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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:ARHGAP26-CTNND1

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: ARHGAP26-CTNND1
FusionPDB ID: 6027
FusionGDB2.0 ID: 6027
HgeneTgene
Gene symbol

ARHGAP26

CTNND1

Gene ID

23092

100528016

Gene nameRho GTPase activating protein 26TMX2-CTNND1 readthrough (NMD candidate)
SynonymsGRAF|GRAF1|OPHN1L|OPHN1L1CAS|CTNND1|p120(cas)|p120(ctn)
Cytomap

5q31.3

11q12.1

Type of geneprotein-codingncRNA
Descriptionrho GTPase-activating protein 26GTPase regulator associated with focal adhesion kinase pp125(FAK)oligophrenin-1-like proteinCadherin-associated Src substrateCatenin delta-1TMX2-CTNND1 readthrough (non-protein coding)p120 catenin
Modification date2020031320200313
UniProtAcc

Q9UNA1

Main function of 5'-partner protein: FUNCTION: GTPase-activating protein for RHOA and CDC42.

O60716

Main function of 5'-partner protein: FUNCTION: Key regulator of cell-cell adhesion that associates with and regulates the cell adhesion properties of both C-, E- and N-cadherins, being critical for their surface stability (PubMed:14610055, PubMed:20371349). Beside cell-cell adhesion, regulates gene transcription through several transcription factors including ZBTB33/Kaiso2 and GLIS2, and the activity of Rho family GTPases and downstream cytoskeletal dynamics (PubMed:10207085, PubMed:20371349). Implicated both in cell transformation by SRC and in ligand-induced receptor signaling through the EGF, PDGF, CSF-1 and ERBB2 receptors (PubMed:17344476). {ECO:0000269|PubMed:10207085, ECO:0000269|PubMed:14610055, ECO:0000269|PubMed:17344476, ECO:0000269|PubMed:20371349}.
Ensembl transtripts involved in fusion geneENST idsENST00000274498, ENST00000378004, 
ENST00000486650, 		ENST00000358694, 
ENST00000360682, ENST00000361332, 
ENST00000361391, ENST00000361796, 
ENST00000399039, ENST00000399050, 
ENST00000415361, ENST00000426142, 
ENST00000428599, ENST00000524630, 
ENST00000525902, ENST00000526357, 
ENST00000526772, ENST00000526938, 
ENST00000527467, ENST00000528232, 
ENST00000528621, ENST00000529526, 
ENST00000529873, ENST00000529919, 
ENST00000529986, ENST00000530094, 
ENST00000530748, ENST00000531014, 
ENST00000532245, ENST00000532463, 
ENST00000532649, ENST00000532787, 
ENST00000532844, ENST00000533667, 
ENST00000534579, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score24 X 18 X 6=259217 X 21 X 10=3570
# samples 2225
** MAII scorelog2(22/2592*10)=-3.55849028935997
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(25/3570*10)=-3.83592407425437
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Fusion gene context

PubMed: ARHGAP26 [Title/Abstract] AND CTNND1 [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: ARHGAP26 [Title/Abstract] AND CTNND1 [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)ARHGAP26(142311690)-CTNND1(57578870), # samples:1
CTNND1(57577695)-ARHGAP26(142393644), # samples:1
Anticipated loss of major functional domain due to fusion event.ARHGAP26-CTNND1 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.
ARHGAP26-CTNND1 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.
ARHGAP26-CTNND1 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.
ARHGAP26-CTNND1 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.
CTNND1-ARHGAP26 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.
CTNND1-ARHGAP26 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


