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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:GFRA3-TTC8

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: GFRA3-TTC8
FusionPDB ID: 32991
FusionGDB2.0 ID: 32991
HgeneTgene
Gene symbol

GFRA3

TTC8

Gene ID

2676

123016

Gene nameGDNF family receptor alpha 3tetratricopeptide repeat domain 8
SynonymsGDNFR3BBS8|RP51
Cytomap

5q31.2

14q31.3

Type of geneprotein-codingprotein-coding
DescriptionGDNF family receptor alpha-3GDNF receptor alpha-3GDNFR-alpha-3GFR-alpha-3GPI-linked receptorglial cell line-derived neurotrophic factor receptor alpha-3tetratricopeptide repeat protein 8Bardet-Biedl syndrome type 8TPR repeat protein 8
Modification date2020031320200313
UniProtAcc

O60609

Main function of 5'-partner protein: FUNCTION: Receptor for the glial cell line-derived neurotrophic factor, ARTN (artemin). Mediates the artemin-induced autophosphorylation and activation of the RET receptor tyrosine kinase. {ECO:0000269|PubMed:9883723}.		.
Ensembl transtripts involved in fusion geneENST idsENST00000274721, ENST00000378362, 
ENST00000338104, ENST00000345383, 
ENST00000346301, ENST00000354441, 
ENST00000358622, ENST00000380656, 
ENST00000536576, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score3 X 8 X 2=484 X 7 X 4=112
# samples 46
** MAII scorelog2(4/48*10)=-0.263034405833794
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(6/112*10)=-0.900464326449086
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Fusion gene context

PubMed: GFRA3 [Title/Abstract] AND TTC8 [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: GFRA3 [Title/Abstract] AND TTC8 [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)GFRA3(137588976)-TTC8(89341370), # samples:3
Anticipated loss of major functional domain due to fusion event.GFRA3-TTC8 seems lost the major protein functional domain in Hgene partner, which is a IUPHAR drug target due to the frame-shifted ORF.
GFRA3-TTC8 seems lost the major protein functional domain in Tgene partner, which is a essential gene due to the frame-shifted ORF.
* DoF score (Degree of Frequency) = # partners X # break points X # cancer types
** MAII score (Major Active Isofusion Index) = log2(# samples/DoF score*10)

check button Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez
PartnerGeneGO IDGO termPubMed ID


