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:LMNA-RAF1

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: LMNA-RAF1
FusionPDB ID: 45796
FusionGDB2.0 ID: 45796
HgeneTgene
Gene symbol

LMNA

RAF1

Gene ID

4000

6037

Gene namelamin A/Cribonuclease A family member 3
SynonymsCDCD1|CDDC|CMD1A|CMT2B1|EMD2|FPL|FPLD|FPLD2|HGPS|IDC|LDP1|LFP|LGMD1B|LMN1|LMNC|LMNL1|MADA|PRO1ECP|RAF1|RNS3
Cytomap

1q22

14q11.2

Type of geneprotein-codingprotein-coding
Descriptionlamin70 kDa laminepididymis secretory sperm binding proteinlamin A/C-like 1mandibuloacral dysplasia type Aprelamin-A/Crenal carcinoma antigen NY-REN-32eosinophil cationic proteinRNase 3cytotoxic ribonucleaseribonuclease 3ribonuclease, RNase A family, 3
Modification date2020032920200313
UniProtAcc

P02545

Main function of 5'-partner protein: FUNCTION: Lamins are components of the nuclear lamina, a fibrous layer on the nucleoplasmic side of the inner nuclear membrane, which is thought to provide a framework for the nuclear envelope and may also interact with chromatin. Lamin A and C are present in equal amounts in the lamina of mammals. Recruited by DNA repair proteins XRCC4 and IFFO1 to the DNA double-strand breaks (DSBs) to prevent chromosome translocation by immobilizing broken DNA ends (PubMed:31548606). Plays an important role in nuclear assembly, chromatin organization, nuclear membrane and telomere dynamics. Required for normal development of peripheral nervous system and skeletal muscle and for muscle satellite cell proliferation (PubMed:10080180, PubMed:22431096, PubMed:10814726, PubMed:11799477, PubMed:18551513). Required for osteoblastogenesis and bone formation (PubMed:12075506, PubMed:15317753, PubMed:18611980). Also prevents fat infiltration of muscle and bone marrow, helping to maintain the volume and strength of skeletal muscle and bone (PubMed:10587585). Required for cardiac homeostasis (PubMed:10580070, PubMed:12927431, PubMed:18611980, PubMed:23666920). {ECO:0000269|PubMed:10080180, ECO:0000269|PubMed:10580070, ECO:0000269|PubMed:10587585, ECO:0000269|PubMed:10814726, ECO:0000269|PubMed:11799477, ECO:0000269|PubMed:12075506, ECO:0000269|PubMed:12927431, ECO:0000269|PubMed:15317753, ECO:0000269|PubMed:18551513, ECO:0000269|PubMed:18611980, ECO:0000269|PubMed:22431096, ECO:0000269|PubMed:23666920, ECO:0000269|PubMed:31548606}.; FUNCTION: Prelamin-A/C can accelerate smooth muscle cell senescence. It acts to disrupt mitosis and induce DNA damage in vascular smooth muscle cells (VSMCs), leading to mitotic failure, genomic instability, and premature senescence.

