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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:SUZ12-NF1

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: SUZ12-NF1
FusionPDB ID: 88244
FusionGDB2.0 ID: 88244
HgeneTgene
Gene symbol

SUZ12

NF1

Gene ID

23512

4763

Gene nameSUZ12 polycomb repressive complex 2 subunitneurofibromin 1
SynonymsCHET9|IMMAS|JJAZ1NFNS|VRNF|WSS
Cytomap

17q11.2

17q11.2

Type of geneprotein-codingprotein-coding
Descriptionpolycomb protein SUZ12chET 9 proteinchromatin precipitated E2F target 9 proteinjoined to JAZF1 proteinsuppressor of zeste 12 protein homologneurofibrominneurofibromatosis 1neurofibromatosis-related protein NF-1truncated neurofibromin 1
Modification date2020031320200322
UniProtAcc

Q15022

Main function of 5'-partner protein: FUNCTION: Polycomb group (PcG) protein. Component of the PRC2 complex, which methylates 'Lys-9' (H3K9me) and 'Lys-27' (H3K27me) of histone H3, leading to transcriptional repression of the affected target gene (PubMed:15225548, PubMed:15231737, PubMed:15385962, PubMed:16618801, PubMed:17344414, PubMed:18285464, PubMed:28229514, PubMed:29499137, PubMed:31959557). The PRC2 complex may also serve as a recruiting platform for DNA methyltransferases, thereby linking two epigenetic repression systems (PubMed:12435631, PubMed:12351676, PubMed:15385962, PubMed:15099518, PubMed:15225548, PubMed:15684044, PubMed:16431907, PubMed:18086877, PubMed:18285464). Genes repressed by the PRC2 complex include HOXC8, HOXA9, MYT1 and CDKN2A (PubMed:15231737, PubMed:16618801, PubMed:17200670, PubMed:31959557). {ECO:0000269|PubMed:12351676, ECO:0000269|PubMed:12435631, ECO:0000269|PubMed:15099518, ECO:0000269|PubMed:15225548, ECO:0000269|PubMed:15231737, ECO:0000269|PubMed:15385962, ECO:0000269|PubMed:15684044, ECO:0000269|PubMed:16431907, ECO:0000269|PubMed:16618801, ECO:0000269|PubMed:17200670, ECO:0000269|PubMed:17344414, ECO:0000269|PubMed:18086877, ECO:0000269|PubMed:18285464, ECO:0000269|PubMed:28229514, ECO:0000269|PubMed:29499137, ECO:0000269|PubMed:31959557}.

P21359

Main function of 5'-partner protein: FUNCTION: Stimulates the GTPase activity of Ras. NF1 shows greater affinity for Ras GAP, but lower specific activity. May be a regulator of Ras activity. {ECO:0000269|PubMed:2121371, ECO:0000269|PubMed:8417346}.
Ensembl transtripts involved in fusion geneENST idsENST00000322652, ENST00000580398, 
ENST00000444181, ENST00000356175, 
ENST00000358273, ENST00000417592, 
ENST00000431387, ENST00000581113, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score15 X 12 X 10=180028 X 30 X 15=12600
# samples 1533
** MAII scorelog2(15/1800*10)=-3.58496250072116
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(33/12600*10)=-5.25481389902883
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Fusion gene context

PubMed: SUZ12 [Title/Abstract] AND NF1 [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: SUZ12 [Title/Abstract] AND NF1 [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)SUZ12(30303633)-NF1(29576002), # samples:3
NF1(29533389)-SUZ12(30293166), # samples:1
Anticipated loss of major functional domain due to fusion event.SUZ12-NF1 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.
SUZ12-NF1 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.
SUZ12-NF1 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.
SUZ12-NF1 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.
NF1-SUZ12 seems lost the major protein functional domain in Hgene partner, which is a CGC due to the frame-shifted ORF.
NF1-SUZ12 seems lost the major protein functional domain in Hgene partner, which is a tumor suppressor due to the frame-shifted ORF.
NF1-SUZ12 seems lost the major protein functional domain in Tgene partner, which is a CGC due to the frame-shifted ORF.
NF1-SUZ12 seems lost the major protein functional domain in Tgene partner, which is a epigenetic factor due to the frame-shifted ORF.
NF1-SUZ12 seems lost the major protein functional domain in Tgene partner, which is a tumor suppressor due to the frame-shifted ORF.
* DoF score (Degree of Frequency) = # partners X # break points X # cancer types
** MAII score (Major Active Isofusion Index) = log2(# samples/DoF score*10)

check button Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez
PartnerGeneGO IDGO termPubMed ID
TgeneNF1

