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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:KCNK5-RUNX2

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: KCNK5-RUNX2
FusionPDB ID: 41475
FusionGDB2.0 ID: 41475
HgeneTgene
Gene symbol

KCNK5

RUNX2

Gene ID

8645

860

Gene namepotassium two pore domain channel subfamily K member 5RUNX family transcription factor 2
SynonymsK2p5.1|KCNK5b|TASK-2|TASK2AML3|CBF-alpha-1|CBFA1|CCD|CCD1|CLCD|OSF-2|OSF2|PEA2aA|PEBP2aA
Cytomap

6p21.2

6p21.1

Type of geneprotein-codingprotein-coding
Descriptionpotassium channel subfamily K member 5K2P5.1 potassium channelTWIK-related acid-sensitive K(+) channel 2TWIK-related acid-sensitive K+ 2TWIK-related acid-sensitive K+ channel 2acid-sensitive potassium channel protein TASK-2potassium channel, subfamirunt-related transcription factor 2PEA2-alpha APEBP2-alpha ASL3-3 enhancer factor 1 alpha A subunitSL3/AKV core-binding factor alpha A subunitacute myeloid leukemia 3 proteincore-binding factor, runt domain, alpha subunit 1oncogene AML-3osteoblast
Modification date2020031320200322
UniProtAcc

O95279

Main function of 5'-partner protein: FUNCTION: pH-dependent, voltage insensitive, outwardly rectifying potassium channel. Outward rectification is lost at high external K(+) concentrations.
.
Ensembl transtripts involved in fusion geneENST idsENST00000359534, ENST00000483243, 
ENST00000352853, ENST00000359524, 
ENST00000371432, ENST00000371436, 
ENST00000371438, ENST00000465038, 
ENST00000541979, ENST00000576263, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score3 X 2 X 3=186 X 6 X 4=144
# samples 36
** MAII scorelog2(3/18*10)=0.736965594166206
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
log2(6/144*10)=-1.26303440583379
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Fusion gene context

PubMed: KCNK5 [Title/Abstract] AND RUNX2 [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: KCNK5 [Title/Abstract] AND RUNX2 [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)KCNK5(39161945)-RUNX2(45479983), # samples:2
Anticipated loss of major functional domain due to fusion event.KCNK5-RUNX2 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.
KCNK5-RUNX2 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.
KCNK5-RUNX2 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.
KCNK5-RUNX2 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
TgeneRUNX2

GO:0045892

negative regulation of transcription, DNA-templated

11965546

TgeneRUNX2

GO:0045893

positive regulation of transcription, DNA-templated

11965546



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/chr6:39161945/chr6:45479983)
- 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 KCNK5 (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 RUNX2 (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)
ENST00000359534KCNK5chr639161945-ENST00000541979RUNX2chr645479983+16149733391613424
ENST00000359534KCNK5chr639161945-ENST00000465038RUNX2chr645479983+16809733391679446
ENST00000359534KCNK5chr639161945-ENST00000352853RUNX2chr645479983+16809733391679446
ENST00000359534KCNK5chr639161945-ENST00000371438RUNX2chr645479983+54549733391679446
ENST00000359534KCNK5chr639161945-ENST00000371436RUNX2chr645479983+17029733391613424
ENST00000359534KCNK5chr639161945-ENST00000576263RUNX2chr645479983+23709733391742467
ENST00000359534KCNK5chr639161945-ENST00000371432RUNX2chr645479983+53909733391613424
ENST00000359534KCNK5chr639161945-ENST00000359524RUNX2chr645479983+54549733391679446

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
ENST00000359534ENST00000541979KCNK5chr639161945-RUNX2chr645479983+0.0103934240.98960656
ENST00000359534ENST00000465038KCNK5chr639161945-RUNX2chr645479983+0.0141934730.9858065
ENST00000359534ENST00000352853KCNK5chr639161945-RUNX2chr645479983+0.0141934730.9858065
ENST00000359534ENST00000371438KCNK5chr639161945-RUNX2chr645479983+0.0013272290.99867284
ENST00000359534ENST00000371436KCNK5chr639161945-RUNX2chr645479983+0.0085853830.9914146
ENST00000359534ENST00000576263KCNK5chr639161945-RUNX2chr645479983+0.017080890.9829191
ENST00000359534ENST00000371432KCNK5chr639161945-RUNX2chr645479983+0.0009097080.9990903
ENST00000359534ENST00000359524KCNK5chr639161945-RUNX2chr645479983+0.0013272290.99867284

