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Fusion Protein:SMARCA4-SMIM7

Fusion Gene and Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: SMARCA4-SMIM7
	FusionPDB ID: 83910
	FusionGDB2.0 ID: 83910
		Hgene	Tgene
	Gene symbol	SMARCA4	SMIM7
	Gene ID	6597	79086
	Gene name	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4	small integral membrane protein 7
	Synonyms	BAF190\|BAF190A\|BRG1\|CSS4\|MRD16\|RTPS2\|SNF2\|SNF2-beta\|SNF2L4\|SNF2LB\|SWI2\|hSNF2b	C19orf42
	Cytomap	19p13.2	19p13.11
	Type of gene	protein-coding	protein-coding
	Description	transcription 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 a	small integral membrane protein 7UPF0608 protein C19orf42
	Modification date	20200315	20200313
	UniProtAcc	.	Q9BQ49 Main function of 5'-partner protein:
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000344626, ENST00000358026, ENST00000413806, ENST00000429416, ENST00000444061, ENST00000450717, ENST00000541122, ENST00000589677, ENST00000590574, ENST00000538456,	ENST00000397349, ENST00000358726, ENST00000487416, ENST00000597711,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	29 X 29 X 17=14297	9 X 10 X 4=360
	# samples	55	8
	** MAII score	log2(55/14297*10)=-4.70013702309346 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(8/360*10)=-2.16992500144231 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Fusion gene context	PubMed: SMARCA4 [Title/Abstract] AND SMIM7 [Title/Abstract] AND fusion [Title/Abstract]
Fusion neoantigen context	PubMed: SMARCA4 [Title/Abstract] AND SMIM7 [Title/Abstract] AND neoantigen [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	SMARCA4(11107220)-SMIM7(16758072), # samples:1
Anticipated loss of major functional domain due to fusion event.	SMARCA4-SMIM7 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-SMIM7 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-SMIM7 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-SMIM7 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)

Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez

Partner	Gene	GO ID	GO term	PubMed ID
Hgene	SMARCA4	GO:0006337	nucleosome disassembly	8895581
Hgene	SMARCA4	GO:0006338	chromatin remodeling	10943845\|11726552
Hgene	SMARCA4	GO:0045892	negative regulation of transcription, DNA-templated	12065415
Hgene	SMARCA4	GO:0045944	positive regulation of transcription by RNA polymerase II	15774904\|17938176
Hgene	SMARCA4	GO:0051091	positive regulation of DNA-binding transcription factor activity	11950834\|17938176
Hgene	SMARCA4	GO:1902661	positive regulation of glucose mediated signaling pathway	22368283

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr19:11107220/chr19:16758072)
- 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.

Retention 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.

Fusion 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.

Fusion gene breakpoints across SMIM7 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

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Fusion Amino Acid Sequences

Fusion information from ORFfinder translation from full-length transcript sequence from FusionPDB.

