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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:SS18L1-CDH4

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: SS18L1-CDH4
FusionPDB ID: 86664
FusionGDB2.0 ID: 86664
HgeneTgene
Gene symbol

SS18L1

CDH4

Gene ID

26039

1002

Gene nameSS18L1 subunit of BAF chromatin remodeling complexcadherin 4
SynonymsCREST|LP2261CAD4|R-CAD|RCAD
Cytomap

20q13.33

20q13.33

Type of geneprotein-codingprotein-coding
Descriptioncalcium-responsive transactivatorSS18-like protein 1SS18L1, nBAF chromatin remodeling complex subunitSYT homolog 1synovial sarcoma translocation gene on chromosome 18-like 1cadherin-4R-cadherincadherin 4, type 1, R-cadherin (retinal)cadherin 4, type 1, preproproteinretinal cadherin
Modification date2020031320200313
UniProtAcc

O75177

Main function of 5'-partner protein: FUNCTION: Transcriptional activator which is required for calcium-dependent dendritic growth and branching in cortical neurons. Recruits CREB-binding protein (CREBBP) to nuclear bodies. Component of the CREST-BRG1 complex, a multiprotein complex that regulates promoter activation by orchestrating a calcium-dependent release of a repressor complex and a recruitment of an activator complex. In resting neurons, transcription of the c-FOS promoter is inhibited by BRG1-dependent recruitment of a phospho-RB1-HDAC1 repressor complex. Upon calcium influx, RB1 is dephosphorylated by calcineurin, which leads to release of the repressor complex. At the same time, there is increased recruitment of CREBBP to the promoter by a CREST-dependent mechanism, which leads to transcriptional activation. The CREST-BRG1 complex also binds to the NR2B promoter, and activity-dependent induction of NR2B expression involves a release of HDAC1 and recruitment of CREBBP (By similarity). {ECO:0000250}.

P55283

Main function of 5'-partner protein: FUNCTION: Cadherins are calcium-dependent cell adhesion proteins. They preferentially interact with themselves in a homophilic manner in connecting cells; cadherins may thus contribute to the sorting of heterogeneous cell types. May play an important role in retinal development.
Ensembl transtripts involved in fusion geneENST idsENST00000331758, ENST00000421564, 
ENST00000370848, ENST00000491916, 
ENST00000360469, ENST00000543233, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score11 X 8 X 7=61616 X 14 X 7=1568
# samples 1221
** MAII scorelog2(12/616*10)=-2.35989594508638
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(21/1568*10)=-2.90046432644909
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Fusion gene context

PubMed: SS18L1 [Title/Abstract] AND CDH4 [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: SS18L1 [Title/Abstract] AND CDH4 [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)SS18L1(60718945)-CDH4(60469966), # samples:2
Anticipated loss of major functional domain due to fusion event.SS18L1-CDH4 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.
SS18L1-CDH4 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.
SS18L1-CDH4 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.
SS18L1-CDH4 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


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/chr20:60718945/chr20:60469966)
- 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 SS18L1 (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 CDH4 (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)
ENST00000421564SS18L1chr2060718945+ENST00000360469CDH4chr2060469965+5497124551824589
ENST00000421564SS18L1chr2060718945+ENST00000543233CDH4chr2060469965+2131124551824589
ENST00000331758SS18L1chr2060718945+ENST00000360469CDH4chr2060469965+546895261795589
ENST00000331758SS18L1chr2060718945+ENST00000543233CDH4chr2060469965+210295261795589
ENST00000421564SS18L1chr2060718945+ENST00000360469CDH4chr2060469966+5497124551824589
ENST00000421564SS18L1chr2060718945+ENST00000543233CDH4chr2060469966+2131124551824589
ENST00000331758SS18L1chr2060718945+ENST00000360469CDH4chr2060469966+546895261795589
ENST00000331758SS18L1chr2060718945+ENST00000543233CDH4chr2060469966+210295261795589
ENST00000421564SS18L1chr2060718944+ENST00000360469CDH4chr2060469965+5497124551824589
ENST00000421564SS18L1chr2060718944+ENST00000543233CDH4chr2060469965+2131124551824589
ENST00000331758SS18L1chr2060718944+ENST00000360469CDH4chr2060469965+546895261795589
ENST00000331758SS18L1chr2060718944+ENST00000543233CDH4chr2060469965+210295261795589