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 KCNK5-RUNX2

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide
KCNK5chr639161945RUNX2chr645479983973211ITISTIGFGDFVADPRQAQSSPPWSY

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Potential FusionNeoAntigen Information of KCNK5-RUNX2 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.
KCNK5-RUNX2_39161945_45479983.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)
KCNK5-RUNX2chr639161945chr645479983973HLA-A66:01FVADPRQAQ0.74020.63911019
KCNK5-RUNX2chr639161945chr645479983973HLA-A34:05FVADPRQAQ0.6120.52311019
KCNK5-RUNX2chr639161945chr645479983973HLA-A34:01FVADPRQAQ0.6120.52311019
KCNK5-RUNX2chr639161945chr645479983973HLA-A26:03FVADPRQAQ0.56320.63771019
KCNK5-RUNX2chr639161945chr645479983973HLA-A66:03FVADPRQAQ0.43870.56131019
KCNK5-RUNX2chr639161945chr645479983973HLA-A66:02FVADPRQAQ0.49920.55871019

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Potential FusionNeoAntigen Information of KCNK5-RUNX2 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.
KCNK5-RUNX2_39161945_45479983.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)
KCNK5-RUNX2chr639161945chr645479983973DRB1-0301FGDFVADPRQAQSSP722
KCNK5-RUNX2chr639161945chr645479983973DRB1-0301GFGDFVADPRQAQSS621
KCNK5-RUNX2chr639161945chr645479983973DRB1-0301GDFVADPRQAQSSPP823
KCNK5-RUNX2chr639161945chr645479983973DRB1-0301IGFGDFVADPRQAQS520
KCNK5-RUNX2chr639161945chr645479983973DRB1-0303FGDFVADPRQAQSSP722
KCNK5-RUNX2chr639161945chr645479983973DRB1-0303GFGDFVADPRQAQSS621
KCNK5-RUNX2chr639161945chr645479983973DRB1-0303GDFVADPRQAQSSPP823
KCNK5-RUNX2chr639161945chr645479983973DRB1-0303IGFGDFVADPRQAQS520
KCNK5-RUNX2chr639161945chr645479983973DRB1-0305FGDFVADPRQAQSSP722
KCNK5-RUNX2chr639161945chr645479983973DRB1-0305GFGDFVADPRQAQSS621
KCNK5-RUNX2chr639161945chr645479983973DRB1-0305GDFVADPRQAQSSPP823
KCNK5-RUNX2chr639161945chr645479983973DRB1-0305IGFGDFVADPRQAQS520
KCNK5-RUNX2chr639161945chr645479983973DRB1-0305TIGFGDFVADPRQAQ419
KCNK5-RUNX2chr639161945chr645479983973DRB1-0305DFVADPRQAQSSPPW924
KCNK5-RUNX2chr639161945chr645479983973DRB1-0307FGDFVADPRQAQSSP722
KCNK5-RUNX2chr639161945chr645479983973DRB1-0307GFGDFVADPRQAQSS621
KCNK5-RUNX2chr639161945chr645479983973DRB1-0307GDFVADPRQAQSSPP823
KCNK5-RUNX2chr639161945chr645479983973DRB1-0307IGFGDFVADPRQAQS520
KCNK5-RUNX2chr639161945chr645479983973DRB1-0310FGDFVADPRQAQSSP722
KCNK5-RUNX2chr639161945chr645479983973DRB1-0310GFGDFVADPRQAQSS621
KCNK5-RUNX2chr639161945chr645479983973DRB1-0310GDFVADPRQAQSSPP823