GO:0043547

positive regulation of GTPase activity

2121371



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/chr17:30303633/chr17:29576002)
- 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 SUZ12 (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 NF1 (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)
ENST00000322652SUZ12chr1730303633+ENST00000356175NF1chr1729576002+915111463756281863
ENST00000322652SUZ12chr1730303633+ENST00000358273NF1chr1729576002+921411463756911884
ENST00000580398SUZ12chr1730303633+ENST00000356175NF1chr1729576002+9033102810855101800
ENST00000580398SUZ12chr1730303633+ENST00000358273NF1chr1729576002+9096102810855731821

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
ENST00000322652ENST00000356175SUZ12chr1730303633+NF1chr1729576002+0.0001762750.99982375
ENST00000322652ENST00000358273SUZ12chr1730303633+NF1chr1729576002+0.000176420.99982363
ENST00000580398ENST00000356175SUZ12chr1730303633+NF1chr1729576002+0.0001673050.99983263
ENST00000580398ENST00000358273SUZ12chr1730303633+NF1chr1729576002+0.000166090.99983394

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 SUZ12-NF1

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

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Potential FusionNeoAntigen Information of SUZ12-NF1 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 SUZ12-NF1 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 SUZ12-NF1

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 SUZ12-NF1

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 SUZ12-NF1

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 SUZ12-NF1

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 SUZ12-NF1

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 SUZ12-NF1

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 SUZ12-NF1

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
HgeneSUZ12C0206727Nerve Sheath Tumors2CTD_human
HgeneSUZ12C0751689Peripheral Nerve Sheath Neoplasm2CTD_human
HgeneSUZ12C0751691Perineurioma2CTD_human
HgeneSUZ12C0001430Adenoma1CTD_human
HgeneSUZ12C0014170Endometrial Neoplasms1CTD_human
HgeneSUZ12C0017636Glioblastoma1CTD_human
HgeneSUZ12C0017638Glioma1CTD_human
HgeneSUZ12C0025202melanoma1CTD_human
HgeneSUZ12C0027809Neurilemmoma1CTD_human
HgeneSUZ12C0027830neurofibroma1CTD_human
HgeneSUZ12C0027962Melanocytic nevus1CTD_human
HgeneSUZ12C0042063Urogenital Abnormalities1GENOMICS_ENGLAND
HgeneSUZ12C0205646Adenoma, Basal Cell1CTD_human
HgeneSUZ12C0205647Follicular adenoma1CTD_human
HgeneSUZ12C0205648Adenoma, Microcystic1CTD_human
HgeneSUZ12C0205649Adenoma, Monomorphic1CTD_human
HgeneSUZ12C0205650Papillary adenoma1CTD_human
HgeneSUZ12C0205651Adenoma, Trabecular1CTD_human
HgeneSUZ12C0206630Endometrial Stromal Sarcoma1ORPHANET
HgeneSUZ12C0259783mixed gliomas1CTD_human
HgeneSUZ12C0265210Weaver syndrome1ORPHANET
HgeneSUZ12C0334588Giant Cell Glioblastoma1CTD_human
HgeneSUZ12C0476089Endometrial Carcinoma1CTD_human
HgeneSUZ12C0545053Advanced bone age1GENOMICS_ENGLAND
HgeneSUZ12C0555198Malignant Glioma1CTD_human
HgeneSUZ12C0557874Global developmental delay1GENOMICS_ENGLAND
HgeneSUZ12C0751374Schwannomatosis, Plexiform1CTD_human
HgeneSUZ12C1621958Glioblastoma Multiforme1CTD_human
HgeneSUZ12C1842581Abnormal corpus callosum morphology1GENOMICS_ENGLAND
HgeneSUZ12C1849265Overgrowth1GENOMICS_ENGLAND
HgeneSUZ12C3714756Intellectual Disability1GENOMICS_ENGLAND
HgeneSUZ12C4018871Abnormality of the respiratory system1GENOMICS_ENGLAND
HgeneSUZ12C4021664Abnormality of the abdominal wall1GENOMICS_ENGLAND
HgeneSUZ12C4021790Abnormality of the skeletal system1GENOMICS_ENGLAND
