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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:NFASC-NTRK1

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: NFASC-NTRK1
FusionPDB ID: 58746
FusionGDB2.0 ID: 58746
HgeneTgene
Gene symbol

NFASC

NTRK1

Gene ID

23114

4914

Gene nameneurofascinneurotrophic receptor tyrosine kinase 1
SynonymsNEDCPMD|NF|NRCAMLMTC|TRK|TRK1|TRKA|Trk-A|p140-TrkA
Cytomap

1q32.1

1q23.1

Type of geneprotein-codingprotein-coding
Descriptionneurofascinneurofascin homologneurofascin isoform 140high affinity nerve growth factor receptorOncogene TRKTRK1-transforming tyrosine kinase proteingp140trkneurotrophic tyrosine kinase, receptor, type 1tropomyosin-related kinase Atyrosine kinase receptor A
Modification date2020031320200313
UniProtAcc

O94856

Main function of 5'-partner protein: FUNCTION: Cell adhesion, ankyrin-binding protein which may be involved in neurite extension, axonal guidance, synaptogenesis, myelination and neuron-glial cell interactions. {ECO:0000250}.

P04629

Main function of 5'-partner protein: FUNCTION: Receptor tyrosine kinase involved in the development and the maturation of the central and peripheral nervous systems through regulation of proliferation, differentiation and survival of sympathetic and nervous neurons. High affinity receptor for NGF which is its primary ligand (PubMed:1850821, PubMed:1849459, PubMed:1281417, PubMed:8325889, PubMed:15488758, PubMed:22649032, PubMed:17196528, PubMed:27445338). Can also bind and be activated by NTF3/neurotrophin-3. However, NTF3 only supports axonal extension through NTRK1 but has no effect on neuron survival (By similarity). Upon dimeric NGF ligand-binding, undergoes homodimerization, autophosphorylation and activation (PubMed:1281417). Recruits, phosphorylates and/or activates several downstream effectors including SHC1, FRS2, SH2B1, SH2B2 and PLCG1 that regulate distinct overlapping signaling cascades driving cell survival and differentiation. Through SHC1 and FRS2 activates a GRB2-Ras-MAPK cascade that regulates cell differentiation and survival. Through PLCG1 controls NF-Kappa-B activation and the transcription of genes involved in cell survival. Through SHC1 and SH2B1 controls a Ras-PI3 kinase-AKT1 signaling cascade that is also regulating survival. In absence of ligand and activation, may promote cell death, making the survival of neurons dependent on trophic factors. {ECO:0000250|UniProtKB:P35739, ECO:0000250|UniProtKB:Q3UFB7, ECO:0000269|PubMed:11244088, ECO:0000269|PubMed:1281417, ECO:0000269|PubMed:15488758, ECO:0000269|PubMed:17196528, ECO:0000269|PubMed:1849459, ECO:0000269|PubMed:1850821, ECO:0000269|PubMed:22649032, ECO:0000269|PubMed:27445338, ECO:0000269|PubMed:27676246, ECO:0000269|PubMed:8155326, ECO:0000269|PubMed:8325889}.; FUNCTION: [Isoform TrkA-III]: Resistant to NGF, it constitutively activates AKT1 and NF-kappa-B and is unable to activate the Ras-MAPK signaling cascade. Antagonizes the anti-proliferative NGF-NTRK1 signaling that promotes neuronal precursors differentiation. Isoform TrkA-III promotes angiogenesis and has oncogenic activity when overexpressed. {ECO:0000269|PubMed:15488758}.
Ensembl transtripts involved in fusion geneENST idsENST00000338515, ENST00000338586, 
ENST00000339876, ENST00000360049, 
ENST00000367169, ENST00000367170, 
ENST00000367171, ENST00000367172, 
ENST00000401399, ENST00000404076, 
ENST00000404907, ENST00000513543, 
ENST00000539706, ENST00000403080, 
ENST00000495396, 		ENST00000531606, 
ENST00000358660, ENST00000368196, 
ENST00000392302, ENST00000524377, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score16 X 10 X 4=64025 X 24 X 13=7800
# samples 2133
** MAII scorelog2(21/640*10)=-1.60768257722124
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(33/7800*10)=-4.56293619439116
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Fusion gene context

