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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:S100A2-FXYD3

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: S100A2-FXYD3
FusionPDB ID: 78868
FusionGDB2.0 ID: 78868
HgeneTgene
Gene symbol

S100A2

FXYD3

Gene ID

6273

5349

Gene nameS100 calcium binding protein A2FXYD domain containing ion transport regulator 3
SynonymsCAN19|S100LMAT8|PLML
Cytomap

1q21.3

19q13.12

Type of geneprotein-codingprotein-coding
Descriptionprotein S100-A2FXYD domain-containing ion transport regulator 3chloride conductance inducer protein Mat-8mammary tumor 8 kDa proteinphospholemman-like proteinsodium/potassium-transporting ATPase subunit FXYD3
Modification date2020031320200313
UniProtAcc.

Q14802

Main function of 5'-partner protein: FUNCTION: Associates with and regulates the activity of the sodium/potassium-transporting ATPase (NKA) which transports Na(+) out of the cell and K(+) into the cell (PubMed:17077088). Reduces glutathionylation of the NKA beta-1 subunit ATP1B1, thus reversing glutathionylation-mediated inhibition of ATP1B1 (PubMed:21454534). Induces a hyperpolarization-activated chloride current when expressed in Xenopus oocytes (PubMed:7836447). {ECO:0000269|PubMed:17077088, ECO:0000269|PubMed:21454534, ECO:0000269|PubMed:7836447}.; FUNCTION: [Isoform 1]: Decreases the apparent K+ and Na+ affinity of the sodium/potassium-transporting ATPase over a large range of membrane potentials. {ECO:0000269|PubMed:17077088}.; FUNCTION: [Isoform 2]: Decreases the apparent K+ affinity of the sodium/potassium-transporting ATPase only at slightly negative and positive membrane potentials and increases the apparent Na+ affinity over a large range of membrane potentials. {ECO:0000269|PubMed:17077088}.
Ensembl transtripts involved in fusion geneENST idsENST00000368707, ENST00000368709, 
ENST00000368710, ENST00000487430, 
ENST00000497140, ENST00000368708, 
ENST00000454903, ENST00000603449, 
ENST00000605552, ENST00000344013, 
ENST00000346446, ENST00000406242, 
ENST00000406988, ENST00000435734, 
ENST00000535103, ENST00000603181, 
ENST00000603524, ENST00000604255, 
ENST00000604404, ENST00000604621, 
ENST00000604804, ENST00000605550, 
ENST00000605677, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score9 X 5 X 4=1809 X 10 X 8=720
# samples 911
** MAII scorelog2(9/180*10)=-1
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(11/720*10)=-2.71049338280502
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Fusion gene context

PubMed: S100A2 [Title/Abstract] AND FXYD3 [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: S100A2 [Title/Abstract] AND FXYD3 [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)S100A2(153533819)-FXYD3(35612126), # samples:1
Anticipated loss of major functional domain due to fusion event.S100A2-FXYD3 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.
S100A2-FXYD3 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.
S100A2-FXYD3 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.
S100A2-FXYD3 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.
S100A2-FXYD3 seems lost the major protein functional domain in Hgene partner, which is a tumor suppressor due to the frame-shifted ORF.
S100A2-FXYD3 seems lost the major protein functional domain in Tgene partner, which is a IUPHAR drug target due to the frame-shifted ORF.
* DoF score (Degree of Frequency) = # partners X # break points X # cancer types
** MAII score (Major Active Isofusion Index) = log2(# samples/DoF score*10)