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/chr5:142311690/chr11:57578870)
- 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 ARHGAP26 (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 CTNND1 (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)
ENST00000378004ARHGAP26chr5142311690+ENST00000524630CTNND1chr1157578870+497014621361731531
ENST00000378004ARHGAP26chr5142311690+ENST00000529919CTNND1chr1157578870+336114621361728530
ENST00000378004ARHGAP26chr5142311690+ENST00000399039CTNND1chr1157578870+376914621361728530
ENST00000378004ARHGAP26chr5142311690+ENST00000360682CTNND1chr1157578870+462714621361755539
ENST00000378004ARHGAP26chr5142311690+ENST00000361796CTNND1chr1157578870+460314621361731531
ENST00000378004ARHGAP26chr5142311690+ENST00000361391CTNND1chr1157578870+462614621361755539
ENST00000378004ARHGAP26chr5142311690+ENST00000530094CTNND1chr1157578870+468914621361818560
ENST00000378004ARHGAP26chr5142311690+ENST00000428599CTNND1chr1157578870+460214621361731531
ENST00000378004ARHGAP26chr5142311690+ENST00000361332CTNND1chr1157578870+468914621361818560
ENST00000378004ARHGAP26chr5142311690+ENST00000527467CTNND1chr1157578870+468914621361818560
ENST00000378004ARHGAP26chr5142311690+ENST00000415361CTNND1chr1157578870+468914621361818560
ENST00000378004ARHGAP26chr5142311690+ENST00000532245CTNND1chr1157578870+460214621361731531
ENST00000378004ARHGAP26chr5142311690+ENST00000532463CTNND1chr1157578870+460214621361731531
ENST00000378004ARHGAP26chr5142311690+ENST00000528232CTNND1chr1157578870+460214621361731531
ENST00000378004ARHGAP26chr5142311690+ENST00000529986CTNND1chr1157578870+460214621361731531
ENST00000378004ARHGAP26chr5142311690+ENST00000531014CTNND1chr1157578870+468914621361818560
ENST00000378004ARHGAP26chr5142311690+ENST00000358694CTNND1chr1157578870+460214621361731531
ENST00000378004ARHGAP26chr5142311690+ENST00000526772CTNND1chr1157578870+460214621361731531
ENST00000378004ARHGAP26chr5142311690+ENST00000532787CTNND1chr1157578870+462614621361755539
ENST00000378004ARHGAP26chr5142311690+ENST00000533667CTNND1chr1157578870+462614621361755539
ENST00000378004ARHGAP26chr5142311690+ENST00000529873CTNND1chr1157578870+462614621361755539
ENST00000378004ARHGAP26chr5142311690+ENST00000525902CTNND1chr1157578870+460214621361731531
ENST00000378004ARHGAP26chr5142311690+ENST00000529526CTNND1chr1157578870+460214621361731531
ENST00000378004ARHGAP26chr5142311690+ENST00000532649CTNND1chr1157578870+460214621361731531
ENST00000378004ARHGAP26chr5142311690+ENST00000426142CTNND1chr1157578870+460214621361731531
ENST00000378004ARHGAP26chr5142311690+ENST00000532844CTNND1chr1157578870+468914621361818560
ENST00000378004ARHGAP26chr5142311690+ENST00000528621CTNND1chr1157578870+460214621361731531
ENST00000378004ARHGAP26chr5142311690+ENST00000399050CTNND1chr1157578870+468914621361818560
ENST00000378004ARHGAP26chr5142311690+ENST00000526357CTNND1chr1157578870+468914621361818560
ENST00000378004ARHGAP26chr5142311690+ENST00000530748CTNND1chr1157578870+460214621361731531
ENST00000378004ARHGAP26chr5142311690+ENST00000534579CTNND1chr1157578870+460214621361731531
ENST00000378004ARHGAP26chr5142311690+ENST00000526938CTNND1chr1157578870+207814621361668510
ENST00000274498ARHGAP26chr5142311690+ENST00000524630CTNND1chr1157578870+499314851591754531
ENST00000274498ARHGAP26chr5142311690+ENST00000529919CTNND1chr1157578870+338414851591751530
ENST00000274498ARHGAP26chr5142311690+ENST00000399039CTNND1chr1157578870+379214851591751530
ENST00000274498ARHGAP26chr5142311690+ENST00000360682CTNND1chr1157578870+465014851591778539
ENST00000274498ARHGAP26chr5142311690+ENST00000361796CTNND1chr1157578870+462614851591754531
ENST00000274498ARHGAP26chr5142311690+ENST00000361391CTNND1chr1157578870+464914851591778539
ENST00000274498ARHGAP26chr5142311690+ENST00000530094CTNND1chr1157578870+471214851591841560
ENST00000274498ARHGAP26chr5142311690+ENST00000428599CTNND1chr1157578870+462514851591754531
ENST00000274498ARHGAP26chr5142311690+ENST00000361332CTNND1chr1157578870+471214851591841560
ENST00000274498ARHGAP26chr5142311690+ENST00000527467CTNND1chr1157578870+471214851591841560
ENST00000274498ARHGAP26chr5142311690+ENST00000415361CTNND1chr1157578870+471214851591841560
ENST00000274498ARHGAP26chr5142311690+ENST00000532245CTNND1chr1157578870+462514851591754531
ENST00000274498ARHGAP26chr5142311690+ENST00000532463CTNND1chr1157578870+462514851591754531
ENST00000274498ARHGAP26chr5142311690+ENST00000528232CTNND1chr1157578870+462514851591754531
ENST00000274498ARHGAP26chr5142311690+ENST00000529986CTNND1chr1157578870+462514851591754531
ENST00000274498ARHGAP26chr5142311690+ENST00000531014CTNND1chr1157578870+471214851591841560
ENST00000274498ARHGAP26chr5142311690+ENST00000358694CTNND1chr1157578870+462514851591754531
ENST00000274498ARHGAP26chr5142311690+ENST00000526772CTNND1chr1157578870+462514851591754531
ENST00000274498ARHGAP26chr5142311690+ENST00000532787CTNND1chr1157578870+464914851591778539
ENST00000274498ARHGAP26chr5142311690+ENST00000533667CTNND1chr1157578870+464914851591778539
ENST00000274498ARHGAP26chr5142311690+ENST00000529873CTNND1chr1157578870+464914851591778539
ENST00000274498ARHGAP26chr5142311690+ENST00000525902CTNND1chr1157578870+462514851591754531
ENST00000274498ARHGAP26chr5142311690+ENST00000529526CTNND1chr1157578870+462514851591754531
ENST00000274498ARHGAP26chr5142311690+ENST00000532649CTNND1chr1157578870+462514851591754531
ENST00000274498ARHGAP26chr5142311690+ENST00000426142CTNND1chr1157578870+462514851591754531
ENST00000274498ARHGAP26chr5142311690+ENST00000532844CTNND1chr1157578870+471214851591841560
ENST00000274498ARHGAP26chr5142311690+ENST00000528621CTNND1chr1157578870+462514851591754531
ENST00000274498ARHGAP26chr5142311690+ENST00000399050CTNND1chr1157578870+471214851591841560
ENST00000274498ARHGAP26chr5142311690+ENST00000526357CTNND1chr1157578870+471214851591841560
ENST00000274498ARHGAP26chr5142311690+ENST00000530748CTNND1chr1157578870+462514851591754531
ENST00000274498ARHGAP26chr5142311690+ENST00000534579CTNND1chr1157578870+462514851591754531
ENST00000274498ARHGAP26chr5142311690+ENST00000526938CTNND1chr1157578870+210114851591691510