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/chr5:137588976/chr14:89341370)
- 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 GFRA3 (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 TTC8 (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)
ENST00000274721GFRA3chr5137588976-ENST00000345383TTC8chr1489341370+214213601151560481
ENST00000274721GFRA3chr5137588976-ENST00000536576TTC8chr1489341370+213813601151560481
ENST00000274721GFRA3chr5137588976-ENST00000346301TTC8chr1489341370+213913601151560481
ENST00000274721GFRA3chr5137588976-ENST00000338104TTC8chr1489341370+213913601151560481
ENST00000274721GFRA3chr5137588976-ENST00000354441TTC8chr1489341370+210213601151560481
ENST00000274721GFRA3chr5137588976-ENST00000380656TTC8chr1489341370+213813601151560481
ENST00000274721GFRA3chr5137588976-ENST00000358622TTC8chr1489341370+213813601151560481
ENST00000378362GFRA3chr5137588976-ENST00000345383TTC8chr1489341370+1943116191361450
ENST00000378362GFRA3chr5137588976-ENST00000536576TTC8chr1489341370+1939116191361450
ENST00000378362GFRA3chr5137588976-ENST00000346301TTC8chr1489341370+1940116191361450
ENST00000378362GFRA3chr5137588976-ENST00000338104TTC8chr1489341370+1940116191361450
ENST00000378362GFRA3chr5137588976-ENST00000354441TTC8chr1489341370+1903116191361450
ENST00000378362GFRA3chr5137588976-ENST00000380656TTC8chr1489341370+1939116191361450
ENST00000378362GFRA3chr5137588976-ENST00000358622TTC8chr1489341370+1939116191361450
ENST00000274721GFRA3chr5137588975-ENST00000345383TTC8chr1489341369+214213601151560481
ENST00000274721GFRA3chr5137588975-ENST00000536576TTC8chr1489341369+213813601151560481
ENST00000274721GFRA3chr5137588975-ENST00000346301TTC8chr1489341369+213913601151560481
ENST00000274721GFRA3chr5137588975-ENST00000338104TTC8chr1489341369+213913601151560481
ENST00000274721GFRA3chr5137588975-ENST00000354441TTC8chr1489341369+210213601151560481
ENST00000274721GFRA3chr5137588975-ENST00000380656TTC8chr1489341369+213813601151560481
ENST00000274721GFRA3chr5137588975-ENST00000358622TTC8chr1489341369+213813601151560481
ENST00000378362GFRA3chr5137588975-ENST00000345383TTC8chr1489341369+1943116191361450
ENST00000378362GFRA3chr5137588975-ENST00000536576TTC8chr1489341369+1939116191361450
ENST00000378362GFRA3chr5137588975-ENST00000346301TTC8chr1489341369+1940116191361450
ENST00000378362GFRA3chr5137588975-ENST00000338104TTC8chr1489341369+1940116191361450
ENST00000378362GFRA3chr5137588975-ENST00000354441TTC8chr1489341369+1903116191361450
ENST00000378362GFRA3chr5137588975-ENST00000380656TTC8chr1489341369+1939116191361450
ENST00000378362GFRA3chr5137588975-ENST00000358622TTC8chr1489341369+1939116191361450
ENST00000274721GFRA3chr5137589455-ENST00000345383TTC8chr1489343638+196912711151314399
ENST00000274721GFRA3chr5137589455-ENST00000346301TTC8chr1489343638+196612711151314399
ENST00000274721GFRA3chr5137589455-ENST00000338104TTC8chr1489343638+196612711151314399
ENST00000378362GFRA3chr5137589455-ENST00000345383TTC8chr1489343638+1770107291115368
ENST00000378362GFRA3chr5137589455-ENST00000346301TTC8chr1489343638+1767107291115368
ENST00000378362GFRA3chr5137589455-ENST00000338104TTC8chr1489343638+1767107291115368
ENST00000274721GFRA3chr5137593328-ENST00000536576TTC8chr1489343638+172610321151113332
ENST00000274721GFRA3chr5137593328-ENST00000354441TTC8chr1489343638+169010321151113332
ENST00000274721GFRA3chr5137593328-ENST00000380656TTC8chr1489343638+172610321151113332
ENST00000274721GFRA3chr5137593328-ENST00000358622TTC8chr1489343638+172610321151113332
ENST00000378362GFRA3chr5137593328-ENST00000536576TTC8chr1489343638+15278339914301
ENST00000378362GFRA3chr5137593328-ENST00000354441TTC8chr1489343638+14918339914301
ENST00000378362GFRA3chr5137593328-ENST00000380656TTC8chr1489343638+15278339914301
ENST00000378362GFRA3chr5137593328-ENST00000358622TTC8chr1489343638+15278339914301

