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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:SMARCA4-KCNMA1

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: SMARCA4-KCNMA1
FusionPDB ID: 83893
FusionGDB2.0 ID: 83893
HgeneTgene
Gene symbol

SMARCA4

KCNMA1

Gene ID

6597

3778

Gene nameSWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4potassium calcium-activated channel subfamily M alpha 1
SynonymsBAF190|BAF190A|BRG1|CSS4|MRD16|RTPS2|SNF2|SNF2-beta|SNF2L4|SNF2LB|SWI2|hSNF2bBKTM|CADEDS|IEG16|KCa1.1|LIWAS|MaxiK|PNKD3|SAKCA|SLO|SLO-ALPHA|SLO1|bA205K10.1|hSlo|mSLO1
Cytomap

19p13.2

10q22.3

Type of geneprotein-codingprotein-coding
Descriptiontranscription activator BRG1ATP-dependent helicase SMARCA4BRG1-associated factor 190ABRM/SWI2-related gene 1SNF2-like 4brahma protein-like 1global transcription activator homologous sequencehomeotic gene regulatormitotic growth and transcription acalcium-activated potassium channel subunit alpha-1uncharacterized proteinBK channel alpha subunitBKCA alpha subunitbig potassium channel alpha subunitcalcium-activated potassium channel, subfamily M subunit alpha-1k(VCA)alphamaxi-K channel HSLOpo
Modification date2020031520200315
UniProtAcc.

Q12791

Main function of 5'-partner protein: FUNCTION: Potassium channel activated by both membrane depolarization or increase in cytosolic Ca(2+) that mediates export of K(+) (PubMed:29330545, PubMed:31152168). It is also activated by the concentration of cytosolic Mg(2+). Its activation dampens the excitatory events that elevate the cytosolic Ca(2+) concentration and/or depolarize the cell membrane. It therefore contributes to repolarization of the membrane potential. Plays a key role in controlling excitability in a number of systems, such as regulation of the contraction of smooth muscle, the tuning of hair cells in the cochlea, regulation of transmitter release, and innate immunity. In smooth muscles, its activation by high level of Ca(2+), caused by ryanodine receptors in the sarcoplasmic reticulum, regulates the membrane potential. In cochlea cells, its number and kinetic properties partly determine the characteristic frequency of each hair cell and thereby helps to establish a tonotopic map. Kinetics of KCNMA1 channels are determined by alternative splicing, phosphorylation status and its combination with modulating beta subunits. Highly sensitive to both iberiotoxin (IbTx) and charybdotoxin (CTX). {ECO:0000269|PubMed:29330545, ECO:0000269|PubMed:31152168}.
Ensembl transtripts involved in fusion geneENST idsENST00000344626, ENST00000358026, 
ENST00000413806, ENST00000429416, 
ENST00000444061, ENST00000450717, 
ENST00000541122, ENST00000589677, 
ENST00000590574, ENST00000538456, 
ENST00000480683, ENST00000481070, 
ENST00000484507, ENST00000286627, 
ENST00000286628, ENST00000354353, 
ENST00000372440, ENST00000372443, 
ENST00000404771, ENST00000404857, 
ENST00000406533, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score29 X 29 X 17=1429718 X 17 X 8=2448
# samples 5521
** MAII scorelog2(55/14297*10)=-4.70013702309346
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(21/2448*10)=-3.54314232502653
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Fusion gene context

PubMed: SMARCA4 [Title/Abstract] AND KCNMA1 [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: SMARCA4 [Title/Abstract] AND KCNMA1 [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)SMARCA4(11114074)-KCNMA1(79397104), # samples:1
Anticipated loss of major functional domain due to fusion event.SMARCA4-KCNMA1 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.
SMARCA4-KCNMA1 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.
SMARCA4-KCNMA1 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.
SMARCA4-KCNMA1 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
HgeneSMARCA4

