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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:C2orf69-ATIC

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: C2orf69-ATIC
FusionPDB ID: 11659
FusionGDB2.0 ID: 11659
HgeneTgene
Gene symbol

C2orf69

ATIC

Gene ID

205327

471

Gene namechromosome 2 open reading frame 695-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolase
Synonyms-AICAR|AICARFT|HEL-S-70p|IMPCHASE|PURH
Cytomap

2q33.1

2q35

Type of geneprotein-codingprotein-coding
DescriptionUPF0565 protein C2orf69bifunctional purine biosynthesis protein PURH5-aminoimidazole-4-carboxamide-1-beta-D-ribonucleotide transformylase/inosinicaseAICAR formyltransferase/IMP cyclohydrolase bifunctional enzymeAICARFT/IMPCHASEepididymis secretory sperm binding protein Li 7
Modification date2020031320200313
UniProtAcc

Q8N8R5

Main function of 5'-partner protein:

P31939

Main function of 5'-partner protein: FUNCTION: Bifunctional enzyme that catalyzes the last two steps of purine biosynthesis (PubMed:11948179, PubMed:14756554). Acts as a transformylase that incorporates a formyl group to the AMP analog AICAR (5-amino-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamide) to produce the intermediate formyl-AICAR (FAICAR) (PubMed:9378707, PubMed:11948179, PubMed:10985775). Can use both 10-formyldihydrofolate and 10-formyltetrahydrofolate as the formyl donor in this reaction (PubMed:10985775). Also catalyzes the cyclization of FAICAR to IMP (PubMed:11948179, PubMed:14756554). Is able to convert thio-AICAR to 6-mercaptopurine ribonucleotide, an inhibitor of purine biosynthesis used in the treatment of human leukemias (PubMed:10985775). Promotes insulin receptor/INSR autophosphorylation and is involved in INSR internalization (PubMed:25687571). {ECO:0000269|PubMed:10985775, ECO:0000269|PubMed:11948179, ECO:0000269|PubMed:14756554, ECO:0000269|PubMed:25687571, ECO:0000269|PubMed:9378707}.
Ensembl transtripts involved in fusion geneENST idsENST00000491721, ENST00000319974, 
ENST00000236959, ENST00000435675, 
ENST00000540518, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score5 X 3 X 2=3010 X 9 X 4=360
# samples 510
** MAII scorelog2(5/30*10)=0.736965594166206
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
log2(10/360*10)=-1.84799690655495
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Fusion gene context

PubMed: C2orf69 [Title/Abstract] AND ATIC [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: C2orf69 [Title/Abstract] AND ATIC [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)C2orf69(200776494)-ATIC(216213817), # samples:1
Anticipated loss of major functional domain due to fusion event.C2orf69-ATIC 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.
C2orf69-ATIC 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.
C2orf69-ATIC 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.
C2orf69-ATIC 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/chr2:200776494/chr2:216213817)
- 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 C2orf69 (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 ATIC (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)
ENST00000319974C2orf69chr2200776494+ENST00000236959ATICchr2216213817+90051639791250
ENST00000319974C2orf69chr2200776494+ENST00000540518ATICchr2216213817+90051639791250
ENST00000319974C2orf69chr2200776494+ENST00000435675ATICchr2216213817+90051639791250

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
ENST00000319974ENST00000236959C2orf69chr2200776494+ATICchr2216213817+0.0014393560.9985606
ENST00000319974ENST00000540518C2orf69chr2200776494+ATICchr2216213817+0.0014393560.9985606
ENST00000319974ENST00000435675C2orf69chr2200776494+ATICchr2216213817+0.0014393560.9985606

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 C2orf69-ATIC

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide
C2orf69chr2200776494ATICchr2216213817516159PQHHVLYFPGDVQDEDLIKWKALFEE

