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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:BCAS3-GRIK2

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: BCAS3-GRIK2
FusionPDB ID: 9211
FusionGDB2.0 ID: 9211
HgeneTgene
Gene symbol

BCAS3

GRIK2

Gene ID

54828

2901

Gene nameBCAS3 microtubule associated cell migration factorglutamate ionotropic receptor kainate type subunit 5
SynonymsGAOB1|MAABEAA2|GRIK2|GluK5|KA2
Cytomap

17q23.2

19q13.2

Type of geneprotein-codingprotein-coding
Descriptionbreast carcinoma-amplified sequence 3BCAS4/BCAS3 fusionRudhirabreast carcinoma amplified sequence 4/3 fusion proteinmetastasis associated antigen of breast cancerprotein Maab1glutamate receptor ionotropic, kainate 5excitatory amino acid receptor 2glutamate receptor KA2
Modification date2020031320200313
UniProtAcc

Q9H6U6

Main function of 5'-partner protein: FUNCTION: Plays a role in angiogenesis. Participates in the regulation of cell polarity and directional endothelial cell migration by mediating both the activation and recruitment of CDC42 and the reorganization of the actin cytoskeleton at the cell leading edge. Promotes filipodia formation (By similarity). Functions synergistically with PELP1 as a transcriptional coactivator of estrogen receptor-responsive genes. Stimulates histone acetyltransferase activity. Binds to chromatin. {ECO:0000250|UniProtKB:Q8CCN5, ECO:0000269|PubMed:17505058}.

Q13002

Main function of 5'-partner protein: FUNCTION: Ionotropic glutamate receptor. L-glutamate acts as an excitatory neurotransmitter at many synapses in the central nervous system. Binding of the excitatory neurotransmitter L-glutamate induces a conformation change, leading to the opening of the cation channel, and thereby converts the chemical signal to an electrical impulse. The receptor then desensitizes rapidly and enters a transient inactive state, characterized by the presence of bound agonist (PubMed:28180184). Modulates cell surface expression of NETO2 (By similarity). {ECO:0000250|UniProtKB:P39087, ECO:0000269|PubMed:28180184}.; FUNCTION: Independent of its ionotropic glutamate receptor activity, acts as a thermoreceptor conferring sensitivity to cold temperatures (PubMed:31474366). Functions in dorsal root ganglion neurons (By similarity). {ECO:0000250|UniProtKB:P39087, ECO:0000269|PubMed:31474366}.
Ensembl transtripts involved in fusion geneENST idsENST00000390652, ENST00000407086, 
ENST00000408905, ENST00000585744, 
ENST00000588462, ENST00000588874, 
ENST00000589222, ENST00000585812, 
ENST00000369134, ENST00000318991, 
ENST00000358361, ENST00000369137, 
ENST00000369138, ENST00000413795, 
ENST00000421544, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score53 X 35 X 17=3153513 X 18 X 5=1170
# samples 6117
** MAII scorelog2(61/31535*10)=-5.69200088030826
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(17/1170*10)=-2.78290187833307
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Fusion gene context

PubMed: BCAS3 [Title/Abstract] AND GRIK2 [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: BCAS3 [Title/Abstract] AND GRIK2 [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)BCAS3(59001861)-GRIK2(102069824), # samples:1
Anticipated loss of major functional domain due to fusion event.BCAS3-GRIK2 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.
BCAS3-GRIK2 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
HgeneBCAS3