KCNK5-RUNX2chr639161945chr645479983973DRB1-0310IGFGDFVADPRQAQS520
KCNK5-RUNX2chr639161945chr645479983973DRB1-0313FGDFVADPRQAQSSP722
KCNK5-RUNX2chr639161945chr645479983973DRB1-0313GFGDFVADPRQAQSS621
KCNK5-RUNX2chr639161945chr645479983973DRB1-0313GDFVADPRQAQSSPP823
KCNK5-RUNX2chr639161945chr645479983973DRB1-0313IGFGDFVADPRQAQS520
KCNK5-RUNX2chr639161945chr645479983973DRB1-0315FGDFVADPRQAQSSP722
KCNK5-RUNX2chr639161945chr645479983973DRB1-0315GFGDFVADPRQAQSS621
KCNK5-RUNX2chr639161945chr645479983973DRB1-0315GDFVADPRQAQSSPP823
KCNK5-RUNX2chr639161945chr645479983973DRB1-0315IGFGDFVADPRQAQS520
KCNK5-RUNX2chr639161945chr645479983973DRB1-0318FGDFVADPRQAQSSP722
KCNK5-RUNX2chr639161945chr645479983973DRB1-0318GFGDFVADPRQAQSS621
KCNK5-RUNX2chr639161945chr645479983973DRB1-0318GDFVADPRQAQSSPP823
KCNK5-RUNX2chr639161945chr645479983973DRB1-0318IGFGDFVADPRQAQS520
KCNK5-RUNX2chr639161945chr645479983973DRB1-0320FGDFVADPRQAQSSP722
KCNK5-RUNX2chr639161945chr645479983973DRB1-0320GFGDFVADPRQAQSS621
KCNK5-RUNX2chr639161945chr645479983973DRB1-0320GDFVADPRQAQSSPP823
KCNK5-RUNX2chr639161945chr645479983973DRB1-0320IGFGDFVADPRQAQS520
KCNK5-RUNX2chr639161945chr645479983973DRB1-0322FGDFVADPRQAQSSP722
KCNK5-RUNX2chr639161945chr645479983973DRB1-0322GFGDFVADPRQAQSS621
KCNK5-RUNX2chr639161945chr645479983973DRB1-0322GDFVADPRQAQSSPP823
KCNK5-RUNX2chr639161945chr645479983973DRB1-0322IGFGDFVADPRQAQS520
KCNK5-RUNX2chr639161945chr645479983973DRB1-0324FGDFVADPRQAQSSP722
KCNK5-RUNX2chr639161945chr645479983973DRB1-0324GFGDFVADPRQAQSS621
KCNK5-RUNX2chr639161945chr645479983973DRB1-0324GDFVADPRQAQSSPP823
KCNK5-RUNX2chr639161945chr645479983973DRB1-0324IGFGDFVADPRQAQS520
KCNK5-RUNX2chr639161945chr645479983973DRB1-0326FGDFVADPRQAQSSP722
KCNK5-RUNX2chr639161945chr645479983973DRB1-0326GFGDFVADPRQAQSS621
KCNK5-RUNX2chr639161945chr645479983973DRB1-0326GDFVADPRQAQSSPP823
KCNK5-RUNX2chr639161945chr645479983973DRB1-0326IGFGDFVADPRQAQS520
KCNK5-RUNX2chr639161945chr645479983973DRB1-0328FGDFVADPRQAQSSP722
KCNK5-RUNX2chr639161945chr645479983973DRB1-0328GFGDFVADPRQAQSS621
KCNK5-RUNX2chr639161945chr645479983973DRB1-0328GDFVADPRQAQSSPP823
KCNK5-RUNX2chr639161945chr645479983973DRB1-0328IGFGDFVADPRQAQS520
KCNK5-RUNX2chr639161945chr645479983973DRB1-0330FGDFVADPRQAQSSP722
KCNK5-RUNX2chr639161945chr645479983973DRB1-0330GFGDFVADPRQAQSS621
KCNK5-RUNX2chr639161945chr645479983973DRB1-0330GDFVADPRQAQSSPP823
KCNK5-RUNX2chr639161945chr645479983973DRB1-0330IGFGDFVADPRQAQS520
KCNK5-RUNX2chr639161945chr645479983973DRB1-0332FGDFVADPRQAQSSP722
