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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:ARID1B-PLEKHG1

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: ARID1B-PLEKHG1
FusionPDB ID: 6413
FusionGDB2.0 ID: 6413
HgeneTgene
Gene symbol

ARID1B

PLEKHG1

Gene ID

57492

57480

Gene nameAT-rich interaction domain 1Bpleckstrin homology and RhoGEF domain containing G1
Synonyms6A3-5|BAF250B|BRIGHT|CSS1|DAN15|ELD/OSA1|MRD12|OSA2|P250RARHGEF41
Cytomap

6q25.3

6q25.1

Type of geneprotein-codingprotein-coding
DescriptionAT-rich interactive domain-containing protein 1BARID domain-containing protein 1BAT rich interactive domain 1B (SWI1-like)BRG1-associated factor 250bBRG1-binding protein ELD/OSA1ELD (eyelid)/OSA proteinpleckstrin homology domain-containing family G member 1pleckstrin homology domain containing, family G (with RhoGef domain) member 1
Modification date2020032020200313
UniProtAcc

Q8NFD5

Main function of 5'-partner protein: FUNCTION: Involved in transcriptional activation and repression of select genes by chromatin remodeling (alteration of DNA-nucleosome topology). Component of SWI/SNF chromatin remodeling complexes that carry out key enzymatic activities, changing chromatin structure by altering DNA-histone contacts within a nucleosome in an ATP-dependent manner. Belongs to the neural progenitors-specific chromatin remodeling complex (npBAF complex) and the neuron-specific chromatin remodeling complex (nBAF complex). During neural development a switch from a stem/progenitor to a postmitotic chromatin remodeling mechanism occurs as neurons exit the cell cycle and become committed to their adult state. The transition from proliferating neural stem/progenitor cells to postmitotic neurons requires a switch in subunit composition of the npBAF and nBAF complexes. As neural progenitors exit mitosis and differentiate into neurons, npBAF complexes which contain ACTL6A/BAF53A and PHF10/BAF45A, are exchanged for homologous alternative ACTL6B/BAF53B and DPF1/BAF45B or DPF3/BAF45C subunits in neuron-specific complexes (nBAF). The npBAF complex is essential for the self-renewal/proliferative capacity of the multipotent neural stem cells. The nBAF complex along with CREST plays a role regulating the activity of genes essential for dendrite growth (By similarity). Binds DNA non-specifically (PubMed:14982958, PubMed:15170388). {ECO:0000250|UniProtKB:E9Q4N7, ECO:0000269|PubMed:14982958, ECO:0000269|PubMed:15170388, ECO:0000303|PubMed:12672490, ECO:0000303|PubMed:22952240, ECO:0000303|PubMed:26601204}.		.
Ensembl transtripts involved in fusion geneENST idsENST00000275248, ENST00000346085, 
ENST00000350026, ENST00000367148, 
ENST00000478761, 		ENST00000358517, 
ENST00000367328, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score27 X 18 X 14=680411 X 13 X 5=715
# samples 3112
** MAII scorelog2(31/6804*10)=-4.45604302038915
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(12/715*10)=-2.57490883605723
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Fusion gene context