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
ENST00000274721ENST00000345383GFRA3chr5137588976-TTC8chr1489341370+0.043756080.95624393
ENST00000274721ENST00000536576GFRA3chr5137588976-TTC8chr1489341370+0.0437450040.95625496
ENST00000274721ENST00000346301GFRA3chr5137588976-TTC8chr1489341370+0.0436377970.95636225
ENST00000274721ENST00000338104GFRA3chr5137588976-TTC8chr1489341370+0.0436377970.95636225
ENST00000274721ENST00000354441GFRA3chr5137588976-TTC8chr1489341370+0.0509057530.9490942
ENST00000274721ENST00000380656GFRA3chr5137588976-TTC8chr1489341370+0.0437450040.95625496
ENST00000274721ENST00000358622GFRA3chr5137588976-TTC8chr1489341370+0.0437450040.95625496
ENST00000378362ENST00000345383GFRA3chr5137588976-TTC8chr1489341370+0.0719082360.9280917
ENST00000378362ENST00000536576GFRA3chr5137588976-TTC8chr1489341370+0.07198150.9280185
ENST00000378362ENST00000346301GFRA3chr5137588976-TTC8chr1489341370+0.0718434750.9281565
ENST00000378362ENST00000338104GFRA3chr5137588976-TTC8chr1489341370+0.0718434750.9281565
ENST00000378362ENST00000354441GFRA3chr5137588976-TTC8chr1489341370+0.083716770.91628325
ENST00000378362ENST00000380656GFRA3chr5137588976-TTC8chr1489341370+0.07198150.9280185
ENST00000378362ENST00000358622GFRA3chr5137588976-TTC8chr1489341370+0.07198150.9280185
ENST00000274721ENST00000345383GFRA3chr5137588975-TTC8chr1489341369+0.043756080.95624393
ENST00000274721ENST00000536576GFRA3chr5137588975-TTC8chr1489341369+0.0437450040.95625496
ENST00000274721ENST00000346301GFRA3chr5137588975-TTC8chr1489341369+0.0436377970.95636225
ENST00000274721ENST00000338104GFRA3chr5137588975-TTC8chr1489341369+0.0436377970.95636225
ENST00000274721ENST00000354441GFRA3chr5137588975-TTC8chr1489341369+0.0509057530.9490942
ENST00000274721ENST00000380656GFRA3chr5137588975-TTC8chr1489341369+0.0437450040.95625496
ENST00000274721ENST00000358622GFRA3chr5137588975-TTC8chr1489341369+0.0437450040.95625496
ENST00000378362ENST00000345383GFRA3chr5137588975-TTC8chr1489341369+0.0719082360.9280917
ENST00000378362ENST00000536576GFRA3chr5137588975-TTC8chr1489341369+0.07198150.9280185
ENST00000378362ENST00000346301GFRA3chr5137588975-TTC8chr1489341369+0.0718434750.9281565
ENST00000378362ENST00000338104GFRA3chr5137588975-TTC8chr1489341369+0.0718434750.9281565
ENST00000378362ENST00000354441GFRA3chr5137588975-TTC8chr1489341369+0.083716770.91628325
ENST00000378362ENST00000380656GFRA3chr5137588975-TTC8chr1489341369+0.07198150.9280185
ENST00000378362ENST00000358622GFRA3chr5137588975-TTC8chr1489341369+0.07198150.9280185
ENST00000274721ENST00000345383GFRA3chr5137589455-TTC8chr1489343638+0.0585252750.9414748
ENST00000274721ENST00000346301GFRA3chr5137589455-TTC8chr1489343638+0.0582942740.9417057
ENST00000274721ENST00000338104GFRA3chr5137589455-TTC8chr1489343638+0.0582942740.9417057
ENST00000378362ENST00000345383GFRA3chr5137589455-TTC8chr1489343638+0.092689240.9073108
ENST00000378362ENST00000346301GFRA3chr5137589455-TTC8chr1489343638+0.0924381760.9075619
ENST00000378362ENST00000338104GFRA3chr5137589455-TTC8chr1489343638+0.0924381760.9075619
ENST00000274721ENST00000536576GFRA3chr5137593328-TTC8chr1489343638+0.130371720.86962825
ENST00000274721ENST00000354441GFRA3chr5137593328-TTC8chr1489343638+0.13935620.8606438
ENST00000274721ENST00000380656GFRA3chr5137593328-TTC8chr1489343638+0.130371720.86962825
ENST00000274721ENST00000358622GFRA3chr5137593328-TTC8chr1489343638+0.130371720.86962825
ENST00000378362ENST00000536576GFRA3chr5137593328-TTC8chr1489343638+0.361725360.6382746
ENST00000378362ENST00000354441GFRA3chr5137593328-TTC8chr1489343638+0.369758670.63024133
ENST00000378362ENST00000380656GFRA3chr5137593328-TTC8chr1489343638+0.361725360.6382746
ENST00000378362ENST00000358622GFRA3chr5137593328-TTC8chr1489343638+0.361725360.6382746

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 GFRA3-TTC8

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide
GFRA3chr5137588975TTC8chr14893413691161383QDWPHPTFAVMAHQARALLQTASSLA
GFRA3chr5137588975TTC8chr14893413691360414QDWPHPTFAVMAHQARALLQTASSLA
GFRA3chr5137588976TTC8chr14893413701161383QDWPHPTFAVMAHQARALLQTASSLA
GFRA3chr5137588976TTC8chr14893413701360414QDWPHPTFAVMAHQARALLQTASSLA
GFRA3chr5137593328TTC8chr14893436381032304CLELRRLCFSDPLCRLEICREAMLLR
GFRA3chr5137593328TTC8chr1489343638833273CLELRRLCFSDPLCRLEICREAMLLR