PubMed: NFASC [Title/Abstract] AND NTRK1 [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: NFASC [Title/Abstract] AND NTRK1 [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)NFASC(204951148)-NTRK1(156844363), # samples:2
Anticipated loss of major functional domain due to fusion event.NFASC-NTRK1 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.
NFASC-NTRK1 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.
NFASC-NTRK1 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.
NFASC-NTRK1 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
TgeneNTRK1

GO:0006468

protein phosphorylation

15488758

TgeneNTRK1

GO:0008285

negative regulation of cell proliferation

15488758

TgeneNTRK1

GO:0010976

positive regulation of neuron projection development

15488758

TgeneNTRK1

GO:0018108

peptidyl-tyrosine phosphorylation

2927393

TgeneNTRK1

GO:0043547

positive regulation of GTPase activity

15488758

TgeneNTRK1

GO:0046579

positive regulation of Ras protein signal transduction

15488758

TgeneNTRK1

GO:0046777

protein autophosphorylation

15488758

TgeneNTRK1

GO:0048011

neurotrophin TRK receptor signaling pathway

15488758

TgeneNTRK1

GO:0051092

positive regulation of NF-kappaB transcription factor activity

15488758

TgeneNTRK1

GO:0070374

positive regulation of ERK1 and ERK2 cascade

15488758

TgeneNTRK1

GO:1904646

cellular response to amyloid-beta

11927634



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/chr1:204951148/chr1:156844363)
- 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 NFASC (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 NTRK1 (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)
ENST00000338586NFASCchr1204951148+ENST00000392302NTRK1chr1156844362+41462798739931328
ENST00000338586NFASCchr1204951148+ENST00000368196NTRK1chr1156844362+42022798739931328
ENST00000338586NFASCchr1204951148+ENST00000524377NTRK1chr1156844362+39942798739931329
ENST00000338586NFASCchr1204951148+ENST00000358660NTRK1chr1156844362+40722798740021331
ENST00000338515NFASCchr1204951148+ENST00000392302NTRK1chr1156844362+41462798739931328
ENST00000338515NFASCchr1204951148+ENST00000368196NTRK1chr1156844362+42022798739931328
ENST00000338515NFASCchr1204951148+ENST00000524377NTRK1chr1156844362+39942798739931329
ENST00000338515NFASCchr1204951148+ENST00000358660NTRK1chr1156844362+40722798740021331
ENST00000367171NFASCchr1204951148+ENST00000392302NTRK1chr1156844362+41012753739481313
ENST00000367171NFASCchr1204951148+ENST00000368196NTRK1chr1156844362+41572753739481313
ENST00000367171NFASCchr1204951148+ENST00000524377NTRK1chr1156844362+39492753739481314
ENST00000367171NFASCchr1204951148+ENST00000358660NTRK1chr1156844362+40272753739571316
ENST00000367169NFASCchr1204951148+ENST00000392302NTRK1chr1156844362+41462798739931328
ENST00000367169NFASCchr1204951148+ENST00000368196NTRK1chr1156844362+42022798739931328
ENST00000367169NFASCchr1204951148+ENST00000524377NTRK1chr1156844362+39942798739931329
ENST00000367169NFASCchr1204951148+ENST00000358660NTRK1chr1156844362+40722798740021331
ENST00000539706NFASCchr1204951148+ENST00000392302NTRK1chr1156844362+41342786739811324
ENST00000539706NFASCchr1204951148+ENST00000368196NTRK1chr1156844362+41902786739811324
ENST00000539706NFASCchr1204951148+ENST00000524377NTRK1chr1156844362+39822786739811325
ENST00000539706NFASCchr1204951148+ENST00000358660NTRK1chr1156844362+40602786739901327
ENST00000339876NFASCchr1204951148+ENST00000392302NTRK1chr1156844362+41462798739931328
ENST00000339876NFASCchr1204951148+ENST00000368196NTRK1chr1156844362+42022798739931328
