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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:KIF13A-PTPRK

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: KIF13A-PTPRK
FusionPDB ID: 42536
FusionGDB2.0 ID: 42536
HgeneTgene
Gene symbol

KIF13A

PTPRK

Gene ID

63971

5796

Gene namekinesin family member 13Aprotein tyrosine phosphatase receptor type K
SynonymsRBKIN|bA500C11.2R-PTP-kappa
Cytomap

6p22.3

6q22.33

Type of geneprotein-codingprotein-coding
Descriptionkinesin-like protein KIF13Ahomolog of mouse KIF13A mannose-6-phosphate receptor transporterkinesin-like protein RBKINreceptor-type tyrosine-protein phosphatase kappadJ480J14.2.1 (protein tyrosine phosphatase, receptor type, K (R-PTP-KAPPA, protein tyrosine phosphatase kappa , protein tyrosine phosphatase kappaprotein-tyrosine phosphatase kappaprotein-tyrosine phospha
Modification date2020031320200322
UniProtAcc

Q9H1H9

Main function of 5'-partner protein: FUNCTION: Plus end-directed microtubule-dependent motor protein involved in intracellular transport and regulating various processes such as mannose-6-phosphate receptor (M6PR) transport to the plasma membrane, endosomal sorting during melanosome biogenesis and cytokinesis. Mediates the transport of M6PR-containing vesicles from trans-Golgi network to the plasma membrane via direct interaction with the AP-1 complex. During melanosome maturation, required for delivering melanogenic enzymes from recycling endosomes to nascent melanosomes by creating peripheral recycling endosomal subdomains in melanocytes. Also required for the abcission step in cytokinesis: mediates translocation of ZFYVE26, and possibly TTC19, to the midbody during cytokinesis. {ECO:0000269|PubMed:19841138, ECO:0000269|PubMed:20208530}.		.
Ensembl transtripts involved in fusion geneENST idsENST00000259711, ENST00000378814, 
ENST00000378816, ENST00000378826, 
ENST00000378843, ENST00000502704, 
ENST00000503342, 		ENST00000524481, 
ENST00000525459, ENST00000368207, 
ENST00000368210, ENST00000368213, 
ENST00000368215, ENST00000368226, 
ENST00000368227, ENST00000532331, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score14 X 12 X 9=151217 X 12 X 9=1836
# samples 1721
** MAII scorelog2(17/1512*10)=-3.15285148808337
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(21/1836*10)=-3.12810482574769
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Fusion gene context

PubMed: KIF13A [Title/Abstract] AND PTPRK [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: KIF13A [Title/Abstract] AND PTPRK [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)KIF13A(17825999)-PTPRK(128718833), # samples:2
Anticipated loss of major functional domain due to fusion event.KIF13A-PTPRK 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.
KIF13A-PTPRK 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.
KIF13A-PTPRK 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.
KIF13A-PTPRK 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
TgenePTPRK