KCNK5-RUNX2chr639161945chr645479983973DRB1-0332GFGDFVADPRQAQSS621
KCNK5-RUNX2chr639161945chr645479983973DRB1-0332GDFVADPRQAQSSPP823
KCNK5-RUNX2chr639161945chr645479983973DRB1-0332IGFGDFVADPRQAQS520
KCNK5-RUNX2chr639161945chr645479983973DRB1-0334FGDFVADPRQAQSSP722
KCNK5-RUNX2chr639161945chr645479983973DRB1-0334GFGDFVADPRQAQSS621
KCNK5-RUNX2chr639161945chr645479983973DRB1-0334GDFVADPRQAQSSPP823
KCNK5-RUNX2chr639161945chr645479983973DRB1-0334IGFGDFVADPRQAQS520
KCNK5-RUNX2chr639161945chr645479983973DRB1-0336FGDFVADPRQAQSSP722
KCNK5-RUNX2chr639161945chr645479983973DRB1-0336GFGDFVADPRQAQSS621
KCNK5-RUNX2chr639161945chr645479983973DRB1-0336GDFVADPRQAQSSPP823
KCNK5-RUNX2chr639161945chr645479983973DRB1-0336IGFGDFVADPRQAQS520
KCNK5-RUNX2chr639161945chr645479983973DRB1-0338FGDFVADPRQAQSSP722
KCNK5-RUNX2chr639161945chr645479983973DRB1-0338GFGDFVADPRQAQSS621
KCNK5-RUNX2chr639161945chr645479983973DRB1-0338GDFVADPRQAQSSPP823
KCNK5-RUNX2chr639161945chr645479983973DRB1-0338IGFGDFVADPRQAQS520
KCNK5-RUNX2chr639161945chr645479983973DRB1-0340FGDFVADPRQAQSSP722
KCNK5-RUNX2chr639161945chr645479983973DRB1-0340GFGDFVADPRQAQSS621
KCNK5-RUNX2chr639161945chr645479983973DRB1-0340GDFVADPRQAQSSPP823
KCNK5-RUNX2chr639161945chr645479983973DRB1-0340IGFGDFVADPRQAQS520
KCNK5-RUNX2chr639161945chr645479983973DRB1-0340TIGFGDFVADPRQAQ419
KCNK5-RUNX2chr639161945chr645479983973DRB1-0340DFVADPRQAQSSPPW924
KCNK5-RUNX2chr639161945chr645479983973DRB1-0342FGDFVADPRQAQSSP722
KCNK5-RUNX2chr639161945chr645479983973DRB1-0342GFGDFVADPRQAQSS621
KCNK5-RUNX2chr639161945chr645479983973DRB1-0342GDFVADPRQAQSSPP823
KCNK5-RUNX2chr639161945chr645479983973DRB1-0342IGFGDFVADPRQAQS520
KCNK5-RUNX2chr639161945chr645479983973DRB1-0344FGDFVADPRQAQSSP722
KCNK5-RUNX2chr639161945chr645479983973DRB1-0344GFGDFVADPRQAQSS621
KCNK5-RUNX2chr639161945chr645479983973DRB1-0344GDFVADPRQAQSSPP823
KCNK5-RUNX2chr639161945chr645479983973DRB1-0344IGFGDFVADPRQAQS520
KCNK5-RUNX2chr639161945chr645479983973DRB1-0346FGDFVADPRQAQSSP722
KCNK5-RUNX2chr639161945chr645479983973DRB1-0346GFGDFVADPRQAQSS621
KCNK5-RUNX2chr639161945chr645479983973DRB1-0346GDFVADPRQAQSSPP823
KCNK5-RUNX2chr639161945chr645479983973DRB1-0346IGFGDFVADPRQAQS520
KCNK5-RUNX2chr639161945chr645479983973DRB1-0348FGDFVADPRQAQSSP722
KCNK5-RUNX2chr639161945chr645479983973DRB1-0348GFGDFVADPRQAQSS621
KCNK5-RUNX2chr639161945chr645479983973DRB1-0348GDFVADPRQAQSSPP823
KCNK5-RUNX2chr639161945chr645479983973DRB1-0348IGFGDFVADPRQAQS520
KCNK5-RUNX2chr639161945chr645479983973DRB1-0350FGDFVADPRQAQSSP722