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
ENST00000421564ENST00000360469SS18L1chr2060718945+CDH4chr2060469965+0.0037072990.99629265
ENST00000421564ENST00000543233SS18L1chr2060718945+CDH4chr2060469965+0.0056665650.9943335
ENST00000331758ENST00000360469SS18L1chr2060718945+CDH4chr2060469965+0.0036097940.99639016
ENST00000331758ENST00000543233SS18L1chr2060718945+CDH4chr2060469965+0.0055981860.9944019
ENST00000421564ENST00000360469SS18L1chr2060718945+CDH4chr2060469966+0.0037072990.99629265
ENST00000421564ENST00000543233SS18L1chr2060718945+CDH4chr2060469966+0.0056665650.9943335
ENST00000331758ENST00000360469SS18L1chr2060718945+CDH4chr2060469966+0.0036097940.99639016
ENST00000331758ENST00000543233SS18L1chr2060718945+CDH4chr2060469966+0.0055981860.9944019
ENST00000421564ENST00000360469SS18L1chr2060718944+CDH4chr2060469965+0.0037072990.99629265
ENST00000421564ENST00000543233SS18L1chr2060718944+CDH4chr2060469965+0.0056665650.9943335
ENST00000331758ENST00000360469SS18L1chr2060718944+CDH4chr2060469965+0.0036097940.99639016
ENST00000331758ENST00000543233SS18L1chr2060718944+CDH4chr2060469965+0.0055981860.9944019

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 SS18L1-CDH4

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide
SS18L1chr2060718944CDH4chr206046996512423RGKGEVTQQTIQKKVQQYTVIVQATD
SS18L1chr2060718944CDH4chr20604699659523RGKGEVTQQTIQKKVQQYTVIVQATD
SS18L1chr2060718945CDH4chr206046996512423RGKGEVTQQTIQKKVQQYTVIVQATD
SS18L1chr2060718945CDH4chr20604699659523RGKGEVTQQTIQKKVQQYTVIVQATD
SS18L1chr2060718945CDH4chr206046996612423RGKGEVTQQTIQKKVQQYTVIVQATD
SS18L1chr2060718945CDH4chr20604699669523RGKGEVTQQTIQKKVQQYTVIVQATD