GO:0006470

protein dephosphorylation

16263724

TgenePTPRK

GO:0007165

signal transduction

16849327

TgenePTPRK

GO:0007179

transforming growth factor beta receptor signaling pathway

15899872

TgenePTPRK

GO:0008285

negative regulation of cell proliferation

15899872|18276111

TgenePTPRK

GO:0010839

negative regulation of keratinocyte proliferation

16263724

TgenePTPRK

GO:0030336

negative regulation of cell migration

18276111

TgenePTPRK

GO:0034394

protein localization to cell surface

18276111

TgenePTPRK

GO:0034614

cellular response to reactive oxygen species

16849327

TgenePTPRK

GO:0034644

cellular response to UV

16849327

TgenePTPRK

GO:0045786

negative regulation of cell cycle

15899872

TgenePTPRK

GO:0045892

negative regulation of transcription, DNA-templated

18276111



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/chr6:17825999/chr6:128718833)
- 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 KIF13A (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 PTPRK (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)
ENST00000378814KIF13Achr617825999-ENST00000368226PTPRKchr6128718833-74571786060082002
ENST00000378814KIF13Achr617825999-ENST00000368227PTPRKchr6128718833-75071786060592019
ENST00000378814KIF13Achr617825999-ENST00000532331PTPRKchr6128718833-73251786060742024
ENST00000378814KIF13Achr617825999-ENST00000368213PTPRKchr6128718833-72771786060262008
ENST00000378814KIF13Achr617825999-ENST00000368210PTPRKchr6128718833-64531786060622020
ENST00000378814KIF13Achr617825999-ENST00000368215PTPRKchr6128718833-63371786060052001
ENST00000378814KIF13Achr617825999-ENST00000368207PTPRKchr6128718833-62191786061042034
ENST00000259711KIF13Achr617825999-ENST00000368226PTPRKchr6128718833-7563189210661142002
ENST00000259711KIF13Achr617825999-ENST00000368227PTPRKchr6128718833-7613189210661652019
ENST00000259711KIF13Achr617825999-ENST00000532331PTPRKchr6128718833-7431189210661802024
ENST00000259711KIF13Achr617825999-ENST00000368213PTPRKchr6128718833-7383189210661322008
ENST00000259711KIF13Achr617825999-ENST00000368210PTPRKchr6128718833-6559189210661682020
ENST00000259711KIF13Achr617825999-ENST00000368215PTPRKchr6128718833-6443189210661112001
ENST00000259711KIF13Achr617825999-ENST00000368207PTPRKchr6128718833-6325189210662102034
ENST00000378843KIF13Achr617825999-ENST00000368226PTPRKchr6128718833-747518041860262002
ENST00000378843KIF13Achr617825999-ENST00000368227PTPRKchr6128718833-752518041860772019
ENST00000378843KIF13Achr617825999-ENST00000532331PTPRKchr6128718833-734318041860922024
ENST00000378843KIF13Achr617825999-ENST00000368213PTPRKchr6128718833-729518041860442008
ENST00000378843KIF13Achr617825999-ENST00000368210PTPRKchr6128718833-647118041860802020
ENST00000378843KIF13Achr617825999-ENST00000368215PTPRKchr6128718833-635518041860232001
ENST00000378843KIF13Achr617825999-ENST00000368207PTPRKchr6128718833-623718041861222034
ENST00000378826KIF13Achr617825999-ENST00000368226PTPRKchr6128718833-747618051960272002
ENST00000378826KIF13Achr617825999-ENST00000368227PTPRKchr6128718833-752618051960782019
ENST00000378826KIF13Achr617825999-ENST00000532331PTPRKchr6128718833-734418051960932024
ENST00000378826KIF13Achr617825999-ENST00000368213PTPRKchr6128718833-729618051960452008
ENST00000378826KIF13Achr617825999-ENST00000368210PTPRKchr6128718833-647218051960812020
ENST00000378826KIF13Achr617825999-ENST00000368215PTPRKchr6128718833-635618051960242001
ENST00000378826KIF13Achr617825999-ENST00000368207PTPRKchr6128718833-623818051961232034
ENST00000378816KIF13Achr617825999-ENST00000368226PTPRKchr6128718833-7562189110561132002
ENST00000378816KIF13Achr617825999-ENST00000368227PTPRKchr6128718833-7612189110561642019
ENST00000378816KIF13Achr617825999-ENST00000532331PTPRKchr6128718833-7430189110561792024
ENST00000378816KIF13Achr617825999-ENST00000368213PTPRKchr6128718833-7382189110561312008
ENST00000378816KIF13Achr617825999-ENST00000368210PTPRKchr6128718833-6558189110561672020
ENST00000378816KIF13Achr617825999-ENST00000368215PTPRKchr6128718833-6442189110561102001
ENST00000378816KIF13Achr617825999-ENST00000368207PTPRKchr6128718833-6324189110562092034