ENST00000339876NFASCchr1204951148+ENST00000524377NTRK1chr1156844362+39942798739931329
ENST00000339876NFASCchr1204951148+ENST00000358660NTRK1chr1156844362+40722798740021331
ENST00000367170NFASCchr1204951148+ENST00000392302NTRK1chr1156844362+41462798739931328
ENST00000367170NFASCchr1204951148+ENST00000368196NTRK1chr1156844362+42022798739931328
ENST00000367170NFASCchr1204951148+ENST00000524377NTRK1chr1156844362+39942798739931329
ENST00000367170NFASCchr1204951148+ENST00000358660NTRK1chr1156844362+40722798740021331
ENST00000360049NFASCchr1204951148+ENST00000392302NTRK1chr1156844362+41342786739811324
ENST00000360049NFASCchr1204951148+ENST00000368196NTRK1chr1156844362+41902786739811324
ENST00000360049NFASCchr1204951148+ENST00000524377NTRK1chr1156844362+39822786739811325
ENST00000360049NFASCchr1204951148+ENST00000358660NTRK1chr1156844362+40602786739901327
ENST00000367172NFASCchr1204951148+ENST00000392302NTRK1chr1156844362+41462798739931328
ENST00000367172NFASCchr1204951148+ENST00000368196NTRK1chr1156844362+42022798739931328
ENST00000367172NFASCchr1204951148+ENST00000524377NTRK1chr1156844362+39942798739931329
ENST00000367172NFASCchr1204951148+ENST00000358660NTRK1chr1156844362+40722798740021331
ENST00000404076NFASCchr1204951148+ENST00000392302NTRK1chr1156844362+4177282922440241266
ENST00000404076NFASCchr1204951148+ENST00000368196NTRK1chr1156844362+4233282922440241266
ENST00000404076NFASCchr1204951148+ENST00000524377NTRK1chr1156844362+4025282922440241267
ENST00000404076NFASCchr1204951148+ENST00000358660NTRK1chr1156844362+4103282922440331269
ENST00000401399NFASCchr1204951148+ENST00000392302NTRK1chr1156844362+40172669138641287
ENST00000401399NFASCchr1204951148+ENST00000368196NTRK1chr1156844362+40732669138641287
ENST00000401399NFASCchr1204951148+ENST00000524377NTRK1chr1156844362+38652669138641288
ENST00000401399NFASCchr1204951148+ENST00000358660NTRK1chr1156844362+39432669138731290
ENST00000404907NFASCchr1204951148+ENST00000392302NTRK1chr1156844362+38962548037431247
ENST00000404907NFASCchr1204951148+ENST00000368196NTRK1chr1156844362+39522548037431247
ENST00000404907NFASCchr1204951148+ENST00000524377NTRK1chr1156844362+37442548037431247
ENST00000404907NFASCchr1204951148+ENST00000358660NTRK1chr1156844362+38222548037521250
ENST00000513543NFASCchr1204951148+ENST00000392302NTRK1chr1156844362+387125233237181228
ENST00000513543NFASCchr1204951148+ENST00000368196NTRK1chr1156844362+392725233237181228
ENST00000513543NFASCchr1204951148+ENST00000524377NTRK1chr1156844362+371925233237181229
ENST00000513543NFASCchr1204951148+ENST00000358660NTRK1chr1156844362+379725233237271231
ENST00000338586NFASCchr1204951148+ENST00000392302NTRK1chr1156844363+41462798739931328
ENST00000338586NFASCchr1204951148+ENST00000368196NTRK1chr1156844363+42022798739931328
ENST00000338586NFASCchr1204951148+ENST00000524377NTRK1chr1156844363+39942798739931329
ENST00000338586NFASCchr1204951148+ENST00000358660NTRK1chr1156844363+40722798740021331
ENST00000338515NFASCchr1204951148+ENST00000392302NTRK1chr1156844363+41462798739931328
ENST00000338515NFASCchr1204951148+ENST00000368196NTRK1chr1156844363+42022798739931328
ENST00000338515NFASCchr1204951148+ENST00000524377NTRK1chr1156844363+39942798739931329
ENST00000338515NFASCchr1204951148+ENST00000358660NTRK1chr1156844363+40722798740021331
ENST00000367171NFASCchr1204951148+ENST00000392302NTRK1chr1156844363+41012753739481313
ENST00000367171NFASCchr1204951148+ENST00000368196NTRK1chr1156844363+41572753739481313
ENST00000367171NFASCchr1204951148+ENST00000524377NTRK1chr1156844363+39492753739481314
