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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:STARD3-NFIX

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: STARD3-NFIX
FusionPDB ID: 87184
FusionGDB2.0 ID: 87184
HgeneTgene
Gene symbol

STARD3

NFIX

Gene ID

10948

4784

Gene nameStAR related lipid transfer domain containing 3nuclear factor I X
SynonymsCAB1|MLN64|es64CTF|MRSHSS|NF-I/X|NF1-X|NF1A|SOTOS2
Cytomap

17q12

19p13.13

Type of geneprotein-codingprotein-coding
DescriptionstAR-related lipid transfer protein 3MLN 64START domain-containing protein 3StAR-related lipid transfer (START) domain containing 3metastatic lymph node gene 64 proteinmetastatic lymph node protein 64steroidogenic acute regulatory protein relatednuclear factor 1 X-typeCCAAT-box-binding transcription factorTGGCA-binding proteinnuclear factor 1/X
Modification date2020031320200329
UniProtAcc

STARD3NL

Main function of 5'-partner protein: 234

Q14938

Main function of 5'-partner protein: FUNCTION: Recognizes and binds the palindromic sequence 5'-TTGGCNNNNNGCCAA-3' present in viral and cellular promoters and in the origin of replication of adenovirus type 2. These proteins are individually capable of activating transcription and replication.
Ensembl transtripts involved in fusion geneENST idsENST00000578232, ENST00000336308, 
ENST00000394250, ENST00000544210, 
ENST00000580611, 		ENST00000360105, 
ENST00000397661, ENST00000585575, 
ENST00000587760, ENST00000592199, 
ENST00000358552, ENST00000587260, 
ENST00000588228, ENST00000588680, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score25 X 11 X 9=247522 X 13 X 10=2860
# samples 3526
** MAII scorelog2(35/2475*10)=-2.82200169802201
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(26/2860*10)=-3.4594316186373
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Fusion gene context

PubMed: STARD3 [Title/Abstract] AND NFIX [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: STARD3 [Title/Abstract] AND NFIX [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)STARD3(37810003)-NFIX(13135835), # samples:2
Anticipated loss of major functional domain due to fusion event.STARD3-NFIX 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.
STARD3-NFIX 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.
STARD3-NFIX 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.
STARD3-NFIX 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
HgeneSTARD3

GO:0030301

cholesterol transport

28377464

HgeneSTARD3

GO:0099044

vesicle tethering to endoplasmic reticulum

24105263|28377464

TgeneNFIX

GO:0000122

negative regulation of transcription by RNA polymerase II

19706729

TgeneNFIX

GO:0045944

positive regulation of transcription by RNA polymerase II

19706729



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/chr17:37810003/chr19:13135835)
- 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 STARD3 (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 NFIX (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)
ENST00000336308STARD3chr1737810003+ENST00000397661NFIXchr1913135835+33234371971735512
ENST00000336308STARD3chr1737810003+ENST00000592199NFIXchr1913135835+19194371971918574
ENST00000336308STARD3chr1737810003+ENST00000587760NFIXchr1913135835+18804371971735512
ENST00000336308STARD3chr1737810003+ENST00000585575NFIXchr1913135835+19194371971918574
ENST00000336308STARD3chr1737810003+ENST00000360105NFIXchr1913135835+57954371971612471
ENST00000544210STARD3chr1737810003+ENST00000397661NFIXchr1913135835+32473611211659512
ENST00000544210STARD3chr1737810003+ENST00000592199NFIXchr1913135835+18433611211842574
ENST00000544210STARD3chr1737810003+ENST00000587760NFIXchr1913135835+18043611211659512
ENST00000544210STARD3chr1737810003+ENST00000585575NFIXchr1913135835+18433611211842574
ENST00000544210STARD3chr1737810003+ENST00000360105NFIXchr1913135835+57193611211536471
ENST00000394250STARD3chr1737810003+ENST00000397661NFIXchr1913135835+32443581181656512
ENST00000394250STARD3chr1737810003+ENST00000592199NFIXchr1913135835+18403581181839574
ENST00000394250STARD3chr1737810003+ENST00000587760NFIXchr1913135835+18013581181656512
ENST00000394250STARD3chr1737810003+ENST00000585575NFIXchr1913135835+18403581181839574
ENST00000394250STARD3chr1737810003+ENST00000360105NFIXchr1913135835+57163581181533471
ENST00000580611STARD3chr1737810003+ENST00000397661NFIXchr1913135835+32353491091647512
ENST00000580611STARD3chr1737810003+ENST00000592199NFIXchr1913135835+18313491091830574
ENST00000580611STARD3chr1737810003+ENST00000587760NFIXchr1913135835+17923491091647512
ENST00000580611STARD3chr1737810003+ENST00000585575NFIXchr1913135835+18313491091830574
ENST00000580611STARD3chr1737810003+ENST00000360105NFIXchr1913135835+57073491091524471

