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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:AGFG1-MFF

Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: AGFG1-MFF
FusionPDB ID: 2868
FusionGDB2.0 ID: 2868
HgeneTgene
Gene symbol

AGFG1

MFF

Gene ID

3267

56947

Gene nameArfGAP with FG repeats 1mitochondrial fission factor
SynonymsHRB|RAB|RIPC2orf33|EMPF2|GL004
Cytomap

2q36.3

2q36.3

Type of geneprotein-codingprotein-coding
Descriptionarf-GAP domain and FG repeat-containing protein 1HIV-1 Rev-binding proteinRab, Rev/Rex activation domain-binding proteinarf-GAP domain and FG repeats-containing protein 1hRIP, Rev interacting proteinnucleoporin-like protein RIPrev-interacting proteimitochondrial fission factor
Modification date2020031320200327
UniProtAcc

P52594

Q9GZY8

Ensembl transtripts involved in fusion geneENST idsENST00000310078, ENST00000373671, 
ENST00000409171, ENST00000409315, 
ENST00000409979, ENST00000486932, 
ENST00000337110, ENST00000349901, 
ENST00000353339, ENST00000354503, 
ENST00000392059, ENST00000409565, 
ENST00000409616, ENST00000476924, 
ENST00000524634, ENST00000304593, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score13 X 9 X 8=9366 X 9 X 4=216
# samples 159
** MAII scorelog2(15/936*10)=-2.64154602908752
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(9/216*10)=-1.26303440583379
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)

PubMed: AGFG1 [Title/Abstract] AND MFF [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)AGFG1(228389631)-MFF(228220393), # samples:2
AGFG1(228337304)-MFF(228220393), # samples:2
Anticipated loss of major functional domain due to fusion event.AGFG1-MFF 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.
AGFG1-MFF 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.
AGFG1-MFF 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.
AGFG1-MFF 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.
AGFG1-MFF seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
AGFG1-MFF 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
TgeneMFF

GO:0090141

positive regulation of mitochondrial fission

23283981|23530241

TgeneMFF

GO:0090314

positive regulation of protein targeting to membrane

23283981


check buttonFusion gene breakpoints across AGFG1 (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 MFF (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
ChimerDB4LUADTCGA-62-A471-01AAGFG1chr2

228389631

-MFFchr2

228220393

+
ChimerDB4LUADTCGA-62-A471-01AAGFG1chr2

228389631

+MFFchr2

228220393

+
ChimerDB4LUADTCGA-62-A471-01AAGFG1chr2

228395926

+MFFchr2

228211942

+
ChimerDB4LUADTCGA-62-A471-01AAGFG1chr2

228395926

+MFFchr2

228220393

+
ChimerDB4LUADTCGA-62-A471AGFG1chr2

228389631

+MFFchr2

228220392

+
ChimerDB4LUADTCGA-62-A471AGFG1chr2

228395926

+MFFchr2

228220392

+
ChimerDB4LUSCTCGA-43-8116-01AAGFG1chr2

228337304

-MFFchr2

228220393

+
ChimerDB4LUSCTCGA-43-8116AGFG1chr2

228337304

+MFFchr2

228220393

+


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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)
ENST00000409979AGFG1chr2228337304+ENST00000304593MFFchr2228220393+137143745653202
ENST00000310078AGFG1chr2228337304+ENST00000304593MFFchr2228220393+136142735643202
ENST00000409315AGFG1chr2228337304+ENST00000304593MFFchr2228220393+115422023436137
ENST00000373671AGFG1chr2228337304+ENST00000304593MFFchr2228220393+115121720433137
ENST00000409171AGFG1chr2228337304+ENST00000304593MFFchr2228220393+115121720433137

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
ENST00000409979ENST00000304593AGFG1chr2228337304+MFFchr2228220393+0.0129206930.9870794
ENST00000310078ENST00000304593AGFG1chr2228337304+MFFchr2228220393+0.0127426880.9872573
ENST00000409315ENST00000304593AGFG1chr2228337304+MFFchr2228220393+0.0118495650.9881505
ENST00000373671ENST00000304593AGFG1chr2228337304+MFFchr2228220393+0.0134576230.98654234
ENST00000409171ENST00000304593AGFG1chr2228337304+MFFchr2228220393+0.0134576230.98654234

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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

>2868_2868_1_AGFG1-MFF_AGFG1_chr2_228337304_ENST00000310078_MFF_chr2_228220393_ENST00000304593_length(amino acids)=202AA_BP=131
MSRLCRLVWPVSPRTTAPGPRRAQYSQAAAAGSGAGGARRRRAAAAARAARGTAGPRRSAARLPALPASSLGAAAMAASAKRKQEEKHLK
MLRDMTGLPHNRKCFDCDQRGPTYVNMTVGSFVCTSCSGSLYGISNIDTTIEGTSDDLTVVDAASLRRQIIKLNRRLQLLEEENKERAKR