ENST00000367171NFASCchr1204951148+ENST00000358660NTRK1chr1156844363+40272753739571316
ENST00000367169NFASCchr1204951148+ENST00000392302NTRK1chr1156844363+41462798739931328
ENST00000367169NFASCchr1204951148+ENST00000368196NTRK1chr1156844363+42022798739931328
ENST00000367169NFASCchr1204951148+ENST00000524377NTRK1chr1156844363+39942798739931329
ENST00000367169NFASCchr1204951148+ENST00000358660NTRK1chr1156844363+40722798740021331
ENST00000539706NFASCchr1204951148+ENST00000392302NTRK1chr1156844363+41342786739811324
ENST00000539706NFASCchr1204951148+ENST00000368196NTRK1chr1156844363+41902786739811324
ENST00000539706NFASCchr1204951148+ENST00000524377NTRK1chr1156844363+39822786739811325
ENST00000539706NFASCchr1204951148+ENST00000358660NTRK1chr1156844363+40602786739901327
ENST00000339876NFASCchr1204951148+ENST00000392302NTRK1chr1156844363+41462798739931328
ENST00000339876NFASCchr1204951148+ENST00000368196NTRK1chr1156844363+42022798739931328
ENST00000339876NFASCchr1204951148+ENST00000524377NTRK1chr1156844363+39942798739931329
ENST00000339876NFASCchr1204951148+ENST00000358660NTRK1chr1156844363+40722798740021331
ENST00000367170NFASCchr1204951148+ENST00000392302NTRK1chr1156844363+41462798739931328
ENST00000367170NFASCchr1204951148+ENST00000368196NTRK1chr1156844363+42022798739931328
ENST00000367170NFASCchr1204951148+ENST00000524377NTRK1chr1156844363+39942798739931329
ENST00000367170NFASCchr1204951148+ENST00000358660NTRK1chr1156844363+40722798740021331
ENST00000360049NFASCchr1204951148+ENST00000392302NTRK1chr1156844363+41342786739811324
ENST00000360049NFASCchr1204951148+ENST00000368196NTRK1chr1156844363+41902786739811324
ENST00000360049NFASCchr1204951148+ENST00000524377NTRK1chr1156844363+39822786739811325
ENST00000360049NFASCchr1204951148+ENST00000358660NTRK1chr1156844363+40602786739901327
ENST00000367172NFASCchr1204951148+ENST00000392302NTRK1chr1156844363+41462798739931328
ENST00000367172NFASCchr1204951148+ENST00000368196NTRK1chr1156844363+42022798739931328
ENST00000367172NFASCchr1204951148+ENST00000524377NTRK1chr1156844363+39942798739931329
ENST00000367172NFASCchr1204951148+ENST00000358660NTRK1chr1156844363+40722798740021331
ENST00000404076NFASCchr1204951148+ENST00000392302NTRK1chr1156844363+4177282922440241266
ENST00000404076NFASCchr1204951148+ENST00000368196NTRK1chr1156844363+4233282922440241266
ENST00000404076NFASCchr1204951148+ENST00000524377NTRK1chr1156844363+4025282922440241267
ENST00000404076NFASCchr1204951148+ENST00000358660NTRK1chr1156844363+4103282922440331269
ENST00000401399NFASCchr1204951148+ENST00000392302NTRK1chr1156844363+40172669138641287
ENST00000401399NFASCchr1204951148+ENST00000368196NTRK1chr1156844363+40732669138641287
ENST00000401399NFASCchr1204951148+ENST00000524377NTRK1chr1156844363+38652669138641288
ENST00000401399NFASCchr1204951148+ENST00000358660NTRK1chr1156844363+39432669138731290
ENST00000404907NFASCchr1204951148+ENST00000392302NTRK1chr1156844363+38962548037431247
ENST00000404907NFASCchr1204951148+ENST00000368196NTRK1chr1156844363+39522548037431247
ENST00000404907NFASCchr1204951148+ENST00000524377NTRK1chr1156844363+37442548037431247
ENST00000404907NFASCchr1204951148+ENST00000358660NTRK1chr1156844363+38222548037521250
ENST00000513543NFASCchr1204951148+ENST00000392302NTRK1chr1156844363+387125233237181228
ENST00000513543NFASCchr1204951148+ENST00000368196NTRK1chr1156844363+392725233237181228
ENST00000513543NFASCchr1204951148+ENST00000524377NTRK1chr1156844363+371925233237181229
ENST00000513543NFASCchr1204951148+ENST00000358660NTRK1chr1156844363+379725233237271231