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Potential FusionNeoAntigen Information of GFRA3-TTC8 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.
GFRA3-TTC8_137588975_89341369.msa
GFRA3-TTC8_137593328_89343638.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)
GFRA3-TTC8chr5137588975chr14893413691360HLA-B15:10AHQARALL0.99750.65591119
GFRA3-TTC8chr5137588975chr14893413691360HLA-A68:03FAVMAHQAR0.98990.6139716
GFRA3-TTC8chr5137588975chr14893413691360HLA-B35:03MAHQARALL0.9760.94321019
GFRA3-TTC8chr5137588975chr14893413691360HLA-A68:05FAVMAHQAR0.97060.6363716
GFRA3-TTC8chr5137588975chr14893413691360HLA-A33:05FAVMAHQAR0.96970.5899716
GFRA3-TTC8chr5137588975chr14893413691360HLA-A33:01FAVMAHQAR0.96970.5899716
GFRA3-TTC8chr5137588975chr14893413691360HLA-B35:04MAHQARALL0.90440.97971019
GFRA3-TTC8chr5137588975chr14893413691360HLA-B35:02MAHQARALL0.90440.97971019
GFRA3-TTC8chr5137588975chr14893413691360HLA-B56:01HPTFAVMAHQA0.96920.7056415
GFRA3-TTC8chr5137588975chr14893413691360HLA-B55:01HPTFAVMAHQA0.94240.5104415
GFRA3-TTC8chr5137588975chr14893413691360HLA-C03:08MAHQARAL0.99980.92441018
GFRA3-TTC8chr5137588975chr14893413691360HLA-C03:19MAHQARAL0.99980.99281018
GFRA3-TTC8chr5137588975chr14893413691360HLA-C12:12MAHQARAL0.99910.97281018
GFRA3-TTC8chr5137588975chr14893413691360HLA-B14:03AHQARALL0.93970.76681119
GFRA3-TTC8chr5137588975chr14893413691360HLA-C03:19MAHQARALL0.99960.99121019
GFRA3-TTC8chr5137588975chr14893413691360HLA-C03:07MAHQARALL0.99940.96871019
GFRA3-TTC8chr5137588975chr14893413691360HLA-C03:08MAHQARALL0.99940.89911019
GFRA3-TTC8chr5137588975chr14893413691360HLA-C15:06MAHQARALL0.99820.92641019
GFRA3-TTC8chr5137588975chr14893413691360HLA-B42:02MAHQARALL0.99450.69861019
GFRA3-TTC8chr5137588975chr14893413691360HLA-B42:01MAHQARALL0.99210.69261019
GFRA3-TTC8chr5137588975chr14893413691360HLA-C12:12MAHQARALL0.99150.96631019
GFRA3-TTC8chr5137588975chr14893413691360HLA-C08:04MAHQARALL0.97710.98081019
GFRA3-TTC8chr5137588975chr14893413691360HLA-C08:13MAHQARALL0.97710.98081019
GFRA3-TTC8chr5137588975chr14893413691360HLA-C06:03MAHQARALL0.97430.99591019
GFRA3-TTC8chr5137588975chr14893413691360HLA-C12:04MAHQARALL0.96850.9951019
GFRA3-TTC8chr5137588975chr14893413691360HLA-C01:17VMAHQARAL0.95330.9688918
GFRA3-TTC8chr5137588975chr14893413691360HLA-C02:06MAHQARALL0.94930.94271019
GFRA3-TTC8chr5137588975chr14893413691360HLA-B35:12MAHQARALL0.90440.97971019
GFRA3-TTC8chr5137588975chr14893413691360HLA-C01:30VMAHQARAL0.89390.9719918
GFRA3-TTC8chr5137588975chr14893413691360HLA-C01:30MAHQARALL0.89150.96921019
GFRA3-TTC8chr5137588975chr14893413691360HLA-C01:17MAHQARALL0.85480.96911019
GFRA3-TTC8chr5137588975chr14893413691360HLA-C03:14MAHQARALL0.80370.98651019