P04049

Main function of 5'-partner protein: FUNCTION: Serine/threonine-protein kinase that acts as a regulatory link between the membrane-associated Ras GTPases and the MAPK/ERK cascade, and this critical regulatory link functions as a switch determining cell fate decisions including proliferation, differentiation, apoptosis, survival and oncogenic transformation. RAF1 activation initiates a mitogen-activated protein kinase (MAPK) cascade that comprises a sequential phosphorylation of the dual-specific MAPK kinases (MAP2K1/MEK1 and MAP2K2/MEK2) and the extracellular signal-regulated kinases (MAPK3/ERK1 and MAPK1/ERK2). The phosphorylated form of RAF1 (on residues Ser-338 and Ser-339, by PAK1) phosphorylates BAD/Bcl2-antagonist of cell death at 'Ser-75'. Phosphorylates adenylyl cyclases: ADCY2, ADCY5 and ADCY6, resulting in their activation. Phosphorylates PPP1R12A resulting in inhibition of the phosphatase activity. Phosphorylates TNNT2/cardiac muscle troponin T. Can promote NF-kB activation and inhibit signal transducers involved in motility (ROCK2), apoptosis (MAP3K5/ASK1 and STK3/MST2), proliferation and angiogenesis (RB1). Can protect cells from apoptosis also by translocating to the mitochondria where it binds BCL2 and displaces BAD/Bcl2-antagonist of cell death. Regulates Rho signaling and migration, and is required for normal wound healing. Plays a role in the oncogenic transformation of epithelial cells via repression of the TJ protein, occludin (OCLN) by inducing the up-regulation of a transcriptional repressor SNAI2/SLUG, which induces down-regulation of OCLN. Restricts caspase activation in response to selected stimuli, notably Fas stimulation, pathogen-mediated macrophage apoptosis, and erythroid differentiation. {ECO:0000269|PubMed:11427728, ECO:0000269|PubMed:11719507, ECO:0000269|PubMed:15385642, ECO:0000269|PubMed:15618521, ECO:0000269|PubMed:15849194, ECO:0000269|PubMed:16892053, ECO:0000269|PubMed:16924233, ECO:0000269|PubMed:9360956}.
Ensembl transtripts involved in fusion geneENST idsENST00000496738, ENST00000361308, 
ENST00000368297, ENST00000368301, 
ENST00000392353, ENST00000368299, 
ENST00000368300, ENST00000448611, 
ENST00000473598, ENST00000347559, 
ENST00000251849, ENST00000442415, 
ENST00000534997, ENST00000542177, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score16 X 16 X 9=230419 X 16 X 7=2128
# samples 2118
** MAII scorelog2(21/2304*10)=-3.45567948377619
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(18/2128*10)=-3.56342933917152
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Fusion gene context

PubMed: LMNA [Title/Abstract] AND RAF1 [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: LMNA [Title/Abstract] AND RAF1 [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)LMNA(156107534)-RAF1(12641914), # samples:2
Anticipated loss of major functional domain due to fusion event.LMNA-RAF1 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.
LMNA-RAF1 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.
LMNA-RAF1 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.
LMNA-RAF1 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.
LMNA-RAF1 seems lost the major protein functional domain in Hgene partner, which is a CGC due to the frame-shifted ORF.
LMNA-RAF1 seems lost the major protein functional domain in Tgene partner, which is a CGC due to the frame-shifted ORF.
LMNA-RAF1 seems lost the major protein functional domain in Tgene partner, which is a IUPHAR drug target due to the frame-shifted ORF.
LMNA-RAF1 seems lost the major protein functional domain in Tgene partner, which is a kinase 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
HgeneLMNA