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


check button Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr1:153533819/chr19:35612126)
- 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 S100A2 (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 FXYD3 (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)
ENST00000487430S100A2chr1153533819-ENST00000605552FXYD3chr1935612126+1378752846295183
ENST00000497140S100A2chr1153533819-ENST00000406242FXYD3chr1935612126+1160697941264225
ENST00000497140S100A2chr1153533819-ENST00000604404FXYD3chr1935612126+1755697839264191
ENST00000497140S100A2chr1153533819-ENST00000435734FXYD3chr1935612126+1832697917264217
ENST00000497140S100A2chr1153533819-ENST00000603181FXYD3chr1935612126+1088697839264191
ENST00000497140S100A2chr1153533819-ENST00000604255FXYD3chr1935612126+1086697839264191
ENST00000497140S100A2chr1153533819-ENST00000346446FXYD3chr1935612126+1832697917264217
ENST00000497140S100A2chr1153533819-ENST00000344013FXYD3chr1935612126+1754697839264191
ENST00000497140S100A2chr1153533819-ENST00000406988FXYD3chr1935612126+1084697839264191
ENST00000497140S100A2chr1153533819-ENST00000605550FXYD3chr1935612126+1159697863264199
ENST00000497140S100A2chr1153533819-ENST00000604804FXYD3chr1935612126+1133697773264169
ENST00000497140S100A2chr1153533819-ENST00000535103FXYD3chr1935612126+1084697839264191
ENST00000497140S100A2chr1153533819-ENST00000603524FXYD3chr1935612126+1170697773264169
ENST00000497140S100A2chr1153533819-ENST00000604621FXYD3chr1935612126+1088697839264191
ENST00000497140S100A2chr1153533819-ENST00000605677FXYD3chr1935612126+1243697941264225
ENST00000368710S100A2chr1153533819-ENST00000406242FXYD3chr1935612126+9164533956129
ENST00000368710S100A2chr1153533819-ENST00000604404FXYD3chr1935612126+15114535952198
ENST00000368710S100A2chr1153533819-ENST00000435734FXYD3chr1935612126+15884533956129
ENST00000368710S100A2chr1153533819-ENST00000603181FXYD3chr1935612126+8444533956129
ENST00000368710S100A2chr1153533819-ENST00000604255FXYD3chr1935612126+8424535952198
ENST00000368710S100A2chr1153533819-ENST00000346446FXYD3chr1935612126+15884533956129
ENST00000368710S100A2chr1153533819-ENST00000344013FXYD3chr1935612126+15104533956129
ENST00000368710S100A2chr1153533819-ENST00000406988FXYD3chr1935612126+8404535952198
ENST00000368710S100A2chr1153533819-ENST00000605550FXYD3chr1935612126+9154536192206
ENST00000368710S100A2chr1153533819-ENST00000604804FXYD3chr1935612126+8894533956129
ENST00000368710S100A2chr1153533819-ENST00000535103FXYD3chr1935612126+8404535952198
ENST00000368710S100A2chr1153533819-ENST00000603524FXYD3chr1935612126+9264535292176
ENST00000368710S100A2chr1153533819-ENST00000604621FXYD3chr1935612126+8444533956129
ENST00000368710S100A2chr1153533819-ENST00000605677FXYD3chr1935612126+9994536972232
ENST00000368709S100A2chr1153533819-ENST00000605552FXYD3chr1935612126+108345755121176
ENST00000368707S100A2chr1153533819-ENST00000406242FXYD3chr1935612126+10195565071169
ENST00000368707S100A2chr1153533819-ENST00000604404FXYD3chr1935612126+1614556698300132
ENST00000368707S100A2chr1153533819-ENST00000435734FXYD3chr1935612126+16915565071169
ENST00000368707S100A2chr1153533819-ENST00000603181FXYD3chr1935612126+9475565071169
ENST00000368707S100A2chr1153533819-ENST00000604255FXYD3chr1935612126+945556698300132
ENST00000368707S100A2chr1153533819-ENST00000346446FXYD3chr1935612126+16915565071169
ENST00000368707S100A2chr1153533819-ENST00000344013FXYD3chr1935612126+16135565071169
ENST00000368707S100A2chr1153533819-ENST00000406988FXYD3chr1935612126+9435565071169
ENST00000368707S100A2chr1153533819-ENST00000605550FXYD3chr1935612126+10185565071169
ENST00000368707S100A2chr1153533819-ENST00000604804FXYD3chr1935612126+9925565071169
ENST00000368707S100A2chr1153533819-ENST00000535103FXYD3chr1935612126+9435565071169
ENST00000368707S100A2chr1153533819-ENST00000603524FXYD3chr1935612126+1029556489833114
ENST00000368707S100A2chr1153533819-ENST00000604621FXYD3chr1935612126+9475565071169
ENST00000368707S100A2chr1153533819-ENST00000605677FXYD3chr1935612126+11025565071169