GO:0043085

positive regulation of catalytic activity

17505058

HgeneBCAS3

GO:0045944

positive regulation of transcription by RNA polymerase II

17505058

HgeneBCAS3

GO:0071391

cellular response to estrogen stimulus

17505058



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/chr17:59001861/chr6:102069824)
- 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 BCAS3 (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 GRIK2 (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)
ENST00000589222BCAS3chr1759001861-ENST00000413795GRIK2chr6102069824+542611556836491193
ENST00000589222BCAS3chr1759001861-ENST00000369138GRIK2chr6102069824+547111556837181216
ENST00000589222BCAS3chr1759001861-ENST00000421544GRIK2chr6102069824+533911556837661232
ENST00000589222BCAS3chr1759001861-ENST00000358361GRIK2chr6102069824+25361155682101677
ENST00000589222BCAS3chr1759001861-ENST00000318991GRIK2chr6102069824+365011556836491194
ENST00000589222BCAS3chr1759001861-ENST00000369137GRIK2chr6102069824+353911556835381157
ENST00000407086BCAS3chr1759001861-ENST00000413795GRIK2chr6102069824+540611354836291193
ENST00000407086BCAS3chr1759001861-ENST00000369138GRIK2chr6102069824+545111354836981216
ENST00000407086BCAS3chr1759001861-ENST00000421544GRIK2chr6102069824+531911354837461232
ENST00000407086BCAS3chr1759001861-ENST00000358361GRIK2chr6102069824+25161135482081677
ENST00000407086BCAS3chr1759001861-ENST00000318991GRIK2chr6102069824+363011354836291193
ENST00000407086BCAS3chr1759001861-ENST00000369137GRIK2chr6102069824+351911354835181156
ENST00000390652BCAS3chr1759001861-ENST00000413795GRIK2chr6102069824+538911183136121193
ENST00000390652BCAS3chr1759001861-ENST00000369138GRIK2chr6102069824+543411183136811216
ENST00000390652BCAS3chr1759001861-ENST00000421544GRIK2chr6102069824+530211183137291232
ENST00000390652BCAS3chr1759001861-ENST00000358361GRIK2chr6102069824+24991118312064677
ENST00000390652BCAS3chr1759001861-ENST00000318991GRIK2chr6102069824+361311183136121194
ENST00000390652BCAS3chr1759001861-ENST00000369137GRIK2chr6102069824+350211183135011157
ENST00000408905BCAS3chr1759001861-ENST00000413795GRIK2chr6102069824+53581087035811193
ENST00000408905BCAS3chr1759001861-ENST00000369138GRIK2chr6102069824+54031087036501216
ENST00000408905BCAS3chr1759001861-ENST00000421544GRIK2chr6102069824+52711087036981232
ENST00000408905BCAS3chr1759001861-ENST00000358361GRIK2chr6102069824+2468108702033677
ENST00000408905BCAS3chr1759001861-ENST00000318991GRIK2chr6102069824+35821087035811193
ENST00000408905BCAS3chr1759001861-ENST00000369137GRIK2chr6102069824+34711087034701156
ENST00000588462BCAS3chr1759001861-ENST00000413795GRIK2chr6102069824+53581087035811193
ENST00000588462BCAS3chr1759001861-ENST00000369138GRIK2chr6102069824+54031087036501216
ENST00000588462BCAS3chr1759001861-ENST00000421544GRIK2chr6102069824+52711087036981232
ENST00000588462BCAS3chr1759001861-ENST00000358361GRIK2chr6102069824+2468108702033677
ENST00000588462BCAS3chr1759001861-ENST00000318991GRIK2chr6102069824+35821087035811193
ENST00000588462BCAS3chr1759001861-ENST00000369137GRIK2chr6102069824+34711087034701156
ENST00000585744BCAS3chr1759001861-ENST00000413795GRIK2chr6102069824+4774503132997994
ENST00000585744BCAS3chr1759001861-ENST00000369138GRIK2chr6102069824+48195031330661017
ENST00000585744BCAS3chr1759001861-ENST00000421544GRIK2chr6102069824+46875031331141033
ENST00000585744BCAS3chr1759001861-ENST00000358361GRIK2chr6102069824+1884503131449478
ENST00000585744BCAS3chr1759001861-ENST00000318991GRIK2chr6102069824+2998503132997995
ENST00000585744BCAS3chr1759001861-ENST00000369137GRIK2chr6102069824+2887503132886958
ENST00000588874BCAS3chr1759001861-ENST00000413795GRIK2chr6102069824+48595881883082964
ENST00000588874BCAS3chr1759001861-ENST00000369138GRIK2chr6102069824+49045881883151987
ENST00000588874BCAS3chr1759001861-ENST00000421544GRIK2chr6102069824+477258818831991003
ENST00000588874BCAS3chr1759001861-ENST00000358361GRIK2chr6102069824+19695881881534448
ENST00000588874BCAS3chr1759001861-ENST00000318991GRIK2chr6102069824+30835881883082965
ENST00000588874BCAS3chr1759001861-ENST00000369137GRIK2chr6102069824+29725881882971928