GO:0006337

nucleosome disassembly

8895581

HgeneSMARCA4

GO:0006338

chromatin remodeling

10943845|11726552

HgeneSMARCA4

GO:0045892

negative regulation of transcription, DNA-templated

12065415

HgeneSMARCA4

GO:0045944

positive regulation of transcription by RNA polymerase II

15774904|17938176

HgeneSMARCA4

GO:0051091

positive regulation of DNA-binding transcription factor activity

11950834|17938176

HgeneSMARCA4

GO:1902661

positive regulation of glucose mediated signaling pathway

22368283

TgeneKCNMA1

GO:0001666

response to hypoxia

15528406

TgeneKCNMA1

GO:0006813

potassium ion transport

7573516|7877450|11245614|12388065|17706472|18458941

TgeneKCNMA1

GO:0006970

response to osmotic stress

10840032|12388065

TgeneKCNMA1

GO:0030007

cellular potassium ion homeostasis

11245614

TgeneKCNMA1

GO:0034465

response to carbon monoxide

15528406

TgeneKCNMA1

GO:0042391

regulation of membrane potential

7877450|7993625

TgeneKCNMA1

GO:0045794

negative regulation of cell volume

12388065

TgeneKCNMA1

GO:0051592

response to calcium ion

12388065|18458941

TgeneKCNMA1

GO:0060073

micturition

11641143

TgeneKCNMA1

GO:0060083

smooth muscle contraction involved in micturition

11641143



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/chr19:11114074/chr10:79397104)
- 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 SMARCA4 (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 KCNMA1 (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)
ENST00000358026SMARCA4chr1911114074+ENST00000404771KCNMA1chr1079397104+599822852632350695
ENST00000358026SMARCA4chr1911114074+ENST00000372440KCNMA1chr1079397104+579522852632350695
ENST00000358026SMARCA4chr1911114074+ENST00000372443KCNMA1chr1079397104+587922852632353696
ENST00000358026SMARCA4chr1911114074+ENST00000286628KCNMA1chr1079397104+808522852632311682
ENST00000358026SMARCA4chr1911114074+ENST00000286627KCNMA1chr1079397104+791122852632311682
ENST00000358026SMARCA4chr1911114074+ENST00000354353KCNMA1chr1079397104+570922852632311682
ENST00000358026SMARCA4chr1911114074+ENST00000404857KCNMA1chr1079397104+564922852632311682
ENST00000358026SMARCA4chr1911114074+ENST00000406533KCNMA1chr1079397104+571222852632311682
ENST00000344626SMARCA4chr1911114074+ENST00000404771KCNMA1chr1079397104+591922061842271695
ENST00000344626SMARCA4chr1911114074+ENST00000372440KCNMA1chr1079397104+571622061842271695
ENST00000344626SMARCA4chr1911114074+ENST00000372443KCNMA1chr1079397104+580022061842274696
ENST00000344626SMARCA4chr1911114074+ENST00000286628KCNMA1chr1079397104+800622061842232682
ENST00000344626SMARCA4chr1911114074+ENST00000286627KCNMA1chr1079397104+783222061842232682
