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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:SON-ITSN1

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: SON-ITSN1
FusionPDB ID: 85157
FusionGDB2.0 ID: 85157
HgeneTgene
Gene symbol

SON

ITSN1

Gene ID

6651

6453

Gene nameSON DNA and RNA binding proteinintersectin 1
SynonymsBASS1|C21orf50|DBP-5|NREBP|SON3|TOKIMSITSN|SH3D1A|SH3P17
Cytomap

21q22.11

21q22.11

Type of geneprotein-codingprotein-coding
Descriptionprotein SONBax antagonist selected in Saccharomyces 1NRE-binding proteinSON DNA binding proteinnegative regulatory element-binding proteinintersectin-1SH3 domain-containing protein 1ASrc homology 3 domain-containing proteinhuman intersectin-SH3 domain-containing protein SH3P17intersectin 1 (SH3 domain protein)intersectin 1 short form variant 3intersectin 1 short form variant, 11inter
Modification date2020031320200313
UniProtAcc

SHH

Main function of 5'-partner protein: 462

Q15811

Main function of 5'-partner protein: FUNCTION: Adapter protein that provides a link between the endocytic membrane traffic and the actin assembly machinery (PubMed:11584276, PubMed:29887380). Acts as guanine nucleotide exchange factor (GEF) for CDC42, and thereby stimulates actin nucleation mediated by WASL and the ARP2/3 complex (PubMed:11584276). Plays a role in the assembly and maturation of clathrin-coated vesicles (By similarity). Recruits FCHSD2 to clathrin-coated pits (PubMed:29887380). Involved in endocytosis of activated EGFR, and probably also other growth factor receptors (By similarity). Involved in endocytosis of integrin beta-1 (ITGB1) and transferrin receptor (TFR); internalization of ITGB1 as DAB2-dependent cargo but not TFR may involve association with DAB2 (PubMed:22648170). Promotes ubiquitination and subsequent degradation of EGFR, and thereby contributes to the down-regulation of EGFR-dependent signaling pathways. In chromaffin cells, required for normal exocytosis of catecholamines. Required for rapid replenishment of release-ready synaptic vesicles at presynaptic active zones (By similarity). Inhibits ARHGAP31 activity toward RAC1 (PubMed:11744688). {ECO:0000250|UniProtKB:Q9WVE9, ECO:0000250|UniProtKB:Q9Z0R4, ECO:0000269|PubMed:11584276, ECO:0000269|PubMed:11744688, ECO:0000269|PubMed:22648170, ECO:0000269|PubMed:29887380}.; FUNCTION: [Isoform 1]: Plays a role in synaptic vesicle endocytosis in brain neurons. {ECO:0000250|UniProtKB:Q9Z0R4}.
Ensembl transtripts involved in fusion geneENST idsENST00000290239, ENST00000470533, 
ENST00000300278, ENST00000356577, 
ENST00000381692, ENST00000381679, 
ENST00000379960, ENST00000381285, 
ENST00000381291, ENST00000381318, 
ENST00000399326, ENST00000399338, 
ENST00000399349, ENST00000399352, 
ENST00000399353, ENST00000399355, 
ENST00000399367, ENST00000437442, 
ENST00000488166, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score12 X 12 X 5=72019 X 21 X 7=2793
# samples 1622
** MAII scorelog2(16/720*10)=-2.16992500144231
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(22/2793*10)=-3.66624014475529
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Fusion gene context

PubMed: SON [Title/Abstract] AND ITSN1 [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: SON [Title/Abstract] AND ITSN1 [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)ITSN1(35154437)-SON(34939462), # samples:3
SON(34948199)-ITSN1(35153764), # samples:1
SON(34948199)-ITSN1(35183278), # samples:1
SON(34948199)-ITSN1(35153765), # samples:1
SON(34932969)-ITSN1(35063151), # samples:1
Anticipated loss of major functional domain due to fusion event.ITSN1-SON 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.
ITSN1-SON 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.
SON-ITSN1 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.
SON-ITSN1 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.
SON-ITSN1 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.
SON-ITSN1 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
HgeneSON