Henst	Tenst	Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand	Seq length (transcript)	BP loci (transcript)	Predicted start (transcript)	Predicted stop (transcript)	Seq length (amino acids)
ENST00000358026	SMARCA4	chr19	11107220	+	ENST00000487416	SMIM7	chr19	16758072	-	4613	2096	263	2176	637
ENST00000358026	SMARCA4	chr19	11107220	+	ENST00000597711	SMIM7	chr19	16758072	-	3016	2096	263	2176	637
ENST00000344626	SMARCA4	chr19	11107220	+	ENST00000487416	SMIM7	chr19	16758072	-	4534	2017	184	2097	637
ENST00000344626	SMARCA4	chr19	11107220	+	ENST00000597711	SMIM7	chr19	16758072	-	2937	2017	184	2097	637
ENST00000429416	SMARCA4	chr19	11107220	+	ENST00000487416	SMIM7	chr19	16758072	-	4610	2093	56	2173	705
ENST00000429416	SMARCA4	chr19	11107220	+	ENST00000597711	SMIM7	chr19	16758072	-	3013	2093	56	2173	705
ENST00000541122	SMARCA4	chr19	11107220	+	ENST00000487416	SMIM7	chr19	16758072	-	4614	2097	255	2177	640
ENST00000541122	SMARCA4	chr19	11107220	+	ENST00000597711	SMIM7	chr19	16758072	-	3017	2097	255	2177	640
ENST00000589677	SMARCA4	chr19	11107220	+	ENST00000487416	SMIM7	chr19	16758072	-	4659	2142	309	2222	637
ENST00000589677	SMARCA4	chr19	11107220	+	ENST00000597711	SMIM7	chr19	16758072	-	3062	2142	309	2222	637
ENST00000444061	SMARCA4	chr19	11107220	+	ENST00000487416	SMIM7	chr19	16758072	-	4425	1908	66	1988	640
ENST00000444061	SMARCA4	chr19	11107220	+	ENST00000597711	SMIM7	chr19	16758072	-	2828	1908	66	1988	640
ENST00000590574	SMARCA4	chr19	11107220	+	ENST00000487416	SMIM7	chr19	16758072	-	4766	2249	416	2329	637
ENST00000590574	SMARCA4	chr19	11107220	+	ENST00000597711	SMIM7	chr19	16758072	-	3169	2249	416	2329	637
ENST00000413806	SMARCA4	chr19	11107220	+	ENST00000487416	SMIM7	chr19	16758072	-	4329	1812	0	1892	630
ENST00000413806	SMARCA4	chr19	11107220	+	ENST00000597711	SMIM7	chr19	16758072	-	2732	1812	0	1892	630
ENST00000450717	SMARCA4	chr19	11107220	+	ENST00000487416	SMIM7	chr19	16758072	-	4329	1812	0	1892	630
ENST00000450717	SMARCA4	chr19	11107220	+	ENST00000597711	SMIM7	chr19	16758072	-	2732	1812	0	1892	630

DeepORF 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.

Henst	Tenst	Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand	No-coding score	Coding score
ENST00000358026	ENST00000487416	SMARCA4	chr19	11107220	+	SMIM7	chr19	16758072	-	0.004370029	0.99563
ENST00000358026	ENST00000597711	SMARCA4	chr19	11107220	+	SMIM7	chr19	16758072	-	0.012056659	0.98794335
ENST00000344626	ENST00000487416	SMARCA4	chr19	11107220	+	SMIM7	chr19	16758072	-	0.004809303	0.99519074
ENST00000344626	ENST00000597711	SMARCA4	chr19	11107220	+	SMIM7	chr19	16758072	-	0.013962228	0.9860378
ENST00000429416	ENST00000487416	SMARCA4	chr19	11107220	+	SMIM7	chr19	16758072	-	0.005345601	0.9946544
ENST00000429416	ENST00000597711	SMARCA4	chr19	11107220	+	SMIM7	chr19	16758072	-	0.015110746	0.98488927
ENST00000541122	ENST00000487416	SMARCA4	chr19	11107220	+	SMIM7	chr19	16758072	-	0.004971094	0.9950289
ENST00000541122	ENST00000597711	SMARCA4	chr19	11107220	+	SMIM7	chr19	16758072	-	0.014813405	0.98518664
ENST00000589677	ENST00000487416	SMARCA4	chr19	11107220	+	SMIM7	chr19	16758072	-	0.004816278	0.99518377
ENST00000589677	ENST00000597711	SMARCA4	chr19	11107220	+	SMIM7	chr19	16758072	-	0.013779992	0.98622
ENST00000444061	ENST00000487416	SMARCA4	chr19	11107220	+	SMIM7	chr19	16758072	-	0.004784391	0.99521565
ENST00000444061	ENST00000597711	SMARCA4	chr19	11107220	+	SMIM7	chr19	16758072	-	0.014462949	0.9855371
ENST00000590574	ENST00000487416	SMARCA4	chr19	11107220	+	SMIM7	chr19	16758072	-	0.004569733	0.99543023
ENST00000590574	ENST00000597711	SMARCA4	chr19	11107220	+	SMIM7	chr19	16758072	-	0.012355899	0.98764414
ENST00000413806	ENST00000487416	SMARCA4	chr19	11107220	+	SMIM7	chr19	16758072	-	0.00435017	0.9956499
ENST00000413806	ENST00000597711	SMARCA4	chr19	11107220	+	SMIM7	chr19	16758072	-	0.013671662	0.9863283
ENST00000450717	ENST00000487416	SMARCA4	chr19	11107220	+	SMIM7	chr19	16758072	-	0.00435017	0.9956499
ENST00000450717	ENST00000597711	SMARCA4	chr19	11107220	+	SMIM7	chr19	16758072	-	0.013671662	0.9863283