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
ENST00000589222ENST00000413795BCAS3chr1759001861-GRIK2chr6102069824+8.18E-050.9999181
ENST00000589222ENST00000369138BCAS3chr1759001861-GRIK2chr6102069824+0.0001210810.9998789
ENST00000589222ENST00000421544BCAS3chr1759001861-GRIK2chr6102069824+0.000118660.99988127
ENST00000589222ENST00000358361BCAS3chr1759001861-GRIK2chr6102069824+0.0003332290.9996668
ENST00000589222ENST00000318991BCAS3chr1759001861-GRIK2chr6102069824+0.0001588070.9998412
ENST00000589222ENST00000369137BCAS3chr1759001861-GRIK2chr6102069824+0.0001199570.9998801
ENST00000407086ENST00000413795BCAS3chr1759001861-GRIK2chr6102069824+8.02E-050.9999198
ENST00000407086ENST00000369138BCAS3chr1759001861-GRIK2chr6102069824+0.0001186610.99988127
ENST00000407086ENST00000421544BCAS3chr1759001861-GRIK2chr6102069824+0.0001162070.9998838
ENST00000407086ENST00000358361BCAS3chr1759001861-GRIK2chr6102069824+0.0003336470.99966633
ENST00000407086ENST00000318991BCAS3chr1759001861-GRIK2chr6102069824+0.0001575450.9998424
ENST00000407086ENST00000369137BCAS3chr1759001861-GRIK2chr6102069824+0.0001192120.9998808
ENST00000390652ENST00000413795BCAS3chr1759001861-GRIK2chr6102069824+7.80E-050.99992204
ENST00000390652ENST00000369138BCAS3chr1759001861-GRIK2chr6102069824+0.0001153140.9998847
ENST00000390652ENST00000421544BCAS3chr1759001861-GRIK2chr6102069824+0.0001130240.999887
ENST00000390652ENST00000358361BCAS3chr1759001861-GRIK2chr6102069824+0.0003296140.9996704
ENST00000390652ENST00000318991BCAS3chr1759001861-GRIK2chr6102069824+0.0001554830.99984455
ENST00000390652ENST00000369137BCAS3chr1759001861-GRIK2chr6102069824+0.0001173080.9998827
ENST00000408905ENST00000413795BCAS3chr1759001861-GRIK2chr6102069824+7.58E-050.9999242
ENST00000408905ENST00000369138BCAS3chr1759001861-GRIK2chr6102069824+0.0001124520.9998876
ENST00000408905ENST00000421544BCAS3chr1759001861-GRIK2chr6102069824+0.0001099970.99988997
ENST00000408905ENST00000358361BCAS3chr1759001861-GRIK2chr6102069824+0.0003375570.9996624
ENST00000408905ENST00000318991BCAS3chr1759001861-GRIK2chr6102069824+0.0001533070.9998467
ENST00000408905ENST00000369137BCAS3chr1759001861-GRIK2chr6102069824+0.0001162660.9998838
ENST00000588462ENST00000413795BCAS3chr1759001861-GRIK2chr6102069824+7.58E-050.9999242
ENST00000588462ENST00000369138BCAS3chr1759001861-GRIK2chr6102069824+0.0001124520.9998876
ENST00000588462ENST00000421544BCAS3chr1759001861-GRIK2chr6102069824+0.0001099970.99988997
ENST00000588462ENST00000358361BCAS3chr1759001861-GRIK2chr6102069824+0.0003375570.9996624
ENST00000588462ENST00000318991BCAS3chr1759001861-GRIK2chr6102069824+0.0001533070.9998467
ENST00000588462ENST00000369137BCAS3chr1759001861-GRIK2chr6102069824+0.0001162660.9998838
ENST00000585744ENST00000413795BCAS3chr1759001861-GRIK2chr6102069824+0.0002451720.99975485
ENST00000585744ENST00000369138BCAS3chr1759001861-GRIK2chr6102069824+0.0002495250.99975044
ENST00000585744ENST00000421544BCAS3chr1759001861-GRIK2chr6102069824+0.0001495240.9998505
ENST00000585744ENST00000358361BCAS3chr1759001861-GRIK2chr6102069824+0.0017402710.9982597
ENST00000585744ENST00000318991BCAS3chr1759001861-GRIK2chr6102069824+0.000596640.99940336
ENST00000585744ENST00000369137BCAS3chr1759001861-GRIK2chr6102069824+0.000883640.99911636
ENST00000588874ENST00000413795BCAS3chr1759001861-GRIK2chr6102069824+0.0002241120.99977595
ENST00000588874ENST00000369138BCAS3chr1759001861-GRIK2chr6102069824+0.0002451980.99975485
ENST00000588874ENST00000421544BCAS3chr1759001861-GRIK2chr6102069824+0.0001484610.99985147
ENST00000588874ENST00000358361BCAS3chr1759001861-GRIK2chr6102069824+0.0014843540.99851567
ENST00000588874ENST00000318991BCAS3chr1759001861-GRIK2chr6102069824+0.0004776880.9995223
ENST00000588874ENST00000369137BCAS3chr1759001861-GRIK2chr6102069824+0.0007106540.9992893

