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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:ARFGEF1-CPA6

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: ARFGEF1-CPA6
FusionPDB ID: 5850
FusionGDB2.0 ID: 5850
HgeneTgene
Gene symbol

ARFGEF1

CPA6

Gene ID

10565

57094

Gene nameADP ribosylation factor guanine nucleotide exchange factor 1carboxypeptidase A6
SynonymsARFGEP1|BIG1|P200CPAH|ETL5|FEB11
Cytomap

8q13.2

8q13.2

Type of geneprotein-codingprotein-coding
Descriptionbrefeldin A-inhibited guanine nucleotide-exchange protein 1ADP-ribosylation factor guanine nucleotide-exchange factor 1 (brefeldin A-inhibited)p200 ARF guanine nucleotide exchange factorcarboxypeptidase A6carboxypeptidase B
Modification date2020031320200313
UniProtAcc

Q9Y6D6

Main function of 5'-partner protein: FUNCTION: Promotes guanine-nucleotide exchange on ARF1 and ARF3. Promotes the activation of ARF1/ARF3 through replacement of GDP with GTP. Involved in vesicular trafficking. Required for the maintenance of Golgi structure; the function may be independent of its GEF activity. Required for the maturaion of integrin beta-1 in the Golgi. Involved in the establishment and persistence of cell polarity during directed cell movement in wound healing. Proposed to act as A kinase-anchoring protein (AKAP) and may mediate crosstalk between Arf and PKA pathways. Inhibits GAP activity of MYO9B probably through competetive RhoA binding. The function in the nucleus remains to be determined. {ECO:0000269|PubMed:12571360, ECO:0000269|PubMed:15644318, ECO:0000269|PubMed:17227842, ECO:0000269|PubMed:20360857, ECO:0000269|PubMed:22084092}.

Q8N4T0

Main function of 5'-partner protein: FUNCTION: May be involved in the proteolytic inactivation of enkephalins and neurotensin in some brain areas. May convert inactive angiotensin I into the biologically active angiotensin II (PubMed:18178555). Releases a C-terminal amino acid, with preference for large hydrophobic C-terminal amino acids and shows only very weak activity toward small amino acids and histidine (PubMed:20855895). {ECO:0000269|PubMed:18178555, ECO:0000269|PubMed:20855895}.
Ensembl transtripts involved in fusion geneENST idsENST00000262215, ENST00000520381, 
ENST00000517955, ENST00000518230, 
ENST00000518549, ENST00000297769, 
ENST00000297770, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score14 X 14 X 6=11767 X 9 X 5=315
# samples 179
** MAII scorelog2(17/1176*10)=-2.79028140869866
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(9/315*10)=-1.8073549220576
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Fusion gene context

PubMed: ARFGEF1 [Title/Abstract] AND CPA6 [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: ARFGEF1 [Title/Abstract] AND CPA6 [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)ARFGEF1(68255399)-CPA6(68334926), # samples:2
Anticipated loss of major functional domain due to fusion event.ARFGEF1-CPA6 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.
ARFGEF1-CPA6 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.
ARFGEF1-CPA6 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.
ARFGEF1-CPA6 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.
ARFGEF1-CPA6 seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
ARFGEF1-CPA6 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
HgeneARFGEF1

GO:0034260

negative regulation of GTPase activity

15644318



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/chr8:68255399/chr8:68334926)
- 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 ARFGEF1 (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 CPA6 (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)
ENST00000520381ARFGEF1chr868150970-ENST00000297769CPA6chr868397024-22921568321957641
ENST00000520381ARFGEF1chr868150970-ENST00000297770CPA6chr868397024-25771568322245737
ENST00000520381ARFGEF1chr868150970-ENST00000518549CPA6chr868397024-22561568321879615
ENST00000262215ARFGEF1chr868150970-ENST00000297769CPA6chr868397024-4252352839039171175
ENST00000262215ARFGEF1chr868150970-ENST00000297770CPA6chr868397024-4537352839042051271
ENST00000262215ARFGEF1chr868150970-ENST00000518549CPA6chr868397024-4216352839038391149