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
ENST00000378814ENST00000368226KIF13Achr617825999-PTPRKchr6128718833-0.0002662360.99973375
ENST00000378814ENST00000368227KIF13Achr617825999-PTPRKchr6128718833-0.0005893510.9994106
ENST00000378814ENST00000532331KIF13Achr617825999-PTPRKchr6128718833-0.0005796480.9994204
ENST00000378814ENST00000368213KIF13Achr617825999-PTPRKchr6128718833-0.0004621140.99953794
ENST00000378814ENST00000368210KIF13Achr617825999-PTPRKchr6128718833-0.0010493460.9989506
ENST00000378814ENST00000368215KIF13Achr617825999-PTPRKchr6128718833-0.0006467620.99935323
ENST00000378814ENST00000368207KIF13Achr617825999-PTPRKchr6128718833-0.0009519450.99904805
ENST00000259711ENST00000368226KIF13Achr617825999-PTPRKchr6128718833-0.0003047130.9996953
ENST00000259711ENST00000368227KIF13Achr617825999-PTPRKchr6128718833-0.0006698910.99933016
ENST00000259711ENST00000532331KIF13Achr617825999-PTPRKchr6128718833-0.000660430.9993395
ENST00000259711ENST00000368213KIF13Achr617825999-PTPRKchr6128718833-0.0005319870.999468
ENST00000259711ENST00000368210KIF13Achr617825999-PTPRKchr6128718833-0.0011859260.9988141
ENST00000259711ENST00000368215KIF13Achr617825999-PTPRKchr6128718833-0.0007306210.9992694
ENST00000259711ENST00000368207KIF13Achr617825999-PTPRKchr6128718833-0.0010679890.99893194
ENST00000378843ENST00000368226KIF13Achr617825999-PTPRKchr6128718833-0.0002773030.99972266
ENST00000378843ENST00000368227KIF13Achr617825999-PTPRKchr6128718833-0.000611150.9993888
ENST00000378843ENST00000532331KIF13Achr617825999-PTPRKchr6128718833-0.0006023070.99939764
ENST00000378843ENST00000368213KIF13Achr617825999-PTPRKchr6128718833-0.0004805120.99951947
ENST00000378843ENST00000368210KIF13Achr617825999-PTPRKchr6128718833-0.0010853530.9989147
ENST00000378843ENST00000368215KIF13Achr617825999-PTPRKchr6128718833-0.0006695890.9993304
ENST00000378843ENST00000368207KIF13Achr617825999-PTPRKchr6128718833-0.0009813950.99901855
ENST00000378826ENST00000368226KIF13Achr617825999-PTPRKchr6128718833-0.0002772760.99972266
ENST00000378826ENST00000368227KIF13Achr617825999-PTPRKchr6128718833-0.0006112050.9993888
ENST00000378826ENST00000532331KIF13Achr617825999-PTPRKchr6128718833-0.0006021840.99939775
ENST00000378826ENST00000368213KIF13Achr617825999-PTPRKchr6128718833-0.0004802890.9995197
ENST00000378826ENST00000368210KIF13Achr617825999-PTPRKchr6128718833-0.0010838620.99891615
ENST00000378826ENST00000368215KIF13Achr617825999-PTPRKchr6128718833-0.0006686810.99933136
ENST00000378826ENST00000368207KIF13Achr617825999-PTPRKchr6128718833-0.0009803590.9990196
ENST00000378816ENST00000368226KIF13Achr617825999-PTPRKchr6128718833-0.0003104880.9996896
ENST00000378816ENST00000368227KIF13Achr617825999-PTPRKchr6128718833-0.0006780430.99932194
ENST00000378816ENST00000532331KIF13Achr617825999-PTPRKchr6128718833-0.000668640.99933136
ENST00000378816ENST00000368213KIF13Achr617825999-PTPRKchr6128718833-0.0005400630.9994599
ENST00000378816ENST00000368210KIF13Achr617825999-PTPRKchr6128718833-0.001206660.99879336
ENST00000378816ENST00000368215KIF13Achr617825999-PTPRKchr6128718833-0.0007435050.99925643
ENST00000378816ENST00000368207KIF13Achr617825999-PTPRKchr6128718833-0.0010862490.99891376