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 BCAS3-GRIK2

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide
BCAS3chr1759001861GRIK2chr61020698241087362HEKPVCCMAFNTSGGIFEYVESGPMG
BCAS3chr1759001861GRIK2chr61020698241118362HEKPVCCMAFNTSGGIFEYVESGPMG
BCAS3chr1759001861GRIK2chr61020698241135362HEKPVCCMAFNTSGGIFEYVESGPMG
BCAS3chr1759001861GRIK2chr61020698241155362HEKPVCCMAFNTSGGIFEYVESGPMG
BCAS3chr1759001861GRIK2chr6102069824588133HEKPVCCMAFNTSGGIFEYVESGPMG

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Potential FusionNeoAntigen Information of BCAS3-GRIK2 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.
BCAS3-GRIK2_59001861_102069824.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)
BCAS3-GRIK2chr1759001861chr61020698241118HLA-B35:08NTSGGIFEY0.98780.88331019
BCAS3-GRIK2chr1759001861chr61020698241118HLA-B15:02NTSGGIFEY0.97440.93231019
BCAS3-GRIK2chr1759001861chr61020698241118HLA-B35:01NTSGGIFEY0.97050.89331019
BCAS3-GRIK2chr1759001861chr61020698241118HLA-A32:13NTSGGIFEY0.13390.84681019
BCAS3-GRIK2chr1759001861chr61020698241118HLA-B15:21NTSGGIFEY0.97440.93251019
BCAS3-GRIK2chr1759001861chr61020698241118HLA-B15:31NTSGGIFEY0.95930.861019
BCAS3-GRIK2chr1759001861chr61020698241118HLA-C15:04NTSGGIFEY0.60940.96291019
BCAS3-GRIK2chr1759001861chr61020698241118HLA-C07:95NTSGGIFEY0.51020.68671019
BCAS3-GRIK2chr1759001861chr61020698241118HLA-C03:14NTSGGIFEY0.21130.97951019
BCAS3-GRIK2chr1759001861chr61020698241118HLA-C12:04NTSGGIFEY0.03440.99551019
BCAS3-GRIK2chr1759001861chr61020698241118HLA-C06:03NTSGGIFEY0.02830.99451019
BCAS3-GRIK2chr1759001861chr61020698241118HLA-C12:12NTSGGIFEY0.01050.88911019
BCAS3-GRIK2chr1759001861chr61020698241118HLA-A68:02TSGGIFEYV0.99160.64511120
BCAS3-GRIK2chr1759001861chr61020698241118HLA-B15:20NTSGGIFEY0.98580.9111019
BCAS3-GRIK2chr1759001861chr61020698241118HLA-A69:01TSGGIFEYV0.98440.82731120
BCAS3-GRIK2chr1759001861chr61020698241118HLA-B35:28NTSGGIFEY0.97520.91621019
BCAS3-GRIK2chr1759001861chr61020698241118HLA-B35:11NTSGGIFEY0.9730.92331019
BCAS3-GRIK2chr1759001861chr61020698241118HLA-B35:23NTSGGIFEY0.97210.9281019
