FusionNeoAntigen Logo

Home

Download

Statistics

Examples

Help

Contact

Terms of Use

Center for Computational Systems Medicine
leaf

Fusion Gene and Fusion Protein Summary

leaf

Fusion Amino Acid Sequences (multiple BPs and multiple gene isoforms)

leaf

Fusion Protein Breakpoint Sequences - (for the Screening of the FusionNeoAntigens)

leaf

Potential FusionNeoAntigens in HLA I - (netMHCpan v4.1 + deepHLApan v1.1)

leaf

Potential FusionNeoAntigens in HLA II - (netMHCIIpan v4.1)

leaf

Fusion Breakpoint 14 AA Peptide Structure - (RoseTTAFold)

leaf

Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D - (Glide)

leaf

Vaccine Design for the FusionNeoAntigens (RNA/protein sequences)

leaf

Potential target of CAR-T therapy development

leaf

Information on the samples that have these potential fusion neoantigens

leaf

Fusion Protein Targeting Drugs - (Manual Curation)

leaf

Fusion Protein Related diseases - (Manual Curation)

Fusion Protein:GFM1-SMARCA2

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: GFM1-SMARCA2
FusionPDB ID: 32948
FusionGDB2.0 ID: 32948
HgeneTgene
Gene symbol

GFM1

SMARCA2

Gene ID

85476

6595

Gene nameG elongation factor mitochondrial 1SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2
SynonymsCOXPD1|EFG|EFG1|EFGM|EGF1|GFM|hEFG1|mtEF-G1BAF190|BRM|NCBRS|SNF2|SNF2L2|SNF2LA|SWI2|Sth1p|hBRM|hSNF2a
Cytomap

3q25.32

9p24.3

Type of geneprotein-codingprotein-coding
Descriptionelongation factor G, mitochondrialG translation elongation factor, mitochondrialmitochondrial elongation factor Gmitochondrial elongation factor G1probable global transcription activator SNF2L2ATP-dependent helicase SMARCA2BAF190BBRG1-associated factor 190BSNF2-alphaSNF2/SWI2-like protein 2SWI/SNF-related matrix-associated actin-dependent regulator of chromatin a2brahma homologglobal transcr
Modification date2020031320200315
UniProtAcc

Q96RP9

Main function of 5'-partner protein: FUNCTION: Mitochondrial GTPase that catalyzes the GTP-dependent ribosomal translocation step during translation elongation. During this step, the ribosome changes from the pre-translocational (PRE) to the post-translocational (POST) state as the newly formed A-site-bound peptidyl-tRNA and P-site-bound deacylated tRNA move to the P and E sites, respectively. Catalyzes the coordinated movement of the two tRNA molecules, the mRNA and conformational changes in the ribosome. Does not mediate the disassembly of ribosomes from messenger RNA at the termination of mitochondrial protein biosynthesis. {ECO:0000255|HAMAP-Rule:MF_03061, ECO:0000269|PubMed:19716793}.
.
Ensembl transtripts involved in fusion geneENST idsENST00000264263, ENST00000478576, 
ENST00000486715, ENST00000490261, 
ENST00000302401, ENST00000324954, 
ENST00000382185, ENST00000382186, 
ENST00000491574, ENST00000349721, 
ENST00000357248, ENST00000382194, 
ENST00000382203, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score7 X 7 X 5=24515 X 14 X 8=1680
# samples 716
** MAII scorelog2(7/245*10)=-1.8073549220576
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(16/1680*10)=-3.39231742277876
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Fusion gene context

PubMed: GFM1 [Title/Abstract] AND SMARCA2 [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: GFM1 [Title/Abstract] AND SMARCA2 [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)GFM1(158362483)-SMARCA2(2086981), # samples:1
Anticipated loss of major functional domain due to fusion event.GFM1-SMARCA2 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.
GFM1-SMARCA2 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.
GFM1-SMARCA2 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.
GFM1-SMARCA2 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
HgeneGFM1