GO:0006397

mRNA processing

21504830

HgeneSON

GO:0043066

negative regulation of apoptotic process

10509013

HgeneSON

GO:0048024

regulation of mRNA splicing, via spliceosome

21504830



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/chr21:35154437/chr21:34939462)
- 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 SON (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 ITSN1 (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)
ENST00000356577SONchr2134948199+ENST00000399353ITSN1chr2135153764+9778769647597473090
ENST00000356577SONchr2134948199+ENST00000381318ITSN1chr2135153764+228277696475112653596
ENST00000356577SONchr2134948199+ENST00000381291ITSN1chr2135153764+11269769647597623095
ENST00000356577SONchr2134948199+ENST00000381285ITSN1chr2135153764+122717696475112653596
ENST00000356577SONchr2134948199+ENST00000399367ITSN1chr2135153764+115597696475112503591
ENST00000356577SONchr2134948199+ENST00000399352ITSN1chr2135153764+11258769647597473090
ENST00000356577SONchr2134948199+ENST00000399355ITSN1chr2135153764+9855769647595493024
ENST00000356577SONchr2134948199+ENST00000399349ITSN1chr2135153764+11043769647595343019
ENST00000356577SONchr2134948199+ENST00000399338ITSN1chr2135153764+9196769647591622895
ENST00000356577SONchr2134948199+ENST00000379960ITSN1chr2135153764+9379769647588442789
ENST00000356577SONchr2134948199+ENST00000437442ITSN1chr2135153764+110917696475110823535
ENST00000356577SONchr2134948199+ENST00000399326ITSN1chr2135153764+11092769647591472890
ENST00000381692SONchr2134948199+ENST00000399353ITSN1chr2135153764+342813464133971118
ENST00000381692SONchr2134948199+ENST00000381318ITSN1chr2135153764+1647713464149151624
ENST00000381692SONchr2134948199+ENST00000381291ITSN1chr2135153764+491913464134121123
ENST00000381692SONchr2134948199+ENST00000381285ITSN1chr2135153764+592113464149151624
ENST00000381692SONchr2134948199+ENST00000399367ITSN1chr2135153764+520913464149001619
ENST00000381692SONchr2134948199+ENST00000399352ITSN1chr2135153764+490813464133971118
ENST00000381692SONchr2134948199+ENST00000399355ITSN1chr2135153764+350513464131991052
ENST00000381692SONchr2134948199+ENST00000399349ITSN1chr2135153764+469313464131841047
ENST00000381692SONchr2134948199+ENST00000399338ITSN1chr2135153764+28461346412812923
ENST00000381692SONchr2134948199+ENST00000379960ITSN1chr2135153764+30291346412494817
ENST00000381692SONchr2134948199+ENST00000437442ITSN1chr2135153764+474113464147321563
ENST00000381692SONchr2134948199+ENST00000399326ITSN1chr2135153764+47421346412797918
ENST00000356577SONchr2134948199+ENST00000399353ITSN1chr2135183278+9070769647590392854
ENST00000356577SONchr2134948199+ENST00000381318ITSN1chr2135183278+221047696475105423355
ENST00000356577SONchr2134948199+ENST00000381291ITSN1chr2135183278+10546769647590392854
ENST00000356577SONchr2134948199+ENST00000381285ITSN1chr2135183278+115487696475105423355
ENST00000356577SONchr2134948199+ENST00000399367ITSN1chr2135183278+108517696475105423355
ENST00000356577SONchr2134948199+ENST00000399352ITSN1chr2135183278+10550769647590392854
ENST00000356577SONchr2134948199+ENST00000399355ITSN1chr2135183278+9132769647588262783
ENST00000356577SONchr2134948199+ENST00000399349ITSN1chr2135183278+10335769647588262783
ENST00000356577SONchr2134948199+ENST00000399338ITSN1chr2135183278+8488769647584542659