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
ENST00000487430ENST00000605552S100A2chr1153533819-FXYD3chr1935612126+0.0399449020.96005505
ENST00000497140ENST00000406242S100A2chr1153533819-FXYD3chr1935612126+0.400250940.5997491
ENST00000497140ENST00000604404S100A2chr1153533819-FXYD3chr1935612126+0.379261940.620738
ENST00000497140ENST00000435734S100A2chr1153533819-FXYD3chr1935612126+0.530246140.46975386
ENST00000497140ENST00000603181S100A2chr1153533819-FXYD3chr1935612126+0.375044230.6249558
ENST00000497140ENST00000604255S100A2chr1153533819-FXYD3chr1935612126+0.36491350.6350865
ENST00000497140ENST00000346446S100A2chr1153533819-FXYD3chr1935612126+0.530246140.46975386
ENST00000497140ENST00000344013S100A2chr1153533819-FXYD3chr1935612126+0.376974050.62302595
ENST00000497140ENST00000406988S100A2chr1153533819-FXYD3chr1935612126+0.361039460.63896054
ENST00000497140ENST00000605550S100A2chr1153533819-FXYD3chr1935612126+0.504338560.4956614
ENST00000497140ENST00000604804S100A2chr1153533819-FXYD3chr1935612126+0.106765510.8932345
ENST00000497140ENST00000535103S100A2chr1153533819-FXYD3chr1935612126+0.361039460.63896054
ENST00000497140ENST00000603524S100A2chr1153533819-FXYD3chr1935612126+0.118980880.8810192
ENST00000497140ENST00000604621S100A2chr1153533819-FXYD3chr1935612126+0.375044230.6249558
ENST00000497140ENST00000605677S100A2chr1153533819-FXYD3chr1935612126+0.360064770.63993526
ENST00000368710ENST00000406242S100A2chr1153533819-FXYD3chr1935612126+0.0401104540.95988953
ENST00000368710ENST00000604404S100A2chr1153533819-FXYD3chr1935612126+0.0435103180.95648974
ENST00000368710ENST00000435734S100A2chr1153533819-FXYD3chr1935612126+0.55620120.44379878
ENST00000368710ENST00000603181S100A2chr1153533819-FXYD3chr1935612126+0.0376357060.96236426
ENST00000368710ENST00000604255S100A2chr1153533819-FXYD3chr1935612126+0.037201190.96279883
ENST00000368710ENST00000346446S100A2chr1153533819-FXYD3chr1935612126+0.55620120.44379878
ENST00000368710ENST00000344013S100A2chr1153533819-FXYD3chr1935612126+0.043787060.9562129
ENST00000368710ENST00000406988S100A2chr1153533819-FXYD3chr1935612126+0.036919170.96308076
ENST00000368710ENST00000605550S100A2chr1153533819-FXYD3chr1935612126+0.0379111020.9620889
ENST00000368710ENST00000604804S100A2chr1153533819-FXYD3chr1935612126+0.0553929320.94460714
ENST00000368710ENST00000535103S100A2chr1153533819-FXYD3chr1935612126+0.036919170.96308076
ENST00000368710ENST00000603524S100A2chr1153533819-FXYD3chr1935612126+0.066005520.9339945
ENST00000368710ENST00000604621S100A2chr1153533819-FXYD3chr1935612126+0.0376357060.96236426
ENST00000368710ENST00000605677S100A2chr1153533819-FXYD3chr1935612126+0.045741710.9542583
ENST00000368709ENST00000605552S100A2chr1153533819-FXYD3chr1935612126+0.024241030.975759
ENST00000368707ENST00000406242S100A2chr1153533819-FXYD3chr1935612126+0.282845350.7171546
ENST00000368707ENST00000604404S100A2chr1153533819-FXYD3chr1935612126+0.494105220.5058948
ENST00000368707ENST00000435734S100A2chr1153533819-FXYD3chr1935612126+0.65278010.34721988
ENST00000368707ENST00000603181S100A2chr1153533819-FXYD3chr1935612126+0.278976950.7210231
ENST00000368707ENST00000604255S100A2chr1153533819-FXYD3chr1935612126+0.2691370.730863
ENST00000368707ENST00000346446S100A2chr1153533819-FXYD3chr1935612126+0.65278010.34721988
ENST00000368707ENST00000344013S100A2chr1153533819-FXYD3chr1935612126+0.49495080.5050492
ENST00000368707ENST00000406988S100A2chr1153533819-FXYD3chr1935612126+0.26670530.73329467
ENST00000368707ENST00000605550S100A2chr1153533819-FXYD3chr1935612126+0.283328120.7166719
ENST00000368707ENST00000604804S100A2chr1153533819-FXYD3chr1935612126+0.164324020.83567595
ENST00000368707ENST00000535103S100A2chr1153533819-FXYD3chr1935612126+0.26670530.73329467
ENST00000368707ENST00000603524S100A2chr1153533819-FXYD3chr1935612126+0.15912320.8408768
ENST00000368707ENST00000604621S100A2chr1153533819-FXYD3chr1935612126+0.278976950.7210231
ENST00000368707ENST00000605677S100A2chr1153533819-FXYD3chr1935612126+0.278946430.7210536

