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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:FNDC3A-ZMYM2

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: FNDC3A-ZMYM2
FusionPDB ID: 30906
FusionGDB2.0 ID: 30906
HgeneTgene
Gene symbol

FNDC3A

ZMYM2

Gene ID

22862

7750

Gene namefibronectin type III domain containing 3Azinc finger MYM-type containing 2
SynonymsFNDC3|HUGO|bA203I16.1|bA203I16.5FIM|MYM|RAMP|SCLL|ZNF198
Cytomap

13q14.2

13q12.11

Type of geneprotein-codingprotein-coding
Descriptionfibronectin type-III domain-containing protein 3Ahuman gene expressed in odontoblastszinc finger MYM-type protein 2fused in myeloproliferative disorders proteinrearranged in an atypical myeloproliferative disorderzinc finger protein 198zinc finger, MYM-type 2
Modification date2020031320200313
UniProtAcc

Q9Y2H6

Main function of 5'-partner protein: FUNCTION: Mediates spermatid-Sertoli adhesion during spermatogenesis. {ECO:0000250}.

Q9UBW7

Main function of 5'-partner protein: FUNCTION: May function as a transcription factor.
Ensembl transtripts involved in fusion geneENST idsENST00000492622, ENST00000541916, 
ENST00000398316, 		ENST00000382871, 
ENST00000382874, ENST00000382881, 
ENST00000382883, ENST00000494061, 
ENST00000382869, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score15 X 12 X 7=12605 X 5 X 4=100
# samples 165
** MAII scorelog2(16/1260*10)=-2.97727992349992
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(5/100*10)=-1
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Fusion gene context

PubMed: FNDC3A [Title/Abstract] AND ZMYM2 [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: FNDC3A [Title/Abstract] AND ZMYM2 [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)FNDC3A(49580425)-ZMYM2(20625573), # samples:1
Anticipated loss of major functional domain due to fusion event.FNDC3A-ZMYM2 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.
FNDC3A-ZMYM2 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.
FNDC3A-ZMYM2 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.
FNDC3A-ZMYM2 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


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/chr13:49580425/chr13:20625573)
- 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 FNDC3A (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 ZMYM2 (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)
ENST00000492622FNDC3Achr1349580425+ENST00000382869ZMYM2chr1320625573+80604042992245648
ENST00000541916FNDC3Achr1349580425+ENST00000382869ZMYM2chr1320625573+7828172672013648

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
ENST00000492622ENST00000382869FNDC3Achr1349580425+ZMYM2chr1320625573+6.64E-050.9999336
ENST00000541916ENST00000382869FNDC3Achr1349580425+ZMYM2chr1320625573+5.61E-050.99994385

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 FNDC3A-ZMYM2

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide
FNDC3Achr1349580425ZMYM2chr132062557317235LSAPIVSADGTQQAARCDCCKSQGTL
FNDC3Achr1349580425ZMYM2chr132062557340435LSAPIVSADGTQQAARCDCCKSQGTL

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Potential FusionNeoAntigen Information of FNDC3A-ZMYM2 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.
FNDC3A-ZMYM2_49580425_20625573.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)
FNDC3A-ZMYM2chr1349580425chr1320625573404HLA-C08:15SADGTQQAA0.9980.9927615
FNDC3A-ZMYM2chr1349580425chr1320625573404HLA-C08:02SADGTQQAA0.9980.9927615