BCAS3-GRIK2chr1759001861chr61020698241118HLA-B35:77NTSGGIFEY0.97050.89331019
BCAS3-GRIK2chr1759001861chr61020698241118HLA-B35:20NTSGGIFEY0.96570.9091019
BCAS3-GRIK2chr1759001861chr61020698241118HLA-A25:01NTSGGIFEY0.89690.83271019
BCAS3-GRIK2chr1759001861chr61020698241118HLA-B15:11NTSGGIFEY0.88090.85291019
BCAS3-GRIK2chr1759001861chr61020698241118HLA-B15:08NTSGGIFEY0.88060.87711019
BCAS3-GRIK2chr1759001861chr61020698241118HLA-B35:43NTSGGIFEY0.84160.87731019
BCAS3-GRIK2chr1759001861chr61020698241118HLA-C03:02NTSGGIFEY0.76610.9531019
BCAS3-GRIK2chr1759001861chr61020698241118HLA-B35:24NTSGGIFEY0.7350.93761019
BCAS3-GRIK2chr1759001861chr61020698241118HLA-C07:22NTSGGIFEY0.71340.70521019
BCAS3-GRIK2chr1759001861chr61020698241118HLA-C15:09NTSGGIFEY0.60940.96291019
BCAS3-GRIK2chr1759001861chr61020698241118HLA-C07:01NTSGGIFEY0.51440.68121019
BCAS3-GRIK2chr1759001861chr61020698241118HLA-B18:04NTSGGIFEY0.30850.88651019
BCAS3-GRIK2chr1759001861chr61020698241118HLA-C16:04NTSGGIFEY0.24780.97261019
BCAS3-GRIK2chr1759001861chr61020698241118HLA-C16:01NTSGGIFEY0.2160.96561019
BCAS3-GRIK2chr1759001861chr61020698241118HLA-C12:02NTSGGIFEY0.18050.96681019
BCAS3-GRIK2chr1759001861chr61020698241118HLA-B18:07NTSGGIFEY0.12270.85971019
BCAS3-GRIK2chr1759001861chr61020698241118HLA-C14:03AFNTSGGIF0.07870.9753817
BCAS3-GRIK2chr1759001861chr61020698241118HLA-C14:02AFNTSGGIF0.07870.9753817
BCAS3-GRIK2chr1759001861chr61020698241118HLA-C16:02NTSGGIFEY0.05940.99081019
BCAS3-GRIK2chr1759001861chr61020698241118HLA-C12:03NTSGGIFEY0.02890.97681019
BCAS3-GRIK2chr1759001861chr61020698241118HLA-C02:10NTSGGIFEY0.00120.97911019
BCAS3-GRIK2chr1759001861chr61020698241118HLA-C02:02NTSGGIFEY0.00120.97911019
BCAS3-GRIK2chr1759001861chr61020698241118HLA-A68:02NTSGGIFEYV0.99840.60421020
BCAS3-GRIK2chr1759001861chr61020698241118HLA-A69:01NTSGGIFEYV0.99690.75641020
BCAS3-GRIK2chr1759001861chr61020698241118HLA-C02:10FNTSGGIFEY0.43810.9857919
BCAS3-GRIK2chr1759001861chr61020698241118HLA-C02:02FNTSGGIFEY0.43810.9857919
BCAS3-GRIK2chr1759001861chr61020698241118HLA-A25:01FNTSGGIFEY0.38410.9504919