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
ENST00000338586ENST00000392302NFASCchr1204951148+NTRK1chr1156844362+0.0020467580.9979532
ENST00000338586ENST00000368196NFASCchr1204951148+NTRK1chr1156844362+0.0019850130.9980149
ENST00000338586ENST00000524377NFASCchr1204951148+NTRK1chr1156844362+0.0021728690.9978271
ENST00000338586ENST00000358660NFASCchr1204951148+NTRK1chr1156844362+0.0019899680.9980101
ENST00000338515ENST00000392302NFASCchr1204951148+NTRK1chr1156844362+0.0020467580.9979532
ENST00000338515ENST00000368196NFASCchr1204951148+NTRK1chr1156844362+0.0019850130.9980149
ENST00000338515ENST00000524377NFASCchr1204951148+NTRK1chr1156844362+0.0021728690.9978271
ENST00000338515ENST00000358660NFASCchr1204951148+NTRK1chr1156844362+0.0019899680.9980101
ENST00000367171ENST00000392302NFASCchr1204951148+NTRK1chr1156844362+0.0016174850.99838257
ENST00000367171ENST00000368196NFASCchr1204951148+NTRK1chr1156844362+0.0015737850.9984262
ENST00000367171ENST00000524377NFASCchr1204951148+NTRK1chr1156844362+0.0017132980.99828666
ENST00000367171ENST00000358660NFASCchr1204951148+NTRK1chr1156844362+0.0018683240.9981317
ENST00000367169ENST00000392302NFASCchr1204951148+NTRK1chr1156844362+0.0020467580.9979532
ENST00000367169ENST00000368196NFASCchr1204951148+NTRK1chr1156844362+0.0019850130.9980149
ENST00000367169ENST00000524377NFASCchr1204951148+NTRK1chr1156844362+0.0021728690.9978271
ENST00000367169ENST00000358660NFASCchr1204951148+NTRK1chr1156844362+0.0019899680.9980101
ENST00000539706ENST00000392302NFASCchr1204951148+NTRK1chr1156844362+0.0016963290.99830365
ENST00000539706ENST00000368196NFASCchr1204951148+NTRK1chr1156844362+0.0016475510.9983525
ENST00000539706ENST00000524377NFASCchr1204951148+NTRK1chr1156844362+0.0017910190.998209
ENST00000539706ENST00000358660NFASCchr1204951148+NTRK1chr1156844362+0.0020638040.99793625
ENST00000339876ENST00000392302NFASCchr1204951148+NTRK1chr1156844362+0.0021936780.9978064
ENST00000339876ENST00000368196NFASCchr1204951148+NTRK1chr1156844362+0.0021278240.9978721
ENST00000339876ENST00000524377NFASCchr1204951148+NTRK1chr1156844362+0.0023266230.99767333
ENST00000339876ENST00000358660NFASCchr1204951148+NTRK1chr1156844362+0.002131040.9978689
ENST00000367170ENST00000392302NFASCchr1204951148+NTRK1chr1156844362+0.0020467580.9979532
ENST00000367170ENST00000368196NFASCchr1204951148+NTRK1chr1156844362+0.0019850130.9980149
ENST00000367170ENST00000524377NFASCchr1204951148+NTRK1chr1156844362+0.0021728690.9978271
ENST00000367170ENST00000358660NFASCchr1204951148+NTRK1chr1156844362+0.0019899680.9980101
ENST00000360049ENST00000392302NFASCchr1204951148+NTRK1chr1156844362+0.0016963290.99830365
ENST00000360049ENST00000368196NFASCchr1204951148+NTRK1chr1156844362+0.0016475510.9983525
ENST00000360049ENST00000524377NFASCchr1204951148+NTRK1chr1156844362+0.0017910190.998209
ENST00000360049ENST00000358660NFASCchr1204951148+NTRK1chr1156844362+0.0020638040.99793625
ENST00000367172ENST00000392302NFASCchr1204951148+NTRK1chr1156844362+0.0020467580.9979532
ENST00000367172ENST00000368196NFASCchr1204951148+NTRK1chr1156844362+0.0019850130.9980149
ENST00000367172ENST00000524377NFASCchr1204951148+NTRK1chr1156844362+0.0021728690.9978271
ENST00000367172ENST00000358660NFASCchr1204951148+NTRK1chr1156844362+0.0019899680.9980101
ENST00000404076ENST00000392302NFASCchr1204951148+NTRK1chr1156844362+0.0022431540.9977569
ENST00000404076ENST00000368196NFASCchr1204951148+NTRK1chr1156844362+0.0021825880.9978174
ENST00000404076ENST00000524377NFASCchr1204951148+NTRK1chr1156844362+0.0023717080.9976283
ENST00000404076ENST00000358660NFASCchr1204951148+NTRK1chr1156844362+0.0025923360.9974076
ENST00000401399ENST00000392302NFASCchr1204951148+NTRK1chr1156844362+0.0024071290.99759287
ENST00000401399ENST00000368196NFASCchr1204951148+NTRK1chr1156844362+0.0023335860.9976665
ENST00000401399ENST00000524377NFASCchr1204951148+NTRK1chr1156844362+0.0025640230.997436
ENST00000401399ENST00000358660NFASCchr1204951148+NTRK1chr1156844362+0.0023419660.997658
ENST00000404907ENST00000392302NFASCchr1204951148+NTRK1chr1156844362+0.0017221450.9982779
ENST00000404907ENST00000368196NFASCchr1204951148+NTRK1chr1156844362+0.0016700890.99832994
ENST00000404907ENST00000524377NFASCchr1204951148+NTRK1chr1156844362+0.001808730.9981913
ENST00000404907ENST00000358660NFASCchr1204951148+NTRK1chr1156844362+0.0020912240.99790883
ENST00000513543ENST00000392302NFASCchr1204951148+NTRK1chr1156844362+0.0017265050.9982735
ENST00000513543ENST00000368196NFASCchr1204951148+NTRK1chr1156844362+0.0016832840.99831676
ENST00000513543ENST00000524377NFASCchr1204951148+NTRK1chr1156844362+0.0018176770.9981823
ENST00000513543ENST00000358660NFASCchr1204951148+NTRK1chr1156844362+0.0021147740.99788517
