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Center for Computational Systems Medicine level2
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Fusion Gene Summary

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Fusion Gene Sample Information

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Fusion ORF Analysis

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Fusion Amino Acid Sequences

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Fusion Protein Functional Features

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Fusion Protein Structure

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pLDDT scores

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Ramachandran Plot of Fusion Protein Structure

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Fusion Protein-Protein Interaction

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Related drugs with this fusion protein

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Related disease with this fusion protein

Fusion Protein:GRB2-PADI1

Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: GRB2-PADI1
FusionPDB ID: 34645
FusionGDB2.0 ID: 34645
HgeneTgene
Gene symbol

GRB2

PADI1

Gene ID

2885

29943

Gene namegrowth factor receptor bound protein 2peptidyl arginine deiminase 1
SynonymsASH|EGFRBP-GRB2|Grb3-3|MST084|MSTP084|NCKAP2HPAD10|PAD1|PDI|PDI1
Cytomap

17q25.1

1p36.13

Type of geneprotein-codingprotein-coding
Descriptiongrowth factor receptor-bound protein 2HT027SH2/SH3 adapter GRB2abundant SRC homologyepidermal growth factor receptor-binding protein GRB2epididymis secretory sperm binding proteingrowth factor receptor-bound protein 3protein Ashprotein-arginine deiminase type-1hPAD-colony 10peptidyl arginine deiminase, type Ipeptidylarginine deiminase Iprotein-arginine deiminase type I
Modification date2020032720200313
UniProtAcc

GAB3

.
Ensembl transtripts involved in fusion geneENST idsENST00000316615, ENST00000316804, 
ENST00000392562, ENST00000392563, 
ENST00000392564, ENST00000462266, 
ENST00000578961, 		ENST00000460293, 
ENST00000375471, ENST00000413717, 
ENST00000536552, ENST00000537499, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score18 X 13 X 11=25742 X 3 X 2=12
# samples 253
** MAII scorelog2(25/2574*10)=-3.36401205355861
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(3/12*10)=1.32192809488736
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context (manual curation of fusion genes in FusionPDB)

PubMed: GRB2 [Title/Abstract] AND PADI1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)GRB2(73317740)-PADI1(17570505), # samples:3
Anticipated loss of major functional domain due to fusion event.GRB2-PADI1 seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF.
GRB2-PADI1 seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF.
GRB2-PADI1 seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame ORF.
GRB2-PADI1 seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame ORF.
GRB2-PADI1 seems lost the major protein functional domain in Tgene partner, which is a epigenetic factor due to the frame-shifted ORF.
GRB2-PADI1 seems lost the major protein functional domain in Tgene partner, which is a IUPHAR drug target 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
TgenePADI1

GO:0018101

protein citrullination

27393304


check buttonFusion gene breakpoints across GRB2 (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 PADI1 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure


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Fusion Gene Sample Information

check buttonFusion gene information from FusionGDB2.0.
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-L5-A4OS-01AGRB2chr17

73317740

-PADI1chr1

17570505

+
ChimerDB4ESCATCGA-L5-A4OSGRB2chr17

73317739

-PADI1chr1

17570504

+
ChimerDB4ESCATCGA-L5-A4OSGRB2chr17

73317740

-PADI1chr1

17570505

+


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Fusion ORF Analysis


check buttonFusion information from ORFfinder translation from full-length transcript sequence from FusionPDB.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandSeq length
(transcript)		BP loci
(transcript)		Predicted start
(transcript)		Predicted stop
(transcript)		Seq length
(amino acids)
ENST00000392562GRB2chr1773317740-ENST00000413717PADI1chr117570505+225212517831484233
ENST00000316804GRB2chr1773317740-ENST00000413717PADI1chr117570505+17717703021003233
ENST00000316615GRB2chr1773317740-ENST00000413717PADI1chr117570505+1704703358936192
ENST00000392563GRB2chr1773317740-ENST00000537499PADI1chr117570505+70937328606192
ENST00000392564GRB2chr1773317740-ENST00000537499PADI1chr117570505+1040704236937233
ENST00000392562GRB2chr1773317739-ENST00000413717PADI1chr117570504+225212517831484233
ENST00000316804GRB2chr1773317739-ENST00000413717PADI1chr117570504+17717703021003233
ENST00000316615GRB2chr1773317739-ENST00000413717PADI1chr117570504+1704703358936192
ENST00000392563GRB2chr1773317739-ENST00000537499PADI1chr117570504+70937328606192
ENST00000392564GRB2chr1773317739-ENST00000537499PADI1chr117570504+1040704236937233