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
ENST00000378004ENST00000524630ARHGAP26chr5142311690+CTNND1chr1157578870+0.0009195660.9990804
ENST00000378004ENST00000529919ARHGAP26chr5142311690+CTNND1chr1157578870+0.0024861630.9975139
ENST00000378004ENST00000399039ARHGAP26chr5142311690+CTNND1chr1157578870+0.0017865570.9982134
ENST00000378004ENST00000360682ARHGAP26chr5142311690+CTNND1chr1157578870+0.0009562330.99904376
ENST00000378004ENST00000361796ARHGAP26chr5142311690+CTNND1chr1157578870+0.0010461510.9989538
ENST00000378004ENST00000361391ARHGAP26chr5142311690+CTNND1chr1157578870+0.000954750.9990452
ENST00000378004ENST00000530094ARHGAP26chr5142311690+CTNND1chr1157578870+0.0008966620.9991033
ENST00000378004ENST00000428599ARHGAP26chr5142311690+CTNND1chr1157578870+0.0010441970.9989557
ENST00000378004ENST00000361332ARHGAP26chr5142311690+CTNND1chr1157578870+0.0008966620.9991033
ENST00000378004ENST00000527467ARHGAP26chr5142311690+CTNND1chr1157578870+0.0008966620.9991033
ENST00000378004ENST00000415361ARHGAP26chr5142311690+CTNND1chr1157578870+0.0008966620.9991033
ENST00000378004ENST00000532245ARHGAP26chr5142311690+CTNND1chr1157578870+0.0010441970.9989557
ENST00000378004ENST00000532463ARHGAP26chr5142311690+CTNND1chr1157578870+0.0010441970.9989557
ENST00000378004ENST00000528232ARHGAP26chr5142311690+CTNND1chr1157578870+0.0010441970.9989557
ENST00000378004ENST00000529986ARHGAP26chr5142311690+CTNND1chr1157578870+0.0010441970.9989557
ENST00000378004ENST00000531014ARHGAP26chr5142311690+CTNND1chr1157578870+0.0008966620.9991033
ENST00000378004ENST00000358694ARHGAP26chr5142311690+CTNND1chr1157578870+0.0010441970.9989557
ENST00000378004ENST00000526772ARHGAP26chr5142311690+CTNND1chr1157578870+0.0010441970.9989557
ENST00000378004ENST00000532787ARHGAP26chr5142311690+CTNND1chr1157578870+0.000954750.9990452
ENST00000378004ENST00000533667ARHGAP26chr5142311690+CTNND1chr1157578870+0.000954750.9990452
ENST00000378004ENST00000529873ARHGAP26chr5142311690+CTNND1chr1157578870+0.000954750.9990452
ENST00000378004ENST00000525902ARHGAP26chr5142311690+CTNND1chr1157578870+0.0010441970.9989557
ENST00000378004ENST00000529526ARHGAP26chr5142311690+CTNND1chr1157578870+0.0010441970.9989557
ENST00000378004ENST00000532649ARHGAP26chr5142311690+CTNND1chr1157578870+0.0010441970.9989557
ENST00000378004ENST00000426142ARHGAP26chr5142311690+CTNND1chr1157578870+0.0010441970.9989557
ENST00000378004ENST00000532844ARHGAP26chr5142311690+CTNND1chr1157578870+0.0008966620.9991033
ENST00000378004ENST00000528621ARHGAP26chr5142311690+CTNND1chr1157578870+0.0010441970.9989557
ENST00000378004ENST00000399050ARHGAP26chr5142311690+CTNND1chr1157578870+0.0008966620.9991033
ENST00000378004ENST00000526357ARHGAP26chr5142311690+CTNND1chr1157578870+0.0008966620.9991033
ENST00000378004ENST00000530748ARHGAP26chr5142311690+CTNND1chr1157578870+0.0010441970.9989557
ENST00000378004ENST00000534579ARHGAP26chr5142311690+CTNND1chr1157578870+0.0010441970.9989557
ENST00000378004ENST00000526938ARHGAP26chr5142311690+CTNND1chr1157578870+0.0022287140.99777126