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
ENST00000520381ENST00000297769ARFGEF1chr868150970-CPA6chr868397024-0.0006411090.99935895
ENST00000520381ENST00000297770ARFGEF1chr868150970-CPA6chr868397024-0.0006389410.9993611
ENST00000520381ENST00000518549ARFGEF1chr868150970-CPA6chr868397024-0.0006918280.9993082
ENST00000262215ENST00000297769ARFGEF1chr868150970-CPA6chr868397024-0.0006633150.99933666
ENST00000262215ENST00000297770ARFGEF1chr868150970-CPA6chr868397024-0.0006560990.99934393
ENST00000262215ENST00000518549ARFGEF1chr868150970-CPA6chr868397024-0.0005145810.9994854

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 ARFGEF1-CPA6

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide
ARFGEF1chr868150970CPA6chr8683970241568512HTDGNYLGNSWHEALLTYKSDPAMRK
ARFGEF1chr868150970CPA6chr86839702435281046HTDGNYLGNSWHEALLTYKSDPAMRK

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Potential FusionNeoAntigen Information of ARFGEF1-CPA6 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.
ARFGEF1-CPA6_68150970_68397024.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)
ARFGEF1-CPA6chr868150970chr8683970243528HLA-B15:18WHEALLTY0.94640.71311018
ARFGEF1-CPA6chr868150970chr8683970243528HLA-A02:11YLGNSWHEA0.99530.7186514
ARFGEF1-CPA6chr868150970chr8683970243528HLA-A02:67YLGNSWHEA0.99520.6817514
ARFGEF1-CPA6chr868150970chr8683970243528HLA-A02:30YLGNSWHEA0.99520.6817514
ARFGEF1-CPA6chr868150970chr8683970243528HLA-A02:24YLGNSWHEA0.99520.6817514
ARFGEF1-CPA6chr868150970chr8683970243528HLA-A02:60YLGNSWHEA0.99520.6444514
ARFGEF1-CPA6chr868150970chr8683970243528HLA-A02:22YLGNSWHEA0.99420.6656514
ARFGEF1-CPA6chr868150970chr8683970243528HLA-A02:27YLGNSWHEA0.99360.7445514
ARFGEF1-CPA6chr868150970chr8683970243528HLA-A02:16YLGNSWHEA0.99160.6319514
ARFGEF1-CPA6chr868150970chr8683970243528HLA-A02:13YLGNSWHEA0.99030.8269514
ARFGEF1-CPA6chr868150970chr8683970243528HLA-A02:19YLGNSWHEA0.98960.5052514
ARFGEF1-CPA6chr868150970chr8683970243528HLA-A02:35YLGNSWHEA0.98540.6998514
ARFGEF1-CPA6chr868150970chr8683970243528HLA-A02:38YLGNSWHEA0.98020.7068514
ARFGEF1-CPA6chr868150970chr8683970243528HLA-B45:01HEALLTYKS0.97840.93531120
ARFGEF1-CPA6chr868150970chr8683970243528HLA-A02:29YLGNSWHEA0.94990.6865514
ARFGEF1-CPA6chr868150970chr8683970243528HLA-B15:02SWHEALLTY0.88320.9134918
ARFGEF1-CPA6chr868150970chr8683970243528HLA-B15:18SWHEALLTY0.21650.7139918
ARFGEF1-CPA6chr868150970chr8683970243528HLA-A02:01YLGNSWHEA0.99520.6817514
ARFGEF1-CPA6chr868150970chr8683970243528HLA-B15:21SWHEALLTY0.88160.8944918
ARFGEF1-CPA6chr868150970chr8683970243528HLA-C07:19SWHEALLTY0.53280.8128918
ARFGEF1-CPA6chr868150970chr8683970243528HLA-C07:95SWHEALLTY0.44850.7236918
ARFGEF1-CPA6chr868150970chr8683970243528HLA-C12:16SWHEALLTY0.42710.9707918
ARFGEF1-CPA6chr868150970chr8683970243528HLA-C07:10SWHEALLTY0.42640.9682918
ARFGEF1-CPA6chr868150970chr8683970243528HLA-C07:80SWHEALLTY0.42460.9661918
ARFGEF1-CPA6chr868150970chr8683970243528HLA-C07:67SWHEALLTY0.42460.9661918
ARFGEF1-CPA6chr868150970chr8683970243528HLA-C07:46SWHEALLTY0.37690.9169918
ARFGEF1-CPA6chr868150970chr8683970243528HLA-C07:27SWHEALLTY0.3710.9606918
ARFGEF1-CPA6chr868150970chr8683970243528HLA-C07:05SWHEALLTY0.19090.9573918
ARFGEF1-CPA6chr868150970chr8683970243528HLA-A02:03YLGNSWHEA0.99540.7651514
ARFGEF1-CPA6chr868150970chr8683970243528HLA-B15:27SWHEALLTY0.5720.8142918
ARFGEF1-CPA6chr868150970chr8683970243528HLA-C07:01SWHEALLTY0.46140.723918
ARFGEF1-CPA6chr868150970chr8683970243528HLA-C07:02SWHEALLTY0.42460.9661918
ARFGEF1-CPA6chr868150970chr8683970243528HLA-C07:22SWHEALLTY0.42050.7177918
ARFGEF1-CPA6chr868150970chr8683970243528HLA-C07:17SWHEALLTY0.40660.971918
ARFGEF1-CPA6chr868150970chr8683970243528HLA-C06:06SWHEALLTY0.01890.9896918
ARFGEF1-CPA6chr868150970chr8683970243528HLA-C14:02SWHEALLTY0.01150.9555918
ARFGEF1-CPA6chr868150970chr8683970243528HLA-C14:03SWHEALLTY0.01150.9555918