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
ENST00000336308ENST00000397661STARD3chr1737810003+NFIXchr1913135835+0.047114690.9528853
ENST00000336308ENST00000592199STARD3chr1737810003+NFIXchr1913135835+0.075595850.92440414
ENST00000336308ENST00000587760STARD3chr1737810003+NFIXchr1913135835+0.070364960.929635
ENST00000336308ENST00000585575STARD3chr1737810003+NFIXchr1913135835+0.075595850.92440414
ENST00000336308ENST00000360105STARD3chr1737810003+NFIXchr1913135835+0.0180282180.9819718
ENST00000544210ENST00000397661STARD3chr1737810003+NFIXchr1913135835+0.0452376460.95476234
ENST00000544210ENST00000592199STARD3chr1737810003+NFIXchr1913135835+0.074723940.92527604
ENST00000544210ENST00000587760STARD3chr1737810003+NFIXchr1913135835+0.068701190.9312988
ENST00000544210ENST00000585575STARD3chr1737810003+NFIXchr1913135835+0.074723940.92527604
ENST00000544210ENST00000360105STARD3chr1737810003+NFIXchr1913135835+0.0173756460.98262435
ENST00000394250ENST00000397661STARD3chr1737810003+NFIXchr1913135835+0.045416070.95458394
ENST00000394250ENST00000592199STARD3chr1737810003+NFIXchr1913135835+0.0751974060.9248026
ENST00000394250ENST00000587760STARD3chr1737810003+NFIXchr1913135835+0.0693012550.9306987
ENST00000394250ENST00000585575STARD3chr1737810003+NFIXchr1913135835+0.0751974060.9248026
ENST00000394250ENST00000360105STARD3chr1737810003+NFIXchr1913135835+0.0173574690.98264253
ENST00000580611ENST00000397661STARD3chr1737810003+NFIXchr1913135835+0.0463979130.95360214
ENST00000580611ENST00000592199STARD3chr1737810003+NFIXchr1913135835+0.0747806360.9252194
ENST00000580611ENST00000587760STARD3chr1737810003+NFIXchr1913135835+0.070279830.9297202
ENST00000580611ENST00000585575STARD3chr1737810003+NFIXchr1913135835+0.0747806360.9252194
ENST00000580611ENST00000360105STARD3chr1737810003+NFIXchr1913135835+0.017473140.98252684

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 STARD3-NFIX

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide
STARD3chr1737810003NFIXchr191313583534978FDLLFISLLWIIELNDEFHPFIEALL
STARD3chr1737810003NFIXchr191313583535878FDLLFISLLWIIELNDEFHPFIEALL
STARD3chr1737810003NFIXchr191313583536178FDLLFISLLWIIELNDEFHPFIEALL
STARD3chr1737810003NFIXchr191313583543778FDLLFISLLWIIELNDEFHPFIEALL