GO:0090343

positive regulation of cell aging

20458013

TgeneRAF1

GO:0002227

innate immune response in mucosa

12860195

TgeneRAF1

GO:0019731

antibacterial humoral response

12860195

TgeneRAF1

GO:0043152

induction of bacterial agglutination

23992292

TgeneRAF1

GO:0045087

innate immune response

23992292

TgeneRAF1

GO:0050829

defense response to Gram-negative bacterium

23992292

TgeneRAF1

GO:0050830

defense response to Gram-positive bacterium

12860195|23992292

TgeneRAF1

GO:0061844

antimicrobial humoral immune response mediated by antimicrobial peptide

12860195



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/chr1:156107534/chr3:12641914)
- 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 LMNA (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 RAF1 (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)
ENST00000368300LMNAchr1156107534+ENST00000251849RAF1chr312641914-39361910833022979
ENST00000368300LMNAchr1156107534+ENST00000442415RAF1chr312641914-37391910833022979
ENST00000368300LMNAchr1156107534+ENST00000534997RAF1chr312641914-32701910833022979
ENST00000368300LMNAchr1156107534+ENST00000542177RAF1chr312641914-32041910833022979
ENST00000368299LMNAchr1156107534+ENST00000251849RAF1chr312641914-39211895683007979
ENST00000368299LMNAchr1156107534+ENST00000442415RAF1chr312641914-37241895683007979
ENST00000368299LMNAchr1156107534+ENST00000534997RAF1chr312641914-32551895683007979
ENST00000368299LMNAchr1156107534+ENST00000542177RAF1chr312641914-31891895683007979
ENST00000448611LMNAchr1156107534+ENST00000251849RAF1chr312641914-3432140682518836
ENST00000448611LMNAchr1156107534+ENST00000442415RAF1chr312641914-3235140682518836
ENST00000448611LMNAchr1156107534+ENST00000534997RAF1chr312641914-2766140682518836
ENST00000448611LMNAchr1156107534+ENST00000542177RAF1chr312641914-2700140682518836
ENST00000473598LMNAchr1156107534+ENST00000251849RAF1chr312641914-35471521842633849
ENST00000473598LMNAchr1156107534+ENST00000442415RAF1chr312641914-33501521842633849
ENST00000473598LMNAchr1156107534+ENST00000534997RAF1chr312641914-28811521842633849
ENST00000473598LMNAchr1156107534+ENST00000542177RAF1chr312641914-28151521842633849

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
ENST00000368300ENST00000251849LMNAchr1156107534+RAF1chr312641914-0.005823040.994177
ENST00000368300ENST00000442415LMNAchr1156107534+RAF1chr312641914-0.0087150620.9912849
ENST00000368300ENST00000534997LMNAchr1156107534+RAF1chr312641914-0.009247230.9907528
ENST00000368300ENST00000542177LMNAchr1156107534+RAF1chr312641914-0.009515260.9904847
ENST00000368299ENST00000251849LMNAchr1156107534+RAF1chr312641914-0.0059804630.9940195
ENST00000368299ENST00000442415LMNAchr1156107534+RAF1chr312641914-0.0089416010.9910584
ENST00000368299ENST00000534997LMNAchr1156107534+RAF1chr312641914-0.0095364650.9904635
ENST00000368299ENST00000542177LMNAchr1156107534+RAF1chr312641914-0.0098304820.99016947
ENST00000448611ENST00000251849LMNAchr1156107534+RAF1chr312641914-0.0149831320.98501694
ENST00000448611ENST00000442415LMNAchr1156107534+RAF1chr312641914-0.0192596760.9807403
ENST00000448611ENST00000534997LMNAchr1156107534+RAF1chr312641914-0.0199795030.9800205
ENST00000448611ENST00000542177LMNAchr1156107534+RAF1chr312641914-0.0206695070.9793305
ENST00000473598ENST00000251849LMNAchr1156107534+RAF1chr312641914-0.0054415720.99455845
ENST00000473598ENST00000442415LMNAchr1156107534+RAF1chr312641914-0.0085069820.99149305
ENST00000473598ENST00000534997LMNAchr1156107534+RAF1chr312641914-0.0091860470.9908139
ENST00000473598ENST00000542177LMNAchr1156107534+RAF1chr312641914-0.0095865080.9904135

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 LMNA-RAF1

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide
LMNAchr1156107534RAF1chr3126419141406466EDEDGDDLLHHHHDAIRSHSESASPS
LMNAchr1156107534RAF1chr3126419141521479EDEDGDDLLHHHHDAIRSHSESASPS
LMNAchr1156107534RAF1chr312641914189574TPLSPTRITRLQEKEDLQELNDRLAV
LMNAchr1156107534RAF1chr312641914191074TPLSPTRITRLQEKEDLQELNDRLAV