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
ENST00000392562ENST00000413717GRB2chr1773317740-PADI1chr117570505+0.0054462110.9945538
ENST00000316804ENST00000413717GRB2chr1773317740-PADI1chr117570505+0.005342120.9946578
ENST00000316615ENST00000413717GRB2chr1773317740-PADI1chr117570505+0.0054129190.99458706
ENST00000392563ENST00000537499GRB2chr1773317740-PADI1chr117570505+0.0012620840.9987379
ENST00000392564ENST00000537499GRB2chr1773317740-PADI1chr117570505+0.0043329220.9956671
ENST00000392562ENST00000413717GRB2chr1773317739-PADI1chr117570504+0.0054462110.9945538
ENST00000316804ENST00000413717GRB2chr1773317739-PADI1chr117570504+0.005342120.9946578
ENST00000316615ENST00000413717GRB2chr1773317739-PADI1chr117570504+0.0054129190.99458706
ENST00000392563ENST00000537499GRB2chr1773317739-PADI1chr117570504+0.0012620840.9987379
ENST00000392564ENST00000537499GRB2chr1773317739-PADI1chr117570504+0.0043329220.9956671

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Fusion Amino Acid Sequences


check button For individual full-length fusion transcript sequence from FusionPDB, we ran ORFfinder and chose the longest ORF among the all predicted ones.
>FusionGDB ID_FusionGDB isoform ID_FGname_Hgene_Hchr_Hbp_Henst_Tgene_Tchr_Tbp_Tenst_length(fusion AA) seq_BP

>34645_34645_1_GRB2-PADI1_GRB2_chr17_73317739_ENST00000316615_PADI1_chr1_17570504_ENST00000413717_length(amino acids)=192AA_BP=114
MEAIAKYDFKATADDELSFKRGDILKVLNEECDQNWYKAELNGKDGFIPKNYIEMKPHPFGNDVQHFKVLRDGAGKYFLWVVKFNSLNEL
VDYHRSTSVSRNQQIFLRDIEQVPQVNMVVLGKYLGIPKPYGPIINGRCCLEEKVQSLLEPLGLHCIFIDDYLSYHELQGEIHCGTNVRR

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

>34645_34645_2_GRB2-PADI1_GRB2_chr17_73317739_ENST00000316804_PADI1_chr1_17570504_ENST00000413717_length(amino acids)=233AA_BP=155
MEAIAKYDFKATADDELSFKRGDILKVLNEECDQNWYKAELNGKDGFIPKNYIEMKPHPWFFGKIPRAKAEEMLSKQRHDGAFLIRESES
APGDFSLSVKFGNDVQHFKVLRDGAGKYFLWVVKFNSLNELVDYHRSTSVSRNQQIFLRDIEQVPQVNMVVLGKYLGIPKPYGPIINGRC

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

>34645_34645_3_GRB2-PADI1_GRB2_chr17_73317739_ENST00000392562_PADI1_chr1_17570504_ENST00000413717_length(amino acids)=233AA_BP=155
MEAIAKYDFKATADDELSFKRGDILKVLNEECDQNWYKAELNGKDGFIPKNYIEMKPHPWFFGKIPRAKAEEMLSKQRHDGAFLIRESES
APGDFSLSVKFGNDVQHFKVLRDGAGKYFLWVVKFNSLNELVDYHRSTSVSRNQQIFLRDIEQVPQVNMVVLGKYLGIPKPYGPIINGRC

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

>34645_34645_4_GRB2-PADI1_GRB2_chr17_73317739_ENST00000392563_PADI1_chr1_17570504_ENST00000537499_length(amino acids)=192AA_BP=114
MEAIAKYDFKATADDELSFKRGDILKVLNEECDQNWYKAELNGKDGFIPKNYIEMKPHPFGNDVQHFKVLRDGAGKYFLWVVKFNSLNEL
VDYHRSTSVSRNQQIFLRDIEQVPQVNMVVLGKYLGIPKPYGPIINGRCCLEEKVQSLLEPLGLHCIFIDDYLSYHELQGEIHCGTNVRR

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

>34645_34645_5_GRB2-PADI1_GRB2_chr17_73317739_ENST00000392564_PADI1_chr1_17570504_ENST00000537499_length(amino acids)=233AA_BP=155
MEAIAKYDFKATADDELSFKRGDILKVLNEECDQNWYKAELNGKDGFIPKNYIEMKPHPWFFGKIPRAKAEEMLSKQRHDGAFLIRESES
APGDFSLSVKFGNDVQHFKVLRDGAGKYFLWVVKFNSLNELVDYHRSTSVSRNQQIFLRDIEQVPQVNMVVLGKYLGIPKPYGPIINGRC