ENST00000356577SONchr2134948199+ENST00000379960ITSN1chr2135183278+8671769647581362553
ENST00000356577SONchr2134948199+ENST00000437442ITSN1chr2135183278+103837696475103743299
ENST00000356577SONchr2134948199+ENST00000399326ITSN1chr2135183278+10384769647584392654
ENST00000381692SONchr2134948199+ENST00000399353ITSN1chr2135183278+27201346412689882
ENST00000381692SONchr2134948199+ENST00000381318ITSN1chr2135183278+1575413464141921383
ENST00000381692SONchr2134948199+ENST00000381291ITSN1chr2135183278+41961346412689882
ENST00000381692SONchr2134948199+ENST00000381285ITSN1chr2135183278+519813464141921383
ENST00000381692SONchr2134948199+ENST00000399367ITSN1chr2135183278+450113464141921383
ENST00000381692SONchr2134948199+ENST00000399352ITSN1chr2135183278+42001346412689882
ENST00000381692SONchr2134948199+ENST00000399355ITSN1chr2135183278+27821346412476811
ENST00000381692SONchr2134948199+ENST00000399349ITSN1chr2135183278+39851346412476811
ENST00000381692SONchr2134948199+ENST00000399338ITSN1chr2135183278+21381346412104687
ENST00000381692SONchr2134948199+ENST00000379960ITSN1chr2135183278+23211346411786581
ENST00000381692SONchr2134948199+ENST00000437442ITSN1chr2135183278+403313464140241327
ENST00000381692SONchr2134948199+ENST00000399326ITSN1chr2135183278+40341346412089682
ENST00000356577SONchr2134948199+ENST00000399353ITSN1chr2135153765+9778769647597473090
ENST00000356577SONchr2134948199+ENST00000381318ITSN1chr2135153765+228277696475112653596
ENST00000356577SONchr2134948199+ENST00000381291ITSN1chr2135153765+11269769647597623095
ENST00000356577SONchr2134948199+ENST00000381285ITSN1chr2135153765+122717696475112653596
ENST00000356577SONchr2134948199+ENST00000399367ITSN1chr2135153765+115597696475112503591
ENST00000356577SONchr2134948199+ENST00000399352ITSN1chr2135153765+11258769647597473090
ENST00000356577SONchr2134948199+ENST00000399355ITSN1chr2135153765+9855769647595493024
ENST00000356577SONchr2134948199+ENST00000399349ITSN1chr2135153765+11043769647595343019
ENST00000356577SONchr2134948199+ENST00000399338ITSN1chr2135153765+9196769647591622895
ENST00000356577SONchr2134948199+ENST00000379960ITSN1chr2135153765+9379769647588442789
ENST00000356577SONchr2134948199+ENST00000437442ITSN1chr2135153765+110917696475110823535
ENST00000356577SONchr2134948199+ENST00000399326ITSN1chr2135153765+11092769647591472890
ENST00000381692SONchr2134948199+ENST00000399353ITSN1chr2135153765+342813464133971118
ENST00000381692SONchr2134948199+ENST00000381318ITSN1chr2135153765+1647713464149151624
ENST00000381692SONchr2134948199+ENST00000381291ITSN1chr2135153765+491913464134121123
ENST00000381692SONchr2134948199+ENST00000381285ITSN1chr2135153765+592113464149151624
ENST00000381692SONchr2134948199+ENST00000399367ITSN1chr2135153765+520913464149001619
ENST00000381692SONchr2134948199+ENST00000399352ITSN1chr2135153765+490813464133971118
ENST00000381692SONchr2134948199+ENST00000399355ITSN1chr2135153765+350513464131991052
ENST00000381692SONchr2134948199+ENST00000399349ITSN1chr2135153765+469313464131841047
ENST00000381692SONchr2134948199+ENST00000399338ITSN1chr2135153765+28461346412812923
ENST00000381692SONchr2134948199+ENST00000379960ITSN1chr2135153765+30291346412494817
ENST00000381692SONchr2134948199+ENST00000437442ITSN1chr2135153765+474113464147321563
ENST00000381692SONchr2134948199+ENST00000399326ITSN1chr2135153765+47421346412797918