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Potential FusionNeoAntigen Information of BCAS3-GRIK2 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.
BCAS3-GRIK2_59001861_102069824.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)
BCAS3-GRIK2chr1759001861chr61020698241118DRB1-0701TSGGIFEYVESGPMG1126
BCAS3-GRIK2chr1759001861chr61020698241118DRB1-0703TSGGIFEYVESGPMG1126
BCAS3-GRIK2chr1759001861chr61020698241118DRB1-0705TSGGIFEYVESGPMG1126
BCAS3-GRIK2chr1759001861chr61020698241118DRB1-0706TSGGIFEYVESGPMG1126
BCAS3-GRIK2chr1759001861chr61020698241118DRB1-0707TSGGIFEYVESGPMG1126
BCAS3-GRIK2chr1759001861chr61020698241118DRB1-0708TSGGIFEYVESGPMG1126
BCAS3-GRIK2chr1759001861chr61020698241118DRB1-0709TSGGIFEYVESGPMG1126
BCAS3-GRIK2chr1759001861chr61020698241118DRB1-0711TSGGIFEYVESGPMG1126
BCAS3-GRIK2chr1759001861chr61020698241118DRB1-0712TSGGIFEYVESGPMG1126
BCAS3-GRIK2chr1759001861chr61020698241118DRB1-0713TSGGIFEYVESGPMG1126
BCAS3-GRIK2chr1759001861chr61020698241118DRB1-0714TSGGIFEYVESGPMG1126
BCAS3-GRIK2chr1759001861chr61020698241118DRB1-0715TSGGIFEYVESGPMG1126
BCAS3-GRIK2chr1759001861chr61020698241118DRB1-0716TSGGIFEYVESGPMG1126
BCAS3-GRIK2chr1759001861chr61020698241118DRB1-0717TSGGIFEYVESGPMG1126
BCAS3-GRIK2chr1759001861chr61020698241118DRB1-0719TSGGIFEYVESGPMG1126
BCAS3-GRIK2chr1759001861chr61020698241118DRB1-0901TSGGIFEYVESGPMG1126
BCAS3-GRIK2chr1759001861chr61020698241118DRB1-0903TSGGIFEYVESGPMG1126
BCAS3-GRIK2chr1759001861chr61020698241118DRB1-0904TSGGIFEYVESGPMG1126
BCAS3-GRIK2chr1759001861chr61020698241118DRB1-0905TSGGIFEYVESGPMG1126
BCAS3-GRIK2chr1759001861chr61020698241118DRB1-0907TSGGIFEYVESGPMG1126
BCAS3-GRIK2chr1759001861chr61020698241118DRB1-0909TSGGIFEYVESGPMG1126

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Fusion breakpoint peptide structures of BCAS3-GRIK2

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
880CMAFNTSGGIFEYVBCAS3GRIK2chr1759001861chr61020698241118

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of BCAS3-GRIK2

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-B14:023BVN880CMAFNTSGGIFEYV-7.15543-7.26883
HLA-B14:023BVN880CMAFNTSGGIFEYV-4.77435-5.80965
HLA-B52:013W39880CMAFNTSGGIFEYV-6.80875-6.92215
HLA-B52:013W39880CMAFNTSGGIFEYV-4.20386-5.23916
HLA-A11:014UQ2880CMAFNTSGGIFEYV-7.5194-8.5547
HLA-A11:014UQ2880CMAFNTSGGIFEYV-6.9601-7.0735
HLA-A24:025HGA880CMAFNTSGGIFEYV-7.52403-7.63743
HLA-A24:025HGA880CMAFNTSGGIFEYV-5.82433-6.85963
HLA-B27:056PYJ880CMAFNTSGGIFEYV-3.28285-4.31815
HLA-B44:053DX8880CMAFNTSGGIFEYV-5.91172-6.94702
HLA-B44:053DX8880CMAFNTSGGIFEYV-4.24346-4.35686