ENST00000338586ENST00000392302NFASCchr1204951148+NTRK1chr1156844363+0.0020467580.9979532
ENST00000338586ENST00000368196NFASCchr1204951148+NTRK1chr1156844363+0.0019850130.9980149
ENST00000338586ENST00000524377NFASCchr1204951148+NTRK1chr1156844363+0.0021728690.9978271
ENST00000338586ENST00000358660NFASCchr1204951148+NTRK1chr1156844363+0.0019899680.9980101
ENST00000338515ENST00000392302NFASCchr1204951148+NTRK1chr1156844363+0.0020467580.9979532
ENST00000338515ENST00000368196NFASCchr1204951148+NTRK1chr1156844363+0.0019850130.9980149
ENST00000338515ENST00000524377NFASCchr1204951148+NTRK1chr1156844363+0.0021728690.9978271
ENST00000338515ENST00000358660NFASCchr1204951148+NTRK1chr1156844363+0.0019899680.9980101
ENST00000367171ENST00000392302NFASCchr1204951148+NTRK1chr1156844363+0.0016174850.99838257
ENST00000367171ENST00000368196NFASCchr1204951148+NTRK1chr1156844363+0.0015737850.9984262
ENST00000367171ENST00000524377NFASCchr1204951148+NTRK1chr1156844363+0.0017132980.99828666
ENST00000367171ENST00000358660NFASCchr1204951148+NTRK1chr1156844363+0.0018683240.9981317
ENST00000367169ENST00000392302NFASCchr1204951148+NTRK1chr1156844363+0.0020467580.9979532
ENST00000367169ENST00000368196NFASCchr1204951148+NTRK1chr1156844363+0.0019850130.9980149
ENST00000367169ENST00000524377NFASCchr1204951148+NTRK1chr1156844363+0.0021728690.9978271
ENST00000367169ENST00000358660NFASCchr1204951148+NTRK1chr1156844363+0.0019899680.9980101
ENST00000539706ENST00000392302NFASCchr1204951148+NTRK1chr1156844363+0.0016963290.99830365
ENST00000539706ENST00000368196NFASCchr1204951148+NTRK1chr1156844363+0.0016475510.9983525
ENST00000539706ENST00000524377NFASCchr1204951148+NTRK1chr1156844363+0.0017910190.998209
ENST00000539706ENST00000358660NFASCchr1204951148+NTRK1chr1156844363+0.0020638040.99793625
ENST00000339876ENST00000392302NFASCchr1204951148+NTRK1chr1156844363+0.0021936780.9978064
ENST00000339876ENST00000368196NFASCchr1204951148+NTRK1chr1156844363+0.0021278240.9978721
ENST00000339876ENST00000524377NFASCchr1204951148+NTRK1chr1156844363+0.0023266230.99767333
ENST00000339876ENST00000358660NFASCchr1204951148+NTRK1chr1156844363+0.002131040.9978689
ENST00000367170ENST00000392302NFASCchr1204951148+NTRK1chr1156844363+0.0020467580.9979532
ENST00000367170ENST00000368196NFASCchr1204951148+NTRK1chr1156844363+0.0019850130.9980149
ENST00000367170ENST00000524377NFASCchr1204951148+NTRK1chr1156844363+0.0021728690.9978271
ENST00000367170ENST00000358660NFASCchr1204951148+NTRK1chr1156844363+0.0019899680.9980101
ENST00000360049ENST00000392302NFASCchr1204951148+NTRK1chr1156844363+0.0016963290.99830365
ENST00000360049ENST00000368196NFASCchr1204951148+NTRK1chr1156844363+0.0016475510.9983525
ENST00000360049ENST00000524377NFASCchr1204951148+NTRK1chr1156844363+0.0017910190.998209
ENST00000360049ENST00000358660NFASCchr1204951148+NTRK1chr1156844363+0.0020638040.99793625
ENST00000367172ENST00000392302NFASCchr1204951148+NTRK1chr1156844363+0.0020467580.9979532
ENST00000367172ENST00000368196NFASCchr1204951148+NTRK1chr1156844363+0.0019850130.9980149
ENST00000367172ENST00000524377NFASCchr1204951148+NTRK1chr1156844363+0.0021728690.9978271
ENST00000367172ENST00000358660NFASCchr1204951148+NTRK1chr1156844363+0.0019899680.9980101
ENST00000404076ENST00000392302NFASCchr1204951148+NTRK1chr1156844363+0.0022431540.9977569
ENST00000404076ENST00000368196NFASCchr1204951148+NTRK1chr1156844363+0.0021825880.9978174
ENST00000404076ENST00000524377NFASCchr1204951148+NTRK1chr1156844363+0.0023717080.9976283
ENST00000404076ENST00000358660NFASCchr1204951148+NTRK1chr1156844363+0.0025923360.9974076
ENST00000401399ENST00000392302NFASCchr1204951148+NTRK1chr1156844363+0.0024071290.99759287
ENST00000401399ENST00000368196NFASCchr1204951148+NTRK1chr1156844363+0.0023335860.9976665
ENST00000401399ENST00000524377NFASCchr1204951148+NTRK1chr1156844363+0.0025640230.997436
ENST00000401399ENST00000358660NFASCchr1204951148+NTRK1chr1156844363+0.0023419660.997658
ENST00000404907ENST00000392302NFASCchr1204951148+NTRK1chr1156844363+0.0017221450.9982779
ENST00000404907ENST00000368196NFASCchr1204951148+NTRK1chr1156844363+0.0016700890.99832994
ENST00000404907ENST00000524377NFASCchr1204951148+NTRK1chr1156844363+0.001808730.9981913
ENST00000404907ENST00000358660NFASCchr1204951148+NTRK1chr1156844363+0.0020912240.99790883
ENST00000513543ENST00000392302NFASCchr1204951148+NTRK1chr1156844363+0.0017265050.9982735
ENST00000513543ENST00000368196NFASCchr1204951148+NTRK1chr1156844363+0.0016832840.99831676
ENST00000513543ENST00000524377NFASCchr1204951148+NTRK1chr1156844363+0.0018176770.9981823
ENST00000513543ENST00000358660NFASCchr1204951148+NTRK1chr1156844363+0.0021147740.99788517