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Potential FusionNeoAntigen Information of C2orf69-ATIC 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.
C2orf69-ATIC_200776494_216213817.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)
C2orf69-ATICchr2200776494chr2216213817516HLA-B57:01VQDEDLIKW0.96480.98761120
C2orf69-ATICchr2200776494chr2216213817516HLA-B58:02VQDEDLIKW0.89610.96941120
C2orf69-ATICchr2200776494chr2216213817516HLA-B44:03VQDEDLIKW0.89330.97231120
C2orf69-ATICchr2200776494chr2216213817516HLA-B47:01VQDEDLIKW0.8790.63311120
C2orf69-ATICchr2200776494chr2216213817516HLA-B58:01VQDEDLIKW0.87730.95971120
C2orf69-ATICchr2200776494chr2216213817516HLA-A32:13VQDEDLIKW0.80590.95091120
C2orf69-ATICchr2200776494chr2216213817516HLA-B13:01VQDEDLIKW0.39110.96051120
C2orf69-ATICchr2200776494chr2216213817516HLA-B38:01VQDEDLIKW0.11320.96171120
C2orf69-ATICchr2200776494chr2216213817516HLA-B35:03FPGDVQDEDL0.95520.9567717
C2orf69-ATICchr2200776494chr2216213817516HLA-B45:01QDEDLIKWKA0.93470.94521222
C2orf69-ATICchr2200776494chr2216213817516HLA-B53:01DVQDEDLIKW0.92560.55451020
C2orf69-ATICchr2200776494chr2216213817516HLA-B35:02FPGDVQDEDL0.83920.9799717
C2orf69-ATICchr2200776494chr2216213817516HLA-B35:04FPGDVQDEDL0.83920.9799717
C2orf69-ATICchr2200776494chr2216213817516HLA-C05:09VQDEDLIKW0.99410.96141120
C2orf69-ATICchr2200776494chr2216213817516HLA-B44:10VQDEDLIKW0.28810.54461120
C2orf69-ATICchr2200776494chr2216213817516HLA-B35:12FPGDVQDEDL0.83920.9799717
C2orf69-ATICchr2200776494chr2216213817516HLA-B39:10FPGDVQDEDL0.7990.9567717
C2orf69-ATICchr2200776494chr2216213817516HLA-C05:01VQDEDLIKW0.99410.96141120
C2orf69-ATICchr2200776494chr2216213817516HLA-B57:10VQDEDLIKW0.96480.98761120
C2orf69-ATICchr2200776494chr2216213817516HLA-B57:04VQDEDLIKW0.91940.82981120
C2orf69-ATICchr2200776494chr2216213817516HLA-B57:02VQDEDLIKW0.90810.91671120
C2orf69-ATICchr2200776494chr2216213817516HLA-B44:13VQDEDLIKW0.89330.97231120
C2orf69-ATICchr2200776494chr2216213817516HLA-B44:26VQDEDLIKW0.89330.97231120
C2orf69-ATICchr2200776494chr2216213817516HLA-B44:07VQDEDLIKW0.89330.97231120
C2orf69-ATICchr2200776494chr2216213817516HLA-B15:13VQDEDLIKW0.64780.69541120
C2orf69-ATICchr2200776494chr2216213817516HLA-B15:24VQDEDLIKW0.60270.91971120
C2orf69-ATICchr2200776494chr2216213817516HLA-B35:28VQDEDLIKW0.57640.97821120
C2orf69-ATICchr2200776494chr2216213817516HLA-B48:02VQDEDLIKW0.51670.9751120
C2orf69-ATICchr2200776494chr2216213817516HLA-B38:05VQDEDLIKW0.11320.96171120
C2orf69-ATICchr2200776494chr2216213817516HLA-B53:02DVQDEDLIKW0.97670.63871020
C2orf69-ATICchr2200776494chr2216213817516HLA-A25:01DVQDEDLIKW0.96950.89181020
C2orf69-ATICchr2200776494chr2216213817516HLA-B15:13DVQDEDLIKW0.89110.76451020
C2orf69-ATICchr2200776494chr2216213817516HLA-B35:09FPGDVQDEDL0.83920.9799717
C2orf69-ATICchr2200776494chr2216213817516HLA-B67:01FPGDVQDEDL0.79640.8888717