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

>2868_2868_2_AGFG1-MFF_AGFG1_chr2_228337304_ENST00000373671_MFF_chr2_228220393_ENST00000304593_length(amino acids)=137AA_BP=66
MPASSLGAAAMAASAKRKQEEKHLKMLRDMTGLPHNRKCFDCDQRGPTYVNMTVGSFVCTSCSGSLYGISNIDTTIEGTSDDLTVVDAAS

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

>2868_2868_3_AGFG1-MFF_AGFG1_chr2_228337304_ENST00000409171_MFF_chr2_228220393_ENST00000304593_length(amino acids)=137AA_BP=66
MPASSLGAAAMAASAKRKQEEKHLKMLRDMTGLPHNRKCFDCDQRGPTYVNMTVGSFVCTSCSGSLYGISNIDTTIEGTSDDLTVVDAAS

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

>2868_2868_4_AGFG1-MFF_AGFG1_chr2_228337304_ENST00000409315_MFF_chr2_228220393_ENST00000304593_length(amino acids)=137AA_BP=66
MPASSLGAAAMAASAKRKQEEKHLKMLRDMTGLPHNRKCFDCDQRGPTYVNMTVGSFVCTSCSGSLYGISNIDTTIEGTSDDLTVVDAAS

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

>2868_2868_5_AGFG1-MFF_AGFG1_chr2_228337304_ENST00000409979_MFF_chr2_228220393_ENST00000304593_length(amino acids)=202AA_BP=131
MSRLCRLVWPVSPRTTAPGPRRAQYSQAAAAGSGAGGARRRRAAAAARAARGTAGPRRSAARLPALPASSLGAAAMAASAKRKQEEKHLK
MLRDMTGLPHNRKCFDCDQRGPTYVNMTVGSFVCTSCSGSLYGISNIDTTIEGTSDDLTVVDAASLRRQIIKLNRRLQLLEEENKERAKR

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

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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/chr2:228389631/chr2:228220393)
- 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
AGFG1

P52594

MFF

Q9GZY8

FUNCTION: Required for vesicle docking or fusion during acrosome biogenesis (By similarity). May play a role in RNA trafficking or localization. In case of infection by HIV-1, acts as a cofactor for viral Rev and promotes movement of Rev-responsive element-containing RNAs from the nuclear periphery to the cytoplasm. This step is essential for HIV-1 replication. {ECO:0000250, ECO:0000269|PubMed:10613896, ECO:0000269|PubMed:14701878, ECO:0000269|PubMed:15749819}.FUNCTION: Plays a role in mitochondrial and peroxisomal fission. Promotes the recruitment and association of the fission mediator dynamin-related protein 1 (DNM1L) to the mitochondrial surface. May be involved in regulation of synaptic vesicle membrane dynamics by recruitment of DNM1L to clathrin-containing vesicles. {ECO:0000269|PubMed:18353969, ECO:0000269|PubMed:23530241}.