ENST00000344626SMARCA4chr1911114074+ENST00000354353KCNMA1chr1079397104+563022061842232682
ENST00000344626SMARCA4chr1911114074+ENST00000404857KCNMA1chr1079397104+557022061842232682
ENST00000344626SMARCA4chr1911114074+ENST00000406533KCNMA1chr1079397104+563322061842232682
ENST00000429416SMARCA4chr1911114074+ENST00000404771KCNMA1chr1079397104+59952282562347763
ENST00000429416SMARCA4chr1911114074+ENST00000372440KCNMA1chr1079397104+57922282562347763
ENST00000429416SMARCA4chr1911114074+ENST00000372443KCNMA1chr1079397104+58762282562350764
ENST00000429416SMARCA4chr1911114074+ENST00000286628KCNMA1chr1079397104+80822282562308750
ENST00000429416SMARCA4chr1911114074+ENST00000286627KCNMA1chr1079397104+79082282562308750
ENST00000429416SMARCA4chr1911114074+ENST00000354353KCNMA1chr1079397104+57062282562308750
ENST00000429416SMARCA4chr1911114074+ENST00000404857KCNMA1chr1079397104+56462282562308750
ENST00000429416SMARCA4chr1911114074+ENST00000406533KCNMA1chr1079397104+57092282562308750
ENST00000541122SMARCA4chr1911114074+ENST00000404771KCNMA1chr1079397104+599922862552351698
ENST00000541122SMARCA4chr1911114074+ENST00000372440KCNMA1chr1079397104+579622862552351698
ENST00000541122SMARCA4chr1911114074+ENST00000372443KCNMA1chr1079397104+588022862552354699
ENST00000541122SMARCA4chr1911114074+ENST00000286628KCNMA1chr1079397104+808622862552312685
ENST00000541122SMARCA4chr1911114074+ENST00000286627KCNMA1chr1079397104+791222862552312685
ENST00000541122SMARCA4chr1911114074+ENST00000354353KCNMA1chr1079397104+571022862552312685
ENST00000541122SMARCA4chr1911114074+ENST00000404857KCNMA1chr1079397104+565022862552312685
ENST00000541122SMARCA4chr1911114074+ENST00000406533KCNMA1chr1079397104+571322862552312685
ENST00000589677SMARCA4chr1911114074+ENST00000404771KCNMA1chr1079397104+604423313092396695
ENST00000589677SMARCA4chr1911114074+ENST00000372440KCNMA1chr1079397104+584123313092396695
ENST00000589677SMARCA4chr1911114074+ENST00000372443KCNMA1chr1079397104+592523313092399696
ENST00000589677SMARCA4chr1911114074+ENST00000286628KCNMA1chr1079397104+813123313092357682
ENST00000589677SMARCA4chr1911114074+ENST00000286627KCNMA1chr1079397104+795723313092357682
ENST00000589677SMARCA4chr1911114074+ENST00000354353KCNMA1chr1079397104+575523313092357682
ENST00000589677SMARCA4chr1911114074+ENST00000404857KCNMA1chr1079397104+569523313092357682
ENST00000589677SMARCA4chr1911114074+ENST00000406533KCNMA1chr1079397104+575823313092357682
ENST00000444061SMARCA4chr1911114074+ENST00000404771KCNMA1chr1079397104+58102097662162698
ENST00000444061SMARCA4chr1911114074+ENST00000372440KCNMA1chr1079397104+56072097662162698