ENST00000274498ENST00000524630ARHGAP26chr5142311690+CTNND1chr1157578870+0.0009248050.9990752
ENST00000274498ENST00000529919ARHGAP26chr5142311690+CTNND1chr1157578870+0.0025225030.9974775
ENST00000274498ENST00000399039ARHGAP26chr5142311690+CTNND1chr1157578870+0.0017979780.99820197
ENST00000274498ENST00000360682ARHGAP26chr5142311690+CTNND1chr1157578870+0.0009625780.9990375
ENST00000274498ENST00000361796ARHGAP26chr5142311690+CTNND1chr1157578870+0.0010573250.9989427
ENST00000274498ENST00000361391ARHGAP26chr5142311690+CTNND1chr1157578870+0.0009611260.99903893
ENST00000274498ENST00000530094ARHGAP26chr5142311690+CTNND1chr1157578870+0.0009085620.9990915
ENST00000274498ENST00000428599ARHGAP26chr5142311690+CTNND1chr1157578870+0.0010551410.9989448
ENST00000274498ENST00000361332ARHGAP26chr5142311690+CTNND1chr1157578870+0.0009085620.9990915
ENST00000274498ENST00000527467ARHGAP26chr5142311690+CTNND1chr1157578870+0.0009085620.9990915
ENST00000274498ENST00000415361ARHGAP26chr5142311690+CTNND1chr1157578870+0.0009085620.9990915
ENST00000274498ENST00000532245ARHGAP26chr5142311690+CTNND1chr1157578870+0.0010551410.9989448
ENST00000274498ENST00000532463ARHGAP26chr5142311690+CTNND1chr1157578870+0.0010551410.9989448
ENST00000274498ENST00000528232ARHGAP26chr5142311690+CTNND1chr1157578870+0.0010551410.9989448
ENST00000274498ENST00000529986ARHGAP26chr5142311690+CTNND1chr1157578870+0.0010551410.9989448
ENST00000274498ENST00000531014ARHGAP26chr5142311690+CTNND1chr1157578870+0.0009085620.9990915
ENST00000274498ENST00000358694ARHGAP26chr5142311690+CTNND1chr1157578870+0.0010551410.9989448
ENST00000274498ENST00000526772ARHGAP26chr5142311690+CTNND1chr1157578870+0.0010551410.9989448
ENST00000274498ENST00000532787ARHGAP26chr5142311690+CTNND1chr1157578870+0.0009611260.99903893
ENST00000274498ENST00000533667ARHGAP26chr5142311690+CTNND1chr1157578870+0.0009611260.99903893
ENST00000274498ENST00000529873ARHGAP26chr5142311690+CTNND1chr1157578870+0.0009611260.99903893
ENST00000274498ENST00000525902ARHGAP26chr5142311690+CTNND1chr1157578870+0.0010551410.9989448
ENST00000274498ENST00000529526ARHGAP26chr5142311690+CTNND1chr1157578870+0.0010551410.9989448
ENST00000274498ENST00000532649ARHGAP26chr5142311690+CTNND1chr1157578870+0.0010551410.9989448
ENST00000274498ENST00000426142ARHGAP26chr5142311690+CTNND1chr1157578870+0.0010551410.9989448
ENST00000274498ENST00000532844ARHGAP26chr5142311690+CTNND1chr1157578870+0.0009085620.9990915
ENST00000274498ENST00000528621ARHGAP26chr5142311690+CTNND1chr1157578870+0.0010551410.9989448
ENST00000274498ENST00000399050ARHGAP26chr5142311690+CTNND1chr1157578870+0.0009085620.9990915
ENST00000274498ENST00000526357ARHGAP26chr5142311690+CTNND1chr1157578870+0.0009085620.9990915
ENST00000274498ENST00000530748ARHGAP26chr5142311690+CTNND1chr1157578870+0.0010551410.9989448
ENST00000274498ENST00000534579ARHGAP26chr5142311690+CTNND1chr1157578870+0.0010551410.9989448
ENST00000274498ENST00000526938ARHGAP26chr5142311690+CTNND1chr1157578870+0.0023353360.9976647