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Potential FusionNeoAntigen Information of ARFGEF1-CPA6 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.
ARFGEF1-CPA6_68150970_68397024.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)
ARFGEF1-CPA6chr868150970chr8683970243528DRB1-0437HEALLTYKSDPAMRK1126
ARFGEF1-CPA6chr868150970chr8683970243528DRB1-0465HEALLTYKSDPAMRK1126
ARFGEF1-CPA6chr868150970chr8683970243528DRB1-0473HEALLTYKSDPAMRK1126
ARFGEF1-CPA6chr868150970chr8683970243528DRB1-0473WHEALLTYKSDPAMR1025
ARFGEF1-CPA6chr868150970chr8683970243528DRB1-1457HEALLTYKSDPAMRK1126
ARFGEF1-CPA6chr868150970chr8683970243528DRB1-1457WHEALLTYKSDPAMR1025
ARFGEF1-CPA6chr868150970chr8683970243528DRB1-1501HEALLTYKSDPAMRK1126
ARFGEF1-CPA6chr868150970chr8683970243528DRB1-1501WHEALLTYKSDPAMR1025
ARFGEF1-CPA6chr868150970chr8683970243528DRB1-1501SWHEALLTYKSDPAM924
ARFGEF1-CPA6chr868150970chr8683970243528DRB1-1502HEALLTYKSDPAMRK1126
ARFGEF1-CPA6chr868150970chr8683970243528DRB1-1502WHEALLTYKSDPAMR1025
ARFGEF1-CPA6chr868150970chr8683970243528DRB1-1503HEALLTYKSDPAMRK1126
ARFGEF1-CPA6chr868150970chr8683970243528DRB1-1503WHEALLTYKSDPAMR1025
ARFGEF1-CPA6chr868150970chr8683970243528DRB1-1504HEALLTYKSDPAMRK1126
ARFGEF1-CPA6chr868150970chr8683970243528DRB1-1504WHEALLTYKSDPAMR1025
ARFGEF1-CPA6chr868150970chr8683970243528DRB1-1504SWHEALLTYKSDPAM924
ARFGEF1-CPA6chr868150970chr8683970243528DRB1-1505HEALLTYKSDPAMRK1126
ARFGEF1-CPA6chr868150970chr8683970243528DRB1-1505WHEALLTYKSDPAMR1025
ARFGEF1-CPA6chr868150970chr8683970243528DRB1-1505SWHEALLTYKSDPAM924
ARFGEF1-CPA6chr868150970chr8683970243528DRB1-1506HEALLTYKSDPAMRK1126
ARFGEF1-CPA6chr868150970chr8683970243528DRB1-1506WHEALLTYKSDPAMR1025
ARFGEF1-CPA6chr868150970chr8683970243528DRB1-1506SWHEALLTYKSDPAM924
ARFGEF1-CPA6chr868150970chr8683970243528DRB1-1507HEALLTYKSDPAMRK1126
ARFGEF1-CPA6chr868150970chr8683970243528DRB1-1507WHEALLTYKSDPAMR1025
ARFGEF1-CPA6chr868150970chr8683970243528DRB1-1507SWHEALLTYKSDPAM924
ARFGEF1-CPA6chr868150970chr8683970243528DRB1-1508HEALLTYKSDPAMRK1126
ARFGEF1-CPA6chr868150970chr8683970243528DRB1-1508WHEALLTYKSDPAMR1025
ARFGEF1-CPA6chr868150970chr8683970243528DRB1-1509HEALLTYKSDPAMRK1126
ARFGEF1-CPA6chr868150970chr8683970243528DRB1-1509WHEALLTYKSDPAMR1025
ARFGEF1-CPA6chr868150970chr8683970243528DRB1-1509SWHEALLTYKSDPAM924