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 S100A2-FXYD3

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide
S100A2chr1153533819FXYD3chr193561212655619GLLMPLSFVFNKLFLSDKNSPFYYGA

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Potential FusionNeoAntigen Information of S100A2-FXYD3 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.
S100A2-FXYD3_153533819_35612126.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)
S100A2-FXYD3chr1153533819chr1935612126556HLA-B57:01LSFVFNKLF0.99810.8587514
S100A2-FXYD3chr1153533819chr1935612126556HLA-B57:03LSFVFNKLF0.99530.9109514
S100A2-FXYD3chr1153533819chr1935612126556HLA-B58:02LSFVFNKLF0.99480.7427514
S100A2-FXYD3chr1153533819chr1935612126556HLA-B15:17LSFVFNKLF0.99120.7822514
S100A2-FXYD3chr1153533819chr1935612126556HLA-B58:01LSFVFNKLF0.99020.6175514
S100A2-FXYD3chr1153533819chr1935612126556HLA-C03:07FVFNKLFL0.99930.9833715
S100A2-FXYD3chr1153533819chr1935612126556HLA-C15:04LSFVFNKLF0.95920.8521514
S100A2-FXYD3chr1153533819chr1935612126556HLA-B15:07KLFLSDKNSPF0.99880.79571122
S100A2-FXYD3chr1153533819chr1935612126556HLA-C03:05FVFNKLFL0.99950.9141715
S100A2-FXYD3chr1153533819chr1935612126556HLA-C17:01FVFNKLFL0.98350.747715
S100A2-FXYD3chr1153533819chr1935612126556HLA-C14:03SFVFNKLF0.91170.9322614
S100A2-FXYD3chr1153533819chr1935612126556HLA-C14:02SFVFNKLF0.91170.9322614
S100A2-FXYD3chr1153533819chr1935612126556HLA-B57:10LSFVFNKLF0.99810.8587514
S100A2-FXYD3chr1153533819chr1935612126556HLA-B57:04LSFVFNKLF0.99440.5507514
S100A2-FXYD3chr1153533819chr1935612126556HLA-B57:02LSFVFNKLF0.96750.7385514
S100A2-FXYD3chr1153533819chr1935612126556HLA-C15:09LSFVFNKLF0.95920.8521514
S100A2-FXYD3chr1153533819chr1935612126556HLA-C14:03SFVFNKLFL0.08490.9426615
S100A2-FXYD3chr1153533819chr1935612126556HLA-C14:02SFVFNKLFL0.08490.9426615
S100A2-FXYD3chr1153533819chr1935612126556HLA-A32:01KLFLSDKNSPF0.9940.91861122