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 NFASC-NTRK1

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide
NFASCchr1204951148NTRK1chr11568443622523831EPESVIGYSGEDYTNSTSGDPVEKKD
NFASCchr1204951148NTRK1chr11568443622548850EPESVIGYSGEDYTNSTSGDPVEKKD
NFASCchr1204951148NTRK1chr11568443622669890EPESVIGYSGEDYTNSTSGDPVEKKD
NFASCchr1204951148NTRK1chr11568443622753916EPESVIGYSGEDYTNSTSGDPVEKKD
NFASCchr1204951148NTRK1chr11568443622786927EPESVIGYSGEDYTNSTSGDPVEKKD
NFASCchr1204951148NTRK1chr11568443622798931EPESVIGYSGEDYTNSTSGDPVEKKD
NFASCchr1204951148NTRK1chr11568443622829869EPESVIGYSGEDYTNSTSGDPVEKKD
NFASCchr1204951148NTRK1chr11568443632523831EPESVIGYSGEDYTNSTSGDPVEKKD
NFASCchr1204951148NTRK1chr11568443632548850EPESVIGYSGEDYTNSTSGDPVEKKD
NFASCchr1204951148NTRK1chr11568443632669890EPESVIGYSGEDYTNSTSGDPVEKKD
NFASCchr1204951148NTRK1chr11568443632753916EPESVIGYSGEDYTNSTSGDPVEKKD
NFASCchr1204951148NTRK1chr11568443632786927EPESVIGYSGEDYTNSTSGDPVEKKD
NFASCchr1204951148NTRK1chr11568443632798931EPESVIGYSGEDYTNSTSGDPVEKKD
NFASCchr1204951148NTRK1chr11568443632829869EPESVIGYSGEDYTNSTSGDPVEKKD