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
ENST00000356577ENST00000399353SONchr2134948199+ITSN1chr2135153764+0.0032078140.99679214
ENST00000356577ENST00000381318SONchr2134948199+ITSN1chr2135153764+0.0006362630.9993637
ENST00000356577ENST00000381291SONchr2134948199+ITSN1chr2135153764+0.0010989820.998901
ENST00000356577ENST00000381285SONchr2134948199+ITSN1chr2135153764+0.0016126950.99838734
ENST00000356577ENST00000399367SONchr2134948199+ITSN1chr2135153764+0.0019067150.9980933
ENST00000356577ENST00000399352SONchr2134948199+ITSN1chr2135153764+0.0020335010.9979665
ENST00000356577ENST00000399355SONchr2134948199+ITSN1chr2135153764+0.0036911480.99630886
ENST00000356577ENST00000399349SONchr2134948199+ITSN1chr2135153764+0.0015067530.9984932
ENST00000356577ENST00000399338SONchr2134948199+ITSN1chr2135153764+0.0027116220.99728835
ENST00000356577ENST00000379960SONchr2134948199+ITSN1chr2135153764+0.0022052220.99779475
ENST00000356577ENST00000437442SONchr2134948199+ITSN1chr2135153764+0.0025413140.99745876
ENST00000356577ENST00000399326SONchr2134948199+ITSN1chr2135153764+0.0024362990.9975637
ENST00000381692ENST00000399353SONchr2134948199+ITSN1chr2135153764+0.001500220.99849975
ENST00000381692ENST00000381318SONchr2134948199+ITSN1chr2135153764+0.0001798970.9998202
ENST00000381692ENST00000381291SONchr2134948199+ITSN1chr2135153764+0.0001917450.99980825
ENST00000381692ENST00000381285SONchr2134948199+ITSN1chr2135153764+0.0005246450.9994754
ENST00000381692ENST00000399367SONchr2134948199+ITSN1chr2135153764+0.0008441350.9991559
ENST00000381692ENST00000399352SONchr2134948199+ITSN1chr2135153764+0.0004067210.9995933
ENST00000381692ENST00000399355SONchr2134948199+ITSN1chr2135153764+0.0013894880.9986105
ENST00000381692ENST00000399349SONchr2134948199+ITSN1chr2135153764+0.0002857620.9997142
ENST00000381692ENST00000399338SONchr2134948199+ITSN1chr2135153764+0.0026539330.99734604
ENST00000381692ENST00000379960SONchr2134948199+ITSN1chr2135153764+0.004865660.9951343
ENST00000381692ENST00000437442SONchr2134948199+ITSN1chr2135153764+0.0011773040.9988226
ENST00000381692ENST00000399326SONchr2134948199+ITSN1chr2135153764+0.0022040910.99779594
ENST00000356577ENST00000399353SONchr2134948199+ITSN1chr2135183278+0.0025744530.9974255
ENST00000356577ENST00000381318SONchr2134948199+ITSN1chr2135183278+0.0005032180.9994968
ENST00000356577ENST00000381291SONchr2134948199+ITSN1chr2135183278+0.0015708820.9984291
ENST00000356577ENST00000381285SONchr2134948199+ITSN1chr2135183278+0.001371030.998629
ENST00000356577ENST00000399367SONchr2134948199+ITSN1chr2135183278+0.0015958520.9984042
ENST00000356577ENST00000399352SONchr2134948199+ITSN1chr2135183278+0.0015584180.99844164
ENST00000356577ENST00000399355SONchr2134948199+ITSN1chr2135183278+0.0018712010.99812883
ENST00000356577ENST00000399349SONchr2134948199+ITSN1chr2135183278+0.0011294070.99887055
ENST00000356577ENST00000399338SONchr2134948199+ITSN1chr2135183278+0.0026787590.9973213
ENST00000356577ENST00000379960SONchr2134948199+ITSN1chr2135183278+0.00288010.9971199
ENST00000356577ENST00000437442SONchr2134948199+ITSN1chr2135183278+0.0018029090.99819714
ENST00000356577ENST00000399326SONchr2134948199+ITSN1chr2135183278+0.00193560.99806446