GFRA3-TTC8chr5137588975chr14893413691360HLA-B54:01HPTFAVMAHQA0.99790.9124415
GFRA3-TTC8chr5137588975chr14893413691360HLA-C03:03MAHQARAL0.99990.99221018
GFRA3-TTC8chr5137588975chr14893413691360HLA-C03:04MAHQARAL0.99990.99221018
GFRA3-TTC8chr5137588975chr14893413691360HLA-C03:17MAHQARAL0.99970.97891018
GFRA3-TTC8chr5137588975chr14893413691360HLA-C16:04MAHQARAL0.99920.99051018
GFRA3-TTC8chr5137588975chr14893413691360HLA-C03:05MAHQARAL0.99910.93661018
GFRA3-TTC8chr5137588975chr14893413691360HLA-B07:13MAHQARAL0.99880.8031018
GFRA3-TTC8chr5137588975chr14893413691360HLA-C12:03MAHQARAL0.99770.99091018
GFRA3-TTC8chr5137588975chr14893413691360HLA-B78:02FAVMAHQA0.99520.956715
GFRA3-TTC8chr5137588975chr14893413691360HLA-C16:01MAHQARAL0.99490.98221018
GFRA3-TTC8chr5137588975chr14893413691360HLA-C16:02MAHQARAL0.99360.99221018
GFRA3-TTC8chr5137588975chr14893413691360HLA-B15:09AHQARALL0.99330.72341119
GFRA3-TTC8chr5137588975chr14893413691360HLA-C03:05MAHQARALL0.99940.93281019
GFRA3-TTC8chr5137588975chr14893413691360HLA-C03:04MAHQARALL0.99940.99061019
GFRA3-TTC8chr5137588975chr14893413691360HLA-C03:17MAHQARALL0.99940.9771019
GFRA3-TTC8chr5137588975chr14893413691360HLA-C03:03MAHQARALL0.99940.99061019
GFRA3-TTC8chr5137588975chr14893413691360HLA-C03:67MAHQARALL0.99930.98451019
GFRA3-TTC8chr5137588975chr14893413691360HLA-C03:02MAHQARALL0.99810.98181019
GFRA3-TTC8chr5137588975chr14893413691360HLA-B07:13MAHQARALL0.9970.80861019
GFRA3-TTC8chr5137588975chr14893413691360HLA-C16:04MAHQARALL0.99330.98811019
GFRA3-TTC8chr5137588975chr14893413691360HLA-C03:67VMAHQARAL0.98890.9869918
GFRA3-TTC8chr5137588975chr14893413691360HLA-C12:03MAHQARALL0.98880.98811019
GFRA3-TTC8chr5137588975chr14893413691360HLA-C03:06MAHQARALL0.97520.99141019
GFRA3-TTC8chr5137588975chr14893413691360HLA-B35:13MAHQARALL0.97520.94661019
GFRA3-TTC8chr5137588975chr14893413691360HLA-C16:01MAHQARALL0.97410.98041019
GFRA3-TTC8chr5137588975chr14893413691360HLA-C12:02MAHQARALL0.96860.98171019
GFRA3-TTC8chr5137588975chr14893413691360HLA-C01:02VMAHQARAL0.95750.9672918
GFRA3-TTC8chr5137588975chr14893413691360HLA-B15:73VMAHQARAL0.9430.9665918
GFRA3-TTC8chr5137588975chr14893413691360HLA-C16:02MAHQARALL0.93680.99131019
GFRA3-TTC8chr5137588975chr14893413691360HLA-B35:09MAHQARALL0.90440.97971019
GFRA3-TTC8chr5137588975chr14893413691360HLA-B51:06MAHQARALL0.87910.52711019
GFRA3-TTC8chr5137588975chr14893413691360HLA-B15:30VMAHQARAL0.87180.9677918
GFRA3-TTC8chr5137588975chr14893413691360HLA-C01:02MAHQARALL0.82920.96791019
GFRA3-TTC8chr5137588975chr14893413691360HLA-B55:02HPTFAVMAHQA0.98350.8431415
GFRA3-TTC8chr5137593328chr14893436381032HLA-A74:09RLCFSDPLCR0.95410.7999515
GFRA3-TTC8chr5137593328chr14893436381032HLA-A74:03RLCFSDPLCR0.95410.7999515