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Potential FusionNeoAntigen Information of C2orf69-ATIC 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.
C2orf69-ATIC_200776494_216213817.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)
C2orf69-ATICchr2200776494chr2216213817516DRB1-0473QHHVLYFPGDVQDED116

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Fusion breakpoint peptide structures of C2orf69-ATIC

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
10629YFPGDVQDEDLIKWC2orf69ATICchr2200776494chr2216213817516

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of C2orf69-ATIC

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-B14:023BVN10629YFPGDVQDEDLIKW-7.15543-7.26883
HLA-B14:023BVN10629YFPGDVQDEDLIKW-4.77435-5.80965
HLA-B52:013W3910629YFPGDVQDEDLIKW-6.80875-6.92215
HLA-B52:013W3910629YFPGDVQDEDLIKW-4.20386-5.23916
HLA-A11:014UQ210629YFPGDVQDEDLIKW-7.5194-8.5547
HLA-A11:014UQ210629YFPGDVQDEDLIKW-6.9601-7.0735
HLA-A24:025HGA10629YFPGDVQDEDLIKW-7.52403-7.63743
HLA-A24:025HGA10629YFPGDVQDEDLIKW-5.82433-6.85963
HLA-B27:056PYJ10629YFPGDVQDEDLIKW-3.28285-4.31815
HLA-B44:053DX810629YFPGDVQDEDLIKW-5.91172-6.94702
HLA-B44:053DX810629YFPGDVQDEDLIKW-4.24346-4.35686

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Vaccine Design for the FusionNeoAntigens of C2orf69-ATIC

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
C2orf69-ATICchr2200776494chr22162138171020DVQDEDLIKWGATGTGCAGGATGAAGATTTGATAAAGTGG
C2orf69-ATICchr2200776494chr22162138171120VQDEDLIKWGTGCAGGATGAAGATTTGATAAAGTGG
C2orf69-ATICchr2200776494chr22162138171222QDEDLIKWKACAGGATGAAGATTTGATAAAGTGGAAGGCA
C2orf69-ATICchr2200776494chr2216213817717FPGDVQDEDLTTCCCTGGGGATGTGCAGGATGAAGATTTG

check button mRNA and peptide sequences of FusionNeoAntigens that have potential interaction with HLA-IIs.
Fusion geneHchrHbpTchrTbpStart in +/-13AAEnd in +/-13AAFusionNeoAntigen peptideFusionNEoAntigen RNA sequence
C2orf69-ATICchr2200776494chr2216213817116QHHVLYFPGDVQDEDCAGCATCACGTCCTCTATTTCCCTGGGGATGTGCAGGATGAAGAT

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Information of the samples that have these potential fusion neoantigens of C2orf69-ATIC

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
STADC2orf69-ATICchr2200776494ENST00000319974chr2216213817ENST00000236959TCGA-BR-8284-01A

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Potential target of CAR-T therapy development for C2orf69-ATIC

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 C2orf69-ATIC

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 C2orf69-ATIC

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
TgeneATICC0001787Osteoporosis, Age-Related1CTD_human
TgeneATICC0003873Rheumatoid Arthritis1CTD_human
TgeneATICC0013221Drug toxicity1CTD_human
TgeneATICC0029456Osteoporosis1CTD_human
TgeneATICC0029459Osteoporosis, Senile1CTD_human
TgeneATICC0041755Adverse reaction to drug1CTD_human
TgeneATICC0155003Blindness, Transient1CTD_human
TgeneATICC0221473Blindness, Hysterical1CTD_human
TgeneATICC0271215Blindness, Legal1CTD_human
TgeneATICC0339730Blindness, Acquired1CTD_human
TgeneATICC0376288Amaurosis1CTD_human
TgeneATICC0456909Blindness1CTD_human
TgeneATICC0750958Blindness, Monocular1CTD_human
TgeneATICC0751406Post-Traumatic Osteoporosis1CTD_human
TgeneATICC1837530AICAR Transformylase Inosine Monophosphate Cyclohydrolase Deficiency1CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
TgeneATICC1879328Blindness both eyes NOS (disorder)1CTD_human
TgeneATICC3714756Intellectual Disability1GENOMICS_ENGLAND