FusionNeoAntigen Logo

Home

Download

Statistics

Examples

Help

Contact

Terms of Use

Center for Computational Systems Medicine
leaf

Fusion Gene and Fusion Protein Summary

leaf

Fusion Amino Acid Sequences (multiple BPs and multiple gene isoforms)

leaf

Fusion Protein Breakpoint Sequences - (for the Screening of the FusionNeoAntigens)

leaf

Potential FusionNeoAntigens in HLA I - (netMHCpan v4.1 + deepHLApan v1.1)

leaf

Potential FusionNeoAntigens in HLA II - (netMHCIIpan v4.1)

leaf

Fusion Breakpoint 14 AA Peptide Structure - (RoseTTAFold)

leaf

Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D - (Glide)

leaf

Vaccine Design for the FusionNeoAntigens (RNA/protein sequences)

leaf

Potential target of CAR-T therapy development

leaf

Information on the samples that have these potential fusion neoantigens

leaf

Fusion Protein Targeting Drugs - (Manual Curation)

leaf

Fusion Protein Related diseases - (Manual Curation)

Fusion Protein:NEK7-SMYD3

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: NEK7-SMYD3
FusionPDB ID: 58545
FusionGDB2.0 ID: 58545
HgeneTgene
Gene symbol

NEK7

SMYD3

Gene ID

140609

64754

Gene nameNIMA related kinase 7SET and MYND domain containing 3
Synonyms-KMT3E|ZMYND1|ZNFN3A1|bA74P14.1
Cytomap

1q31.3

1q44

Type of geneprotein-codingprotein-coding
Descriptionserine/threonine-protein kinase Nek7NIMA (never in mitosis gene a)-related kinase 7never in mitosis A-related kinase 7nimA-related protein kinase 7histone-lysine N-methyltransferase SMYD3SET and MYND domain-containing protein 3bA74P14.1 (novel protein)zinc finger MYND domain-containing protein 1zinc finger protein, subfamily 3A (MYND domain containing), 1zinc finger, MYND domain containing 1
Modification date2020031320200320
UniProtAcc

Q8TDX7

Main function of 5'-partner protein: FUNCTION: Protein kinase which plays an important role in mitotic cell cycle progression (PubMed:17101132). Required for microtubule nucleation activity of the centrosome, robust mitotic spindle formation and cytokinesis (PubMed:17586473, PubMed:19414596). Phosphorylates RPS6KB1 (By similarity). Phosphorylates EML4 at 'Ser-146', promoting its dissociation from microtubules during mitosis which is required for efficient chromosome congression (PubMed:31409757). {ECO:0000250|UniProtKB:D3ZBE5, ECO:0000269|PubMed:17101132, ECO:0000269|PubMed:17586473, ECO:0000269|PubMed:19414596, ECO:0000269|PubMed:31409757}.
.
Ensembl transtripts involved in fusion geneENST idsENST00000417895, ENST00000367383, 
ENST00000367385, ENST00000538004, 
ENST00000388985, ENST00000490107, 
ENST00000541742, ENST00000366517, 
ENST00000403792, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score12 X 5 X 8=48029 X 14 X 17=6902
# samples 1247
** MAII scorelog2(12/480*10)=-2
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(47/6902*10)=-3.87628181187052
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Fusion gene context

PubMed: NEK7 [Title/Abstract] AND SMYD3 [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: NEK7 [Title/Abstract] AND SMYD3 [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)NEK7(198201767)-SMYD3(246093239), # samples:3
Anticipated loss of major functional domain due to fusion event.NEK7-SMYD3 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.
NEK7-SMYD3 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.
NEK7-SMYD3 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.
NEK7-SMYD3 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
HgeneNEK7

GO:0006468

protein phosphorylation

12840024



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/chr1:198201767/chr1:246093239)
- 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 NEK7 (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 SMYD3 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure


Top

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)
ENST00000367385NEK7chr1198201767+ENST00000541742SMYD3chr1246093239-13783993271154275
ENST00000367385NEK7chr1198201767+ENST00000490107SMYD3chr1246093239-13763993271154275
ENST00000367385NEK7chr1198201767+ENST00000388985SMYD3chr1246093239-11553993271154275
ENST00000538004NEK7chr1198201767+ENST00000541742SMYD3chr1246093239-1163184112939275
ENST00000538004NEK7chr1198201767+ENST00000490107SMYD3chr1246093239-1161184112939275
ENST00000538004NEK7chr1198201767+ENST00000388985SMYD3chr1246093239-940184112939276
ENST00000367383NEK7chr1198201767+ENST00000541742SMYD3chr1246093239-1220241169996275
ENST00000367383NEK7chr1198201767+ENST00000490107SMYD3chr1246093239-1218241169996275
ENST00000367383NEK7chr1198201767+ENST00000388985SMYD3chr1246093239-997241169996276