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-SMIM7

+/-13 AA sequence from the breakpoints of the fusion protein sequences.

Hgene	Hchr	Hbp	Tgene	Tchr	Tbp	Length(fusion protein)	BP in fusion protein	Peptide
SMARCA4	chr19	11107220	SMIM7	chr19	16758072	1812	604	AEGQTPAIGPDGEAVRLLNPSDETRN
SMARCA4	chr19	11107220	SMIM7	chr19	16758072	1908	614	AEGQTPAIGPDGEAVRLLNPSDETRN
SMARCA4	chr19	11107220	SMIM7	chr19	16758072	2017	611	AEGQTPAIGPDGEAVRLLNPSDETRN
SMARCA4	chr19	11107220	SMIM7	chr19	16758072	2093	24	EKRDAHSAPGPARRGGGGAGKSTAPA
SMARCA4	chr19	11107220	SMIM7	chr19	16758072	2096	611	AEGQTPAIGPDGEAVRLLNPSDETRN
SMARCA4	chr19	11107220	SMIM7	chr19	16758072	2097	614	AEGQTPAIGPDGEAVRLLNPSDETRN
SMARCA4	chr19	11107220	SMIM7	chr19	16758072	2142	611	AEGQTPAIGPDGEAVRLLNPSDETRN
SMARCA4	chr19	11107220	SMIM7	chr19	16758072	2249	611	AEGQTPAIGPDGEAVRLLNPSDETRN

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Potential FusionNeoAntigen Information of SMARCA4-SMIM7 in HLA I

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.

SMARCA4-SMIM7_11107220_16758072.msa

Potential FusionNeoAntigen Information
* We used NetMHCpan v4.1 (%rank<0.5) and deepHLApan v1.1 (immunogenic score>0.5)