Top

Potential FusionNeoAntigen Information of LMNA-RAF1 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.
LMNA-RAF1_156107534_12641914.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)
LMNA-RAF1chr1156107534chr3126419141895HLA-B27:05TRITRLQEK0.99930.7327514
LMNA-RAF1chr1156107534chr3126419141895HLA-B27:07TRLQEKEDL0.99730.5791817
LMNA-RAF1chr1156107534chr3126419141895HLA-B13:01QEKEDLQEL0.99380.96171120
LMNA-RAF1chr1156107534chr3126419141895HLA-B50:02QEKEDLQEL0.9870.64381120
LMNA-RAF1chr1156107534chr3126419141895HLA-B39:24TRLQEKEDL0.98510.5893817
LMNA-RAF1chr1156107534chr3126419141895HLA-B44:03QEKEDLQEL0.98090.98261120
LMNA-RAF1chr1156107534chr3126419141895HLA-B39:01TRLQEKEDL0.97520.9424817
LMNA-RAF1chr1156107534chr3126419141895HLA-B45:01QEKEDLQEL0.95770.93151120
LMNA-RAF1chr1156107534chr3126419141895HLA-B47:01QEKEDLQEL0.95730.69881120
LMNA-RAF1chr1156107534chr3126419141895HLA-B38:02TRLQEKEDL0.94550.9807817
LMNA-RAF1chr1156107534chr3126419141895HLA-B18:01QEKEDLQEL0.82340.93381120
LMNA-RAF1chr1156107534chr3126419141406HLA-B08:09DLLHHHHDA0.80490.694615
LMNA-RAF1chr1156107534chr3126419141895HLA-B39:13QEKEDLQEL0.77930.97171120
LMNA-RAF1chr1156107534chr3126419141406HLA-B15:10HHHDAIRSH0.70960.5751019
LMNA-RAF1chr1156107534chr3126419141895HLA-B50:01QEKEDLQEL0.5520.88541120
LMNA-RAF1chr1156107534chr3126419141406HLA-B15:18HHHDAIRSH0.51890.69791019
LMNA-RAF1chr1156107534chr3126419141895HLA-B41:01QEKEDLQEL0.47990.91241120
LMNA-RAF1chr1156107534chr3126419141406HLA-B15:03HHHDAIRSH0.46760.73881019
LMNA-RAF1chr1156107534chr3126419141406HLA-B15:18HHHHDAIRSH0.81240.7043919
LMNA-RAF1chr1156107534chr3126419141895HLA-A02:22RLQEKEDLQEL0.99780.5848920
LMNA-RAF1chr1156107534chr3126419141895HLA-A02:27RLQEKEDLQEL0.9950.6482920
LMNA-RAF1chr1156107534chr3126419141895HLA-A02:13RLQEKEDLQEL0.99420.7772920
LMNA-RAF1chr1156107534chr3126419141895HLA-A02:11RLQEKEDLQEL0.98650.6761920
LMNA-RAF1chr1156107534chr3126419141895HLA-A02:60RLQEKEDLQEL0.98640.6372920
LMNA-RAF1chr1156107534chr3126419141895HLA-A02:67RLQEKEDLQEL0.98630.638920
LMNA-RAF1chr1156107534chr3126419141895HLA-A02:30RLQEKEDLQEL0.98630.638920
LMNA-RAF1chr1156107534chr3126419141895HLA-A02:24RLQEKEDLQEL0.98630.638920
LMNA-RAF1chr1156107534chr3126419141895HLA-A02:04RLQEKEDLQEL0.98090.7211920
LMNA-RAF1chr1156107534chr3126419141895HLA-A02:29RLQEKEDLQEL0.93330.6357920
LMNA-RAF1chr1156107534chr3126419141895HLA-A02:20RLQEKEDLQEL0.9170.6449920
LMNA-RAF1chr1156107534chr3126419141895HLA-B40:01RLQEKEDLQEL0.77240.64920
LMNA-RAF1chr1156107534chr3126419141895HLA-B39:13RLQEKEDLQEL0.59550.987920
LMNA-RAF1chr1156107534chr3126419141895HLA-B40:06QEKEDLQEL0.99920.71951120
LMNA-RAF1chr1156107534chr3126419141895HLA-B27:14TRITRLQEK0.99720.6655514
LMNA-RAF1chr1156107534chr3126419141895HLA-B39:12TRLQEKEDL0.96890.945817
LMNA-RAF1chr1156107534chr3126419141895HLA-B39:08QEKEDLQEL0.87260.82991120