GFRA3-TTC8chr5137593328chr14893436381032HLA-A74:11RLCFSDPLCR0.95410.7999515
GFRA3-TTC8chr5137593328chr14893436381032HLA-A31:06RLCFSDPLCR0.94260.6549515
GFRA3-TTC8chr5137593328chr14893436381032HLA-B27:05RRLCFSDPLCR0.99990.82415
GFRA3-TTC8chr5137593328chr14893436381032HLA-C04:07FSDPLCRL10.8034816
GFRA3-TTC8chr5137593328chr14893436381032HLA-C08:15FSDPLCRL10.9069816
GFRA3-TTC8chr5137593328chr14893436381032HLA-C04:10FSDPLCRL10.8244816
GFRA3-TTC8chr5137593328chr14893436381032HLA-C05:09FSDPLCRL10.9421816
GFRA3-TTC8chr5137593328chr14893436381032HLA-C03:07FSDPLCRL0.99980.9774816
GFRA3-TTC8chr5137593328chr14893436381032HLA-C03:19FSDPLCRL0.99980.9901816
GFRA3-TTC8chr5137593328chr14893436381032HLA-C15:06FSDPLCRL0.99960.9048816
GFRA3-TTC8chr5137593328chr14893436381032HLA-C04:06FSDPLCRL0.99960.8139816
GFRA3-TTC8chr5137593328chr14893436381032HLA-C08:04FSDPLCRL0.9990.878816
GFRA3-TTC8chr5137593328chr14893436381032HLA-C08:13FSDPLCRL0.9990.878816
GFRA3-TTC8chr5137593328chr14893436381032HLA-C04:14FSDPLCRL0.9980.7796816
GFRA3-TTC8chr5137593328chr14893436381032HLA-C08:03FSDPLCRL0.98160.9657816
GFRA3-TTC8chr5137593328chr14893436381032HLA-C05:09FSDPLCRLEI0.99990.9268818
GFRA3-TTC8chr5137593328chr14893436381032HLA-C08:15FSDPLCRLEI0.99980.9332818
GFRA3-TTC8chr5137593328chr14893436381032HLA-B27:14RRLCFSDPLCR0.99990.8486415
GFRA3-TTC8chr5137593328chr14893436381032HLA-B27:03RRLCFSDPLCR0.99730.8389415
GFRA3-TTC8chr5137593328chr14893436381032HLA-C05:01FSDPLCRL10.9421816
GFRA3-TTC8chr5137593328chr14893436381032HLA-C04:01FSDPLCRL10.8034816
GFRA3-TTC8chr5137593328chr14893436381032HLA-C04:03FSDPLCRL10.8497816
GFRA3-TTC8chr5137593328chr14893436381032HLA-C08:02FSDPLCRL10.9069816
GFRA3-TTC8chr5137593328chr14893436381032HLA-C18:01FSDPLCRL10.8525816
GFRA3-TTC8chr5137593328chr14893436381032HLA-C03:03FSDPLCRL0.99980.9902816
GFRA3-TTC8chr5137593328chr14893436381032HLA-C03:04FSDPLCRL0.99980.9902816
GFRA3-TTC8chr5137593328chr14893436381032HLA-C15:05FSDPLCRL0.99950.8738816
GFRA3-TTC8chr5137593328chr14893436381032HLA-C04:04FSDPLCRL0.99950.7733816
GFRA3-TTC8chr5137593328chr14893436381032HLA-C03:06FSDPLCRL0.99810.988816
GFRA3-TTC8chr5137593328chr14893436381032HLA-C08:01FSDPLCRL0.98160.9657816
GFRA3-TTC8chr5137593328chr14893436381032HLA-C17:01FSDPLCRL0.94740.7418816
GFRA3-TTC8chr5137593328chr14893436381032HLA-B07:13FSDPLCRL0.40720.7587816
GFRA3-TTC8chr5137593328chr14893436381032HLA-C05:01FSDPLCRLEI0.99990.9268818
GFRA3-TTC8chr5137593328chr14893436381032HLA-C08:02FSDPLCRLEI0.99980.9332818
GFRA3-TTC8chr5137593328chr14893436381032HLA-A74:01RLCFSDPLCR0.95410.7999515
GFRA3-TTC8chr5137593328chr14893436381032HLA-A03:02RLCFSDPLCR0.91310.5189515
GFRA3-TTC8chr5137593328chr14893436381032HLA-B27:10RRLCFSDPLCR0.99990.8969415