PubMed: ARID1B [Title/Abstract] AND PLEKHG1 [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: ARID1B [Title/Abstract] AND PLEKHG1 [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)ARID1B(157256710)-PLEKHG1(151089774), # samples:3
Anticipated loss of major functional domain due to fusion event.ARID1B-PLEKHG1 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.
ARID1B-PLEKHG1 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.
ARID1B-PLEKHG1 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.
ARID1B-PLEKHG1 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/chr6:157256710/chr6:151089774)
- 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 ARID1B (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 PLEKHG1 (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)
ENST00000350026ARID1Bchr6157256710+ENST00000367328PLEKHG1chr6151089774+85131999157451914
ENST00000350026ARID1Bchr6157256710+ENST00000358517PLEKHG1chr6151089774+85131999157451914
ENST00000346085ARID1Bchr6157256710+ENST00000367328PLEKHG1chr6151089774+85522038157841927
ENST00000346085ARID1Bchr6157256710+ENST00000358517PLEKHG1chr6151089774+85522038157841927
ENST00000367148ARID1Bchr6157256710+ENST00000367328PLEKHG1chr6151089774+85121998057441914
ENST00000367148ARID1Bchr6157256710+ENST00000358517PLEKHG1chr6151089774+85121998057441914
ENST00000275248ARID1Bchr6157256710+ENST00000367328PLEKHG1chr6151089774+849019767757221881
ENST00000275248ARID1Bchr6157256710+ENST00000358517PLEKHG1chr6151089774+849019767757221881
ENST00000350026ARID1Bchr6157256710+ENST00000367328PLEKHG1chr6151089773+85131999157451914
ENST00000350026ARID1Bchr6157256710+ENST00000358517PLEKHG1chr6151089773+85131999157451914
ENST00000346085ARID1Bchr6157256710+ENST00000367328PLEKHG1chr6151089773+85522038157841927
ENST00000346085ARID1Bchr6157256710+ENST00000358517PLEKHG1chr6151089773+85522038157841927
ENST00000367148ARID1Bchr6157256710+ENST00000367328PLEKHG1chr6151089773+85121998057441914
ENST00000367148ARID1Bchr6157256710+ENST00000358517PLEKHG1chr6151089773+85121998057441914
ENST00000275248ARID1Bchr6157256710+ENST00000367328PLEKHG1chr6151089773+849019767757221881
ENST00000275248ARID1Bchr6157256710+ENST00000358517PLEKHG1chr6151089773+849019767757221881
ENST00000350026ARID1Bchr6157256709+ENST00000367328PLEKHG1chr6151089773+85131999157451914
ENST00000350026ARID1Bchr6157256709+ENST00000358517PLEKHG1chr6151089773+85131999157451914
ENST00000346085ARID1Bchr6157256709+ENST00000367328PLEKHG1chr6151089773+85522038157841927
ENST00000346085ARID1Bchr6157256709+ENST00000358517PLEKHG1chr6151089773+85522038157841927
ENST00000367148ARID1Bchr6157256709+ENST00000367328PLEKHG1chr6151089773+85121998057441914
ENST00000367148ARID1Bchr6157256709+ENST00000358517PLEKHG1chr6151089773+85121998057441914
ENST00000275248ARID1Bchr6157256709+ENST00000367328PLEKHG1chr6151089773+849019767757221881
ENST00000275248ARID1Bchr6157256709+ENST00000358517PLEKHG1chr6151089773+849019767757221881