LMNA-RAF1chr1156107534chr3126419141406HLA-C07:46HHHDAIRSH0.50630.86771019
LMNA-RAF1chr1156107534chr3126419141406HLA-B15:21HHHDAIRSH0.12040.86941019
LMNA-RAF1chr1156107534chr3126419141406HLA-C12:16HHHDAIRSH0.00040.96031019
LMNA-RAF1chr1156107534chr3126419141895HLA-A02:01RLQEKEDLQEL0.98630.638920
LMNA-RAF1chr1156107534chr3126419141895HLA-B40:03RLQEKEDLQEL0.97160.6422920
LMNA-RAF1chr1156107534chr3126419141895HLA-B39:08RLQEKEDLQEL0.930.9274920
LMNA-RAF1chr1156107534chr3126419141895HLA-B27:10TRITRLQEK0.9990.8653514
LMNA-RAF1chr1156107534chr3126419141895HLA-B40:04QEKEDLQEL0.9990.76711120
LMNA-RAF1chr1156107534chr3126419141895HLA-B39:31TRLQEKEDL0.98180.9425817
LMNA-RAF1chr1156107534chr3126419141895HLA-B44:13QEKEDLQEL0.98090.98261120
LMNA-RAF1chr1156107534chr3126419141895HLA-B44:26QEKEDLQEL0.98090.98261120
LMNA-RAF1chr1156107534chr3126419141895HLA-B44:07QEKEDLQEL0.98090.98261120
LMNA-RAF1chr1156107534chr3126419141895HLA-B18:11QEKEDLQEL0.88550.94811120
LMNA-RAF1chr1156107534chr3126419141895HLA-B39:11QEKEDLQEL0.84610.78781120
LMNA-RAF1chr1156107534chr3126419141895HLA-B41:03QEKEDLQEL0.83920.60851120
LMNA-RAF1chr1156107534chr3126419141895HLA-B18:04QEKEDLQEL0.83620.93891120
LMNA-RAF1chr1156107534chr3126419141895HLA-B18:07QEKEDLQEL0.82550.89541120
LMNA-RAF1chr1156107534chr3126419141895HLA-B18:05QEKEDLQEL0.82340.93381120
LMNA-RAF1chr1156107534chr3126419141895HLA-B18:08QEKEDLQEL0.82180.90541120
LMNA-RAF1chr1156107534chr3126419141895HLA-B39:02QEKEDLQEL0.80320.9711120
LMNA-RAF1chr1156107534chr3126419141895HLA-B18:03QEKEDLQEL0.80.92561120
LMNA-RAF1chr1156107534chr3126419141895HLA-B18:06QEKEDLQEL0.78970.93421120
LMNA-RAF1chr1156107534chr3126419141895HLA-B39:31QEKEDLQEL0.78910.96081120
LMNA-RAF1chr1156107534chr3126419141406HLA-C07:17HHHDAIRSH0.67770.95771019
LMNA-RAF1chr1156107534chr3126419141895HLA-B48:02QEKEDLQEL0.58560.97981120
LMNA-RAF1chr1156107534chr3126419141895HLA-B15:53QEKEDLQEL0.56770.88141120
LMNA-RAF1chr1156107534chr3126419141895HLA-B50:04QEKEDLQEL0.5520.88541120
LMNA-RAF1chr1156107534chr3126419141895HLA-B50:05QEKEDLQEL0.5520.88541120
LMNA-RAF1chr1156107534chr3126419141895HLA-B15:30LQEKEDLQEL0.94250.96471020
LMNA-RAF1chr1156107534chr3126419141895HLA-B15:73LQEKEDLQEL0.94150.96861020
LMNA-RAF1chr1156107534chr3126419141895HLA-B41:03LQEKEDLQEL0.45870.64041020
LMNA-RAF1chr1156107534chr3126419141895HLA-A02:03RLQEKEDLQEL0.99840.7194920
LMNA-RAF1chr1156107534chr3126419141895HLA-A02:14RLQEKEDLQEL0.98090.661920
LMNA-RAF1chr1156107534chr3126419141895HLA-B41:03RLQEKEDLQEL0.87440.7028920
LMNA-RAF1chr1156107534chr3126419141895HLA-B40:04RLQEKEDLQEL0.87360.8369920
LMNA-RAF1chr1156107534chr3126419141895HLA-B40:21RLQEKEDLQEL0.84710.8145920
LMNA-RAF1chr1156107534chr3126419141895HLA-B40:36RLQEKEDLQEL0.77220.6009920
LMNA-RAF1chr1156107534chr3126419141895HLA-B40:49RLQEKEDLQEL0.74860.6812920