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

>34645_34645_6_GRB2-PADI1_GRB2_chr17_73317740_ENST00000316615_PADI1_chr1_17570505_ENST00000413717_length(amino acids)=192AA_BP=114
MEAIAKYDFKATADDELSFKRGDILKVLNEECDQNWYKAELNGKDGFIPKNYIEMKPHPFGNDVQHFKVLRDGAGKYFLWVVKFNSLNEL
VDYHRSTSVSRNQQIFLRDIEQVPQVNMVVLGKYLGIPKPYGPIINGRCCLEEKVQSLLEPLGLHCIFIDDYLSYHELQGEIHCGTNVRR

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

>34645_34645_7_GRB2-PADI1_GRB2_chr17_73317740_ENST00000316804_PADI1_chr1_17570505_ENST00000413717_length(amino acids)=233AA_BP=155
MEAIAKYDFKATADDELSFKRGDILKVLNEECDQNWYKAELNGKDGFIPKNYIEMKPHPWFFGKIPRAKAEEMLSKQRHDGAFLIRESES
APGDFSLSVKFGNDVQHFKVLRDGAGKYFLWVVKFNSLNELVDYHRSTSVSRNQQIFLRDIEQVPQVNMVVLGKYLGIPKPYGPIINGRC

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

>34645_34645_8_GRB2-PADI1_GRB2_chr17_73317740_ENST00000392562_PADI1_chr1_17570505_ENST00000413717_length(amino acids)=233AA_BP=155
MEAIAKYDFKATADDELSFKRGDILKVLNEECDQNWYKAELNGKDGFIPKNYIEMKPHPWFFGKIPRAKAEEMLSKQRHDGAFLIRESES
APGDFSLSVKFGNDVQHFKVLRDGAGKYFLWVVKFNSLNELVDYHRSTSVSRNQQIFLRDIEQVPQVNMVVLGKYLGIPKPYGPIINGRC

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

>34645_34645_9_GRB2-PADI1_GRB2_chr17_73317740_ENST00000392563_PADI1_chr1_17570505_ENST00000537499_length(amino acids)=192AA_BP=114
MEAIAKYDFKATADDELSFKRGDILKVLNEECDQNWYKAELNGKDGFIPKNYIEMKPHPFGNDVQHFKVLRDGAGKYFLWVVKFNSLNEL
VDYHRSTSVSRNQQIFLRDIEQVPQVNMVVLGKYLGIPKPYGPIINGRCCLEEKVQSLLEPLGLHCIFIDDYLSYHELQGEIHCGTNVRR

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

>34645_34645_10_GRB2-PADI1_GRB2_chr17_73317740_ENST00000392564_PADI1_chr1_17570505_ENST00000537499_length(amino acids)=233AA_BP=155
MEAIAKYDFKATADDELSFKRGDILKVLNEECDQNWYKAELNGKDGFIPKNYIEMKPHPWFFGKIPRAKAEEMLSKQRHDGAFLIRESES
APGDFSLSVKFGNDVQHFKVLRDGAGKYFLWVVKFNSLNELVDYHRSTSVSRNQQIFLRDIEQVPQVNMVVLGKYLGIPKPYGPIINGRC

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

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Fusion Protein Functional Features


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/chr17:73317740/chr1:17570505)
- 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
GRB2

GAB3

.
586FUNCTION: 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.

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.
- Retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneGRB2chr17:73317739chr1:17570504ENST00000316615-451_58115.0177.0DomainSH3 1
HgeneGRB2chr17:73317739chr1:17570504ENST00000316804-561_58156.0218.0DomainSH3 1
HgeneGRB2chr17:73317739chr1:17570504ENST00000316804-5660_152156.0218.0DomainSH2
HgeneGRB2chr17:73317739chr1:17570504ENST00000392562-561_58156.0218.0DomainSH3 1
HgeneGRB2chr17:73317739chr1:17570504ENST00000392562-5660_152156.0218.0DomainSH2
HgeneGRB2chr17:73317739chr1:17570504ENST00000392563-341_58115.0177.0DomainSH3 1
HgeneGRB2chr17:73317739chr1:17570504ENST00000392564-451_58156.0218.0DomainSH3 1
HgeneGRB2chr17:73317739chr1:17570504ENST00000392564-4560_152156.0218.0DomainSH2
HgeneGRB2chr17:73317740chr1:17570505ENST00000316615-451_58115.0177.0DomainSH3 1
HgeneGRB2chr17:73317740chr1:17570505ENST00000316804-561_58156.0218.0DomainSH3 1
HgeneGRB2chr17:73317740chr1:17570505ENST00000316804-5660_152156.0218.0DomainSH2
HgeneGRB2chr17:73317740chr1:17570505ENST00000392562-561_58156.0218.0DomainSH3 1
HgeneGRB2chr17:73317740chr1:17570505ENST00000392562-5660_152156.0218.0DomainSH2
HgeneGRB2chr17:73317740chr1:17570505ENST00000392563-341_58115.0177.0DomainSH3 1
HgeneGRB2chr17:73317740chr1:17570505ENST00000392564-451_58156.0218.0DomainSH3 1
HgeneGRB2chr17:73317740chr1:17570505ENST00000392564-4560_152156.0218.0DomainSH2

