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Center for Computational Systems Medicine
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Fusion Gene and Fusion Protein Summary

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Fusion Amino Acid Sequences (multiple BPs and multiple gene isoforms)

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Fusion Protein Breakpoint Sequences - (for the Screening of the FusionNeoAntigens)

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Potential FusionNeoAntigens in HLA I - (netMHCpan v4.1 + deepHLApan v1.1)

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Potential FusionNeoAntigens in HLA II - (netMHCIIpan v4.1)

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Fusion Breakpoint 14 AA Peptide Structure - (RoseTTAFold)

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D - (Glide)

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Vaccine Design for the FusionNeoAntigens (RNA/protein sequences)

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Potential target of CAR-T therapy development

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Information on the samples that have these potential fusion neoantigens

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Fusion Protein Targeting Drugs - (Manual Curation)

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Fusion Protein Related diseases - (Manual Curation)

Fusion Protein:ARHGEF12-TOR1AIP2

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: ARHGEF12-TOR1AIP2
FusionPDB ID: 6217
FusionGDB2.0 ID: 6217
HgeneTgene
Gene symbol

ARHGEF12

TOR1AIP2

Gene ID

23365

163590

Gene nameRho guanine nucleotide exchange factor 12torsin 1A interacting protein 2
SynonymsLARG|PRO2792IFRG15|LULL1|NET9
Cytomap

11q23.3

1q25.2

Type of geneprotein-codingprotein-coding
Descriptionrho guanine nucleotide exchange factor 12Rho guanine nucleotide exchange factor (GEF) 12leukemia-associated RhoGEFleukemia-associated rho guanine nucleotide exchange factortorsin-1A-interacting protein 2interferon alpha responsive protein15 kDa interferon-responsive proteininterferon responsive gene 15lumenal domain like LAP1torsin A interacting protein 2
Modification date2020031320200313
UniProtAcc

Q9NZN5

Main function of 5'-partner protein: FUNCTION: May play a role in the regulation of RhoA GTPase by guanine nucleotide-binding alpha-12 (GNA12) and alpha-13 (GNA13). Acts as guanine nucleotide exchange factor (GEF) for RhoA GTPase and may act as GTPase-activating protein (GAP) for GNA12 and GNA13. {ECO:0000269|PubMed:11094164}.
.
Ensembl transtripts involved in fusion geneENST idsENST00000356641, ENST00000397843, 
ENST00000532993, 
ENST00000482587, 
ENST00000367612, ENST00000609928, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score16 X 13 X 9=18725 X 5 X 3=75
# samples 215
** MAII scorelog2(21/1872*10)=-3.15611920191728
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(5/75*10)=-0.584962500721156
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Fusion gene context

PubMed: ARHGEF12 [Title/Abstract] AND TOR1AIP2 [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: ARHGEF12 [Title/Abstract] AND TOR1AIP2 [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)ARHGEF12(120348235)-TOR1AIP2(179816771), # samples:1
Anticipated loss of major functional domain due to fusion event.ARHGEF12-TOR1AIP2 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.
ARHGEF12-TOR1AIP2 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.
* 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
HgeneARHGEF12

GO:0007186

G protein-coupled receptor signaling pathway

15755723

TgeneTOR1AIP2

GO:0032781

positive regulation of ATPase activity

23569223|24275647

TgeneTOR1AIP2

GO:0090435

protein localization to nuclear envelope

19339278



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/chr11:120348235/chr1:179816771)
- 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 buttonRetention analysis results 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, are available here.

check buttonFusion gene breakpoints across ARHGEF12 (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 TOR1AIP2 (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 Amino Acid Sequences


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)
ENST00000397843ARHGEF12chr11120348235+ENST00000367612TOR1AIP2chr1179816771-10662369816645571463
ENST00000397843ARHGEF12chr11120348235+ENST00000609928TOR1AIP2chr1179816771-6698369816645571463
ENST00000356641ARHGEF12chr11120348235+ENST00000367612TOR1AIP2chr1179816771-104463482743411444
ENST00000356641ARHGEF12chr11120348235+ENST00000609928TOR1AIP2chr1179816771-64823482743411444
ENST00000532993ARHGEF12chr11120348235+ENST00000367612TOR1AIP2chr1179816771-10657369323045521440
ENST00000532993ARHGEF12chr11120348235+ENST00000609928TOR1AIP2chr1179816771-6693369323045521440