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 ARHGAP26-CTNND1

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide
ARHGAP26chr5142311690CTNND1chr11575788701462442RRLWMEAMDGREPVNLNNASRSQSSH
ARHGAP26chr5142311690CTNND1chr11575788701485442RRLWMEAMDGREPVNLNNASRSQSSH

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Potential FusionNeoAntigen Information of ARHGAP26-CTNND1 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.
ARHGAP26-CTNND1_142311690_57578870.msa

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)
ARHGAP26-CTNND1chr5142311690chr11575788701485HLA-B41:01REPVNLNNA0.44380.8341019
ARHGAP26-CTNND1chr5142311690chr11575788701485HLA-B50:01REPVNLNNA0.07250.66291019
ARHGAP26-CTNND1chr5142311690chr11575788701485HLA-B40:06REPVNLNNA0.9930.6571019
ARHGAP26-CTNND1chr5142311690chr11575788701485HLA-B78:01EAMDGREPV0.9730.9248514
ARHGAP26-CTNND1chr5142311690chr11575788701485HLA-B51:08EAMDGREPV0.97280.8052514
ARHGAP26-CTNND1chr5142311690chr11575788701485HLA-C05:09AMDGREPVNL10.9631616
ARHGAP26-CTNND1chr5142311690chr11575788701485HLA-A02:07AMDGREPVNL0.90750.6826616
ARHGAP26-CTNND1chr5142311690chr11575788701485HLA-A68:02EAMDGREPV0.99710.6202514
ARHGAP26-CTNND1chr5142311690chr11575788701485HLA-A69:01EAMDGREPV0.99060.7005514
ARHGAP26-CTNND1chr5142311690chr11575788701485HLA-B78:02EAMDGREPV0.97840.9444514
ARHGAP26-CTNND1chr5142311690chr11575788701485HLA-B50:04REPVNLNNA0.07250.66291019
ARHGAP26-CTNND1chr5142311690chr11575788701485HLA-B50:05REPVNLNNA0.07250.66291019
ARHGAP26-CTNND1chr5142311690chr11575788701485HLA-C04:03AMDGREPVNL10.8139616
ARHGAP26-CTNND1chr5142311690chr11575788701485HLA-C05:01AMDGREPVNL10.9631616