Fusion gene	Hchr	Hbp	Tgene	Tchr	Tbp	HLA I	FusionNeoAntigen peptide	Binding score	Immunogenic score	Neoantigen start (at BP 13)	Neoantigen end (at BP 13)
SMARCA4-SMIM7	chr19	11107220	chr19	16758072	2093	HLA-A68:24	HSAPGPARR	0.9983	0.8319	5	14
SMARCA4-SMIM7	chr19	11107220	chr19	16758072	2093	HLA-A68:03	HSAPGPARR	0.9975	0.8292	5	14
SMARCA4-SMIM7	chr19	11107220	chr19	16758072	2093	HLA-A11:10	HSAPGPARR	0.9943	0.5844	5	14
SMARCA4-SMIM7	chr19	11107220	chr19	16758072	2093	HLA-A68:08	HSAPGPARR	0.9922	0.8489	5	14
SMARCA4-SMIM7	chr19	11107220	chr19	16758072	2093	HLA-A66:01	HSAPGPARR	0.9921	0.7608	5	14
SMARCA4-SMIM7	chr19	11107220	chr19	16758072	2017	HLA-B45:01	GEAVRLLNP	0.9916	0.8032	11	20
SMARCA4-SMIM7	chr19	11107220	chr19	16758072	2093	HLA-A68:06	HSAPGPARR	0.9884	0.755	5	14
SMARCA4-SMIM7	chr19	11107220	chr19	16758072	2093	HLA-A68:05	HSAPGPARR	0.9855	0.8412	5	14
SMARCA4-SMIM7	chr19	11107220	chr19	16758072	2093	HLA-A74:03	HSAPGPARR	0.9819	0.9	5	14
SMARCA4-SMIM7	chr19	11107220	chr19	16758072	2093	HLA-A74:11	HSAPGPARR	0.9819	0.9	5	14
SMARCA4-SMIM7	chr19	11107220	chr19	16758072	2093	HLA-A74:09	HSAPGPARR	0.9819	0.9	5	14
SMARCA4-SMIM7	chr19	11107220	chr19	16758072	2093	HLA-A31:06	HSAPGPARR	0.9817	0.8333	5	14
SMARCA4-SMIM7	chr19	11107220	chr19	16758072	2093	HLA-A31:02	HSAPGPARR	0.9777	0.9096	5	14
SMARCA4-SMIM7	chr19	11107220	chr19	16758072	2017	HLA-B50:02	GEAVRLLNP	0.9738	0.6742	11	20
SMARCA4-SMIM7	chr19	11107220	chr19	16758072	2093	HLA-B27:05	RRGGGGAGK	0.9724	0.6102	12	21
SMARCA4-SMIM7	chr19	11107220	chr19	16758072	2017	HLA-B07:05	GPDGEAVRL	0.9591	0.6967	8	17
SMARCA4-SMIM7	chr19	11107220	chr19	16758072	2093	HLA-A34:05	HSAPGPARR	0.9582	0.8463	5	14
SMARCA4-SMIM7	chr19	11107220	chr19	16758072	2093	HLA-A34:01	HSAPGPARR	0.9582	0.8463	5	14
SMARCA4-SMIM7	chr19	11107220	chr19	16758072	2093	HLA-A34:02	HSAPGPARR	0.9533	0.6756	5	14
SMARCA4-SMIM7	chr19	11107220	chr19	16758072	2093	HLA-A11:04	HSAPGPARR	0.9399	0.606	5	14
SMARCA4-SMIM7	chr19	11107220	chr19	16758072	2093	HLA-A66:03	HSAPGPARR	0.9268	0.8857	5	14
SMARCA4-SMIM7	chr19	11107220	chr19	16758072	2093	HLA-A33:05	HSAPGPARR	0.916	0.7375	5	14
SMARCA4-SMIM7	chr19	11107220	chr19	16758072	2093	HLA-A33:01	HSAPGPARR	0.916	0.7375	5	14
SMARCA4-SMIM7	chr19	11107220	chr19	16758072	2093	HLA-A26:03	HSAPGPARR	0.8599	0.7965	5	14
SMARCA4-SMIM7	chr19	11107220	chr19	16758072	2017	HLA-B35:03	GPDGEAVRL	0.856	0.9598	8	17
SMARCA4-SMIM7	chr19	11107220	chr19	16758072	2017	HLA-B35:08	GPDGEAVRL	0.8225	0.9197	8	17
SMARCA4-SMIM7	chr19	11107220	chr19	16758072	2017	HLA-B35:04	GPDGEAVRL	0.5823	0.976	8	17