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Potential FusionNeoAntigen Information of SS18L1-CDH4 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.
SS18L1-CDH4_60718944_60469965.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)
SS18L1-CDH4chr2060718944chr206046996595HLA-B15:01IQKKVQQY0.99990.75141018
SS18L1-CDH4chr2060718944chr206046996595HLA-B15:25IQKKVQQY0.99740.77521018
SS18L1-CDH4chr2060718944chr206046996595HLA-B15:01TIQKKVQQY0.9980.7795918
SS18L1-CDH4chr2060718944chr206046996595HLA-B15:25TIQKKVQQY0.99620.8346918
SS18L1-CDH4chr2060718944chr206046996595HLA-B15:02TIQKKVQQY0.98660.8459918
SS18L1-CDH4chr2060718944chr206046996595HLA-B13:02TQQTIQKKV0.75350.7697615
SS18L1-CDH4chr2060718944chr206046996595HLA-B13:01TQQTIQKKV0.55530.9353615
SS18L1-CDH4chr2060718944chr206046996595HLA-B52:01TQQTIQKKV0.20810.8374615
SS18L1-CDH4chr2060718944chr206046996595HLA-A32:13TIQKKVQQY0.10890.9215918
SS18L1-CDH4chr2060718944chr206046996595HLA-B15:17QTIQKKVQQY0.97250.8092818
SS18L1-CDH4chr2060718944chr206046996595HLA-B13:02IQKKVQQYTV0.48510.65141020
SS18L1-CDH4chr2060718944chr206046996595HLA-B15:01QQTIQKKVQQY0.99970.7742718
SS18L1-CDH4chr2060718944chr206046996595HLA-B15:04IQKKVQQY0.99870.80531018
SS18L1-CDH4chr2060718944chr206046996595HLA-B15:05IQKKVQQY0.94550.72971018
SS18L1-CDH4chr2060718944chr206046996595HLA-B15:21TIQKKVQQY0.98430.8204918
SS18L1-CDH4chr2060718944chr206046996595HLA-B15:07TIQKKVQQY0.97560.5561918
SS18L1-CDH4chr2060718944chr206046996595HLA-B15:05TIQKKVQQY0.93020.8324918
SS18L1-CDH4chr2060718944chr206046996595HLA-B15:31TIQKKVQQY0.84470.8342918
SS18L1-CDH4chr2060718944chr206046996595HLA-B15:04TIQKKVQQY0.7510.8188918
SS18L1-CDH4chr2060718944chr206046996595HLA-B15:04IQKKVQQYT0.66060.77671019
SS18L1-CDH4chr2060718944chr206046996595HLA-C15:04TIQKKVQQY0.61430.788918
SS18L1-CDH4chr2060718944chr206046996595HLA-B51:07TQQTIQKKV0.16960.7637615
SS18L1-CDH4chr2060718944chr206046996595HLA-B44:08QQTIQKKVQQY0.97030.5133718
SS18L1-CDH4chr2060718944chr206046996595HLA-B15:27IQKKVQQY0.99990.79721018
SS18L1-CDH4chr2060718944chr206046996595HLA-B15:125IQKKVQQY0.99990.75141018
SS18L1-CDH4chr2060718944chr206046996595HLA-B15:34IQKKVQQY0.99990.75141018
SS18L1-CDH4chr2060718944chr206046996595HLA-B15:135IQKKVQQY0.99990.76991018
SS18L1-CDH4chr2060718944chr206046996595HLA-B15:33IQKKVQQY0.99990.75141018
SS18L1-CDH4chr2060718944chr206046996595HLA-B15:50IQKKVQQY0.99980.78031018
SS18L1-CDH4chr2060718944chr206046996595HLA-B15:24IQKKVQQY0.99970.79311018
SS18L1-CDH4chr2060718944chr206046996595HLA-B15:12IQKKVQQY0.99940.80071018
SS18L1-CDH4chr2060718944chr206046996595HLA-B15:35IQKKVQQY0.9990.73291018
SS18L1-CDH4chr2060718944chr206046996595HLA-B15:53IQKKVQQY0.9990.72911018
SS18L1-CDH4chr2060718944chr206046996595HLA-B15:39IQKKVQQY0.99780.57861018
SS18L1-CDH4chr2060718944chr206046996595HLA-B15:54IQKKVQQY0.99740.69591018