ENST00000444061SMARCA4chr1911114074+ENST00000372443KCNMA1chr1079397104+56912097662165699
ENST00000444061SMARCA4chr1911114074+ENST00000286628KCNMA1chr1079397104+78972097662123685
ENST00000444061SMARCA4chr1911114074+ENST00000286627KCNMA1chr1079397104+77232097662123685
ENST00000444061SMARCA4chr1911114074+ENST00000354353KCNMA1chr1079397104+55212097662123685
ENST00000444061SMARCA4chr1911114074+ENST00000404857KCNMA1chr1079397104+54612097662123685
ENST00000444061SMARCA4chr1911114074+ENST00000406533KCNMA1chr1079397104+55242097662123685
ENST00000590574SMARCA4chr1911114074+ENST00000404771KCNMA1chr1079397104+615124384162503695
ENST00000590574SMARCA4chr1911114074+ENST00000372440KCNMA1chr1079397104+594824384162503695
ENST00000590574SMARCA4chr1911114074+ENST00000372443KCNMA1chr1079397104+603224384162506696
ENST00000590574SMARCA4chr1911114074+ENST00000286628KCNMA1chr1079397104+823824384162464682
ENST00000590574SMARCA4chr1911114074+ENST00000286627KCNMA1chr1079397104+806424384162464682
ENST00000590574SMARCA4chr1911114074+ENST00000354353KCNMA1chr1079397104+586224384162464682
ENST00000590574SMARCA4chr1911114074+ENST00000404857KCNMA1chr1079397104+580224384162464682
ENST00000590574SMARCA4chr1911114074+ENST00000406533KCNMA1chr1079397104+586524384162464682
ENST00000413806SMARCA4chr1911114074+ENST00000404771KCNMA1chr1079397104+5714200102066688
ENST00000413806SMARCA4chr1911114074+ENST00000372440KCNMA1chr1079397104+5511200102066688
ENST00000413806SMARCA4chr1911114074+ENST00000372443KCNMA1chr1079397104+5595200102069689
ENST00000413806SMARCA4chr1911114074+ENST00000286628KCNMA1chr1079397104+7801200102027675
ENST00000413806SMARCA4chr1911114074+ENST00000286627KCNMA1chr1079397104+7627200102027675
ENST00000413806SMARCA4chr1911114074+ENST00000354353KCNMA1chr1079397104+5425200102027675
ENST00000413806SMARCA4chr1911114074+ENST00000404857KCNMA1chr1079397104+5365200102027675
ENST00000413806SMARCA4chr1911114074+ENST00000406533KCNMA1chr1079397104+5428200102027675
ENST00000450717SMARCA4chr1911114074+ENST00000404771KCNMA1chr1079397104+5714200102066688
ENST00000450717SMARCA4chr1911114074+ENST00000372440KCNMA1chr1079397104+5511200102066688
ENST00000450717SMARCA4chr1911114074+ENST00000372443KCNMA1chr1079397104+5595200102069689
ENST00000450717SMARCA4chr1911114074+ENST00000286628KCNMA1chr1079397104+7801200102027675
ENST00000450717SMARCA4chr1911114074+ENST00000286627KCNMA1chr1079397104+7627200102027675
ENST00000450717SMARCA4chr1911114074+ENST00000354353KCNMA1chr1079397104+5425200102027675
ENST00000450717SMARCA4chr1911114074+ENST00000404857KCNMA1chr1079397104+5365200102027675
ENST00000450717SMARCA4chr1911114074+ENST00000406533KCNMA1chr1079397104+5428200102027675