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Potential FusionNeoAntigen Information of NFASC-NTRK1 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.

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)

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Potential FusionNeoAntigen Information of NFASC-NTRK1 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 NFASC-NTRK1

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.

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of NFASC-NTRK1

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

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Vaccine Design for the FusionNeoAntigens of NFASC-NTRK1

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

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 NFASC-NTRK1

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

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Potential target of CAR-T therapy development for NFASC-NTRK1

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
TgeneNTRK1chr1:204951148chr1:156844362ENST00000368196716424_4390791.0TransmembraneHelical
TgeneNTRK1chr1:204951148chr1:156844362ENST00000392302817424_4390761.0TransmembraneHelical
TgeneNTRK1chr1:204951148chr1:156844362ENST00000524377817424_4390797.0TransmembraneHelical
TgeneNTRK1chr1:204951148chr1:156844363ENST00000368196716424_4390791.0TransmembraneHelical
TgeneNTRK1chr1:204951148chr1:156844363ENST00000392302817424_4390761.0TransmembraneHelical
TgeneNTRK1chr1:204951148chr1:156844363ENST00000524377817424_4390797.0TransmembraneHelical

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 NFASC-NTRK1

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 NFASC-NTRK1

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
TgeneNTRK1C0020074HSAN Type IV17CTD_human;GENOMICS_ENGLAND;UNIPROT
TgeneNTRK1C0238463Papillary thyroid carcinoma3ORPHANET
TgeneNTRK1C0002768Congenital Pain Insensitivity1ORPHANET
TgeneNTRK1C0005586Bipolar Disorder1CTD_human
TgeneNTRK1C0005587Depression, Bipolar1CTD_human
TgeneNTRK1C0017638Glioma1CTD_human
TgeneNTRK1C0020075Hereditary Sensory Autonomic Neuropathy, Type 51CTD_human;ORPHANET
TgeneNTRK1C0024713Manic Disorder1CTD_human
TgeneNTRK1C0027796Neuralgia1CTD_human
TgeneNTRK1C0027819Neuroblastoma1CTD_human
TgeneNTRK1C0033958Psychosis, Brief Reactive1CTD_human
TgeneNTRK1C0033975Psychotic Disorders1CTD_human
TgeneNTRK1C0036337Schizoaffective Disorder1CTD_human
TgeneNTRK1C0036341Schizophrenia1CTD_human
TgeneNTRK1C0036358Schizophreniform Disorders1CTD_human
TgeneNTRK1C0038870Neuralgia, Supraorbital1CTD_human
TgeneNTRK1C0042656Neuralgia, Vidian1CTD_human
TgeneNTRK1C0234247Neuralgia, Atypical1CTD_human
TgeneNTRK1C0234249Neuralgia, Stump1CTD_human
TgeneNTRK1C0259783mixed gliomas1CTD_human
TgeneNTRK1C0273115Lung Injury1CTD_human
TgeneNTRK1C0338831Manic1CTD_human
TgeneNTRK1C0423711Neuralgia, Perineal1CTD_human
TgeneNTRK1C0423712Neuralgia, Iliohypogastric Nerve1CTD_human
TgeneNTRK1C0555198Malignant Glioma1CTD_human
TgeneNTRK1C0598589Inherited neuropathies1GENOMICS_ENGLAND
TgeneNTRK1C0751371Neuralgia, Ilioinguinal1CTD_human
TgeneNTRK1C0751372Nerve Pain1CTD_human
TgeneNTRK1C0751373Paroxysmal Nerve Pain1CTD_human
TgeneNTRK1C0752347Lewy Body Disease1CTD_human
TgeneNTRK1C1833921Familial medullary thyroid carcinoma1CTD_human;GENOMICS_ENGLAND;ORPHANET
TgeneNTRK1C2350344Chronic Lung Injury1CTD_human