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Potential FusionNeoAntigen Information of GFRA3-TTC8 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.
GFRA3-TTC8_137588975_89341369.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)
GFRA3-TTC8chr5137588975chr14893413691360DRB1-1172PHPTFAVMAHQARAL318
GFRA3-TTC8chr5137588975chr14893413691360DRB1-1172WPHPTFAVMAHQARA217
GFRA3-TTC8chr5137588975chr14893413691360DRB1-1385WPHPTFAVMAHQARA217
GFRA3-TTC8chr5137588975chr14893413691360DRB1-1385PHPTFAVMAHQARAL318
GFRA3-TTC8chr5137588975chr14893413691360DRB1-1386PHPTFAVMAHQARAL318
GFRA3-TTC8chr5137588975chr14893413691360DRB1-1386WPHPTFAVMAHQARA217
GFRA3-TTC8chr5137588975chr14893413691360DRB1-1386HPTFAVMAHQARALL419
GFRA3-TTC8chr5137588975chr14893413691360DRB1-1402PHPTFAVMAHQARAL318
GFRA3-TTC8chr5137588975chr14893413691360DRB1-1402WPHPTFAVMAHQARA217
GFRA3-TTC8chr5137588975chr14893413691360DRB1-1402HPTFAVMAHQARALL419
GFRA3-TTC8chr5137588975chr14893413691360DRB1-1403PHPTFAVMAHQARAL318
GFRA3-TTC8chr5137588975chr14893413691360DRB1-1403WPHPTFAVMAHQARA217
GFRA3-TTC8chr5137588975chr14893413691360DRB1-1419WPHPTFAVMAHQARA217
GFRA3-TTC8chr5137588975chr14893413691360DRB1-1419PHPTFAVMAHQARAL318
GFRA3-TTC8chr5137588975chr14893413691360DRB1-1424PHPTFAVMAHQARAL318
GFRA3-TTC8chr5137588975chr14893413691360DRB1-1424WPHPTFAVMAHQARA217
GFRA3-TTC8chr5137588975chr14893413691360DRB1-1430PHPTFAVMAHQARAL318
GFRA3-TTC8chr5137588975chr14893413691360DRB1-1430WPHPTFAVMAHQARA217
GFRA3-TTC8chr5137588975chr14893413691360DRB1-1440PHPTFAVMAHQARAL318
GFRA3-TTC8chr5137588975chr14893413691360DRB1-1440WPHPTFAVMAHQARA217
GFRA3-TTC8chr5137588975chr14893413691360DRB1-1441PHPTFAVMAHQARAL318
GFRA3-TTC8chr5137588975chr14893413691360DRB1-1441WPHPTFAVMAHQARA217
GFRA3-TTC8chr5137588975chr14893413691360DRB1-1441HPTFAVMAHQARALL419
GFRA3-TTC8chr5137588975chr14893413691360DRB1-1447PHPTFAVMAHQARAL318
GFRA3-TTC8chr5137588975chr14893413691360DRB1-1447WPHPTFAVMAHQARA217
GFRA3-TTC8chr5137588975chr14893413691360DRB1-1447HPTFAVMAHQARALL419
GFRA3-TTC8chr5137588975chr14893413691360DRB1-1467PHPTFAVMAHQARAL318
GFRA3-TTC8chr5137588975chr14893413691360DRB1-1467WPHPTFAVMAHQARA217
GFRA3-TTC8chr5137588975chr14893413691360DRB1-1467HPTFAVMAHQARALL419
GFRA3-TTC8chr5137588975chr14893413691360DRB1-1477PHPTFAVMAHQARAL318
GFRA3-TTC8chr5137588975chr14893413691360DRB1-1477WPHPTFAVMAHQARA217
GFRA3-TTC8chr5137588975chr14893413691360DRB1-1489PHPTFAVMAHQARAL318
GFRA3-TTC8chr5137588975chr14893413691360DRB1-1489WPHPTFAVMAHQARA217
GFRA3-TTC8chr5137588975chr14893413691360DRB1-1489HPTFAVMAHQARALL419
GFRA3-TTC8chr5137588975chr14893413691360DRB1-1494PHPTFAVMAHQARAL318
GFRA3-TTC8chr5137588975chr14893413691360DRB1-1494WPHPTFAVMAHQARA217
GFRA3-TTC8chr5137588975chr14893413691360DRB1-1494HPTFAVMAHQARALL419
GFRA3-TTC8chr5137588975chr14893413691360DRB1-1498PHPTFAVMAHQARAL318
GFRA3-TTC8chr5137588975chr14893413691360DRB1-1498WPHPTFAVMAHQARA217
GFRA3-TTC8chr5137588975chr14893413691360DRB1-1498HPTFAVMAHQARALL419