Top

Potential FusionNeoAntigen Information of LMNA-RAF1 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 LMNA-RAF1

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
1233DLLHHHHDAIRSHSLMNARAF1chr1156107534chr3126419141406
File nameBPseqHgeneTgeneHchrHbpTchrTbpAAlen
7952RITRLQEKEDLQELLMNARAF1chr1156107534chr3126419141895

Top

Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of LMNA-RAF1

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-B14:023BVN1233DLLHHHHDAIRSHS-7.9962-8.1096
HLA-B14:023BVN1233DLLHHHHDAIRSHS-5.70842-6.74372
HLA-B52:013W391233DLLHHHHDAIRSHS-6.83737-6.95077
HLA-B52:013W391233DLLHHHHDAIRSHS-4.4836-5.5189
HLA-A11:014UQ21233DLLHHHHDAIRSHS-10.0067-10.1201
HLA-A11:014UQ21233DLLHHHHDAIRSHS-9.03915-10.0745
HLA-A24:025HGA1233DLLHHHHDAIRSHS-6.56204-6.67544
HLA-A24:025HGA1233DLLHHHHDAIRSHS-5.42271-6.45801
HLA-B44:053DX81233DLLHHHHDAIRSHS-7.85648-8.89178
HLA-B44:053DX81233DLLHHHHDAIRSHS-5.3978-5.5112
HLA-A02:016TDR1233DLLHHHHDAIRSHS-3.37154-4.40684
HLA-B14:023BVN7952RITRLQEKEDLQEL-7.9962-8.1096
HLA-B14:023BVN7952RITRLQEKEDLQEL-5.70842-6.74372
HLA-B52:013W397952RITRLQEKEDLQEL-6.83737-6.95077
HLA-B52:013W397952RITRLQEKEDLQEL-4.4836-5.5189
HLA-A11:014UQ27952RITRLQEKEDLQEL-10.0067-10.1201
HLA-A11:014UQ27952RITRLQEKEDLQEL-9.03915-10.0745
HLA-A24:025HGA7952RITRLQEKEDLQEL-6.56204-6.67544
HLA-A24:025HGA7952RITRLQEKEDLQEL-5.42271-6.45801
HLA-B44:053DX87952RITRLQEKEDLQEL-7.85648-8.89178
HLA-B44:053DX87952RITRLQEKEDLQEL-5.3978-5.5112
HLA-A02:016TDR7952RITRLQEKEDLQEL-3.37154-4.40684

Top

Vaccine Design for the FusionNeoAntigens of LMNA-RAF1

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
LMNA-RAF1chr1156107534chr3126419141019HHHDAIRSHCACCACCACGATGCAATTCGAAGTCAC
LMNA-RAF1chr1156107534chr3126419141020LQEKEDLQELCACCACCACGATGCAATTCGAAGTCACAGC
LMNA-RAF1chr1156107534chr3126419141120QEKEDLQELCACCACGATGCAATTCGAAGTCACAGC
LMNA-RAF1chr1156107534chr312641914514TRITRLQEKGATGACCTGCTCCATCACCACCACGAT
LMNA-RAF1chr1156107534chr312641914615DLLHHHHDAGACCTGCTCCATCACCACCACGATGCA
LMNA-RAF1chr1156107534chr312641914817TRLQEKEDLCTCCATCACCACCACGATGCAATTCGA
LMNA-RAF1chr1156107534chr312641914919HHHHDAIRSHCATCACCACCACGATGCAATTCGAAGTCAC
LMNA-RAF1chr1156107534chr312641914920RLQEKEDLQELCATCACCACCACGATGCAATTCGAAGTCACAGC