ENST00000381692ENST00000399353SONchr2134948199+ITSN1chr2135183278+0.0015775460.9984225
ENST00000381692ENST00000381318SONchr2134948199+ITSN1chr2135183278+0.0001211970.99987876
ENST00000381692ENST00000381291SONchr2134948199+ITSN1chr2135183278+0.0004694450.99953055
ENST00000381692ENST00000381285SONchr2134948199+ITSN1chr2135183278+0.0003111610.99968886
ENST00000381692ENST00000399367SONchr2134948199+ITSN1chr2135183278+0.0004871690.9995128
ENST00000381692ENST00000399352SONchr2134948199+ITSN1chr2135183278+0.0004658710.99953413
ENST00000381692ENST00000399355SONchr2134948199+ITSN1chr2135183278+0.0019028230.99809724
ENST00000381692ENST00000399349SONchr2134948199+ITSN1chr2135183278+0.0006233320.9993767
ENST00000381692ENST00000399338SONchr2134948199+ITSN1chr2135183278+0.0039535120.9960465
ENST00000381692ENST00000379960SONchr2134948199+ITSN1chr2135183278+0.0038250180.99617493
ENST00000381692ENST00000437442SONchr2134948199+ITSN1chr2135183278+0.0005554280.99944454
ENST00000381692ENST00000399326SONchr2134948199+ITSN1chr2135183278+0.0035921880.9964078
ENST00000356577ENST00000399353SONchr2134948199+ITSN1chr2135153765+0.0032078140.99679214
ENST00000356577ENST00000381318SONchr2134948199+ITSN1chr2135153765+0.0006362630.9993637
ENST00000356577ENST00000381291SONchr2134948199+ITSN1chr2135153765+0.0010989820.998901
ENST00000356577ENST00000381285SONchr2134948199+ITSN1chr2135153765+0.0016126950.99838734
ENST00000356577ENST00000399367SONchr2134948199+ITSN1chr2135153765+0.0019067150.9980933
ENST00000356577ENST00000399352SONchr2134948199+ITSN1chr2135153765+0.0020335010.9979665
ENST00000356577ENST00000399355SONchr2134948199+ITSN1chr2135153765+0.0036911480.99630886
ENST00000356577ENST00000399349SONchr2134948199+ITSN1chr2135153765+0.0015067530.9984932
ENST00000356577ENST00000399338SONchr2134948199+ITSN1chr2135153765+0.0027116220.99728835
ENST00000356577ENST00000379960SONchr2134948199+ITSN1chr2135153765+0.0022052220.99779475
ENST00000356577ENST00000437442SONchr2134948199+ITSN1chr2135153765+0.0025413140.99745876
ENST00000356577ENST00000399326SONchr2134948199+ITSN1chr2135153765+0.0024362990.9975637
ENST00000381692ENST00000399353SONchr2134948199+ITSN1chr2135153765+0.001500220.99849975
ENST00000381692ENST00000381318SONchr2134948199+ITSN1chr2135153765+0.0001798970.9998202
ENST00000381692ENST00000381291SONchr2134948199+ITSN1chr2135153765+0.0001917450.99980825
ENST00000381692ENST00000381285SONchr2134948199+ITSN1chr2135153765+0.0005246450.9994754
ENST00000381692ENST00000399367SONchr2134948199+ITSN1chr2135153765+0.0008441350.9991559
ENST00000381692ENST00000399352SONchr2134948199+ITSN1chr2135153765+0.0004067210.9995933
ENST00000381692ENST00000399355SONchr2134948199+ITSN1chr2135153765+0.0013894880.9986105
ENST00000381692ENST00000399349SONchr2134948199+ITSN1chr2135153765+0.0002857620.9997142
ENST00000381692ENST00000399338SONchr2134948199+ITSN1chr2135153765+0.0026539330.99734604
ENST00000381692ENST00000379960SONchr2134948199+ITSN1chr2135153765+0.004865660.9951343
ENST00000381692ENST00000437442SONchr2134948199+ITSN1chr2135153765+0.0011773040.9988226
ENST00000381692ENST00000399326SONchr2134948199+ITSN1chr2135153765+0.0022040910.99779594