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
ENST00000350026ENST00000367328ARID1Bchr6157256710+PLEKHG1chr6151089774+0.0008964930.9991035
ENST00000350026ENST00000358517ARID1Bchr6157256710+PLEKHG1chr6151089774+0.0008964930.9991035
ENST00000346085ENST00000367328ARID1Bchr6157256710+PLEKHG1chr6151089774+0.0009134950.9990865
ENST00000346085ENST00000358517ARID1Bchr6157256710+PLEKHG1chr6151089774+0.0009134950.9990865
ENST00000367148ENST00000367328ARID1Bchr6157256710+PLEKHG1chr6151089774+0.000894210.99910575
ENST00000367148ENST00000358517ARID1Bchr6157256710+PLEKHG1chr6151089774+0.000894210.99910575
ENST00000275248ENST00000367328ARID1Bchr6157256710+PLEKHG1chr6151089774+0.0010253360.9989747
ENST00000275248ENST00000358517ARID1Bchr6157256710+PLEKHG1chr6151089774+0.0010253360.9989747
ENST00000350026ENST00000367328ARID1Bchr6157256710+PLEKHG1chr6151089773+0.0008964930.9991035
ENST00000350026ENST00000358517ARID1Bchr6157256710+PLEKHG1chr6151089773+0.0008964930.9991035
ENST00000346085ENST00000367328ARID1Bchr6157256710+PLEKHG1chr6151089773+0.0009134950.9990865
ENST00000346085ENST00000358517ARID1Bchr6157256710+PLEKHG1chr6151089773+0.0009134950.9990865
ENST00000367148ENST00000367328ARID1Bchr6157256710+PLEKHG1chr6151089773+0.000894210.99910575
ENST00000367148ENST00000358517ARID1Bchr6157256710+PLEKHG1chr6151089773+0.000894210.99910575
ENST00000275248ENST00000367328ARID1Bchr6157256710+PLEKHG1chr6151089773+0.0010253360.9989747
ENST00000275248ENST00000358517ARID1Bchr6157256710+PLEKHG1chr6151089773+0.0010253360.9989747
ENST00000350026ENST00000367328ARID1Bchr6157256709+PLEKHG1chr6151089773+0.0008964930.9991035
ENST00000350026ENST00000358517ARID1Bchr6157256709+PLEKHG1chr6151089773+0.0008964930.9991035
ENST00000346085ENST00000367328ARID1Bchr6157256709+PLEKHG1chr6151089773+0.0009134950.9990865
ENST00000346085ENST00000358517ARID1Bchr6157256709+PLEKHG1chr6151089773+0.0009134950.9990865
ENST00000367148ENST00000367328ARID1Bchr6157256709+PLEKHG1chr6151089773+0.000894210.99910575
ENST00000367148ENST00000358517ARID1Bchr6157256709+PLEKHG1chr6151089773+0.000894210.99910575
ENST00000275248ENST00000367328ARID1Bchr6157256709+PLEKHG1chr6151089773+0.0010253360.9989747
ENST00000275248ENST00000358517ARID1Bchr6157256709+PLEKHG1chr6151089773+0.0010253360.9989747

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 ARID1B-PLEKHG1

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide
ARID1Bchr6157256709PLEKHG1chr61510897731976236GQQSPGMGMMHSASAAAAGAPGSMDP
ARID1Bchr6157256709PLEKHG1chr61510897731998269GQQSPGMGMMHSASAAAAGAPGSMDP
ARID1Bchr6157256709PLEKHG1chr61510897731999269GQQSPGMGMMHSASAAAAGAPGSMDP
ARID1Bchr6157256709PLEKHG1chr61510897732038269GQQSPGMGMMHSASAAAAGAPGSMDP
ARID1Bchr6157256710PLEKHG1chr61510897731976236GQQSPGMGMMHSASAAAAGAPGSMDP
ARID1Bchr6157256710PLEKHG1chr61510897731998269GQQSPGMGMMHSASAAAAGAPGSMDP
ARID1Bchr6157256710PLEKHG1chr61510897731999269GQQSPGMGMMHSASAAAAGAPGSMDP
ARID1Bchr6157256710PLEKHG1chr61510897732038269GQQSPGMGMMHSASAAAAGAPGSMDP
ARID1Bchr6157256710PLEKHG1chr61510897741976236GQQSPGMGMMHSASAAAAGAPGSMDP
ARID1Bchr6157256710PLEKHG1chr61510897741998269GQQSPGMGMMHSASAAAAGAPGSMDP
ARID1Bchr6157256710PLEKHG1chr61510897741999269GQQSPGMGMMHSASAAAAGAPGSMDP
ARID1Bchr6157256710PLEKHG1chr61510897742038269GQQSPGMGMMHSASAAAAGAPGSMDP