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Potential FusionNeoAntigen Information of FNDC3A-ZMYM2 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.
FNDC3A-ZMYM2_49580425_20625573.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)
FNDC3A-ZMYM2chr1349580425chr1320625573404DRB1-0401SAPIVSADGTQQAAR116
FNDC3A-ZMYM2chr1349580425chr1320625573404DRB1-0403SAPIVSADGTQQAAR116
FNDC3A-ZMYM2chr1349580425chr1320625573404DRB1-0413SAPIVSADGTQQAAR116
FNDC3A-ZMYM2chr1349580425chr1320625573404DRB1-0413LSAPIVSADGTQQAA015
FNDC3A-ZMYM2chr1349580425chr1320625573404DRB1-0413APIVSADGTQQAARC217
FNDC3A-ZMYM2chr1349580425chr1320625573404DRB1-0422SAPIVSADGTQQAAR116
FNDC3A-ZMYM2chr1349580425chr1320625573404DRB1-0422APIVSADGTQQAARC217
FNDC3A-ZMYM2chr1349580425chr1320625573404DRB1-0422LSAPIVSADGTQQAA015
FNDC3A-ZMYM2chr1349580425chr1320625573404DRB1-0427SAPIVSADGTQQAAR116
FNDC3A-ZMYM2chr1349580425chr1320625573404DRB1-0433SAPIVSADGTQQAAR116
FNDC3A-ZMYM2chr1349580425chr1320625573404DRB1-0434SAPIVSADGTQQAAR116
FNDC3A-ZMYM2chr1349580425chr1320625573404DRB1-0435SAPIVSADGTQQAAR116
FNDC3A-ZMYM2chr1349580425chr1320625573404DRB1-0438SAPIVSADGTQQAAR116
FNDC3A-ZMYM2chr1349580425chr1320625573404DRB1-0439SAPIVSADGTQQAAR116
FNDC3A-ZMYM2chr1349580425chr1320625573404DRB1-0440SAPIVSADGTQQAAR116
FNDC3A-ZMYM2chr1349580425chr1320625573404DRB1-0441SAPIVSADGTQQAAR116
FNDC3A-ZMYM2chr1349580425chr1320625573404DRB1-0444SAPIVSADGTQQAAR116
FNDC3A-ZMYM2chr1349580425chr1320625573404DRB1-0444LSAPIVSADGTQQAA015
FNDC3A-ZMYM2chr1349580425chr1320625573404DRB1-0446SAPIVSADGTQQAAR116
FNDC3A-ZMYM2chr1349580425chr1320625573404DRB1-0449SAPIVSADGTQQAAR116
FNDC3A-ZMYM2chr1349580425chr1320625573404DRB1-0450SAPIVSADGTQQAAR116
FNDC3A-ZMYM2chr1349580425chr1320625573404DRB1-0451SAPIVSADGTQQAAR116
FNDC3A-ZMYM2chr1349580425chr1320625573404DRB1-0452SAPIVSADGTQQAAR116
FNDC3A-ZMYM2chr1349580425chr1320625573404DRB1-0455SAPIVSADGTQQAAR116
FNDC3A-ZMYM2chr1349580425chr1320625573404DRB1-0460SAPIVSADGTQQAAR116
FNDC3A-ZMYM2chr1349580425chr1320625573404DRB1-0463SAPIVSADGTQQAAR116
FNDC3A-ZMYM2chr1349580425chr1320625573404DRB1-0464SAPIVSADGTQQAAR116
FNDC3A-ZMYM2chr1349580425chr1320625573404DRB1-0468SAPIVSADGTQQAAR116
FNDC3A-ZMYM2chr1349580425chr1320625573404DRB1-0470SAPIVSADGTQQAAR116
FNDC3A-ZMYM2chr1349580425chr1320625573404DRB1-0471SAPIVSADGTQQAAR116
FNDC3A-ZMYM2chr1349580425chr1320625573404DRB1-0472SAPIVSADGTQQAAR116
FNDC3A-ZMYM2chr1349580425chr1320625573404DRB1-0473SAPIVSADGTQQAAR116
FNDC3A-ZMYM2chr1349580425chr1320625573404DRB1-0476SAPIVSADGTQQAAR116
FNDC3A-ZMYM2chr1349580425chr1320625573404DRB1-0478SAPIVSADGTQQAAR116
FNDC3A-ZMYM2chr1349580425chr1320625573404DRB1-0479SAPIVSADGTQQAAR116
FNDC3A-ZMYM2chr1349580425chr1320625573404DRB1-0485SAPIVSADGTQQAAR116
FNDC3A-ZMYM2chr1349580425chr1320625573404DRB3-0204SAPIVSADGTQQAAR116

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Fusion breakpoint peptide structures of FNDC3A-ZMYM2

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
8374SADGTQQAARCDCCFNDC3AZMYM2chr1349580425chr1320625573404

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of FNDC3A-ZMYM2

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-B14:023BVN8374SADGTQQAARCDCC-7.9962-8.1096
HLA-B14:023BVN8374SADGTQQAARCDCC-5.70842-6.74372
HLA-B52:013W398374SADGTQQAARCDCC-6.83737-6.95077
HLA-B52:013W398374SADGTQQAARCDCC-4.4836-5.5189
HLA-A11:014UQ28374SADGTQQAARCDCC-10.0067-10.1201
HLA-A11:014UQ28374SADGTQQAARCDCC-9.03915-10.0745
HLA-A24:025HGA8374SADGTQQAARCDCC-6.56204-6.67544
HLA-A24:025HGA8374SADGTQQAARCDCC-5.42271-6.45801
HLA-B44:053DX88374SADGTQQAARCDCC-7.85648-8.89178
HLA-B44:053DX88374SADGTQQAARCDCC-5.3978-5.5112
HLA-A02:016TDR8374SADGTQQAARCDCC-3.37154-4.40684

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Vaccine Design for the FusionNeoAntigens of FNDC3A-ZMYM2

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
FNDC3A-ZMYM2chr1349580425chr1320625573615SADGTQQAAAGTGCAGATGGAACACAACAGGCTGCA

check button mRNA and peptide sequences of FusionNeoAntigens that have potential interaction with HLA-IIs.
Fusion geneHchrHbpTchrTbpStart in +/-13AAEnd in +/-13AAFusionNeoAntigen peptideFusionNEoAntigen RNA sequence
FNDC3A-ZMYM2chr1349580425chr1320625573015LSAPIVSADGTQQAATTGTCTGCCCCTATTGTAAGTGCAGATGGAACACAACAGGCTGCA
FNDC3A-ZMYM2chr1349580425chr1320625573116SAPIVSADGTQQAARTCTGCCCCTATTGTAAGTGCAGATGGAACACAACAGGCTGCAAGG
FNDC3A-ZMYM2chr1349580425chr1320625573217APIVSADGTQQAARCGCCCCTATTGTAAGTGCAGATGGAACACAACAGGCTGCAAGGTGT

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Information of the samples that have these potential fusion neoantigens of FNDC3A-ZMYM2

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
BRCAFNDC3A-ZMYM2chr1349580425ENST00000492622chr1320625573ENST00000382869TCGA-A8-A096-01A

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Potential target of CAR-T therapy development for FNDC3A-ZMYM2

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

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Related Drugs to FNDC3A-ZMYM2

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 FNDC3A-ZMYM2

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
TgeneZMYM2C0020796Profound Mental Retardation1CTD_human
TgeneZMYM2C0025363Mental Retardation, Psychosocial1CTD_human
TgeneZMYM2C0027022Myeloproliferative disease1CTD_human
TgeneZMYM2C0917816Mental deficiency1CTD_human
TgeneZMYM2C3714756Intellectual Disability1CTD_human