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
ENST00000397843ENST00000367612ARHGEF12chr11120348235+TOR1AIP2chr1179816771-0.0003579320.999642
ENST00000397843ENST00000609928ARHGEF12chr11120348235+TOR1AIP2chr1179816771-0.0005796720.9994204
ENST00000356641ENST00000367612ARHGEF12chr11120348235+TOR1AIP2chr1179816771-0.0003075030.99969256
ENST00000356641ENST00000609928ARHGEF12chr11120348235+TOR1AIP2chr1179816771-0.0005061370.99949384
ENST00000532993ENST00000367612ARHGEF12chr11120348235+TOR1AIP2chr1179816771-0.0005162970.9994837
ENST00000532993ENST00000609928ARHGEF12chr11120348235+TOR1AIP2chr1179816771-0.000845940.9991541

check button Predicted full-length fusion amino acid sequences. For individual full-length fusion transcript sequence from FusionPDB, we ran ORFfinder and chose the longest ORF among all the predicted ones.

Get the fusion protein sequences from here.

Fusion protein sequence information is available in the fasta format.
>FusionGDB ID_FusionGDB isoform ID_FGname_Hgene_Hchr_Hbp_Henst_Tgene_Tchr_Tbp_Tenst_length(fusion AA) seq_BP

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Fusion Protein Breakpoint Sequences for ARHGEF12-TOR1AIP2

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide
ARHGEF12chr11120348235TOR1AIP2chr117981677134821156KEEQHGISVTGLQSPEAGSHPQQTQK
ARHGEF12chr11120348235TOR1AIP2chr117981677134821158EQHGISVTGLQSPEAGSHPQQTQKLE
ARHGEF12chr11120348235TOR1AIP2chr117981677136931152KEEQHGISVTGLQSPEAGSHPQQTQK
ARHGEF12chr11120348235TOR1AIP2chr117981677136931154EQHGISVTGLQSPEAGSHPQQTQKLE
ARHGEF12chr11120348235TOR1AIP2chr117981677136981175KEEQHGISVTGLQSPEAGSHPQQTQK
ARHGEF12chr11120348235TOR1AIP2chr117981677136981177EQHGISVTGLQSPEAGSHPQQTQKLE

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Potential FusionNeoAntigen Information of ARHGEF12-TOR1AIP2 in HLA I

check button Multiple sequence alignments of the potential FusionNeoAntigens per fusion breakpoints. If the MSA is empty, then it means that there were predicted fusion neoantigens in this fusion breakpoint, but those predicted fusion neoantigens were not across the breakpoint, which is not fusion-specific.

check button Potential FusionNeoAntigen Information
* We used NetMHCpan v4.1 (%rank<0.5) and deepHLApan v1.1 (immunogenic score>0.5)
Fusion geneHchrHbpTgeneTchrTbpHLA IFusionNeoAntigen peptideBinding scoreImmunogenic scoreNeoantigen start (at BP 13)Neoantigen end (at BP 13)

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Potential FusionNeoAntigen Information of ARHGEF12-TOR1AIP2 in HLA II

check button Multiple sequence alignments of the potential FusionNeoAntigens per fusion breakpoints. If the MSA is empty, then it means that there were predicted fusion neoantigens in this fusion breakpoint, but those predicted fusion neoantigens were not across the breakpoint, which is not fusion-specific.
ARHGEF12-TOR1AIP2_120348235_179816771.msa

check button Potential FusionNeoAntigen Information
* We used NetMHCIIpan v4.1 (%rank<0.5).
Fusion geneHchrHbpTgeneTchrTbpHLA IIFusionNeoAntigen peptideNeoantigen start (at BP 13)Neoantigen end (at BP 13)
ARHGEF12-TOR1AIP2chr11120348235chr11798167713482DRB1-0440GISVTGLQSPEAGSH520
ARHGEF12-TOR1AIP2chr11120348235chr11798167713482DRB1-0440HGISVTGLQSPEAGS419
ARHGEF12-TOR1AIP2chr11120348235chr11798167713482DRB1-0442GISVTGLQSPEAGSH520
ARHGEF12-TOR1AIP2chr11120348235chr11798167713482DRB1-0444GISVTGLQSPEAGSH520
ARHGEF12-TOR1AIP2chr11120348235chr11798167713482DRB1-0455GISVTGLQSPEAGSH520
ARHGEF12-TOR1AIP2chr11120348235chr11798167713482DRB1-0455HGISVTGLQSPEAGS419
ARHGEF12-TOR1AIP2chr11120348235chr11798167713482DRB1-0456GISVTGLQSPEAGSH520
ARHGEF12-TOR1AIP2chr11120348235chr11798167713482DRB1-0458GISVTGLQSPEAGSH520
ARHGEF12-TOR1AIP2chr11120348235chr11798167713482DRB1-0468GISVTGLQSPEAGSH520
ARHGEF12-TOR1AIP2chr11120348235chr11798167713482DRB1-0468HGISVTGLQSPEAGS419
ARHGEF12-TOR1AIP2chr11120348235chr11798167713482DRB1-0470GISVTGLQSPEAGSH520
ARHGEF12-TOR1AIP2chr11120348235chr11798167713482DRB1-0479GISVTGLQSPEAGSH520
ARHGEF12-TOR1AIP2chr11120348235chr11798167713482DRB1-0479HGISVTGLQSPEAGS419
ARHGEF12-TOR1AIP2chr11120348235chr11798167713482DRB1-1002GISVTGLQSPEAGSH520
ARHGEF12-TOR1AIP2chr11120348235chr11798167713482DRB1-1002HGISVTGLQSPEAGS419