SMARCA4-SMIM7	chr19	11107220	chr19	16758072	2017	HLA-B35:02	GPDGEAVRL	0.5823	0.976	8	17
SMARCA4-SMIM7	chr19	11107220	chr19	16758072	2017	HLA-B41:01	GEAVRLLNP	0.4861	0.7397	11	20
SMARCA4-SMIM7	chr19	11107220	chr19	16758072	2017	HLA-B50:01	GEAVRLLNP	0.112	0.6475	11	20
SMARCA4-SMIM7	chr19	11107220	chr19	16758072	2017	HLA-B81:01	GPDGEAVRL	0.08	0.6663	8	17
SMARCA4-SMIM7	chr19	11107220	chr19	16758072	2017	HLA-B82:01	GPDGEAVRL	0.022	0.5155	8	17
SMARCA4-SMIM7	chr19	11107220	chr19	16758072	2017	HLA-B35:03	IGPDGEAVRL	0.829	0.9159	7	17
SMARCA4-SMIM7	chr19	11107220	chr19	16758072	2017	HLA-B35:04	IGPDGEAVRL	0.6681	0.9673	7	17
SMARCA4-SMIM7	chr19	11107220	chr19	16758072	2017	HLA-B35:02	IGPDGEAVRL	0.6681	0.9673	7	17
SMARCA4-SMIM7	chr19	11107220	chr19	16758072	2093	HLA-A31:06	AHSAPGPARR	0.4282	0.8003	4	14
SMARCA4-SMIM7	chr19	11107220	chr19	16758072	2017	HLA-B35:04	GPDGEAVRLL	0.3311	0.9576	8	18
SMARCA4-SMIM7	chr19	11107220	chr19	16758072	2017	HLA-B35:02	GPDGEAVRLL	0.3311	0.9576	8	18
SMARCA4-SMIM7	chr19	11107220	chr19	16758072	2093	HLA-A68:06	DAHSAPGPARR	0.9991	0.8619	3	14
SMARCA4-SMIM7	chr19	11107220	chr19	16758072	2093	HLA-A33:05	DAHSAPGPARR	0.9988	0.8201	3	14
SMARCA4-SMIM7	chr19	11107220	chr19	16758072	2093	HLA-A33:01	DAHSAPGPARR	0.9988	0.8201	3	14
SMARCA4-SMIM7	chr19	11107220	chr19	16758072	2093	HLA-A68:24	DAHSAPGPARR	0.9986	0.89	3	14
SMARCA4-SMIM7	chr19	11107220	chr19	16758072	2093	HLA-A68:03	DAHSAPGPARR	0.9982	0.8927	3	14
SMARCA4-SMIM7	chr19	11107220	chr19	16758072	2093	HLA-A68:05	DAHSAPGPARR	0.992	0.8972	3	14
SMARCA4-SMIM7	chr19	11107220	chr19	16758072	2093	HLA-A68:01	HSAPGPARR	0.9983	0.8319	5	14
SMARCA4-SMIM7	chr19	11107220	chr19	16758072	2017	HLA-C04:07	GPDGEAVRL	0.9951	0.9638	8	17
SMARCA4-SMIM7	chr19	11107220	chr19	16758072	2017	HLA-C04:10	GPDGEAVRL	0.9948	0.9543	8	17
SMARCA4-SMIM7	chr19	11107220	chr19	16758072	2093	HLA-A11:01	HSAPGPARR	0.9905	0.5902	5	14
SMARCA4-SMIM7	chr19	11107220	chr19	16758072	2017	HLA-C08:15	GPDGEAVRL	0.9904	0.9914	8	17
SMARCA4-SMIM7	chr19	11107220	chr19	16758072	2017	HLA-B40:06	GEAVRLLNP	0.9903	0.7031	11	20
SMARCA4-SMIM7	chr19	11107220	chr19	16758072	2093	HLA-A33:03	HSAPGPARR	0.9892	0.7456	5	14
SMARCA4-SMIM7	chr19	11107220	chr19	16758072	2093	HLA-A31:01	HSAPGPARR	0.9883	0.8827	5	14
SMARCA4-SMIM7	chr19	11107220	chr19	16758072	2093	HLA-B27:14	RRGGGGAGK	0.9477	0.5999	12	21
SMARCA4-SMIM7	chr19	11107220	chr19	16758072	2017	HLA-B07:12	GPDGEAVRL	0.8419	0.8056	8	17
SMARCA4-SMIM7	chr19	11107220	chr19	16758072	2017	HLA-B56:04	GPDGEAVRL	0.7301	0.502	8	17
SMARCA4-SMIM7	chr19	11107220	chr19	16758072	2017	HLA-B35:12	GPDGEAVRL	0.5823	0.976	8	17