ARFGEF1-CPA6chr868150970chr8683970243528DRB1-1510HEALLTYKSDPAMRK1126
ARFGEF1-CPA6chr868150970chr8683970243528DRB1-1510WHEALLTYKSDPAMR1025
ARFGEF1-CPA6chr868150970chr8683970243528DRB1-1511HEALLTYKSDPAMRK1126
ARFGEF1-CPA6chr868150970chr8683970243528DRB1-1511WHEALLTYKSDPAMR1025
ARFGEF1-CPA6chr868150970chr8683970243528DRB1-1512HEALLTYKSDPAMRK1126
ARFGEF1-CPA6chr868150970chr8683970243528DRB1-1512WHEALLTYKSDPAMR1025
ARFGEF1-CPA6chr868150970chr8683970243528DRB1-1512SWHEALLTYKSDPAM924
ARFGEF1-CPA6chr868150970chr8683970243528DRB1-1513HEALLTYKSDPAMRK1126
ARFGEF1-CPA6chr868150970chr8683970243528DRB1-1513WHEALLTYKSDPAMR1025
ARFGEF1-CPA6chr868150970chr8683970243528DRB1-1513SWHEALLTYKSDPAM924
ARFGEF1-CPA6chr868150970chr8683970243528DRB1-1514HEALLTYKSDPAMRK1126
ARFGEF1-CPA6chr868150970chr8683970243528DRB1-1514WHEALLTYKSDPAMR1025
ARFGEF1-CPA6chr868150970chr8683970243528DRB1-1515HEALLTYKSDPAMRK1126
ARFGEF1-CPA6chr868150970chr8683970243528DRB1-1515WHEALLTYKSDPAMR1025
ARFGEF1-CPA6chr868150970chr8683970243528DRB1-1516HEALLTYKSDPAMRK1126
ARFGEF1-CPA6chr868150970chr8683970243528DRB1-1516WHEALLTYKSDPAMR1025
ARFGEF1-CPA6chr868150970chr8683970243528DRB1-1516SWHEALLTYKSDPAM924
ARFGEF1-CPA6chr868150970chr8683970243528DRB1-1518HEALLTYKSDPAMRK1126
ARFGEF1-CPA6chr868150970chr8683970243528DRB1-1518WHEALLTYKSDPAMR1025
ARFGEF1-CPA6chr868150970chr8683970243528DRB1-1518SWHEALLTYKSDPAM924
ARFGEF1-CPA6chr868150970chr8683970243528DRB1-1519HEALLTYKSDPAMRK1126
ARFGEF1-CPA6chr868150970chr8683970243528DRB1-1519WHEALLTYKSDPAMR1025
ARFGEF1-CPA6chr868150970chr8683970243528DRB1-1520HEALLTYKSDPAMRK1126
ARFGEF1-CPA6chr868150970chr8683970243528DRB1-1520WHEALLTYKSDPAMR1025
ARFGEF1-CPA6chr868150970chr8683970243528DRB1-1520SWHEALLTYKSDPAM924
ARFGEF1-CPA6chr868150970chr8683970243528DRB1-1521HEALLTYKSDPAMRK1126
ARFGEF1-CPA6chr868150970chr8683970243528DRB1-1521WHEALLTYKSDPAMR1025
ARFGEF1-CPA6chr868150970chr8683970243528DRB1-1522HEALLTYKSDPAMRK1126
ARFGEF1-CPA6chr868150970chr8683970243528DRB1-1522WHEALLTYKSDPAMR1025
ARFGEF1-CPA6chr868150970chr8683970243528DRB1-1522SWHEALLTYKSDPAM924
ARFGEF1-CPA6chr868150970chr8683970243528DRB1-1523HEALLTYKSDPAMRK1126
ARFGEF1-CPA6chr868150970chr8683970243528DRB1-1523WHEALLTYKSDPAMR1025
ARFGEF1-CPA6chr868150970chr8683970243528DRB1-1524HEALLTYKSDPAMRK1126
ARFGEF1-CPA6chr868150970chr8683970243528DRB1-1524WHEALLTYKSDPAMR1025