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
HgeneAGFG1chr2:228337304chr2:228220393ENST00000310078+11329_5255.666666666666664563.0Zinc fingerC4-type
HgeneAGFG1chr2:228337304chr2:228220393ENST00000373671+11229_5255.666666666666664523.0Zinc fingerC4-type
HgeneAGFG1chr2:228337304chr2:228220393ENST00000409171+11329_5255.666666666666664561.0Zinc fingerC4-type
TgeneMFFchr2:228337304chr2:228220393ENST0000030459369291_322219.66666666666666292.0Coiled coilOntology_term=ECO:0000255
TgeneMFFchr2:228337304chr2:228220393ENST0000033711058291_322171.66666666666666244.0Coiled coilOntology_term=ECO:0000255
TgeneMFFchr2:228337304chr2:228220393ENST0000034990158291_322166.66666666666666239.0Coiled coilOntology_term=ECO:0000255
TgeneMFFchr2:228337304chr2:228220393ENST00000353339811291_322270.6666666666667343.0Coiled coilOntology_term=ECO:0000255
TgeneMFFchr2:228337304chr2:228220393ENST0000035450347291_322146.66666666666666219.0Coiled coilOntology_term=ECO:0000255
TgeneMFFchr2:228337304chr2:228220393ENST00000392059811291_322270.6666666666667343.0Coiled coilOntology_term=ECO:0000255
TgeneMFFchr2:228337304chr2:228220393ENST0000040956536291_322146.66666666666666219.0Coiled coilOntology_term=ECO:0000255
TgeneMFFchr2:228337304chr2:228220393ENST0000040961669291_322166.66666666666666239.0Coiled coilOntology_term=ECO:0000255
TgeneMFFchr2:228337304chr2:228220393ENST0000030459369341_342219.66666666666666292.0Topological domainMitochondrial intermembrane
TgeneMFFchr2:228337304chr2:228220393ENST0000033711058341_342171.66666666666666244.0Topological domainMitochondrial intermembrane
TgeneMFFchr2:228337304chr2:228220393ENST0000034990158341_342166.66666666666666239.0Topological domainMitochondrial intermembrane
TgeneMFFchr2:228337304chr2:228220393ENST00000353339811341_342270.6666666666667343.0Topological domainMitochondrial intermembrane
TgeneMFFchr2:228337304chr2:228220393ENST0000035450347341_342146.66666666666666219.0Topological domainMitochondrial intermembrane
TgeneMFFchr2:228337304chr2:228220393ENST00000392059811341_342270.6666666666667343.0Topological domainMitochondrial intermembrane
TgeneMFFchr2:228337304chr2:228220393ENST0000040956536341_342146.66666666666666219.0Topological domainMitochondrial intermembrane
TgeneMFFchr2:228337304chr2:228220393ENST0000040961669341_342166.66666666666666239.0Topological domainMitochondrial intermembrane
TgeneMFFchr2:228337304chr2:228220393ENST0000030459369323_340219.66666666666666292.0TransmembraneHelical%3B Anchor for type IV membrane protein
TgeneMFFchr2:228337304chr2:228220393ENST0000033711058323_340171.66666666666666244.0TransmembraneHelical%3B Anchor for type IV membrane protein
TgeneMFFchr2:228337304chr2:228220393ENST0000034990158323_340166.66666666666666239.0TransmembraneHelical%3B Anchor for type IV membrane protein
TgeneMFFchr2:228337304chr2:228220393ENST00000353339811323_340270.6666666666667343.0TransmembraneHelical%3B Anchor for type IV membrane protein
TgeneMFFchr2:228337304chr2:228220393ENST0000035450347323_340146.66666666666666219.0TransmembraneHelical%3B Anchor for type IV membrane protein
TgeneMFFchr2:228337304chr2:228220393ENST00000392059811323_340270.6666666666667343.0TransmembraneHelical%3B Anchor for type IV membrane protein
TgeneMFFchr2:228337304chr2:228220393ENST0000040956536323_340146.66666666666666219.0TransmembraneHelical%3B Anchor for type IV membrane protein
TgeneMFFchr2:228337304chr2:228220393ENST0000040961669323_340166.66666666666666239.0TransmembraneHelical%3B Anchor for type IV membrane protein

- Not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneAGFG1chr2:228337304chr2:228220393ENST00000310078+11311_13555.666666666666664563.0DomainArf-GAP
HgeneAGFG1chr2:228337304chr2:228220393ENST00000373671+11211_13555.666666666666664523.0DomainArf-GAP
HgeneAGFG1chr2:228337304chr2:228220393ENST00000409171+11311_13555.666666666666664561.0DomainArf-GAP
TgeneMFFchr2:228337304chr2:228220393ENST00000304593691_322219.66666666666666292.0Topological domainCytoplasmic
TgeneMFFchr2:228337304chr2:228220393ENST00000337110581_322171.66666666666666244.0Topological domainCytoplasmic
TgeneMFFchr2:228337304chr2:228220393ENST00000349901581_322166.66666666666666239.0Topological domainCytoplasmic
TgeneMFFchr2:228337304chr2:228220393ENST000003533398111_322270.6666666666667343.0Topological domainCytoplasmic
TgeneMFFchr2:228337304chr2:228220393ENST00000354503471_322146.66666666666666219.0Topological domainCytoplasmic
TgeneMFFchr2:228337304chr2:228220393ENST000003920598111_322270.6666666666667343.0Topological domainCytoplasmic
TgeneMFFchr2:228337304chr2:228220393ENST00000409565361_322146.66666666666666219.0Topological domainCytoplasmic
TgeneMFFchr2:228337304chr2:228220393ENST00000409616691_322166.66666666666666239.0Topological domainCytoplasmic


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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 >>>273_AGFG1_228337304_MFF_228220393_ranked_0.pdbAGFG1228337304228337304ENST00000304593MFFchr2228220393+
MSRLCRLVWPVSPRTTAPGPRRAQYSQAAAAGSGAGGARRRRAAAAARAARGTAGPRRSAARLPALPASSLGAAAMAASAKRKQEEKHLK
MLRDMTGLPHNRKCFDCDQRGPTYVNMTVGSFVCTSCSGSLYGISNIDTTIEGTSDDLTVVDAASLRRQIIKLNRRLQLLEEENKERAKR
202


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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.
AGFG1_pLDDT.png
all structure
all structure
MFF_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
AGFG1
MFF


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 AGFG1-MFF


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 AGFG1-MFF


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