KCNK5-RUNX2chr639161945chr645479983973DRB1-0350GFGDFVADPRQAQSS621
KCNK5-RUNX2chr639161945chr645479983973DRB1-0350GDFVADPRQAQSSPP823
KCNK5-RUNX2chr639161945chr645479983973DRB1-0350IGFGDFVADPRQAQS520
KCNK5-RUNX2chr639161945chr645479983973DRB1-0352FGDFVADPRQAQSSP722
KCNK5-RUNX2chr639161945chr645479983973DRB1-0352GFGDFVADPRQAQSS621
KCNK5-RUNX2chr639161945chr645479983973DRB1-0352GDFVADPRQAQSSPP823
KCNK5-RUNX2chr639161945chr645479983973DRB1-0352IGFGDFVADPRQAQS520
KCNK5-RUNX2chr639161945chr645479983973DRB1-0354FGDFVADPRQAQSSP722
KCNK5-RUNX2chr639161945chr645479983973DRB1-0354GFGDFVADPRQAQSS621
KCNK5-RUNX2chr639161945chr645479983973DRB1-0354GDFVADPRQAQSSPP823
KCNK5-RUNX2chr639161945chr645479983973DRB1-0354IGFGDFVADPRQAQS520
KCNK5-RUNX2chr639161945chr645479983973DRB1-0434FGDFVADPRQAQSSP722
KCNK5-RUNX2chr639161945chr645479983973DRB1-0466FGDFVADPRQAQSSP722
KCNK5-RUNX2chr639161945chr645479983973DRB1-0466GFGDFVADPRQAQSS621
KCNK5-RUNX2chr639161945chr645479983973DRB1-0466GDFVADPRQAQSSPP823
KCNK5-RUNX2chr639161945chr645479983973DRB1-0466IGFGDFVADPRQAQS520
KCNK5-RUNX2chr639161945chr645479983973DRB1-0466DFVADPRQAQSSPPW924
KCNK5-RUNX2chr639161945chr645479983973DRB1-0466TIGFGDFVADPRQAQ419
KCNK5-RUNX2chr639161945chr645479983973DRB1-0802FGDFVADPRQAQSSP722
KCNK5-RUNX2chr639161945chr645479983973DRB1-0802GFGDFVADPRQAQSS621
KCNK5-RUNX2chr639161945chr645479983973DRB1-0803FGDFVADPRQAQSSP722
KCNK5-RUNX2chr639161945chr645479983973DRB1-0805FGDFVADPRQAQSSP722
KCNK5-RUNX2chr639161945chr645479983973DRB1-0805GFGDFVADPRQAQSS621
KCNK5-RUNX2chr639161945chr645479983973DRB1-0808FGDFVADPRQAQSSP722
KCNK5-RUNX2chr639161945chr645479983973DRB1-0809FGDFVADPRQAQSSP722
KCNK5-RUNX2chr639161945chr645479983973DRB1-0809GFGDFVADPRQAQSS621
KCNK5-RUNX2chr639161945chr645479983973DRB1-0811FGDFVADPRQAQSSP722
KCNK5-RUNX2chr639161945chr645479983973DRB1-0813FGDFVADPRQAQSSP722
KCNK5-RUNX2chr639161945chr645479983973DRB1-0813GFGDFVADPRQAQSS621
KCNK5-RUNX2chr639161945chr645479983973DRB1-0813GDFVADPRQAQSSPP823
KCNK5-RUNX2chr639161945chr645479983973DRB1-0813IGFGDFVADPRQAQS520
KCNK5-RUNX2chr639161945chr645479983973DRB1-0814FGDFVADPRQAQSSP722
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KCNK5-RUNX2chr639161945chr645479983973DRB1-1467GFGDFVADPRQAQSS621
KCNK5-RUNX2chr639161945chr645479983973DRB1-1467GDFVADPRQAQSSPP823
KCNK5-RUNX2chr639161945chr645479983973DRB1-1468FGDFVADPRQAQSSP722
KCNK5-RUNX2chr639161945chr645479983973DRB1-1469FGDFVADPRQAQSSP722
KCNK5-RUNX2chr639161945chr645479983973DRB1-1469GFGDFVADPRQAQSS621