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Potential FusionNeoAntigen Information of ARID1B-PLEKHG1 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.
ARID1B-PLEKHG1_157256709_151089773.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)
ARID1B-PLEKHG1chr6157256709chr61510897731976HLA-B39:06MHSASAAA0.99940.8416917
ARID1B-PLEKHG1chr6157256709chr61510897731976HLA-B39:06MHSASAAAA0.99690.9022918
ARID1B-PLEKHG1chr6157256709chr61510897731976HLA-B39:01MHSASAAAA0.99480.9387918
ARID1B-PLEKHG1chr6157256709chr61510897731976HLA-B08:09MGMMHSASA0.98870.8047615
ARID1B-PLEKHG1chr6157256709chr61510897731976HLA-B15:10MHSASAAAA0.940.549918
ARID1B-PLEKHG1chr6157256709chr61510897731976HLA-B15:37MHSASAAAA0.43960.601918
ARID1B-PLEKHG1chr6157256709chr61510897731976HLA-B39:05MHSASAAAA0.98970.931918
ARID1B-PLEKHG1chr6157256709chr61510897731976HLA-B15:09MHSASAAAA0.9740.9434918
ARID1B-PLEKHG1chr6157256709chr61510897731976HLA-B39:11MHSASAAAA0.580.9308918

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Potential FusionNeoAntigen Information of ARID1B-PLEKHG1 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.
ARID1B-PLEKHG1_157256709_151089773.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)
ARID1B-PLEKHG1chr6157256709chr61510897731976DRB1-0902GMGMMHSASAAAAGA520
ARID1B-PLEKHG1chr6157256709chr61510897731976DRB1-0902MGMMHSASAAAAGAP621

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Fusion breakpoint peptide structures of ARID1B-PLEKHG1

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
5916MGMMHSASAAAAGAARID1BPLEKHG1chr6157256709chr61510897731976

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of ARID1B-PLEKHG1

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-B14:023BVN5916MGMMHSASAAAAGA-6.11479-7.15009
HLA-B14:023BVN5916MGMMHSASAAAAGA-4.76706-4.88046
HLA-B52:013W395916MGMMHSASAAAAGA-6.87405-6.98745
HLA-B52:013W395916MGMMHSASAAAAGA-5.3619-6.3972
HLA-A11:014UQ25916MGMMHSASAAAAGA-9.79836-9.91176
HLA-A24:025HGA5916MGMMHSASAAAAGA-8.83847-8.95187
HLA-A24:025HGA5916MGMMHSASAAAAGA-8.05027-9.08557
HLA-B44:053DX85916MGMMHSASAAAAGA-7.51915-7.63255
HLA-B44:053DX85916MGMMHSASAAAAGA-4.45384-5.48914
HLA-A02:016TDR5916MGMMHSASAAAAGA-2.8902-3.9255

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Vaccine Design for the FusionNeoAntigens of ARID1B-PLEKHG1

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
ARID1B-PLEKHG1chr6157256709chr6151089773615MGMMHSASAGAAAGACCATCAAGTTTACCAGATTAC
ARID1B-PLEKHG1chr6157256709chr6151089773917MHSASAAATCAAGTTTACCAGATTACCTTGAC
ARID1B-PLEKHG1chr6157256709chr6151089773918MHSASAAAATCAAGTTTACCAGATTACCTTGACTGC

check button mRNA and peptide sequences of FusionNeoAntigens that have potential interaction with HLA-IIs.
Fusion geneHchrHbpTchrTbpStart in +/-13AAEnd in +/-13AAFusionNeoAntigen peptideFusionNEoAntigen RNA sequence
ARID1B-PLEKHG1chr6157256709chr6151089773520GMGMMHSASAAAAGACAAGAAAGACCATCAAGTTTACCAGATTACCTTGACTGCATCAGG
ARID1B-PLEKHG1chr6157256709chr6151089773621MGMMHSASAAAAGAPGAAAGACCATCAAGTTTACCAGATTACCTTGACTGCATCAGGGAC

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Information of the samples that have these potential fusion neoantigens of ARID1B-PLEKHG1

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
BRCAARID1B-PLEKHG1chr6157256709ENST00000275248chr6151089773ENST00000358517TCGA-E9-A248-01A

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Potential target of CAR-T therapy development for ARID1B-PLEKHG1

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 ARID1B-PLEKHG1

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 ARID1B-PLEKHG1

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