- Not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneGRB2chr17:73317739chr1:17570504ENST00000316615-45156_215115.0177.0DomainSH3 2
HgeneGRB2chr17:73317739chr1:17570504ENST00000316615-4560_152115.0177.0DomainSH2
HgeneGRB2chr17:73317739chr1:17570504ENST00000316804-56156_215156.0218.0DomainSH3 2
HgeneGRB2chr17:73317739chr1:17570504ENST00000392562-56156_215156.0218.0DomainSH3 2
HgeneGRB2chr17:73317739chr1:17570504ENST00000392563-34156_215115.0177.0DomainSH3 2
HgeneGRB2chr17:73317739chr1:17570504ENST00000392563-3460_152115.0177.0DomainSH2
HgeneGRB2chr17:73317739chr1:17570504ENST00000392564-45156_215156.0218.0DomainSH3 2
HgeneGRB2chr17:73317740chr1:17570505ENST00000316615-45156_215115.0177.0DomainSH3 2
HgeneGRB2chr17:73317740chr1:17570505ENST00000316615-4560_152115.0177.0DomainSH2
HgeneGRB2chr17:73317740chr1:17570505ENST00000316804-56156_215156.0218.0DomainSH3 2
HgeneGRB2chr17:73317740chr1:17570505ENST00000392562-56156_215156.0218.0DomainSH3 2
HgeneGRB2chr17:73317740chr1:17570505ENST00000392563-34156_215115.0177.0DomainSH3 2
HgeneGRB2chr17:73317740chr1:17570505ENST00000392563-3460_152115.0177.0DomainSH2
HgeneGRB2chr17:73317740chr1:17570505ENST00000392564-45156_215156.0218.0DomainSH3 2


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Fusion Protein Structures

check button PDB and CIF files of the predicted fusion proteins
* Here we show the 3D structure of the fusion proteins using Mol*. AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. Model confidence is shown from the pLDDT values per residue. pLDDT corresponds to the model’s prediction of its score on the local Distance Difference Test. It is a measure of local accuracy (from AlphfaFold website). To color code individual residues, we transformed individual PDB files into CIF format.
Fusion protein PDB link (fusion AA seq ID in FusionPDB)HgeneHchrHbpHstrandTgeneTchrTbpTstrandAA seqLen(AA seq)
PDB file >>>360_GRB2_73317740_PADI1_17570505_ranked_0.pdbGRB27331773973317740ENST00000537499PADI1chr117570505+
MEAIAKYDFKATADDELSFKRGDILKVLNEECDQNWYKAELNGKDGFIPKNYIEMKPHPWFFGKIPRAKAEEMLSKQRHDGAFLIRESES
APGDFSLSVKFGNDVQHFKVLRDGAGKYFLWVVKFNSLNELVDYHRSTSVSRNQQIFLRDIEQVPQVNMVVLGKYLGIPKPYGPIINGRC
233


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pLDDT score distribution

check button pLDDT score distribution of the predicted wild-type structures of two partner proteins from AlphaFold2
* AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100.
GRB2_pLDDT.png
all structure
all structure
PADI1_pLDDT.png
all structure
all structure

check button pLDDT score distribution of the predicted fusion protein structures from AlphaFold2
* AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100.
all structure


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Ramachandran Plot of Fusion Protein Structure


check button Ramachandran plot of the torsional angles - phi (φ)and psi (ψ) - of the residues (amino acids) contained in this fusion protein peptide.
Fusion AA seq ID in FusionPDB and their Ramachandran plots

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Fusion Protein-Protein Interaction


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 from validated records (BIOGRID-3.4.160)
GenePPI interactors


check button Protein-protein interactors based on sequence similarity (STRING)
GeneSTRING network
GRB2
PADI1


check button - Retained interactions in fusion protein (protein functional feature from UniProt).
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenStill interaction with


check button - Lost interactions due to fusion (protein functional feature from UniProt).
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


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Related Drugs to GRB2-PADI1


check button Drugs used for this fusion-positive patient.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)
HgeneTgeneDrugSourcePMID

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Related Diseases to GRB2-PADI1


check button Diseases that have this fusion gene.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)
HgeneTgeneDiseaseSourcePMID

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