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Potential FusionNeoAntigen Information of ARHGAP26-CTNND1 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.
ARHGAP26-CTNND1_142311690_57578870.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)
ARHGAP26-CTNND1chr5142311690chr11575788701485DRB3-0201REPVNLNNASRSQSS1025
ARHGAP26-CTNND1chr5142311690chr11575788701485DRB3-0201GREPVNLNNASRSQS924
ARHGAP26-CTNND1chr5142311690chr11575788701485DRB3-0201DGREPVNLNNASRSQ823
ARHGAP26-CTNND1chr5142311690chr11575788701485DRB3-0201EPVNLNNASRSQSSH1126
ARHGAP26-CTNND1chr5142311690chr11575788701485DRB3-0202REPVNLNNASRSQSS1025
ARHGAP26-CTNND1chr5142311690chr11575788701485DRB3-0202GREPVNLNNASRSQS924
ARHGAP26-CTNND1chr5142311690chr11575788701485DRB3-0202DGREPVNLNNASRSQ823
ARHGAP26-CTNND1chr5142311690chr11575788701485DRB3-0204REPVNLNNASRSQSS1025
ARHGAP26-CTNND1chr5142311690chr11575788701485DRB3-0204GREPVNLNNASRSQS924
ARHGAP26-CTNND1chr5142311690chr11575788701485DRB3-0204DGREPVNLNNASRSQ823
ARHGAP26-CTNND1chr5142311690chr11575788701485DRB3-0204EPVNLNNASRSQSSH1126
ARHGAP26-CTNND1chr5142311690chr11575788701485DRB3-0205REPVNLNNASRSQSS1025
ARHGAP26-CTNND1chr5142311690chr11575788701485DRB3-0205GREPVNLNNASRSQS924
ARHGAP26-CTNND1chr5142311690chr11575788701485DRB3-0209REPVNLNNASRSQSS1025
ARHGAP26-CTNND1chr5142311690chr11575788701485DRB3-0209GREPVNLNNASRSQS924
ARHGAP26-CTNND1chr5142311690chr11575788701485DRB3-0210REPVNLNNASRSQSS1025
ARHGAP26-CTNND1chr5142311690chr11575788701485DRB3-0210GREPVNLNNASRSQS924
ARHGAP26-CTNND1chr5142311690chr11575788701485DRB3-0210DGREPVNLNNASRSQ823
ARHGAP26-CTNND1chr5142311690chr11575788701485DRB3-0211REPVNLNNASRSQSS1025
ARHGAP26-CTNND1chr5142311690chr11575788701485DRB3-0211GREPVNLNNASRSQS924
ARHGAP26-CTNND1chr5142311690chr11575788701485DRB3-0211DGREPVNLNNASRSQ823
ARHGAP26-CTNND1chr5142311690chr11575788701485DRB3-0212REPVNLNNASRSQSS1025
ARHGAP26-CTNND1chr5142311690chr11575788701485DRB3-0212GREPVNLNNASRSQS924
ARHGAP26-CTNND1chr5142311690chr11575788701485DRB3-0212DGREPVNLNNASRSQ823
ARHGAP26-CTNND1chr5142311690chr11575788701485DRB3-0213REPVNLNNASRSQSS1025
ARHGAP26-CTNND1chr5142311690chr11575788701485DRB3-0213GREPVNLNNASRSQS924
ARHGAP26-CTNND1chr5142311690chr11575788701485DRB3-0213DGREPVNLNNASRSQ823
ARHGAP26-CTNND1chr5142311690chr11575788701485DRB3-0214REPVNLNNASRSQSS1025
ARHGAP26-CTNND1chr5142311690chr11575788701485DRB3-0214GREPVNLNNASRSQS924
ARHGAP26-CTNND1chr5142311690chr11575788701485DRB3-0214DGREPVNLNNASRSQ823
ARHGAP26-CTNND1chr5142311690chr11575788701485DRB3-0214EPVNLNNASRSQSSH1126
ARHGAP26-CTNND1chr5142311690chr11575788701485DRB3-0215REPVNLNNASRSQSS1025