ARFGEF1-CPA6chr868150970chr8683970243528DRB1-1524SWHEALLTYKSDPAM924
ARFGEF1-CPA6chr868150970chr8683970243528DRB1-1525HEALLTYKSDPAMRK1126
ARFGEF1-CPA6chr868150970chr8683970243528DRB1-1526HEALLTYKSDPAMRK1126
ARFGEF1-CPA6chr868150970chr8683970243528DRB1-1526WHEALLTYKSDPAMR1025
ARFGEF1-CPA6chr868150970chr8683970243528DRB1-1527HEALLTYKSDPAMRK1126
ARFGEF1-CPA6chr868150970chr8683970243528DRB1-1528HEALLTYKSDPAMRK1126
ARFGEF1-CPA6chr868150970chr8683970243528DRB1-1528WHEALLTYKSDPAMR1025
ARFGEF1-CPA6chr868150970chr8683970243528DRB1-1528SWHEALLTYKSDPAM924
ARFGEF1-CPA6chr868150970chr8683970243528DRB1-1529HEALLTYKSDPAMRK1126
ARFGEF1-CPA6chr868150970chr8683970243528DRB1-1529WHEALLTYKSDPAMR1025
ARFGEF1-CPA6chr868150970chr8683970243528DRB1-1530HEALLTYKSDPAMRK1126
ARFGEF1-CPA6chr868150970chr8683970243528DRB1-1530WHEALLTYKSDPAMR1025
ARFGEF1-CPA6chr868150970chr8683970243528DRB1-1531HEALLTYKSDPAMRK1126
ARFGEF1-CPA6chr868150970chr8683970243528DRB1-1531WHEALLTYKSDPAMR1025
ARFGEF1-CPA6chr868150970chr8683970243528DRB1-1532HEALLTYKSDPAMRK1126
ARFGEF1-CPA6chr868150970chr8683970243528DRB1-1532WHEALLTYKSDPAMR1025
ARFGEF1-CPA6chr868150970chr8683970243528DRB1-1532SWHEALLTYKSDPAM924
ARFGEF1-CPA6chr868150970chr8683970243528DRB1-1533HEALLTYKSDPAMRK1126
ARFGEF1-CPA6chr868150970chr8683970243528DRB1-1533WHEALLTYKSDPAMR1025
ARFGEF1-CPA6chr868150970chr8683970243528DRB1-1533SWHEALLTYKSDPAM924
ARFGEF1-CPA6chr868150970chr8683970243528DRB1-1535HEALLTYKSDPAMRK1126
ARFGEF1-CPA6chr868150970chr8683970243528DRB1-1535WHEALLTYKSDPAMR1025
ARFGEF1-CPA6chr868150970chr8683970243528DRB1-1535SWHEALLTYKSDPAM924
ARFGEF1-CPA6chr868150970chr8683970243528DRB1-1536HEALLTYKSDPAMRK1126
ARFGEF1-CPA6chr868150970chr8683970243528DRB1-1536WHEALLTYKSDPAMR1025
ARFGEF1-CPA6chr868150970chr8683970243528DRB1-1536SWHEALLTYKSDPAM924
ARFGEF1-CPA6chr868150970chr8683970243528DRB1-1537HEALLTYKSDPAMRK1126
ARFGEF1-CPA6chr868150970chr8683970243528DRB1-1537WHEALLTYKSDPAMR1025
ARFGEF1-CPA6chr868150970chr8683970243528DRB1-1537SWHEALLTYKSDPAM924
ARFGEF1-CPA6chr868150970chr8683970243528DRB1-1538HEALLTYKSDPAMRK1126
ARFGEF1-CPA6chr868150970chr8683970243528DRB1-1538WHEALLTYKSDPAMR1025
ARFGEF1-CPA6chr868150970chr8683970243528DRB1-1539HEALLTYKSDPAMRK1126
ARFGEF1-CPA6chr868150970chr8683970243528DRB1-1539WHEALLTYKSDPAMR1025