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Potential FusionNeoAntigen Information of S100A2-FXYD3 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.
S100A2-FXYD3_153533819_35612126.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)
S100A2-FXYD3chr1153533819chr1935612126556DRB1-0305NKLFLSDKNSPFYYG1025
S100A2-FXYD3chr1153533819chr1935612126556DRB1-0305FNKLFLSDKNSPFYY924
S100A2-FXYD3chr1153533819chr1935612126556DRB1-0305VFNKLFLSDKNSPFY823
S100A2-FXYD3chr1153533819chr1935612126556DRB1-0338NKLFLSDKNSPFYYG1025
S100A2-FXYD3chr1153533819chr1935612126556DRB1-0338FNKLFLSDKNSPFYY924
S100A2-FXYD3chr1153533819chr1935612126556DRB1-0338VFNKLFLSDKNSPFY823
S100A2-FXYD3chr1153533819chr1935612126556DRB1-0338KLFLSDKNSPFYYGA1126
S100A2-FXYD3chr1153533819chr1935612126556DRB1-0340NKLFLSDKNSPFYYG1025
S100A2-FXYD3chr1153533819chr1935612126556DRB1-0340FNKLFLSDKNSPFYY924
S100A2-FXYD3chr1153533819chr1935612126556DRB1-0434NKLFLSDKNSPFYYG1025
S100A2-FXYD3chr1153533819chr1935612126556DRB1-0466NKLFLSDKNSPFYYG1025
S100A2-FXYD3chr1153533819chr1935612126556DRB1-0472NKLFLSDKNSPFYYG1025
S100A2-FXYD3chr1153533819chr1935612126556DRB1-0825NKLFLSDKNSPFYYG1025
S100A2-FXYD3chr1153533819chr1935612126556DRB1-1447PLSFVFNKLFLSDKN419
S100A2-FXYD3chr1153533819chr1935612126556DRB1-1448NKLFLSDKNSPFYYG1025
S100A2-FXYD3chr1153533819chr1935612126556DRB1-1448FNKLFLSDKNSPFYY924
S100A2-FXYD3chr1153533819chr1935612126556DRB1-1493NKLFLSDKNSPFYYG1025
S100A2-FXYD3chr1153533819chr1935612126556DRB1-1498PLSFVFNKLFLSDKN419
S100A2-FXYD3chr1153533819chr1935612126556DRB3-0101NKLFLSDKNSPFYYG1025
S100A2-FXYD3chr1153533819chr1935612126556DRB3-0101FNKLFLSDKNSPFYY924
S100A2-FXYD3chr1153533819chr1935612126556DRB3-0101VFNKLFLSDKNSPFY823
S100A2-FXYD3chr1153533819chr1935612126556DRB3-0101KLFLSDKNSPFYYGA1126
S100A2-FXYD3chr1153533819chr1935612126556DRB3-0101FVFNKLFLSDKNSPF722
S100A2-FXYD3chr1153533819chr1935612126556DRB3-0104NKLFLSDKNSPFYYG1025
S100A2-FXYD3chr1153533819chr1935612126556DRB3-0104FNKLFLSDKNSPFYY924
S100A2-FXYD3chr1153533819chr1935612126556DRB3-0104VFNKLFLSDKNSPFY823
S100A2-FXYD3chr1153533819chr1935612126556DRB3-0104KLFLSDKNSPFYYGA1126
S100A2-FXYD3chr1153533819chr1935612126556DRB3-0104FVFNKLFLSDKNSPF722
S100A2-FXYD3chr1153533819chr1935612126556DRB3-0105NKLFLSDKNSPFYYG1025
S100A2-FXYD3chr1153533819chr1935612126556DRB3-0105FNKLFLSDKNSPFYY924
S100A2-FXYD3chr1153533819chr1935612126556DRB3-0105VFNKLFLSDKNSPFY823