ARHGAP26-CTNND1chr5142311690chr11575788701485DRB3-0215GREPVNLNNASRSQS924
ARHGAP26-CTNND1chr5142311690chr11575788701485DRB3-0215DGREPVNLNNASRSQ823
ARHGAP26-CTNND1chr5142311690chr11575788701485DRB3-0216REPVNLNNASRSQSS1025
ARHGAP26-CTNND1chr5142311690chr11575788701485DRB3-0216GREPVNLNNASRSQS924
ARHGAP26-CTNND1chr5142311690chr11575788701485DRB3-0217REPVNLNNASRSQSS1025
ARHGAP26-CTNND1chr5142311690chr11575788701485DRB3-0217GREPVNLNNASRSQS924
ARHGAP26-CTNND1chr5142311690chr11575788701485DRB3-0217DGREPVNLNNASRSQ823
ARHGAP26-CTNND1chr5142311690chr11575788701485DRB3-0217EPVNLNNASRSQSSH1126
ARHGAP26-CTNND1chr5142311690chr11575788701485DRB3-0218REPVNLNNASRSQSS1025
ARHGAP26-CTNND1chr5142311690chr11575788701485DRB3-0218GREPVNLNNASRSQS924
ARHGAP26-CTNND1chr5142311690chr11575788701485DRB3-0218DGREPVNLNNASRSQ823
ARHGAP26-CTNND1chr5142311690chr11575788701485DRB3-0219REPVNLNNASRSQSS1025
ARHGAP26-CTNND1chr5142311690chr11575788701485DRB3-0219GREPVNLNNASRSQS924
ARHGAP26-CTNND1chr5142311690chr11575788701485DRB3-0219DGREPVNLNNASRSQ823
ARHGAP26-CTNND1chr5142311690chr11575788701485DRB3-0220REPVNLNNASRSQSS1025
ARHGAP26-CTNND1chr5142311690chr11575788701485DRB3-0220GREPVNLNNASRSQS924
ARHGAP26-CTNND1chr5142311690chr11575788701485DRB3-0220DGREPVNLNNASRSQ823
ARHGAP26-CTNND1chr5142311690chr11575788701485DRB3-0221REPVNLNNASRSQSS1025
ARHGAP26-CTNND1chr5142311690chr11575788701485DRB3-0221GREPVNLNNASRSQS924
ARHGAP26-CTNND1chr5142311690chr11575788701485DRB3-0222REPVNLNNASRSQSS1025
ARHGAP26-CTNND1chr5142311690chr11575788701485DRB3-0222GREPVNLNNASRSQS924
ARHGAP26-CTNND1chr5142311690chr11575788701485DRB3-0222DGREPVNLNNASRSQ823
ARHGAP26-CTNND1chr5142311690chr11575788701485DRB3-0223REPVNLNNASRSQSS1025
ARHGAP26-CTNND1chr5142311690chr11575788701485DRB3-0223GREPVNLNNASRSQS924
ARHGAP26-CTNND1chr5142311690chr11575788701485DRB3-0223DGREPVNLNNASRSQ823
ARHGAP26-CTNND1chr5142311690chr11575788701485DRB3-0224REPVNLNNASRSQSS1025
ARHGAP26-CTNND1chr5142311690chr11575788701485DRB3-0224GREPVNLNNASRSQS924
ARHGAP26-CTNND1chr5142311690chr11575788701485DRB3-0224DGREPVNLNNASRSQ823
ARHGAP26-CTNND1chr5142311690chr11575788701485DRB3-0224EPVNLNNASRSQSSH1126
ARHGAP26-CTNND1chr5142311690chr11575788701485DRB3-0225REPVNLNNASRSQSS1025
ARHGAP26-CTNND1chr5142311690chr11575788701485DRB3-0225GREPVNLNNASRSQS924
ARHGAP26-CTNND1chr5142311690chr11575788701485DRB3-0225DGREPVNLNNASRSQ823
ARHGAP26-CTNND1chr5142311690chr11575788701485DRB3-0301REPVNLNNASRSQSS1025
ARHGAP26-CTNND1chr5142311690chr11575788701485DRB3-0301GREPVNLNNASRSQS924
ARHGAP26-CTNND1chr5142311690chr11575788701485DRB3-0301DGREPVNLNNASRSQ823