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 SON-ITSN1

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide
SONchr2134948199ITSN1chr21351537647696392AMELPGPPATSMPELQGPPVTPVLEL
SONchr2134948199ITSN1chr21351537657696392AMELPGPPATSMPELQGPPVTPVLEL
SONchr2134948199ITSN1chr21351832787696392AMELPGPPATSMPELQGPPVTPVLEL

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Potential FusionNeoAntigen Information of SON-ITSN1 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.
SON-ITSN1_34948199_35153764.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)
SON-ITSN1chr2134948199chr21351537647696HLA-B56:01MPELQGPPV0.99240.75431120
SON-ITSN1chr2134948199chr21351537647696HLA-B51:02MPELQGPPV0.99070.8611120
SON-ITSN1chr2134948199chr21351537647696HLA-B35:03MPELQGPPV0.98170.92571120
SON-ITSN1chr2134948199chr21351537647696HLA-B35:02MPELQGPPV0.9810.98541120
SON-ITSN1chr2134948199chr21351537647696HLA-B35:04MPELQGPPV0.9810.98541120
SON-ITSN1chr2134948199chr21351537647696HLA-B35:08MPELQGPPV0.96530.86881120
SON-ITSN1chr2134948199chr21351537647696HLA-B51:01MPELQGPPV0.96380.95631120
SON-ITSN1chr2134948199chr21351537647696HLA-B35:03PPATSMPEL0.67160.6961615
SON-ITSN1chr2134948199chr21351537647696HLA-B82:01MPELQGPPV0.5870.62221120
SON-ITSN1chr2134948199chr21351537647696HLA-B35:02PPATSMPEL0.41810.8485615
SON-ITSN1chr2134948199chr21351537647696HLA-B35:04PPATSMPEL0.41810.8485615
SON-ITSN1chr2134948199chr21351537647696HLA-B56:01MPELQGPPVT0.95340.84691121
SON-ITSN1chr2134948199chr21351537647696HLA-B54:01MPELQGPPV0.99840.92741120
SON-ITSN1chr2134948199chr21351537647696HLA-B35:12MPELQGPPV0.9810.98541120
SON-ITSN1chr2134948199chr21351537647696HLA-B78:01MPELQGPPV0.97880.98491120
SON-ITSN1chr2134948199chr21351537647696HLA-B56:04MPELQGPPV0.97450.89051120
SON-ITSN1chr2134948199chr21351537647696HLA-B51:08MPELQGPPV0.95110.86991120
SON-ITSN1chr2134948199chr21351537647696HLA-B42:02MPELQGPPV0.80370.92871120
SON-ITSN1chr2134948199chr21351537647696HLA-B42:01MPELQGPPV0.7250.92251120
SON-ITSN1chr2134948199chr21351537647696HLA-B39:10MPELQGPPV0.6870.9941120
SON-ITSN1chr2134948199chr21351537647696HLA-B35:12PPATSMPEL0.41810.8485615
SON-ITSN1chr2134948199chr21351537647696HLA-B39:10PPATSMPEL0.09140.8302615
SON-ITSN1chr2134948199chr21351537647696HLA-B54:01MPELQGPPVT0.98760.95311121
SON-ITSN1chr2134948199chr21351537647696HLA-A02:07SMPELQGPPV0.95720.66211020
SON-ITSN1chr2134948199chr21351537647696HLA-B54:01MPELQGPPVTP0.99960.97311122
SON-ITSN1chr2134948199chr21351537647696HLA-B35:22MPELQGPPV0.99310.82741120
SON-ITSN1chr2134948199chr21351537647696HLA-B55:02MPELQGPPV0.98570.82811120
SON-ITSN1chr2134948199chr21351537647696HLA-B59:01MPELQGPPV0.98520.94321120
SON-ITSN1chr2134948199chr21351537647696HLA-B35:09MPELQGPPV0.9810.98541120
SON-ITSN1chr2134948199chr21351537647696HLA-B55:04MPELQGPPV0.97670.91120
SON-ITSN1chr2134948199chr21351537647696HLA-B56:05MPELQGPPV0.97470.93011120
SON-ITSN1chr2134948199chr21351537647696HLA-B56:02MPELQGPPV0.97450.89051120
SON-ITSN1chr2134948199chr21351537647696HLA-B78:02MPELQGPPV0.97450.98991120
SON-ITSN1chr2134948199chr21351537647696HLA-B51:21MPELQGPPV0.97140.9451120
SON-ITSN1chr2134948199chr21351537647696HLA-B51:09MPELQGPPV0.97120.9471120
SON-ITSN1chr2134948199chr21351537647696HLA-B51:29MPELQGPPV0.96970.75551120
SON-ITSN1chr2134948199chr21351537647696HLA-B51:05MPELQGPPV0.96770.59281120
SON-ITSN1chr2134948199chr21351537647696HLA-B51:14MPELQGPPV0.96510.88611120
SON-ITSN1chr2134948199chr21351537647696HLA-B51:13MPELQGPPV0.96280.89641120
SON-ITSN1chr2134948199chr21351537647696HLA-B67:01MPELQGPPV0.80560.99141120
SON-ITSN1chr2134948199chr21351537647696HLA-B82:02MPELQGPPV0.5870.62221120
SON-ITSN1chr2134948199chr21351537647696HLA-B35:09PPATSMPEL0.41810.8485615
SON-ITSN1chr2134948199chr21351537647696HLA-B67:01PPATSMPEL0.09770.6118615
SON-ITSN1chr2134948199chr21351537647696HLA-B55:02MPELQGPPVT0.9280.88561121
SON-ITSN1chr2134948199chr21351537647696HLA-B55:02MPELQGPPVTP0.99060.93781122