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
ENST00000358026ENST00000404771SMARCA4chr1911114074+KCNMA1chr1079397104+0.0070984640.9929015
ENST00000358026ENST00000372440SMARCA4chr1911114074+KCNMA1chr1079397104+0.0075548960.9924452
ENST00000358026ENST00000372443SMARCA4chr1911114074+KCNMA1chr1079397104+0.0072715360.9927285
ENST00000358026ENST00000286628SMARCA4chr1911114074+KCNMA1chr1079397104+0.0025437570.99745625
ENST00000358026ENST00000286627SMARCA4chr1911114074+KCNMA1chr1079397104+0.0026812460.9973188
ENST00000358026ENST00000354353SMARCA4chr1911114074+KCNMA1chr1079397104+0.0089072060.99109274
ENST00000358026ENST00000404857SMARCA4chr1911114074+KCNMA1chr1079397104+0.0086319920.991368
ENST00000358026ENST00000406533SMARCA4chr1911114074+KCNMA1chr1079397104+0.0084495740.99155045
ENST00000344626ENST00000404771SMARCA4chr1911114074+KCNMA1chr1079397104+0.0073337770.9926662
ENST00000344626ENST00000372440SMARCA4chr1911114074+KCNMA1chr1079397104+0.0077600810.99223995
ENST00000344626ENST00000372443SMARCA4chr1911114074+KCNMA1chr1079397104+0.007465790.99253416
ENST00000344626ENST00000286628SMARCA4chr1911114074+KCNMA1chr1079397104+0.0025960810.9974039
ENST00000344626ENST00000286627SMARCA4chr1911114074+KCNMA1chr1079397104+0.0027376380.99726236
ENST00000344626ENST00000354353SMARCA4chr1911114074+KCNMA1chr1079397104+0.0091259170.99087405
ENST00000344626ENST00000404857SMARCA4chr1911114074+KCNMA1chr1079397104+0.0087449250.99125504
ENST00000344626ENST00000406533SMARCA4chr1911114074+KCNMA1chr1079397104+0.008732740.99126726
ENST00000429416ENST00000404771SMARCA4chr1911114074+KCNMA1chr1079397104+0.0077112080.99228877
ENST00000429416ENST00000372440SMARCA4chr1911114074+KCNMA1chr1079397104+0.0081207860.99187917
ENST00000429416ENST00000372443SMARCA4chr1911114074+KCNMA1chr1079397104+0.0078350880.99216485
ENST00000429416ENST00000286628SMARCA4chr1911114074+KCNMA1chr1079397104+0.0027498210.99725014
ENST00000429416ENST00000286627SMARCA4chr1911114074+KCNMA1chr1079397104+0.0028727510.99712723
ENST00000429416ENST00000354353SMARCA4chr1911114074+KCNMA1chr1079397104+0.0095001770.9904998
ENST00000429416ENST00000404857SMARCA4chr1911114074+KCNMA1chr1079397104+0.0091118250.99088824
ENST00000429416ENST00000406533SMARCA4chr1911114074+KCNMA1chr1079397104+0.0091777110.9908223
ENST00000541122ENST00000404771SMARCA4chr1911114074+KCNMA1chr1079397104+0.007367290.9926327
ENST00000541122ENST00000372440SMARCA4chr1911114074+KCNMA1chr1079397104+0.007843750.99215627
ENST00000541122ENST00000372443SMARCA4chr1911114074+KCNMA1chr1079397104+0.0075511030.9924489
ENST00000541122ENST00000286628SMARCA4chr1911114074+KCNMA1chr1079397104+0.0026592970.99734074
ENST00000541122ENST00000286627SMARCA4chr1911114074+KCNMA1chr1079397104+0.0028020810.99719787
ENST00000541122ENST00000354353SMARCA4chr1911114074+KCNMA1chr1079397104+0.0092538860.99074614
ENST00000541122ENST00000404857SMARCA4chr1911114074+KCNMA1chr1079397104+0.0088999950.9911
ENST00000541122ENST00000406533SMARCA4chr1911114074+KCNMA1chr1079397104+0.0088426980.9911573
ENST00000589677ENST00000404771SMARCA4chr1911114074+KCNMA1chr1079397104+0.0069881960.9930118
ENST00000589677ENST00000372440SMARCA4chr1911114074+KCNMA1chr1079397104+0.0073501220.99264985
ENST00000589677ENST00000372443SMARCA4chr1911114074+KCNMA1chr1079397104+0.007098690.99290127
ENST00000589677ENST00000286628SMARCA4chr1911114074+KCNMA1chr1079397104+0.0025963420.9974037