TgeneNF1C0027831Neurofibromatosis 144CTD_human;GENOMICS_ENGLAND;UNIPROT
TgeneNF1C1708353Hereditary Paraganglioma-Pheochromocytoma Syndrome10CLINGEN
TgeneNF1C0349639Juvenile Myelomonocytic Leukemia7CTD_human;GENOMICS_ENGLAND;ORPHANET
TgeneNF1C2931482Neurofibromatosis-Noonan syndrome6CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
TgeneNF1C0553586Cafe-au-lait macules with pulmonary stenosis5CTD_human;GENOMICS_ENGLAND;ORPHANET
TgeneNF1C0162678Neurofibromatoses3CGI;CTD_human;GENOMICS_ENGLAND
TgeneNF1C0004114Astrocytoma2CTD_human
TgeneNF1C0023467Leukemia, Myelocytic, Acute2CTD_human
TgeneNF1C0025202melanoma2CGI;CTD_human
TgeneNF1C0026998Acute Myeloid Leukemia, M12CTD_human
TgeneNF1C0205768Subependymal Giant Cell Astrocytoma2CTD_human
TgeneNF1C0206727Nerve Sheath Tumors2CTD_human
TgeneNF1C0280783Juvenile Pilocytic Astrocytoma2CTD_human
TgeneNF1C0280785Diffuse Astrocytoma2CTD_human
TgeneNF1C0334579Anaplastic astrocytoma2CTD_human
TgeneNF1C0334580Protoplasmic astrocytoma2CTD_human
TgeneNF1C0334581Gemistocytic astrocytoma2CTD_human
TgeneNF1C0334582Fibrillary Astrocytoma2CTD_human
TgeneNF1C0334583Pilocytic Astrocytoma2CTD_human
TgeneNF1C0338070Childhood Cerebral Astrocytoma2CTD_human
TgeneNF1C0547065Mixed oligoastrocytoma2CTD_human
TgeneNF1C0750935Cerebral Astrocytoma2CTD_human
TgeneNF1C0750936Intracranial Astrocytoma2CTD_human
TgeneNF1C0751689Peripheral Nerve Sheath Neoplasm2CTD_human
TgeneNF1C0751691Perineurioma2CTD_human
TgeneNF1C1704230Grade I Astrocytoma2CTD_human
TgeneNF1C1834235NEUROFIBROMATOSIS, FAMILIAL SPINAL2CTD_human;GENOMICS_ENGLAND;UNIPROT
TgeneNF1C1879321Acute Myeloid Leukemia (AML-M2)2CTD_human
TgeneNF1C0001430Adenoma1CTD_human
TgeneNF1C0004352Autistic Disorder1CTD_human
TgeneNF1C0016057Fibrosarcoma1CTD_human
TgeneNF1C0017636Glioblastoma1CTD_human
TgeneNF1C0017638Glioma1CGI;CTD_human
TgeneNF1C0020796Profound Mental Retardation1CTD_human
TgeneNF1C0023186Learning Disorders1CTD_human
TgeneNF1C0023827liposarcoma1CTD_human
TgeneNF1C0025363Mental Retardation, Psychosocial1CTD_human
TgeneNF1C0026654Moyamoya Disease1GENOMICS_ENGLAND
TgeneNF1C0027809Neurilemmoma1CTD_human
TgeneNF1C0027830neurofibroma1CTD_human
TgeneNF1C0027962Melanocytic nevus1CTD_human
TgeneNF1C0028326Noonan Syndrome1GENOMICS_ENGLAND
TgeneNF1C0031511Pheochromocytoma1CTD_human
TgeneNF1C0035320Retinal Neovascularization1CTD_human
TgeneNF1C0205646Adenoma, Basal Cell1CTD_human
TgeneNF1C0205647Follicular adenoma1CTD_human
TgeneNF1C0205648Adenoma, Microcystic1CTD_human
TgeneNF1C0205649Adenoma, Monomorphic1CTD_human
TgeneNF1C0205650Papillary adenoma1CTD_human
TgeneNF1C0205651Adenoma, Trabecular1CTD_human
TgeneNF1C0205824Liposarcoma, Dedifferentiated1CTD_human
TgeneNF1C0205825Liposarcoma, Pleomorphic1CTD_human
TgeneNF1C0205944Sarcoma, Epithelioid1CTD_human
TgeneNF1C0205945Sarcoma, Spindle Cell1CTD_human
TgeneNF1C0259783mixed gliomas1CTD_human
TgeneNF1C0334588Giant Cell Glioblastoma1CTD_human
TgeneNF1C0555198Malignant Glioma1CTD_human
TgeneNF1C0751262Adult Learning Disorders1CTD_human
TgeneNF1C0751263Learning Disturbance1CTD_human
TgeneNF1C0751265Learning Disabilities1CTD_human
TgeneNF1C0751374Schwannomatosis, Plexiform1CTD_human
TgeneNF1C0917816Mental deficiency1CTD_human
TgeneNF1C0917817Neurofibromatosis 31CTD_human
TgeneNF1C1257877Pheochromocytoma, Extra-Adrenal1CTD_human
TgeneNF1C1261473Sarcoma1CTD_human
TgeneNF1C1330966Developmental Academic Disorder1CTD_human
TgeneNF1C1370889Liposarcoma, well differentiated1CTD_human
TgeneNF1C1621958Glioblastoma Multiforme1CTD_human
TgeneNF1C3150928NF1 Microdeletion Syndrome1ORPHANET
TgeneNF1C3714756Intellectual Disability1CTD_human