KCNK5-RUNX2chr639161945chr645479983973DRB1-1469GDFVADPRQAQSSPP823
KCNK5-RUNX2chr639161945chr645479983973DRB1-1469IGFGDFVADPRQAQS520
KCNK5-RUNX2chr639161945chr645479983973DRB1-1476FGDFVADPRQAQSSP722
KCNK5-RUNX2chr639161945chr645479983973DRB1-1476GFGDFVADPRQAQSS621
KCNK5-RUNX2chr639161945chr645479983973DRB1-1477FGDFVADPRQAQSSP722
KCNK5-RUNX2chr639161945chr645479983973DRB1-1477GFGDFVADPRQAQSS621
KCNK5-RUNX2chr639161945chr645479983973DRB1-1477GDFVADPRQAQSSPP823
KCNK5-RUNX2chr639161945chr645479983973DRB1-1477IGFGDFVADPRQAQS520
KCNK5-RUNX2chr639161945chr645479983973DRB1-1479FGDFVADPRQAQSSP722
KCNK5-RUNX2chr639161945chr645479983973DRB1-1479GFGDFVADPRQAQSS621
KCNK5-RUNX2chr639161945chr645479983973DRB1-1480FGDFVADPRQAQSSP722
KCNK5-RUNX2chr639161945chr645479983973DRB1-1485FGDFVADPRQAQSSP722
KCNK5-RUNX2chr639161945chr645479983973DRB1-1485GFGDFVADPRQAQSS621
KCNK5-RUNX2chr639161945chr645479983973DRB1-1485GDFVADPRQAQSSPP823
KCNK5-RUNX2chr639161945chr645479983973DRB1-1489FGDFVADPRQAQSSP722
KCNK5-RUNX2chr639161945chr645479983973DRB1-1489GFGDFVADPRQAQSS621
KCNK5-RUNX2chr639161945chr645479983973DRB1-1489GDFVADPRQAQSSPP823
KCNK5-RUNX2chr639161945chr645479983973DRB1-1489IGFGDFVADPRQAQS520
KCNK5-RUNX2chr639161945chr645479983973DRB1-1493FGDFVADPRQAQSSP722
KCNK5-RUNX2chr639161945chr645479983973DRB1-1493GFGDFVADPRQAQSS621
KCNK5-RUNX2chr639161945chr645479983973DRB1-1493GDFVADPRQAQSSPP823
KCNK5-RUNX2chr639161945chr645479983973DRB1-1493IGFGDFVADPRQAQS520
KCNK5-RUNX2chr639161945chr645479983973DRB1-1494FGDFVADPRQAQSSP722
KCNK5-RUNX2chr639161945chr645479983973DRB1-1494GFGDFVADPRQAQSS621
KCNK5-RUNX2chr639161945chr645479983973DRB1-1494GDFVADPRQAQSSPP823
KCNK5-RUNX2chr639161945chr645479983973DRB1-1494IGFGDFVADPRQAQS520
KCNK5-RUNX2chr639161945chr645479983973DRB1-1498FGDFVADPRQAQSSP722
KCNK5-RUNX2chr639161945chr645479983973DRB1-1498GFGDFVADPRQAQSS621
KCNK5-RUNX2chr639161945chr645479983973DRB1-1498GDFVADPRQAQSSPP823
KCNK5-RUNX2chr639161945chr645479983973DRB1-1498IGFGDFVADPRQAQS520
KCNK5-RUNX2chr639161945chr645479983973DRB3-0114FGDFVADPRQAQSSP722
KCNK5-RUNX2chr639161945chr645479983973DRB3-0114GFGDFVADPRQAQSS621
KCNK5-RUNX2chr639161945chr645479983973DRB3-0114GDFVADPRQAQSSPP823
KCNK5-RUNX2chr639161945chr645479983973DRB3-0114IGFGDFVADPRQAQS520
KCNK5-RUNX2chr639161945chr645479983973DRB5-0111TIGFGDFVADPRQAQ419
KCNK5-RUNX2chr639161945chr645479983973DRB5-0111STIGFGDFVADPRQA318
KCNK5-RUNX2chr639161945chr645479983973DRB5-0203TIGFGDFVADPRQAQ419
KCNK5-RUNX2chr639161945chr645479983973DRB5-0203STIGFGDFVADPRQA318