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
ENST00000367385ENST00000541742NEK7chr1198201767+SMYD3chr1246093239-0.0027292220.99727076
ENST00000367385ENST00000490107NEK7chr1198201767+SMYD3chr1246093239-0.0028346760.99716526
ENST00000367385ENST00000388985NEK7chr1198201767+SMYD3chr1246093239-0.0027252250.9972748
ENST00000538004ENST00000541742NEK7chr1198201767+SMYD3chr1246093239-0.0019222990.99807775
ENST00000538004ENST00000490107NEK7chr1198201767+SMYD3chr1246093239-0.0020247720.9979753
ENST00000538004ENST00000388985NEK7chr1198201767+SMYD3chr1246093239-0.0016340790.99836594
ENST00000367383ENST00000541742NEK7chr1198201767+SMYD3chr1246093239-0.0019743970.99802566
ENST00000367383ENST00000490107NEK7chr1198201767+SMYD3chr1246093239-0.002038940.99796104
ENST00000367383ENST00000388985NEK7chr1198201767+SMYD3chr1246093239-0.0017706070.99822944

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

Top

Fusion Protein Breakpoint Sequences for NEK7-SMYD3

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide
NEK7chr1198201767SMYD3chr124609323918423QGMQGPPVPQFQPQVICNSFTICNAE
NEK7chr1198201767SMYD3chr124609323924123QGMQGPPVPQFQPQVICNSFTICNAE
NEK7chr1198201767SMYD3chr124609323939923QGMQGPPVPQFQPQVICNSFTICNAE

Top

Potential FusionNeoAntigen Information of NEK7-SMYD3 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.
NEK7-SMYD3_198201767_246093239.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)
NEK7-SMYD3chr1198201767chr1246093239241HLA-B51:01VPQFQPQV0.99330.793715
NEK7-SMYD3chr1198201767chr1246093239241HLA-B52:01PQFQPQVI0.93150.8967816
NEK7-SMYD3chr1198201767chr1246093239241HLA-B51:02VPQFQPQV0.91860.7028715
NEK7-SMYD3chr1198201767chr1246093239241HLA-B35:01QPQVICNSF0.9640.75111120
NEK7-SMYD3chr1198201767chr1246093239241HLA-B35:08QPQVICNSF0.94760.72091120
NEK7-SMYD3chr1198201767chr1246093239241HLA-B35:03VPQFQPQVI0.84880.7492716
NEK7-SMYD3chr1198201767chr1246093239241HLA-B35:02VPQFQPQVI0.82630.9137716
NEK7-SMYD3chr1198201767chr1246093239241HLA-B35:04VPQFQPQVI0.82630.9137716
NEK7-SMYD3chr1198201767chr1246093239241HLA-B35:04QPQVICNSF0.43860.75751120
NEK7-SMYD3chr1198201767chr1246093239241HLA-B35:02QPQVICNSF0.43860.75751120
NEK7-SMYD3chr1198201767chr1246093239241HLA-B81:01VPQFQPQVI0.25540.5912716
NEK7-SMYD3chr1198201767chr1246093239241HLA-B08:09VPQFQPQVI0.19470.7721716
NEK7-SMYD3chr1198201767chr1246093239241HLA-B78:01VPQFQPQV0.98660.9216715
NEK7-SMYD3chr1198201767chr1246093239241HLA-B51:08VPQFQPQV0.95190.6334715
NEK7-SMYD3chr1198201767chr1246093239241HLA-B51:07VPQFQPQVI0.98210.7896716
NEK7-SMYD3chr1198201767chr1246093239241HLA-B78:01VPQFQPQVI0.9820.6395716
NEK7-SMYD3chr1198201767chr1246093239241HLA-B51:08VPQFQPQVI0.90290.5352716
NEK7-SMYD3chr1198201767chr1246093239241HLA-B35:12VPQFQPQVI0.82630.9137716
NEK7-SMYD3chr1198201767chr1246093239241HLA-B07:12VPQFQPQVI0.76540.5718716
NEK7-SMYD3chr1198201767chr1246093239241HLA-B07:04VPQFQPQVI0.64970.5554716
NEK7-SMYD3chr1198201767chr1246093239241HLA-B35:12QPQVICNSF0.43860.75751120
NEK7-SMYD3chr1198201767chr1246093239241HLA-B42:02VPQFQPQVI0.35940.7566716
NEK7-SMYD3chr1198201767chr1246093239241HLA-B42:01VPQFQPQVI0.30870.7445716
NEK7-SMYD3chr1198201767chr1246093239241HLA-B39:10QPQVICNSF0.19110.72461120
NEK7-SMYD3chr1198201767chr1246093239241HLA-B39:10VPQFQPQVI0.15760.9208716
NEK7-SMYD3chr1198201767chr1246093239241HLA-B78:02VPQFQPQV0.99320.9468715
NEK7-SMYD3chr1198201767chr1246093239241HLA-B51:13VPQFQPQV0.99260.7323715
NEK7-SMYD3chr1198201767chr1246093239241HLA-B51:14VPQFQPQV0.99120.7399715
NEK7-SMYD3chr1198201767chr1246093239241HLA-B51:21VPQFQPQV0.9780.8222715
NEK7-SMYD3chr1198201767chr1246093239241HLA-B51:29VPQFQPQV0.9560.6003715
NEK7-SMYD3chr1198201767chr1246093239241HLA-B51:09VPQFQPQV0.93350.7549715
NEK7-SMYD3chr1198201767chr1246093239241HLA-B59:01VPQFQPQV0.41970.7492715
NEK7-SMYD3chr1198201767chr1246093239241HLA-B78:02VPQFQPQVI0.98690.7517716
NEK7-SMYD3chr1198201767chr1246093239241HLA-B35:77QPQVICNSF0.9640.75111120
NEK7-SMYD3chr1198201767chr1246093239241HLA-B35:23QPQVICNSF0.96390.70231120
NEK7-SMYD3chr1198201767chr1246093239241HLA-B35:22VPQFQPQVI0.95320.5238716
NEK7-SMYD3chr1198201767chr1246093239241HLA-B35:11QPQVICNSF0.93180.75461120
NEK7-SMYD3chr1198201767chr1246093239241HLA-B35:17QPQVICNSF0.91930.60771120
NEK7-SMYD3chr1198201767chr1246093239241HLA-B35:30QPQVICNSF0.91930.60771120
NEK7-SMYD3chr1198201767chr1246093239241HLA-B35:24QPQVICNSF0.8930.70021120
NEK7-SMYD3chr1198201767chr1246093239241HLA-B35:13VPQFQPQVI0.84910.7579716
NEK7-SMYD3chr1198201767chr1246093239241HLA-B35:09VPQFQPQVI0.82630.9137716
NEK7-SMYD3chr1198201767chr1246093239241HLA-B55:04VPQFQPQVI0.5150.5631716
NEK7-SMYD3chr1198201767chr1246093239241HLA-B15:08QPQVICNSF0.44690.67471120
NEK7-SMYD3chr1198201767chr1246093239241HLA-B35:09QPQVICNSF0.43860.75751120
NEK7-SMYD3chr1198201767chr1246093239241HLA-B35:43QPQVICNSF0.42660.67141120
NEK7-SMYD3chr1198201767chr1246093239241HLA-B15:11QPQVICNSF0.41480.67261120
NEK7-SMYD3chr1198201767chr1246093239241HLA-B18:07QPQVICNSF0.27130.59441120
NEK7-SMYD3chr1198201767chr1246093239241HLA-B67:01VPQFQPQVI0.19860.9188716
NEK7-SMYD3chr1198201767chr1246093239241HLA-B08:12VPQFQPQVI0.16350.8626716
NEK7-SMYD3chr1198201767chr1246093239241HLA-B15:27FQPQVICNSF0.99960.77881020
NEK7-SMYD3chr1198201767chr1246093239241HLA-B15:24FQPQVICNSF0.99940.72591020
NEK7-SMYD3chr1198201767chr1246093239241HLA-B15:12FQPQVICNSF0.99580.76111020