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Potential FusionNeoAntigen Information of STARD3-NFIX 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.
STARD3-NFIX_37810003_13135835.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)
STARD3-NFIXchr1737810003chr1913135835437HLA-A02:04SLLWIIEL0.95660.6896614
STARD3-NFIXchr1737810003chr1913135835437HLA-B35:08WIIELNDEF0.99320.8662918
STARD3-NFIXchr1737810003chr1913135835437HLA-B35:01WIIELNDEF0.98550.9179918
STARD3-NFIXchr1737810003chr1913135835437HLA-B35:08ELNDEFHPF0.97680.89581221
STARD3-NFIXchr1737810003chr1913135835437HLA-B15:02ELNDEFHPF0.97120.88161221
STARD3-NFIXchr1737810003chr1913135835437HLA-B35:01ELNDEFHPF0.91570.92081221
STARD3-NFIXchr1737810003chr1913135835437HLA-B15:31WIIELNDEF0.98430.9064918
STARD3-NFIXchr1737810003chr1913135835437HLA-B15:21ELNDEFHPF0.97120.86231221
STARD3-NFIXchr1737810003chr1913135835437HLA-B15:31ELNDEFHPF0.92320.81531221
STARD3-NFIXchr1737810003chr1913135835437HLA-B15:08WIIELNDEF0.9970.921918
STARD3-NFIXchr1737810003chr1913135835437HLA-C03:05ISLLWIIEL0.99660.9093514
STARD3-NFIXchr1737810003chr1913135835437HLA-C15:02ISLLWIIEL0.99650.8485514
STARD3-NFIXchr1737810003chr1913135835437HLA-B35:77WIIELNDEF0.98550.9179918
STARD3-NFIXchr1737810003chr1913135835437HLA-B35:23WIIELNDEF0.98540.9143918
STARD3-NFIXchr1737810003chr1913135835437HLA-A25:01ELNDEFHPF0.98290.91381221
STARD3-NFIXchr1737810003chr1913135835437HLA-B15:11ELNDEFHPF0.98250.77131221
STARD3-NFIXchr1737810003chr1913135835437HLA-B35:20WIIELNDEF0.98230.9365918
STARD3-NFIXchr1737810003chr1913135835437HLA-B15:08ELNDEFHPF0.98140.78291221
STARD3-NFIXchr1737810003chr1913135835437HLA-B35:43ELNDEFHPF0.97550.78741221
STARD3-NFIXchr1737810003chr1913135835437HLA-B15:12ELNDEFHPF0.97040.83171221
STARD3-NFIXchr1737810003chr1913135835437HLA-B35:23ELNDEFHPF0.91670.89991221
STARD3-NFIXchr1737810003chr1913135835437HLA-B35:77ELNDEFHPF0.91570.92081221
STARD3-NFIXchr1737810003chr1913135835437HLA-B35:20ELNDEFHPF0.91410.93081221
STARD3-NFIXchr1737810003chr1913135835437HLA-B35:24ELNDEFHPF0.82650.93711221
STARD3-NFIXchr1737810003chr1913135835437HLA-C17:01ISLLWIIEL0.60420.9207514
STARD3-NFIXchr1737810003chr1913135835437HLA-B18:04ELNDEFHPF0.53610.93831221
STARD3-NFIXchr1737810003chr1913135835437HLA-B08:12ELNDEFHPF0.24630.86981221
STARD3-NFIXchr1737810003chr1913135835437HLA-B18:11IELNDEFHPF0.98810.91461121

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Potential FusionNeoAntigen Information of STARD3-NFIX 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 STARD3-NFIX

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
8766SLLWIIELNDEFHPSTARD3NFIXchr1737810003chr1913135835437

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of STARD3-NFIX

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-B14:023BVN8766SLLWIIELNDEFHP-7.15543-7.26883
HLA-B14:023BVN8766SLLWIIELNDEFHP-4.77435-5.80965
HLA-B52:013W398766SLLWIIELNDEFHP-6.80875-6.92215
HLA-B52:013W398766SLLWIIELNDEFHP-4.20386-5.23916
HLA-A11:014UQ28766SLLWIIELNDEFHP-7.5194-8.5547
HLA-A11:014UQ28766SLLWIIELNDEFHP-6.9601-7.0735
HLA-A24:025HGA8766SLLWIIELNDEFHP-7.52403-7.63743
HLA-A24:025HGA8766SLLWIIELNDEFHP-5.82433-6.85963
HLA-B27:056PYJ8766SLLWIIELNDEFHP-3.28285-4.31815
HLA-B44:053DX88766SLLWIIELNDEFHP-5.91172-6.94702
HLA-B44:053DX88766SLLWIIELNDEFHP-4.24346-4.35686

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Vaccine Design for the FusionNeoAntigens of STARD3-NFIX

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
STARD3-NFIXchr1737810003chr19131358351121IELNDEFHPFCTGAATGATGAGTTCCACCCGTTCATCGAG
STARD3-NFIXchr1737810003chr19131358351221ELNDEFHPFAATGATGAGTTCCACCCGTTCATCGAG
STARD3-NFIXchr1737810003chr1913135835514ISLLWIIELCTGCTCTGGATCATCGAACTGAATGAT
STARD3-NFIXchr1737810003chr1913135835614SLLWIIELCTCTGGATCATCGAACTGAATGAT
STARD3-NFIXchr1737810003chr1913135835918WIIELNDEFATCGAACTGAATGATGAGTTCCACCCG

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 STARD3-NFIX

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
BRCASTARD3-NFIXchr1737810003ENST00000336308chr1913135835ENST00000360105TCGA-A2-A1G1-01A

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Potential target of CAR-T therapy development for STARD3-NFIX

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
HgeneSTARD3chr17:37810003chr19:13135835ENST00000336308+21552_7273446.0TransmembraneHelical
HgeneSTARD3chr17:37810003chr19:13135835ENST00000394250+21452_7273428.0TransmembraneHelical
HgeneSTARD3chr17:37810003chr19:13135835ENST00000544210+21552_7273446.0TransmembraneHelical

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 STARD3-NFIX

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 STARD3-NFIX

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