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Fusion breakpoint peptide structures of KCNK5-RUNX2

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
2771GFGDFVADPRQAQSKCNK5RUNX2chr639161945chr645479983973

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of KCNK5-RUNX2

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-B14:023BVN2771GFGDFVADPRQAQS-7.24289-7.35629
HLA-B14:023BVN2771GFGDFVADPRQAQS-6.44411-7.47941
HLA-B52:013W392771GFGDFVADPRQAQS-6.85231-6.96571
HLA-B52:013W392771GFGDFVADPRQAQS-5.09533-6.13063
HLA-A11:014UQ22771GFGDFVADPRQAQS-8.61576-8.72916
HLA-A24:025HGA2771GFGDFVADPRQAQS-6.80714-7.84244
HLA-A24:025HGA2771GFGDFVADPRQAQS-6.33574-6.44914
HLA-B44:053DX82771GFGDFVADPRQAQS-7.01739-7.13079
HLA-B44:053DX82771GFGDFVADPRQAQS-3.37818-4.41348

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Vaccine Design for the FusionNeoAntigens of KCNK5-RUNX2

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
KCNK5-RUNX2chr639161945chr6454799831019FVADPRQAQTTGTGGCCGACCCCAGGCAGGCACAGT

check button mRNA and peptide sequences of FusionNeoAntigens that have potential interaction with HLA-IIs.
Fusion geneHchrHbpTchrTbpStart in +/-13AAEnd in +/-13AAFusionNeoAntigen peptideFusionNEoAntigen RNA sequence
KCNK5-RUNX2chr639161945chr645479983318STIGFGDFVADPRQACCACCATCGGCTTCGGTGACTTTGTGGCCGACCCCAGGCAGGCAC
KCNK5-RUNX2chr639161945chr645479983419TIGFGDFVADPRQAQCCATCGGCTTCGGTGACTTTGTGGCCGACCCCAGGCAGGCACAGT
KCNK5-RUNX2chr639161945chr645479983520IGFGDFVADPRQAQSTCGGCTTCGGTGACTTTGTGGCCGACCCCAGGCAGGCACAGTCTT
KCNK5-RUNX2chr639161945chr645479983621GFGDFVADPRQAQSSGCTTCGGTGACTTTGTGGCCGACCCCAGGCAGGCACAGTCTTCCC
KCNK5-RUNX2chr639161945chr645479983722FGDFVADPRQAQSSPTCGGTGACTTTGTGGCCGACCCCAGGCAGGCACAGTCTTCCCCGC
KCNK5-RUNX2chr639161945chr645479983823GDFVADPRQAQSSPPGTGACTTTGTGGCCGACCCCAGGCAGGCACAGTCTTCCCCGCCGT
KCNK5-RUNX2chr639161945chr645479983924DFVADPRQAQSSPPWACTTTGTGGCCGACCCCAGGCAGGCACAGTCTTCCCCGCCGTGGT

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Information of the samples that have these potential fusion neoantigens of KCNK5-RUNX2

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
KIRPKCNK5-RUNX2chr639161945ENST00000359534chr645479983ENST00000352853TCGA-B9-A69E-01A

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Potential target of CAR-T therapy development for KCNK5-RUNX2

check button Predicted 3D structure. We used RoseTTAFold.
241_KCNK5-RUNX2_1de0e_pred.pdb


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
HgeneKCNK5chr6:39161945chr6:45479983ENST00000359534-4585_112211500.0IntramembranePore-forming%3B Name%3DPore-forming 1
HgeneKCNK5chr6:39161945chr6:45479983ENST00000359534-45113_133211500.0TransmembraneHelical
HgeneKCNK5chr6:39161945chr6:45479983ENST00000359534-45158_180211500.0TransmembraneHelical
HgeneKCNK5chr6:39161945chr6:45479983ENST00000359534-458_26211500.0TransmembraneHelical

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
KCNK5chr639161945ENST00000359534RUNX2chr645479983ENST00000352853
KCNK5chr639161945ENST00000359534RUNX2chr645479983ENST00000371432
KCNK5chr639161945ENST00000359534RUNX2chr645479983ENST00000576263

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Related Drugs to KCNK5-RUNX2

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 KCNK5-RUNX2

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