ENST00000589677ENST00000286627SMARCA4chr1911114074+KCNMA1chr1079397104+0.0027205660.99727947
ENST00000589677ENST00000354353SMARCA4chr1911114074+KCNMA1chr1079397104+0.008624420.9913756
ENST00000589677ENST00000404857SMARCA4chr1911114074+KCNMA1chr1079397104+0.0082678480.9917321
ENST00000589677ENST00000406533SMARCA4chr1911114074+KCNMA1chr1079397104+0.0082750260.99172497
ENST00000444061ENST00000404771SMARCA4chr1911114074+KCNMA1chr1079397104+0.007196220.99280375
ENST00000444061ENST00000372440SMARCA4chr1911114074+KCNMA1chr1079397104+0.0075947090.99240524
ENST00000444061ENST00000372443SMARCA4chr1911114074+KCNMA1chr1079397104+0.0073250730.9926749
ENST00000444061ENST00000286628SMARCA4chr1911114074+KCNMA1chr1079397104+0.0025309610.99746907
ENST00000444061ENST00000286627SMARCA4chr1911114074+KCNMA1chr1079397104+0.0026620660.9973379
ENST00000444061ENST00000354353SMARCA4chr1911114074+KCNMA1chr1079397104+0.0088930170.99110705
ENST00000444061ENST00000404857SMARCA4chr1911114074+KCNMA1chr1079397104+0.0084858280.9915141
ENST00000444061ENST00000406533SMARCA4chr1911114074+KCNMA1chr1079397104+0.0085721060.99142784
ENST00000590574ENST00000404771SMARCA4chr1911114074+KCNMA1chr1079397104+0.007082140.99291784
ENST00000590574ENST00000372440SMARCA4chr1911114074+KCNMA1chr1079397104+0.0074710810.9925289
ENST00000590574ENST00000372443SMARCA4chr1911114074+KCNMA1chr1079397104+0.0072059230.9927941
ENST00000590574ENST00000286628SMARCA4chr1911114074+KCNMA1chr1079397104+0.0025850710.99741495
ENST00000590574ENST00000286627SMARCA4chr1911114074+KCNMA1chr1079397104+0.002712360.99728763
ENST00000590574ENST00000354353SMARCA4chr1911114074+KCNMA1chr1079397104+0.0087802130.9912198
ENST00000590574ENST00000404857SMARCA4chr1911114074+KCNMA1chr1079397104+0.0085170190.9914829
ENST00000590574ENST00000406533SMARCA4chr1911114074+KCNMA1chr1079397104+0.0084600150.99154
ENST00000413806ENST00000404771SMARCA4chr1911114074+KCNMA1chr1079397104+0.0069744270.99302554
ENST00000413806ENST00000372440SMARCA4chr1911114074+KCNMA1chr1079397104+0.0073912080.9926087
ENST00000413806ENST00000372443SMARCA4chr1911114074+KCNMA1chr1079397104+0.0071089680.9928911
ENST00000413806ENST00000286628SMARCA4chr1911114074+KCNMA1chr1079397104+0.0024527720.9975472
ENST00000413806ENST00000286627SMARCA4chr1911114074+KCNMA1chr1079397104+0.0025807860.99741924
ENST00000413806ENST00000354353SMARCA4chr1911114074+KCNMA1chr1079397104+0.0087259320.99127406
ENST00000413806ENST00000404857SMARCA4chr1911114074+KCNMA1chr1079397104+0.0083390230.99166095
ENST00000413806ENST00000406533SMARCA4chr1911114074+KCNMA1chr1079397104+0.0083151110.9916849
ENST00000450717ENST00000404771SMARCA4chr1911114074+KCNMA1chr1079397104+0.0069744270.99302554
ENST00000450717ENST00000372440SMARCA4chr1911114074+KCNMA1chr1079397104+0.0073912080.9926087
ENST00000450717ENST00000372443SMARCA4chr1911114074+KCNMA1chr1079397104+0.0071089680.9928911
ENST00000450717ENST00000286628SMARCA4chr1911114074+KCNMA1chr1079397104+0.0024527720.9975472
ENST00000450717ENST00000286627SMARCA4chr1911114074+KCNMA1chr1079397104+0.0025807860.99741924
ENST00000450717ENST00000354353SMARCA4chr1911114074+KCNMA1chr1079397104+0.0087259320.99127406
ENST00000450717ENST00000404857SMARCA4chr1911114074+KCNMA1chr1079397104+0.0083390230.99166095
ENST00000450717ENST00000406533SMARCA4chr1911114074+KCNMA1chr1079397104+0.0083151110.9916849