Top

Potential FusionNeoAntigen Information of NEK7-SMYD3 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)

Top

Fusion breakpoint peptide structures of NEK7-SMYD3

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
7085PVPQFQPQVICNSFNEK7SMYD3chr1198201767chr1246093239241

Top

Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of NEK7-SMYD3

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-B14:023BVN7085PVPQFQPQVICNSF-4.62424-5.65954
HLA-B14:023BVN7085PVPQFQPQVICNSF-4.1114-4.2248
HLA-B52:013W397085PVPQFQPQVICNSF-6.8001-6.9135
HLA-B52:013W397085PVPQFQPQVICNSF-6.46104-7.49634
HLA-A24:025HGA7085PVPQFQPQVICNSF-9.1447-9.2581
HLA-A24:025HGA7085PVPQFQPQVICNSF-6.01279-7.04809
HLA-B44:053DX87085PVPQFQPQVICNSF-5.02862-5.14202
HLA-B44:053DX87085PVPQFQPQVICNSF-4.60714-5.64244

Top

Vaccine Design for the FusionNeoAntigens of NEK7-SMYD3

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
NEK7-SMYD3chr1198201767chr12460932391020FQPQVICNSFCAACCACAGGTGATCTGCAACTCTTTCACC
NEK7-SMYD3chr1198201767chr12460932391120QPQVICNSFCCACAGGTGATCTGCAACTCTTTCACC
NEK7-SMYD3chr1198201767chr1246093239715VPQFQPQVCCTCAGTTCCAACCACAGGTGATC
NEK7-SMYD3chr1198201767chr1246093239716VPQFQPQVICCTCAGTTCCAACCACAGGTGATCTGC
NEK7-SMYD3chr1198201767chr1246093239816PQFQPQVICAGTTCCAACCACAGGTGATCTGC

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

Top

Information of the samples that have these potential fusion neoantigens of NEK7-SMYD3

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
SARCNEK7-SMYD3chr1198201767ENST00000367383chr1246093239ENST00000388985TCGA-QQ-A5VC-01A

Top

Potential target of CAR-T therapy development for NEK7-SMYD3

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

Top

Related Drugs to NEK7-SMYD3

check button Drugs used for this fusion-positive patient.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)
HgeneTgeneDrugSourcePMID

Top

Related Diseases to NEK7-SMYD3

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