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Fusion breakpoint peptide structures of GFRA3-TTC8

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
4811LCFSDPLCRLEICRGFRA3TTC8chr5137593328chr14893436381032
File nameBPseqHgeneTgeneHchrHbpTchrTbpAAlen
9325TFAVMAHQARALLQGFRA3TTC8chr5137588975chr14893413691360

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of GFRA3-TTC8

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-B14:023BVN4811LCFSDPLCRLEICR-7.9962-8.1096
HLA-B14:023BVN4811LCFSDPLCRLEICR-5.70842-6.74372
HLA-B52:013W394811LCFSDPLCRLEICR-6.83737-6.95077
HLA-B52:013W394811LCFSDPLCRLEICR-4.4836-5.5189
HLA-A11:014UQ24811LCFSDPLCRLEICR-10.0067-10.1201
HLA-A11:014UQ24811LCFSDPLCRLEICR-9.03915-10.0745
HLA-A24:025HGA4811LCFSDPLCRLEICR-6.56204-6.67544
HLA-A24:025HGA4811LCFSDPLCRLEICR-5.42271-6.45801
HLA-B44:053DX84811LCFSDPLCRLEICR-7.85648-8.89178
HLA-B44:053DX84811LCFSDPLCRLEICR-5.3978-5.5112
HLA-A02:016TDR4811LCFSDPLCRLEICR-3.37154-4.40684
HLA-B14:023BVN9325TFAVMAHQARALLQ-7.9962-8.1096
HLA-B14:023BVN9325TFAVMAHQARALLQ-5.70842-6.74372
HLA-B52:013W399325TFAVMAHQARALLQ-6.83737-6.95077
HLA-B52:013W399325TFAVMAHQARALLQ-4.4836-5.5189
HLA-A11:014UQ29325TFAVMAHQARALLQ-10.0067-10.1201
HLA-A11:014UQ29325TFAVMAHQARALLQ-9.03915-10.0745
HLA-A24:025HGA9325TFAVMAHQARALLQ-6.56204-6.67544
HLA-A24:025HGA9325TFAVMAHQARALLQ-5.42271-6.45801
HLA-B44:053DX89325TFAVMAHQARALLQ-7.85648-8.89178
HLA-B44:053DX89325TFAVMAHQARALLQ-5.3978-5.5112
HLA-A02:016TDR9325TFAVMAHQARALLQ-3.37154-4.40684

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Vaccine Design for the FusionNeoAntigens of GFRA3-TTC8

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
GFRA3-TTC8chr5137588975chr14893413691018MAHQARALGCACACCAGGCAAGGGCACTATTA
GFRA3-TTC8chr5137588975chr14893413691019MAHQARALLGCACACCAGGCAAGGGCACTATTACAA
GFRA3-TTC8chr5137588975chr14893413691119AHQARALLCACCAGGCAAGGGCACTATTACAA
GFRA3-TTC8chr5137588975chr1489341369415HPTFAVMAHQACCTACCTTTGCTGTGATGGCACACCAGGCAAGG
GFRA3-TTC8chr5137588975chr1489341369715FAVMAHQAGCTGTGATGGCACACCAGGCAAGG
GFRA3-TTC8chr5137588975chr1489341369716FAVMAHQARGCTGTGATGGCACACCAGGCAAGGGCA
GFRA3-TTC8chr5137588975chr1489341369918VMAHQARALATGGCACACCAGGCAAGGGCACTATTA
GFRA3-TTC8chr5137593328chr1489343638415RRLCFSDPLCRCCTCTGCTTCTCCGACCCGCTTTGCAGATTGGA
GFRA3-TTC8chr5137593328chr1489343638515RLCFSDPLCRCTGCTTCTCCGACCCGCTTTGCAGATTGGA
GFRA3-TTC8chr5137593328chr1489343638816FSDPLCRLCGACCCGCTTTGCAGATTGGAGAT
GFRA3-TTC8chr5137593328chr1489343638818FSDPLCRLEICGACCCGCTTTGCAGATTGGAGATCTGCAG

check button mRNA and peptide sequences of FusionNeoAntigens that have potential interaction with HLA-IIs.
Fusion geneHchrHbpTchrTbpStart in +/-13AAEnd in +/-13AAFusionNeoAntigen peptideFusionNEoAntigen RNA sequence
GFRA3-TTC8chr5137588975chr1489341369217WPHPTFAVMAHQARACCACACCCTACCTTTGCTGTGATGGCACACCAGGCAAGGGCACTA
GFRA3-TTC8chr5137588975chr1489341369318PHPTFAVMAHQARALCACCCTACCTTTGCTGTGATGGCACACCAGGCAAGGGCACTATTA
GFRA3-TTC8chr5137588975chr1489341369419HPTFAVMAHQARALLCCTACCTTTGCTGTGATGGCACACCAGGCAAGGGCACTATTACAA

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Information of the samples that have these potential fusion neoantigens of GFRA3-TTC8

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
PCPGGFRA3-TTC8chr5137588975ENST00000274721chr1489341369ENST00000338104TCGA-TT-A6YN
PCPGGFRA3-TTC8chr5137593328ENST00000274721chr1489343638ENST00000354441TCGA-TT-A6YN-01A

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Potential target of CAR-T therapy development for GFRA3-TTC8

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 GFRA3-TTC8

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 GFRA3-TTC8

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