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Potential FusionNeoAntigen Information of SON-ITSN1 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 SON-ITSN1

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
6844PPATSMPELQGPPVSONITSN1chr2134948199chr21351537647696

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of SON-ITSN1

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-B14:023BVN6844PPATSMPELQGPPV-8.55667-8.74867
HLA-B14:023BVN6844PPATSMPELQGPPV-3.49457-4.25557
HLA-B52:013W396844PPATSMPELQGPPV-7.26725-7.45925
HLA-B52:013W396844PPATSMPELQGPPV-4.01461-4.77561
HLA-A24:025HGA6844PPATSMPELQGPPV-7.65911-8.42011
HLA-A24:025HGA6844PPATSMPELQGPPV-7.10204-7.29404
HLA-B44:053DX86844PPATSMPELQGPPV-7.5556-8.3166
HLA-B44:053DX86844PPATSMPELQGPPV-2.76159-2.95359

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Vaccine Design for the FusionNeoAntigens of SON-ITSN1

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
SON-ITSN1chr2134948199chr21351537641020SMPELQGPPVCTCTTTAGGGAATCTCAGCAAATGCTTGGA
SON-ITSN1chr2134948199chr21351537641120MPELQGPPVTTTAGGGAATCTCAGCAAATGCTTGGA
SON-ITSN1chr2134948199chr21351537641121MPELQGPPVTTTTAGGGAATCTCAGCAAATGCTTGGAAGA
SON-ITSN1chr2134948199chr21351537641122MPELQGPPVTPTTTAGGGAATCTCAGCAAATGCTTGGAAGACTT
SON-ITSN1chr2134948199chr2135153764615PPATSMPELCGCAAACATTTTCTCTTTAGGGAATCT

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 SON-ITSN1

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
SKCMSON-ITSN1chr2134948199ENST00000356577chr2135153764ENST00000381285TCGA-DA-A1I7

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Potential target of CAR-T therapy development for SON-ITSN1

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 SON-ITSN1

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 SON-ITSN1

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