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 LMNA-RAF1

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
SKCMLMNA-RAF1chr1156107534ENST00000368299chr312641914ENST00000251849TCGA-EB-A5SF-01A
SKCMLMNA-RAF1chr1156107534ENST00000448611chr312641914ENST00000251849TCGA-EB-A5SF-01A

Top

Potential target of CAR-T therapy development for LMNA-RAF1

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 LMNA-RAF1

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

Top

Related Diseases to LMNA-RAF1

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
TgeneRAF1C0028326Noonan Syndrome10CLINGEN;CTD_human;GENOMICS_ENGLAND;ORPHANET
TgeneRAF1C0175704LEOPARD Syndrome7CLINGEN;CTD_human;GENOMICS_ENGLAND
TgeneRAF1C1969057Noonan Syndrome 54CTD_human;GENOMICS_ENGLAND;UNIPROT
TgeneRAF1C1969056LEOPARD SYNDROME 23CTD_human;GENOMICS_ENGLAND;UNIPROT
TgeneRAF1C0007194Hypertrophic Cardiomyopathy2CTD_human
TgeneRAF1C0041409Turner Syndrome, Male2CTD_human
TgeneRAF1C1519086Pilomyxoid astrocytoma2ORPHANET
TgeneRAF1C1527404Female Pseudo-Turner Syndrome2CTD_human
TgeneRAF1C4551472Hypertrophic obstructive cardiomyopathy2CTD_human
TgeneRAF1C4551602Noonan Syndrome 12CTD_human
TgeneRAF1C0006142Malignant neoplasm of breast1CTD_human
TgeneRAF1C0007131Non-Small Cell Lung Carcinoma1CTD_human
TgeneRAF1C0007193Cardiomyopathy, Dilated1CTD_human
TgeneRAF1C0017638Glioma1CTD_human
TgeneRAF1C0020429Hyperalgesia1CTD_human
TgeneRAF1C0022665Kidney Neoplasm1CTD_human
TgeneRAF1C0023903Liver neoplasms1CTD_human
TgeneRAF1C0024121Lung Neoplasms1CTD_human
TgeneRAF1C0242379Malignant neoplasm of lung1CTD_human
TgeneRAF1C0259783mixed gliomas1CTD_human
TgeneRAF1C0340427Familial dilated cardiomyopathy1ORPHANET
TgeneRAF1C0345904Malignant neoplasm of liver1CTD_human
TgeneRAF1C0345967Malignant mesothelioma1CTD_human
TgeneRAF1C0458247Allodynia1CTD_human
TgeneRAF1C0555198Malignant Glioma1CTD_human
TgeneRAF1C0587248Costello syndrome (disorder)1CLINGEN
TgeneRAF1C0678222Breast Carcinoma1CTD_human
TgeneRAF1C0740457Malignant neoplasm of kidney1CTD_human
TgeneRAF1C0751211Hyperalgesia, Primary1CTD_human
TgeneRAF1C0751212Hyperalgesia, Secondary1CTD_human
TgeneRAF1C0751213Tactile Allodynia1CTD_human
TgeneRAF1C0751214Hyperalgesia, Thermal1CTD_human
TgeneRAF1C1257931Mammary Neoplasms, Human1CTD_human
TgeneRAF1C1275081Cardio-facio-cutaneous syndrome1CLINGEN
TgeneRAF1C1449563Cardiomyopathy, Familial Idiopathic1CTD_human
TgeneRAF1C1458155Mammary Neoplasms1CTD_human
TgeneRAF1C2936719Mechanical Allodynia1CTD_human
TgeneRAF1C4014656CARDIOMYOPATHY, DILATED, 1NN1CTD_human;UNIPROT
TgeneRAF1C4551484Leopard Syndrome 11CTD_human;GENOMICS_ENGLAND
TgeneRAF1C4704874Mammary Carcinoma, Human1CTD_human
TgeneRAF1C4721610Carcinoma, Ovarian Epithelial1CTD_human