ARFGEF1-CPA6chr868150970chr8683970243528DRB1-1540HEALLTYKSDPAMRK1126
ARFGEF1-CPA6chr868150970chr8683970243528DRB1-1540WHEALLTYKSDPAMR1025
ARFGEF1-CPA6chr868150970chr8683970243528DRB1-1540SWHEALLTYKSDPAM924
ARFGEF1-CPA6chr868150970chr8683970243528DRB1-1541HEALLTYKSDPAMRK1126
ARFGEF1-CPA6chr868150970chr8683970243528DRB1-1541WHEALLTYKSDPAMR1025
ARFGEF1-CPA6chr868150970chr8683970243528DRB1-1541SWHEALLTYKSDPAM924
ARFGEF1-CPA6chr868150970chr8683970243528DRB1-1542HEALLTYKSDPAMRK1126
ARFGEF1-CPA6chr868150970chr8683970243528DRB1-1542WHEALLTYKSDPAMR1025
ARFGEF1-CPA6chr868150970chr8683970243528DRB1-1542SWHEALLTYKSDPAM924
ARFGEF1-CPA6chr868150970chr8683970243528DRB1-1543HEALLTYKSDPAMRK1126
ARFGEF1-CPA6chr868150970chr8683970243528DRB1-1543WHEALLTYKSDPAMR1025
ARFGEF1-CPA6chr868150970chr8683970243528DRB1-1543SWHEALLTYKSDPAM924
ARFGEF1-CPA6chr868150970chr8683970243528DRB1-1544HEALLTYKSDPAMRK1126
ARFGEF1-CPA6chr868150970chr8683970243528DRB1-1544WHEALLTYKSDPAMR1025
ARFGEF1-CPA6chr868150970chr8683970243528DRB1-1545HEALLTYKSDPAMRK1126
ARFGEF1-CPA6chr868150970chr8683970243528DRB1-1545WHEALLTYKSDPAMR1025
ARFGEF1-CPA6chr868150970chr8683970243528DRB1-1545SWHEALLTYKSDPAM924
ARFGEF1-CPA6chr868150970chr8683970243528DRB1-1546HEALLTYKSDPAMRK1126
ARFGEF1-CPA6chr868150970chr8683970243528DRB1-1546WHEALLTYKSDPAMR1025
ARFGEF1-CPA6chr868150970chr8683970243528DRB1-1546SWHEALLTYKSDPAM924
ARFGEF1-CPA6chr868150970chr8683970243528DRB1-1547HEALLTYKSDPAMRK1126
ARFGEF1-CPA6chr868150970chr8683970243528DRB1-1547WHEALLTYKSDPAMR1025
ARFGEF1-CPA6chr868150970chr8683970243528DRB1-1548HEALLTYKSDPAMRK1126
ARFGEF1-CPA6chr868150970chr8683970243528DRB1-1548WHEALLTYKSDPAMR1025
ARFGEF1-CPA6chr868150970chr8683970243528DRB1-1548SWHEALLTYKSDPAM924
ARFGEF1-CPA6chr868150970chr8683970243528DRB1-1549HEALLTYKSDPAMRK1126
ARFGEF1-CPA6chr868150970chr8683970243528DRB1-1549WHEALLTYKSDPAMR1025
ARFGEF1-CPA6chr868150970chr8683970243528DRB1-1549SWHEALLTYKSDPAM924
ARFGEF1-CPA6chr868150970chr8683970243528DRB1-1615HEALLTYKSDPAMRK1126
ARFGEF1-CPA6chr868150970chr8683970243528DRB5-0106HEALLTYKSDPAMRK1126
ARFGEF1-CPA6chr868150970chr8683970243528DRB5-0202HEALLTYKSDPAMRK1126
ARFGEF1-CPA6chr868150970chr8683970243528DRB5-0204HEALLTYKSDPAMRK1126
ARFGEF1-CPA6chr868150970chr8683970243528DRB5-0204WHEALLTYKSDPAMR1025
ARFGEF1-CPA6chr868150970chr8683970243528DRB5-0205HEALLTYKSDPAMRK1126