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Fusion breakpoint peptide structures of ARHGEF12-TOR1AIP2

check button3D structures of the fusion breakpoint peptide of 14AA sequence that have potential fusion neoantigens
* The minimum length of the amino acid sequence in RoseTTAFold is 14AA. Here, we predicted the 14AA fusion protein breakpoint sequence not the fusion neoantigen peptide, which is shorter than 14 AA.

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of ARHGEF12-TOR1AIP2

check buttonVirtual screening between 25 HLAs (from PDB) and FusionNeoAntigens
* We used Glide to predict the interaction between HLAs and neoantigens.
HLA allelePDB IDFile nameBPseqDocking scoreGlide score

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Vaccine Design for the FusionNeoAntigens of ARHGEF12-TOR1AIP2

check button mRNA and peptide sequences of FusionNeoAntigens that have potential interaction with HLA-Is.
Fusion geneHchrHbpTchrTbpStart in +/-13AAEnd in +/-13AAFusionNeoAntigen peptide sequenceFusionNeoAntigen RNA sequence

check button mRNA and peptide sequences of FusionNeoAntigens that have potential interaction with HLA-IIs.
Fusion geneHchrHbpTchrTbpStart in +/-13AAEnd in +/-13AAFusionNeoAntigen peptideFusionNEoAntigen RNA sequence
ARHGEF12-TOR1AIP2chr11120348235chr1179816771419HGISVTGLQSPEAGSTTTCAGTCACTGGTTTGCAGAGTCCAGAGGCTGGAAGTCATCCAC
ARHGEF12-TOR1AIP2chr11120348235chr1179816771520GISVTGLQSPEAGSHCAGTCACTGGTTTGCAGAGTCCAGAGGCTGGAAGTCATCCACAAC

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Information of the samples that have these potential fusion neoantigens of ARHGEF12-TOR1AIP2

check button These samples were reported as having these fusion breakpoints. For individual breakpoints, we checked the open reading frames considering multiple gene isoforms and chose the in-frame fusion genes only. Then, we made fusion protein sequences and predicted the fusion neoantigens. These fusion-positive samples may have these potential fusion neoantigens.
Cancer typeFusion geneHchrHbpHenstTchrTbpTenstSample

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Potential target of CAR-T therapy development for ARHGEF12-TOR1AIP2

check button Predicted 3D structure. We used RoseTTAFold.

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, to provide the retention of the transmembrane domain, we only show the protein feature retention information of those transmembrane features


* Minus value of BPloci means that the break point is located before the CDS.
- In-frame and retained 'Transmembrane'.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
TgeneTOR1AIP2chr11:120348235chr1:179816771ENST0000036761236215_2350471.0TransmembraneHelical

check button Subcellular localization prediction of the transmembrane domain retained fusion proteins
* We used DeepLoc 1.0. The order of the X-axis of the barplot is as follows: Entry_ID, Localization, Type, Nucleus, Cytoplasm, Extracellular, Mitochondrion, Cell_membrane, Endoplasmic_reticulum, Plastid, Golgi.apparatus, Lysosome.Vacuole, Peroxisome. Y-axis is the output score of DeepLoc. Clicking the image will open a new tab with a large image.
HgeneHchrHbpHenstTgeneTchrTbpTenstDeepLoc result

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Related Drugs to ARHGEF12-TOR1AIP2

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 ARHGEF12-TOR1AIP2

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
HgeneARHGEF12C0043094Weight Gain1CTD_human