GO:0070125

mitochondrial translational elongation

19716793

TgeneSMARCA2

GO:0008285

negative regulation of cell proliferation

14660596

TgeneSMARCA2

GO:0045892

negative regulation of transcription, DNA-templated

12065415

TgeneSMARCA2

GO:0045893

positive regulation of transcription, DNA-templated

17984088

TgeneSMARCA2

GO:0045944

positive regulation of transcription by RNA polymerase II

15774904



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/chr3:158362483/chr9:2086981)
- 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 GFM1 (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 SMARCA2 (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)
ENST00000486715GFM1chr3158362483+ENST00000357248SMARCA2chr92086981+294621962060654
ENST00000486715GFM1chr3158362483+ENST00000349721SMARCA2chr92086981+300021962114672
ENST00000486715GFM1chr3158362483+ENST00000382203SMARCA2chr92086981+300021962114672
ENST00000486715GFM1chr3158362483+ENST00000382194SMARCA2chr92086981+289921962060654
ENST00000478576GFM1chr3158362483+ENST00000357248SMARCA2chr92086981+294621962060654
ENST00000478576GFM1chr3158362483+ENST00000349721SMARCA2chr92086981+300021962114672
ENST00000478576GFM1chr3158362483+ENST00000382203SMARCA2chr92086981+300021962114672
ENST00000478576GFM1chr3158362483+ENST00000382194SMARCA2chr92086981+289921962060654
ENST00000264263GFM1chr3158362483+ENST00000357248SMARCA2chr92086981+294621962060654
ENST00000264263GFM1chr3158362483+ENST00000349721SMARCA2chr92086981+300021962114672
ENST00000264263GFM1chr3158362483+ENST00000382203SMARCA2chr92086981+300021962114672
ENST00000264263GFM1chr3158362483+ENST00000382194SMARCA2chr92086981+289921962060654

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
ENST00000486715ENST00000357248GFM1chr3158362483+SMARCA2chr92086981+0.0004706420.99952936
ENST00000486715ENST00000349721GFM1chr3158362483+SMARCA2chr92086981+0.0005134980.99948645
ENST00000486715ENST00000382203GFM1chr3158362483+SMARCA2chr92086981+0.0005134980.99948645
ENST00000486715ENST00000382194GFM1chr3158362483+SMARCA2chr92086981+0.0005916930.99940836
ENST00000478576ENST00000357248GFM1chr3158362483+SMARCA2chr92086981+0.0004706420.99952936
ENST00000478576ENST00000349721GFM1chr3158362483+SMARCA2chr92086981+0.0005134980.99948645
ENST00000478576ENST00000382203GFM1chr3158362483+SMARCA2chr92086981+0.0005134980.99948645
ENST00000478576ENST00000382194GFM1chr3158362483+SMARCA2chr92086981+0.0005916930.99940836
ENST00000264263ENST00000357248GFM1chr3158362483+SMARCA2chr92086981+0.0004706420.99952936
ENST00000264263ENST00000349721GFM1chr3158362483+SMARCA2chr92086981+0.0005134980.99948645
ENST00000264263ENST00000382203GFM1chr3158362483+SMARCA2chr92086981+0.0005134980.99948645
ENST00000264263ENST00000382194GFM1chr3158362483+SMARCA2chr92086981+0.0005916930.99940836

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

Top

Fusion Protein Breakpoint Sequences for GFM1-SMARCA2

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

Top

Potential FusionNeoAntigen Information of GFM1-SMARCA2 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)

Top

Potential FusionNeoAntigen Information of GFM1-SMARCA2 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)

Top

Fusion breakpoint peptide structures of GFM1-SMARCA2

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.

Top

Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of GFM1-SMARCA2

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

Top

Vaccine Design for the FusionNeoAntigens of GFM1-SMARCA2

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

Top

Information of the samples that have these potential fusion neoantigens of GFM1-SMARCA2

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

Top

Potential target of CAR-T therapy development for GFM1-SMARCA2

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

Top

Related Drugs to GFM1-SMARCA2

check button Drugs used for this fusion-positive patient.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)
HgeneTgeneDrugSourcePMID

Top

Related Diseases to GFM1-SMARCA2

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