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Fusion breakpoint peptide structures of ARFGEF1-CPA6

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
5019LGNSWHEALLTYKSARFGEF1CPA6chr868150970chr8683970243528

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of ARFGEF1-CPA6

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-B14:023BVN5019LGNSWHEALLTYKS-7.9962-8.1096
HLA-B14:023BVN5019LGNSWHEALLTYKS-5.70842-6.74372
HLA-B52:013W395019LGNSWHEALLTYKS-6.83737-6.95077
HLA-B52:013W395019LGNSWHEALLTYKS-4.4836-5.5189
HLA-A11:014UQ25019LGNSWHEALLTYKS-10.0067-10.1201
HLA-A11:014UQ25019LGNSWHEALLTYKS-9.03915-10.0745
HLA-A24:025HGA5019LGNSWHEALLTYKS-6.56204-6.67544
HLA-A24:025HGA5019LGNSWHEALLTYKS-5.42271-6.45801
HLA-B44:053DX85019LGNSWHEALLTYKS-7.85648-8.89178
HLA-B44:053DX85019LGNSWHEALLTYKS-5.3978-5.5112
HLA-A02:016TDR5019LGNSWHEALLTYKS-3.37154-4.40684

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Vaccine Design for the FusionNeoAntigens of ARFGEF1-CPA6

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
ARFGEF1-CPA6chr868150970chr8683970241018WHEALLTYTGGCATGAGGCTCTTCTAACATAT
ARFGEF1-CPA6chr868150970chr8683970241120HEALLTYKSCATGAGGCTCTTCTAACATATAAGAGT
ARFGEF1-CPA6chr868150970chr868397024514YLGNSWHEATATTTAGGAAATTCATGGCATGAGGCT
ARFGEF1-CPA6chr868150970chr868397024918SWHEALLTYTCATGGCATGAGGCTCTTCTAACATAT

check button mRNA and peptide sequences of FusionNeoAntigens that have potential interaction with HLA-IIs.
Fusion geneHchrHbpTchrTbpStart in +/-13AAEnd in +/-13AAFusionNeoAntigen peptideFusionNEoAntigen RNA sequence
ARFGEF1-CPA6chr868150970chr8683970241025WHEALLTYKSDPAMRTGGCATGAGGCTCTTCTAACATATAAGAGTGACCCAGCCATGAGA
ARFGEF1-CPA6chr868150970chr8683970241126HEALLTYKSDPAMRKCATGAGGCTCTTCTAACATATAAGAGTGACCCAGCCATGAGAAAA
ARFGEF1-CPA6chr868150970chr868397024924SWHEALLTYKSDPAMTCATGGCATGAGGCTCTTCTAACATATAAGAGTGACCCAGCCATG

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Information of the samples that have these potential fusion neoantigens of ARFGEF1-CPA6

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
BRCAARFGEF1-CPA6chr868150970ENST00000262215chr868397024ENST00000297769TCGA-A8-A09N-01A

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Potential target of CAR-T therapy development for ARFGEF1-CPA6

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 ARFGEF1-CPA6

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 ARFGEF1-CPA6

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