S100A2-FXYD3chr1153533819chr1935612126556DRB3-0105KLFLSDKNSPFYYGA1126
S100A2-FXYD3chr1153533819chr1935612126556DRB3-0105FVFNKLFLSDKNSPF722
S100A2-FXYD3chr1153533819chr1935612126556DRB3-0108NKLFLSDKNSPFYYG1025
S100A2-FXYD3chr1153533819chr1935612126556DRB3-0108FNKLFLSDKNSPFYY924
S100A2-FXYD3chr1153533819chr1935612126556DRB3-0108VFNKLFLSDKNSPFY823
S100A2-FXYD3chr1153533819chr1935612126556DRB3-0108KLFLSDKNSPFYYGA1126
S100A2-FXYD3chr1153533819chr1935612126556DRB3-0108FVFNKLFLSDKNSPF722
S100A2-FXYD3chr1153533819chr1935612126556DRB3-0109NKLFLSDKNSPFYYG1025
S100A2-FXYD3chr1153533819chr1935612126556DRB3-0109FNKLFLSDKNSPFYY924
S100A2-FXYD3chr1153533819chr1935612126556DRB3-0109VFNKLFLSDKNSPFY823
S100A2-FXYD3chr1153533819chr1935612126556DRB3-0109KLFLSDKNSPFYYGA1126
S100A2-FXYD3chr1153533819chr1935612126556DRB3-0111NKLFLSDKNSPFYYG1025
S100A2-FXYD3chr1153533819chr1935612126556DRB3-0111FNKLFLSDKNSPFYY924
S100A2-FXYD3chr1153533819chr1935612126556DRB3-0111VFNKLFLSDKNSPFY823
S100A2-FXYD3chr1153533819chr1935612126556DRB3-0111KLFLSDKNSPFYYGA1126
S100A2-FXYD3chr1153533819chr1935612126556DRB3-0111FVFNKLFLSDKNSPF722
S100A2-FXYD3chr1153533819chr1935612126556DRB3-0112NKLFLSDKNSPFYYG1025
S100A2-FXYD3chr1153533819chr1935612126556DRB3-0112FNKLFLSDKNSPFYY924
S100A2-FXYD3chr1153533819chr1935612126556DRB3-0112VFNKLFLSDKNSPFY823
S100A2-FXYD3chr1153533819chr1935612126556DRB3-0112KLFLSDKNSPFYYGA1126
S100A2-FXYD3chr1153533819chr1935612126556DRB3-0112FVFNKLFLSDKNSPF722
S100A2-FXYD3chr1153533819chr1935612126556DRB3-0113NKLFLSDKNSPFYYG1025
S100A2-FXYD3chr1153533819chr1935612126556DRB3-0113FNKLFLSDKNSPFYY924
S100A2-FXYD3chr1153533819chr1935612126556DRB3-0113VFNKLFLSDKNSPFY823
S100A2-FXYD3chr1153533819chr1935612126556DRB3-0113KLFLSDKNSPFYYGA1126
S100A2-FXYD3chr1153533819chr1935612126556DRB3-0113FVFNKLFLSDKNSPF722
S100A2-FXYD3chr1153533819chr1935612126556DRB3-0114NKLFLSDKNSPFYYG1025
S100A2-FXYD3chr1153533819chr1935612126556DRB3-0114FNKLFLSDKNSPFYY924
S100A2-FXYD3chr1153533819chr1935612126556DRB3-0114VFNKLFLSDKNSPFY823
S100A2-FXYD3chr1153533819chr1935612126556DRB3-0114KLFLSDKNSPFYYGA1126
S100A2-FXYD3chr1153533819chr1935612126556DRB3-0114FVFNKLFLSDKNSPF722
S100A2-FXYD3chr1153533819chr1935612126556DRB3-0205PLSFVFNKLFLSDKN419
S100A2-FXYD3chr1153533819chr1935612126556DRB3-0303NKLFLSDKNSPFYYG1025
S100A2-FXYD3chr1153533819chr1935612126556DRB3-0303FNKLFLSDKNSPFYY924
S100A2-FXYD3chr1153533819chr1935612126556DRB3-0303VFNKLFLSDKNSPFY823

