2931760Acrocallosal syndrome, Schinzel type2ORPHANET
HgeneGLI3C3887487Postaxial polydactyly type A2CTD_human;GENOMICS_ENGLAND;ORPHANET
HgeneGLI3C4282400Polydactyly, Postaxial, Type A12CTD_human;GENOMICS_ENGLAND;UNIPROT
HgeneGLI3C0011999Diastematomyelia1CTD_human
HgeneGLI3C0024623Malignant neoplasm of stomach1CTD_human
HgeneGLI3C0027794Neural Tube Defects1CTD_human
HgeneGLI3C0027806Neurenteric Cyst1CTD_human
HgeneGLI3C0038356Stomach Neoplasms1CTD_human
HgeneGLI3C0080218Tethered Cord Syndrome1CTD_human
HgeneGLI3C0152234Iniencephaly1CTD_human
HgeneGLI3C0152426Craniorachischisis1CTD_human
HgeneGLI3C0162835Hypopigmentation disorder1CTD_human
HgeneGLI3C0238198Gastrointestinal Stromal Tumors1CTD_human
HgeneGLI3C0265553Polysyndactyly1ORPHANET
HgeneGLI3C0265633Congenital absence of tibia1ORPHANET
HgeneGLI3C0266453Exencephaly1CTD_human
HgeneGLI3C0342418Hypothalamic hamartomas1CTD_human;GENOMICS_ENGLAND
HgeneGLI3C0344479Spinal Cord Myelodysplasia1CTD_human
HgeneGLI3C0702169Acrania1CTD_human
HgeneGLI3C1708349Hereditary Diffuse Gastric Cancer1CTD_human
HgeneGLI3C3179349Gastrointestinal Stromal Sarcoma1CTD_human
HgeneGLI3C3495676Anorectal Malformations1GENOMICS_ENGLAND
TgeneGLI3C0265306Greig cephalopolysyndactyly syndrome13CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
TgeneGLI3C0265220Pallister-Hall syndrome6CTD_human;GENOMICS_ENGLAND
TgeneGLI3C0152427Polydactyly2CTD_human;GENOMICS_ENGLAND
TgeneGLI3C0796147Acrocallosal Syndrome2ORPHANET
TgeneGLI3C1868111Polydactyly, preaxial 42CTD_human;GENOMICS_ENGLAND;ORPHANET
TgeneGLI3C1868120POSTAXIAL POLYDACTYLY, TYPE B2CTD_human;ORPHANET
TgeneGLI3C2931760Acrocallosal syndrome, Schinzel type2ORPHANET
TgeneGLI3C3887487Postaxial polydactyly type A2CTD_human;GENOMICS_ENGLAND;ORPHANET
TgeneGLI3C4282400Polydactyly, Postaxial, Type A12CTD_human;GENOMICS_ENGLAND;UNIPROT
TgeneGLI3C0011999Diastematomyelia1CTD_human
TgeneGLI3C0024623Malignant neoplasm of stomach1CTD_human
TgeneGLI3C0027794Neural Tube Defects1CTD_human
TgeneGLI3C0027806Neurenteric Cyst1CTD_human
TgeneGLI3C0038356Stomach Neoplasms1CTD_human
TgeneGLI3C0080218Tethered Cord Syndrome1CTD_human
TgeneGLI3C0152234Iniencephaly1CTD_human
TgeneGLI3C0152426Craniorachischisis1CTD_human
TgeneGLI3C0162835Hypopigmentation disorder1CTD_human
TgeneGLI3C0238198Gastrointestinal Stromal Tumors1CTD_human
TgeneGLI3C0265553Polysyndactyly1ORPHANET
TgeneGLI3C0265633Congenital absence of tibia1ORPHANET
TgeneGLI3C0266453Exencephaly1CTD_human
TgeneGLI3C0342418Hypothalamic hamartomas1CTD_human;GENOMICS_ENGLAND
TgeneGLI3C0344479Spinal Cord Myelodysplasia1CTD_human
TgeneGLI3C0702169Acrania1CTD_human
TgeneGLI3C1708349Hereditary Diffuse Gastric Cancer1CTD_human
TgeneGLI3C3179349Gastrointestinal Stromal Sarcoma1CTD_human
TgeneGLI3C3495676Anorectal Malformations1GENOMICS_ENGLAND