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 SMARCA4-KCNMA1

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide
SMARCA4chr1911114074KCNMA1chr1079397104228223EEKRDAHSAPGPARRGGGGAGKSTAP

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Potential FusionNeoAntigen Information of SMARCA4-KCNMA1 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 SMARCA4-KCNMA1 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 SMARCA4-KCNMA1

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 SMARCA4-KCNMA1

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 SMARCA4-KCNMA1

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 SMARCA4-KCNMA1

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 SMARCA4-KCNMA1

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
TgeneKCNMA1chr19:11114074chr10:79397104ENST00000286627027336_35801179.0IntramembranePore-forming%3B Name%3DP region
TgeneKCNMA1chr19:11114074chr10:79397104ENST00000286628028336_35801237.0IntramembranePore-forming%3B Name%3DP region
TgeneKCNMA1chr19:11114074chr10:79397104ENST00000404857028336_35801220.0IntramembranePore-forming%3B Name%3DP region
TgeneKCNMA1chr19:11114074chr10:79397104ENST0000048068302336_3580169.0IntramembranePore-forming%3B Name%3DP region
TgeneKCNMA1chr19:11114074chr10:79397104ENST00000286627027179_19901179.0TransmembraneHelical%3B Name%3DSegment S1
TgeneKCNMA1chr19:11114074chr10:79397104ENST00000286627027215_23501179.0TransmembraneHelical%3B Name%3DSegment S2
TgeneKCNMA1chr19:11114074chr10:79397104ENST00000286627027240_26001179.0TransmembraneHelical%3B Name%3DSegment S3
TgeneKCNMA1chr19:11114074chr10:79397104ENST00000286627027265_28501179.0TransmembraneHelical%3B Name%3DSegment S4
TgeneKCNMA1chr19:11114074chr10:79397104ENST00000286627027301_32101179.0TransmembraneHelical%3B Name%3DSegment S5
TgeneKCNMA1chr19:11114074chr10:79397104ENST00000286627027368_38801179.0TransmembraneHelical%3B Name%3DSegment S6
TgeneKCNMA1chr19:11114074chr10:79397104ENST0000028662702787_10701179.0TransmembraneHelical%3B Name%3DSegment S0
TgeneKCNMA1chr19:11114074chr10:79397104ENST00000286628028179_19901237.0TransmembraneHelical%3B Name%3DSegment S1
TgeneKCNMA1chr19:11114074chr10:79397104ENST00000286628028215_23501237.0TransmembraneHelical%3B Name%3DSegment S2
TgeneKCNMA1chr19:11114074chr10:79397104ENST00000286628028240_26001237.0TransmembraneHelical%3B Name%3DSegment S3
TgeneKCNMA1chr19:11114074chr10:79397104ENST00000286628028265_28501237.0TransmembraneHelical%3B Name%3DSegment S4
TgeneKCNMA1chr19:11114074chr10:79397104ENST00000286628028301_32101237.0TransmembraneHelical%3B Name%3DSegment S5
TgeneKCNMA1chr19:11114074chr10:79397104ENST00000286628028368_38801237.0TransmembraneHelical%3B Name%3DSegment S6
TgeneKCNMA1chr19:11114074chr10:79397104ENST0000028662802887_10701237.0TransmembraneHelical%3B Name%3DSegment S0
TgeneKCNMA1chr19:11114074chr10:79397104ENST00000404857028179_19901220.0TransmembraneHelical%3B Name%3DSegment S1
TgeneKCNMA1chr19:11114074chr10:79397104ENST00000404857028215_23501220.0TransmembraneHelical%3B Name%3DSegment S2
TgeneKCNMA1chr19:11114074chr10:79397104ENST00000404857028240_26001220.0TransmembraneHelical%3B Name%3DSegment S3
TgeneKCNMA1chr19:11114074chr10:79397104ENST00000404857028265_28501220.0TransmembraneHelical%3B Name%3DSegment S4
TgeneKCNMA1chr19:11114074chr10:79397104ENST00000404857028301_32101220.0TransmembraneHelical%3B Name%3DSegment S5
TgeneKCNMA1chr19:11114074chr10:79397104ENST00000404857028368_38801220.0TransmembraneHelical%3B Name%3DSegment S6
TgeneKCNMA1chr19:11114074chr10:79397104ENST0000040485702887_10701220.0TransmembraneHelical%3B Name%3DSegment S0
TgeneKCNMA1chr19:11114074chr10:79397104ENST0000048068302179_1990169.0TransmembraneHelical%3B Name%3DSegment S1
TgeneKCNMA1chr19:11114074chr10:79397104ENST0000048068302215_2350169.0TransmembraneHelical%3B Name%3DSegment S2
TgeneKCNMA1chr19:11114074chr10:79397104ENST0000048068302240_2600169.0TransmembraneHelical%3B Name%3DSegment S3
TgeneKCNMA1chr19:11114074chr10:79397104ENST0000048068302265_2850169.0TransmembraneHelical%3B Name%3DSegment S4
TgeneKCNMA1chr19:11114074chr10:79397104ENST0000048068302301_3210169.0TransmembraneHelical%3B Name%3DSegment S5
TgeneKCNMA1chr19:11114074chr10:79397104ENST0000048068302368_3880169.0TransmembraneHelical%3B Name%3DSegment S6
TgeneKCNMA1chr19:11114074chr10:79397104ENST000004806830287_1070169.0TransmembraneHelical%3B Name%3DSegment S0

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 SMARCA4-KCNMA1

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 SMARCA4-KCNMA1

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