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Vaccine Design for the FusionNeoAntigens of BCAS3-GRIK2

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
BCAS3-GRIK2chr1759001861chr61020698241019NTSGGIFEYATACAAGTGGTGGTATTTTTGAATATG
BCAS3-GRIK2chr1759001861chr61020698241020NTSGGIFEYVATACAAGTGGTGGTATTTTTGAATATGTGG
BCAS3-GRIK2chr1759001861chr61020698241120TSGGIFEYVCAAGTGGTGGTATTTTTGAATATGTGG
BCAS3-GRIK2chr1759001861chr6102069824817AFNTSGGIFCTTTTAATACAAGTGGTGGTATTTTTG
BCAS3-GRIK2chr1759001861chr6102069824919FNTSGGIFEYTTAATACAAGTGGTGGTATTTTTGAATATG

check button mRNA and peptide sequences of FusionNeoAntigens that have potential interaction with HLA-IIs.
Fusion geneHchrHbpTchrTbpStart in +/-13AAEnd in +/-13AAFusionNeoAntigen peptideFusionNEoAntigen RNA sequence
BCAS3-GRIK2chr1759001861chr61020698241126TSGGIFEYVESGPMGCAAGTGGTGGTATTTTTGAATATGTGGAATCTGGCCCAATGGGAG

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Information of the samples that have these potential fusion neoantigens of BCAS3-GRIK2

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
BRCABCAS3-GRIK2chr1759001861ENST00000390652chr6102069824ENST00000318991TCGA-AN-A0XW-01A

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Potential target of CAR-T therapy development for BCAS3-GRIK2

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
TgeneGRIK2chr17:59001861chr6:102069824ENST00000318991016562_5820870.0TransmembraneHelical
TgeneGRIK2chr17:59001861chr6:102069824ENST00000318991016636_6560870.0TransmembraneHelical
TgeneGRIK2chr17:59001861chr6:102069824ENST00000318991016820_8400870.0TransmembraneHelical
TgeneGRIK2chr17:59001861chr6:102069824ENST00000369137015562_5820833.0TransmembraneHelical
TgeneGRIK2chr17:59001861chr6:102069824ENST00000369137015636_6560833.0TransmembraneHelical
TgeneGRIK2chr17:59001861chr6:102069824ENST00000369137015820_8400833.0TransmembraneHelical
TgeneGRIK2chr17:59001861chr6:102069824ENST00000369138017562_58201270.3333333333333TransmembraneHelical
TgeneGRIK2chr17:59001861chr6:102069824ENST00000369138017636_65601270.3333333333333TransmembraneHelical
TgeneGRIK2chr17:59001861chr6:102069824ENST00000369138017820_84001270.3333333333333TransmembraneHelical
TgeneGRIK2chr17:59001861chr6:102069824ENST00000413795017562_58201247.3333333333333TransmembraneHelical
TgeneGRIK2chr17:59001861chr6:102069824ENST00000413795017636_65601247.3333333333333TransmembraneHelical
TgeneGRIK2chr17:59001861chr6:102069824ENST00000413795017820_84001247.3333333333333TransmembraneHelical
TgeneGRIK2chr17:59001861chr6:102069824ENST00000421544016562_5820909.0TransmembraneHelical
TgeneGRIK2chr17:59001861chr6:102069824ENST00000421544016636_6560909.0TransmembraneHelical
TgeneGRIK2chr17:59001861chr6:102069824ENST00000421544016820_8400909.0TransmembraneHelical

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

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Related Drugs to BCAS3-GRIK2

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 BCAS3-GRIK2

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