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Fusion breakpoint peptide structures of S100A2-FXYD3

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
8569SFVFNKLFLSDKNSS100A2FXYD3chr1153533819chr1935612126556

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of S100A2-FXYD3

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-B14:023BVN8569SFVFNKLFLSDKNS-7.9962-8.1096
HLA-B14:023BVN8569SFVFNKLFLSDKNS-5.70842-6.74372
HLA-B52:013W398569SFVFNKLFLSDKNS-6.83737-6.95077
HLA-B52:013W398569SFVFNKLFLSDKNS-4.4836-5.5189
HLA-A11:014UQ28569SFVFNKLFLSDKNS-10.0067-10.1201
HLA-A11:014UQ28569SFVFNKLFLSDKNS-9.03915-10.0745
HLA-A24:025HGA8569SFVFNKLFLSDKNS-6.56204-6.67544
HLA-A24:025HGA8569SFVFNKLFLSDKNS-5.42271-6.45801
HLA-B44:053DX88569SFVFNKLFLSDKNS-7.85648-8.89178
HLA-B44:053DX88569SFVFNKLFLSDKNS-5.3978-5.5112
HLA-A02:016TDR8569SFVFNKLFLSDKNS-3.37154-4.40684

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Vaccine Design for the FusionNeoAntigens of S100A2-FXYD3

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
S100A2-FXYD3chr1153533819chr19356121261122KLFLSDKNSPFTGTCTGATAAAAACAGTCCTTTCTACTATGGTG
S100A2-FXYD3chr1153533819chr1935612126514LSFVFNKLFTATTCAATAAACTTTTTTTGTCTGATA
S100A2-FXYD3chr1153533819chr1935612126614SFVFNKLFTCAATAAACTTTTTTTGTCTGATA
S100A2-FXYD3chr1153533819chr1935612126615SFVFNKLFLTCAATAAACTTTTTTTGTCTGATAAAA
S100A2-FXYD3chr1153533819chr1935612126715FVFNKLFLATAAACTTTTTTTGTCTGATAAAA

check button mRNA and peptide sequences of FusionNeoAntigens that have potential interaction with HLA-IIs.
Fusion geneHchrHbpTchrTbpStart in +/-13AAEnd in +/-13AAFusionNeoAntigen peptideFusionNEoAntigen RNA sequence
S100A2-FXYD3chr1153533819chr19356121261025NKLFLSDKNSPFYYGTTTTGTCTGATAAAAACAGTCCTTTCTACTATGGTGCTCCATATA
S100A2-FXYD3chr1153533819chr19356121261126KLFLSDKNSPFYYGATGTCTGATAAAAACAGTCCTTTCTACTATGGTGCTCCATATATAT
S100A2-FXYD3chr1153533819chr1935612126419PLSFVFNKLFLSDKNTTGTATTCAATAAACTTTTTTTGTCTGATAAAAACAGTCCTTTCT
S100A2-FXYD3chr1153533819chr1935612126722FVFNKLFLSDKNSPFATAAACTTTTTTTGTCTGATAAAAACAGTCCTTTCTACTATGGTG
S100A2-FXYD3chr1153533819chr1935612126823VFNKLFLSDKNSPFYAACTTTTTTTGTCTGATAAAAACAGTCCTTTCTACTATGGTGCTC
S100A2-FXYD3chr1153533819chr1935612126924FNKLFLSDKNSPFYYTTTTTTTGTCTGATAAAAACAGTCCTTTCTACTATGGTGCTCCAT

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Information of the samples that have these potential fusion neoantigens of S100A2-FXYD3

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
HNSCS100A2-FXYD3chr1153533819ENST00000368707chr1935612126ENST00000603524TCGA-D6-A4ZB-01A

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Potential target of CAR-T therapy development for S100A2-FXYD3

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
TgeneFXYD3chr1:153533819chr19:35612126ENST000003440133939_59088.0TransmembraneHelical
TgeneFXYD3chr1:153533819chr19:35612126ENST000003464462739_590114.0TransmembraneHelical
TgeneFXYD3chr1:153533819chr19:35612126ENST000004062423639_59097.0TransmembraneHelical
TgeneFXYD3chr1:153533819chr19:35612126ENST000004069882839_59088.0TransmembraneHelical
TgeneFXYD3chr1:153533819chr19:35612126ENST000004357344939_590114.0TransmembraneHelical
TgeneFXYD3chr1:153533819chr19:35612126ENST000004549033539_59062.0TransmembraneHelical
TgeneFXYD3chr1:153533819chr19:35612126ENST0000060318141039_59088.0TransmembraneHelical
TgeneFXYD3chr1:153533819chr19:35612126ENST000006034492439_59062.0TransmembraneHelical
TgeneFXYD3chr1:153533819chr19:35612126ENST000006044043939_59088.0TransmembraneHelical
TgeneFXYD3chr1:153533819chr19:35612126ENST000006046212839_59088.0TransmembraneHelical
TgeneFXYD3chr1:153533819chr19:35612126ENST000006055523539_59062.0TransmembraneHelical
TgeneFXYD3chr1:153533819chr19:35612126ENST000006056771439_59097.0TransmembraneHelical

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 S100A2-FXYD3

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 S100A2-FXYD3

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