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Fusion breakpoint peptide structures of ARHGAP26-CTNND1

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.
File nameBPseqHgeneTgeneHchrHbpTchrTbpAAlen
426AMDGREPVNLNNASARHGAP26CTNND1chr5142311690chr11575788701485

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of ARHGAP26-CTNND1

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
HLA-B14:023BVN426AMDGREPVNLNNAS-7.15543-7.26883
HLA-B14:023BVN426AMDGREPVNLNNAS-4.77435-5.80965
HLA-B52:013W39426AMDGREPVNLNNAS-6.80875-6.92215
HLA-B52:013W39426AMDGREPVNLNNAS-4.20386-5.23916
HLA-A11:014UQ2426AMDGREPVNLNNAS-7.5194-8.5547
HLA-A11:014UQ2426AMDGREPVNLNNAS-6.9601-7.0735
HLA-A24:025HGA426AMDGREPVNLNNAS-7.52403-7.63743
HLA-A24:025HGA426AMDGREPVNLNNAS-5.82433-6.85963
HLA-B27:056PYJ426AMDGREPVNLNNAS-3.28285-4.31815
HLA-B44:053DX8426AMDGREPVNLNNAS-5.91172-6.94702
HLA-B44:053DX8426AMDGREPVNLNNAS-4.24346-4.35686

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Vaccine Design for the FusionNeoAntigens of ARHGAP26-CTNND1

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
ARHGAP26-CTNND1chr5142311690chr11575788701019REPVNLNNACGGGAACCTGTGAATCTAAACAATGCT
ARHGAP26-CTNND1chr5142311690chr1157578870514EAMDGREPVGAAGCCATGGATGGCCGGGAACCTGTG
ARHGAP26-CTNND1chr5142311690chr1157578870616AMDGREPVNLGCCATGGATGGCCGGGAACCTGTGAATCTA

check button mRNA and peptide sequences of FusionNeoAntigens that have potential interaction with HLA-IIs.
Fusion geneHchrHbpTchrTbpStart in +/-13AAEnd in +/-13AAFusionNeoAntigen peptideFusionNEoAntigen RNA sequence
ARHGAP26-CTNND1chr5142311690chr11575788701025REPVNLNNASRSQSSCGGGAACCTGTGAATCTAAACAATGCTTCCCGAAGCCAGAGCAGT
ARHGAP26-CTNND1chr5142311690chr11575788701126EPVNLNNASRSQSSHGAACCTGTGAATCTAAACAATGCTTCCCGAAGCCAGAGCAGTCAT
ARHGAP26-CTNND1chr5142311690chr1157578870823DGREPVNLNNASRSQGATGGCCGGGAACCTGTGAATCTAAACAATGCTTCCCGAAGCCAG
ARHGAP26-CTNND1chr5142311690chr1157578870924GREPVNLNNASRSQSGGCCGGGAACCTGTGAATCTAAACAATGCTTCCCGAAGCCAGAGC

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Information of the samples that have these potential fusion neoantigens of ARHGAP26-CTNND1

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
Non-CancerARHGAP26-CTNND1chr5142311690ENST00000274498chr1157578870ENST000003586945373N

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Potential target of CAR-T therapy development for ARHGAP26-CTNND1

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

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 ARHGAP26-CTNND1

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 ARHGAP26-CTNND1

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
HgeneARHGAP26C0033975Psychotic Disorders1PSYGENET