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 KIF13A-PTPRK

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide
KIF13Achr617825999PTPRKchr61287188331786595AQMEVIMKTLNSNGGCTFDDGPGACD
KIF13Achr617825999PTPRKchr61287188331804595AQMEVIMKTLNSNGGCTFDDGPGACD
KIF13Achr617825999PTPRKchr61287188331805595AQMEVIMKTLNSNGGCTFDDGPGACD
KIF13Achr617825999PTPRKchr61287188331891595AQMEVIMKTLNSNGGCTFDDGPGACD
KIF13Achr617825999PTPRKchr61287188331892595AQMEVIMKTLNSNGGCTFDDGPGACD

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Potential FusionNeoAntigen Information of KIF13A-PTPRK 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.
KIF13A-PTPRK_17825999_128718833.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)
KIF13A-PTPRKchr617825999chr61287188331892HLA-B57:01KTLNSNGGCTF0.99970.7754718
KIF13A-PTPRKchr617825999chr61287188331892HLA-B57:03KTLNSNGGCTF0.99820.7614718
KIF13A-PTPRKchr617825999chr61287188331892HLA-B15:17KTLNSNGGCTF0.99780.681718
KIF13A-PTPRKchr617825999chr61287188331892HLA-B57:10KTLNSNGGCTF0.99970.7754718
KIF13A-PTPRKchr617825999chr61287188331892HLA-B57:04KTLNSNGGCTF0.9990.5545718
KIF13A-PTPRKchr617825999chr61287188331892HLA-B57:02KTLNSNGGCTF0.99440.7101718

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Potential FusionNeoAntigen Information of KIF13A-PTPRK 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.

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)

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Fusion breakpoint peptide structures of KIF13A-PTPRK

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
5945MKTLNSNGGCTFDDKIF13APTPRKchr617825999chr61287188331892

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of KIF13A-PTPRK

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-B14:023BVN5945MKTLNSNGGCTFDD-6.01316-6.12656
HLA-B14:023BVN5945MKTLNSNGGCTFDD-3.92858-4.96388
HLA-B52:013W395945MKTLNSNGGCTFDD-5.92102-6.95632
HLA-B52:013W395945MKTLNSNGGCTFDD-4.84472-4.95812
HLA-A24:025HGA5945MKTLNSNGGCTFDD-8.26357-9.29887
HLA-A24:025HGA5945MKTLNSNGGCTFDD-7.03366-7.14706
HLA-B44:053DX85945MKTLNSNGGCTFDD-6.13971-6.25311
HLA-B44:053DX85945MKTLNSNGGCTFDD-5.20728-6.24258
HLA-A02:016TDR5945MKTLNSNGGCTFDD-5.28864-5.40204

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Vaccine Design for the FusionNeoAntigens of KIF13A-PTPRK

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
KIF13A-PTPRKchr617825999chr6128718833718KTLNSNGGCTFAAACCCTGAATAGTAATGGTGGCTGTACTTTTG

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

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Information of the samples that have these potential fusion neoantigens of KIF13A-PTPRK

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
LUADKIF13A-PTPRKchr617825999ENST00000259711chr6128718833ENST00000368207TCGA-44-7671-01A

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Potential target of CAR-T therapy development for KIF13A-PTPRK

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
TgenePTPRKchr6:17825999chr6:128718833ENST00000368213031753_77401447.0TransmembraneHelical
TgenePTPRKchr6:17825999chr6:128718833ENST00000368215030753_77401440.0TransmembraneHelical
TgenePTPRKchr6:17825999chr6:128718833ENST00000368226030753_77401441.0TransmembraneHelical

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 KIF13A-PTPRK

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 KIF13A-PTPRK

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