SS18L1-CDH4chr2060718944chr206046996595HLA-B15:20IQKKVQQY0.94550.82351018
SS18L1-CDH4chr2060718944chr206046996595HLA-B35:28IQKKVQQY0.930.82981018
SS18L1-CDH4chr2060718944chr206046996595HLA-B18:04IQKKVQQY0.89760.86131018
SS18L1-CDH4chr2060718944chr206046996595HLA-B18:06IQKKVQQY0.87470.85531018
SS18L1-CDH4chr2060718944chr206046996595HLA-B48:02IQKKVQQY0.71970.80861018
SS18L1-CDH4chr2060718944chr206046996595HLA-B15:34TIQKKVQQY0.9980.7795918
SS18L1-CDH4chr2060718944chr206046996595HLA-B15:125TIQKKVQQY0.9980.7795918
SS18L1-CDH4chr2060718944chr206046996595HLA-B15:33TIQKKVQQY0.9980.7795918
SS18L1-CDH4chr2060718944chr206046996595HLA-B15:27TIQKKVQQY0.99790.8294918
SS18L1-CDH4chr2060718944chr206046996595HLA-B15:135TIQKKVQQY0.99770.7951918
SS18L1-CDH4chr2060718944chr206046996595HLA-B15:50TIQKKVQQY0.99680.8044918
SS18L1-CDH4chr2060718944chr206046996595HLA-B15:39TIQKKVQQY0.99580.6744918
SS18L1-CDH4chr2060718944chr206046996595HLA-B15:11TIQKKVQQY0.99230.7476918
SS18L1-CDH4chr2060718944chr206046996595HLA-B15:08TIQKKVQQY0.9910.7321918
SS18L1-CDH4chr2060718944chr206046996595HLA-B15:24TIQKKVQQY0.9870.8107918
SS18L1-CDH4chr2060718944chr206046996595HLA-B15:12TIQKKVQQY0.98670.8372918
SS18L1-CDH4chr2060718944chr206046996595HLA-B35:43TIQKKVQQY0.98310.7392918
SS18L1-CDH4chr2060718944chr206046996595HLA-B35:11TIQKKVQQY0.98120.8213918
SS18L1-CDH4chr2060718944chr206046996595HLA-B15:35TIQKKVQQY0.97420.7508918
SS18L1-CDH4chr2060718944chr206046996595HLA-A30:01VTQQTIQKK0.93370.5808514
SS18L1-CDH4chr2060718944chr206046996595HLA-B15:20TIQKKVQQY0.9330.8865918
SS18L1-CDH4chr2060718944chr206046996595HLA-B35:28TIQKKVQQY0.90280.8944918
SS18L1-CDH4chr2060718944chr206046996595HLA-B15:13TIQKKVQQY0.8930.5847918
SS18L1-CDH4chr2060718944chr206046996595HLA-B35:20TIQKKVQQY0.84640.9115918
SS18L1-CDH4chr2060718944chr206046996595HLA-C03:02TIQKKVQQY0.7420.939918
SS18L1-CDH4chr2060718944chr206046996595HLA-C15:09TIQKKVQQY0.61430.788918
SS18L1-CDH4chr2060718944chr206046996595HLA-A25:01TIQKKVQQY0.50610.7139918
SS18L1-CDH4chr2060718944chr206046996595HLA-C12:02TIQKKVQQY0.45020.9457918
SS18L1-CDH4chr2060718944chr206046996595HLA-C02:02TIQKKVQQY0.07450.9691918
SS18L1-CDH4chr2060718944chr206046996595HLA-C02:10TIQKKVQQY0.07450.9691918
SS18L1-CDH4chr2060718944chr206046996595HLA-B57:04QTIQKKVQQY0.97930.6976818
SS18L1-CDH4chr2060718944chr206046996595HLA-A25:01QTIQKKVQQY0.7110.795818
SS18L1-CDH4chr2060718944chr206046996595HLA-B15:34QQTIQKKVQQY0.99970.7742718
SS18L1-CDH4chr2060718944chr206046996595HLA-B15:125QQTIQKKVQQY0.99970.7742718
SS18L1-CDH4chr2060718944chr206046996595HLA-B15:135QQTIQKKVQQY0.99970.7921718
SS18L1-CDH4chr2060718944chr206046996595HLA-B15:33QQTIQKKVQQY0.99970.7742718
SS18L1-CDH4chr2060718944chr206046996595HLA-B15:50QQTIQKKVQQY0.99960.8721718
SS18L1-CDH4chr2060718944chr206046996595HLA-B15:12QQTIQKKVQQY0.99840.7904718
SS18L1-CDH4chr2060718944chr206046996595HLA-B15:53QQTIQKKVQQY0.99540.7609718

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Potential FusionNeoAntigen Information of SS18L1-CDH4 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.
SS18L1-CDH4_60718944_60469965.msa

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)
SS18L1-CDH4chr2060718944chr206046996595DRB1-0465QKKVQQYTVIVQATD1126
SS18L1-CDH4chr2060718944chr206046996595DRB1-0473QKKVQQYTVIVQATD1126
SS18L1-CDH4chr2060718944chr206046996595DRB1-1457QKKVQQYTVIVQATD1126

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Fusion breakpoint peptide structures of SS18L1-CDH4

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
9581TQQTIQKKVQQYTVSS18L1CDH4chr2060718944chr206046996595

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of SS18L1-CDH4

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-B14:023BVN9581TQQTIQKKVQQYTV-7.15543-7.26883
HLA-B14:023BVN9581TQQTIQKKVQQYTV-4.77435-5.80965
HLA-B52:013W399581TQQTIQKKVQQYTV-6.80875-6.92215
HLA-B52:013W399581TQQTIQKKVQQYTV-4.20386-5.23916
HLA-A11:014UQ29581TQQTIQKKVQQYTV-7.5194-8.5547
HLA-A11:014UQ29581TQQTIQKKVQQYTV-6.9601-7.0735
HLA-A24:025HGA9581TQQTIQKKVQQYTV-7.52403-7.63743
HLA-A24:025HGA9581TQQTIQKKVQQYTV-5.82433-6.85963
HLA-B27:056PYJ9581TQQTIQKKVQQYTV-3.28285-4.31815
HLA-B44:053DX89581TQQTIQKKVQQYTV-5.91172-6.94702
HLA-B44:053DX89581TQQTIQKKVQQYTV-4.24346-4.35686

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Vaccine Design for the FusionNeoAntigens of SS18L1-CDH4

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
SS18L1-CDH4chr2060718944chr20604699651018IQKKVQQYATCCAGAAGAAAGTTCAGCAGTAC
SS18L1-CDH4chr2060718944chr20604699651019IQKKVQQYTATCCAGAAGAAAGTTCAGCAGTACACA
SS18L1-CDH4chr2060718944chr20604699651020IQKKVQQYTVATCCAGAAGAAAGTTCAGCAGTACACAGTC
SS18L1-CDH4chr2060718944chr2060469965514VTQQTIQKKGTTACGCAGCAAACCATCCAGAAGAAA
SS18L1-CDH4chr2060718944chr2060469965615TQQTIQKKVACGCAGCAAACCATCCAGAAGAAAGTT
SS18L1-CDH4chr2060718944chr2060469965718QQTIQKKVQQYCAGCAAACCATCCAGAAGAAAGTTCAGCAGTAC
SS18L1-CDH4chr2060718944chr2060469965818QTIQKKVQQYCAAACCATCCAGAAGAAAGTTCAGCAGTAC
SS18L1-CDH4chr2060718944chr2060469965918TIQKKVQQYACCATCCAGAAGAAAGTTCAGCAGTAC

check button mRNA and peptide sequences of FusionNeoAntigens that have potential interaction with HLA-IIs.
Fusion geneHchrHbpTchrTbpStart in +/-13AAEnd in +/-13AAFusionNeoAntigen peptideFusionNEoAntigen RNA sequence
SS18L1-CDH4chr2060718944chr20604699651126QKKVQQYTVIVQATDCAGAAGAAAGTTCAGCAGTACACAGTCATCGTTCAGGCCACAGAT

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Information of the samples that have these potential fusion neoantigens of SS18L1-CDH4

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
BRCASS18L1-CDH4chr2060718944ENST00000331758chr2060469965ENST00000360469TCGA-E2-A1LL-01A

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Potential target of CAR-T therapy development for SS18L1-CDH4

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
TgeneCDH4chr20:60718944chr20:60469965ENST00000360469616735_7560917.0TransmembraneHelical
TgeneCDH4chr20:60718944chr20:60469965ENST00000543233515735_7560843.0TransmembraneHelical
TgeneCDH4chr20:60718945chr20:60469965ENST00000360469616735_7560917.0TransmembraneHelical
TgeneCDH4chr20:60718945chr20:60469965ENST00000543233515735_7560843.0TransmembraneHelical
TgeneCDH4chr20:60718945chr20:60469966ENST00000360469616735_7560917.0TransmembraneHelical
TgeneCDH4chr20:60718945chr20:60469966ENST00000543233515735_7560843.0TransmembraneHelical

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 SS18L1-CDH4

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 SS18L1-CDH4

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
HgeneSS18L1C1862939AMYOTROPHIC LATERAL SCLEROSIS 11GENOMICS_ENGLAND