SMARCA4-SMIM7	chr19	11107220	chr19	16758072	2017	HLA-B39:10	GPDGEAVRL	0.3947	0.9339	8	17
SMARCA4-SMIM7	chr19	11107220	chr19	16758072	2017	HLA-C08:15	IGPDGEAVRL	0.9992	0.9657	7	17
SMARCA4-SMIM7	chr19	11107220	chr19	16758072	2017	HLA-C01:17	IGPDGEAVRL	0.9967	0.9348	7	17
SMARCA4-SMIM7	chr19	11107220	chr19	16758072	2017	HLA-B35:12	IGPDGEAVRL	0.6681	0.9673	7	17
SMARCA4-SMIM7	chr19	11107220	chr19	16758072	2017	HLA-B39:10	IGPDGEAVRL	0.6522	0.8519	7	17
SMARCA4-SMIM7	chr19	11107220	chr19	16758072	2017	HLA-B35:12	GPDGEAVRLL	0.3311	0.9576	8	18
SMARCA4-SMIM7	chr19	11107220	chr19	16758072	2093	HLA-A68:01	DAHSAPGPARR	0.9986	0.89	3	14
SMARCA4-SMIM7	chr19	11107220	chr19	16758072	2017	HLA-B39:10	TPAIGPDGEAV	0.9535	0.9322	4	15
SMARCA4-SMIM7	chr19	11107220	chr19	16758072	2017	HLA-C04:03	GPDGEAVRL	0.9957	0.9712	8	17
SMARCA4-SMIM7	chr19	11107220	chr19	16758072	2017	HLA-C04:01	GPDGEAVRL	0.9951	0.9638	8	17
SMARCA4-SMIM7	chr19	11107220	chr19	16758072	2017	HLA-C18:01	GPDGEAVRL	0.9939	0.9626	8	17
SMARCA4-SMIM7	chr19	11107220	chr19	16758072	2093	HLA-A11:02	HSAPGPARR	0.9905	0.5902	5	14
SMARCA4-SMIM7	chr19	11107220	chr19	16758072	2017	HLA-C08:02	GPDGEAVRL	0.9904	0.9914	8	17
SMARCA4-SMIM7	chr19	11107220	chr19	16758072	2093	HLA-A74:01	HSAPGPARR	0.9819	0.9	5	14
SMARCA4-SMIM7	chr19	11107220	chr19	16758072	2093	HLA-B27:10	RRGGGGAGK	0.9398	0.7829	12	21
SMARCA4-SMIM7	chr19	11107220	chr19	16758072	2093	HLA-A66:02	HSAPGPARR	0.889	0.8684	5	14
SMARCA4-SMIM7	chr19	11107220	chr19	16758072	2017	HLA-B35:13	GPDGEAVRL	0.7856	0.9618	8	17
SMARCA4-SMIM7	chr19	11107220	chr19	16758072	2017	HLA-B56:02	GPDGEAVRL	0.7301	0.502	8	17
SMARCA4-SMIM7	chr19	11107220	chr19	16758072	2017	HLA-B35:22	GPDGEAVRL	0.679	0.602	8	17
SMARCA4-SMIM7	chr19	11107220	chr19	16758072	2017	HLA-B35:09	GPDGEAVRL	0.5823	0.976	8	17
SMARCA4-SMIM7	chr19	11107220	chr19	16758072	2017	HLA-B39:11	GPDGEAVRL	0.4533	0.8836	8	17
SMARCA4-SMIM7	chr19	11107220	chr19	16758072	2017	HLA-B67:01	GPDGEAVRL	0.4507	0.9021	8	17
SMARCA4-SMIM7	chr19	11107220	chr19	16758072	2017	HLA-B50:05	GEAVRLLNP	0.112	0.6475	11	20
SMARCA4-SMIM7	chr19	11107220	chr19	16758072	2017	HLA-B50:04	GEAVRLLNP	0.112	0.6475	11	20
SMARCA4-SMIM7	chr19	11107220	chr19	16758072	2017	HLA-B82:02	GPDGEAVRL	0.022	0.5155	8	17
SMARCA4-SMIM7	chr19	11107220	chr19	16758072	2017	HLA-C08:02	IGPDGEAVRL	0.9992	0.9657	7	17
SMARCA4-SMIM7	chr19	11107220	chr19	16758072	2017	HLA-C01:03	IGPDGEAVRL	0.999	0.8439	7	17
SMARCA4-SMIM7	chr19	11107220	chr19	16758072	2017	HLA-C01:02	IGPDGEAVRL	0.9978	0.9341	7	17
SMARCA4-SMIM7	chr19	11107220	chr19	16758072	2017	HLA-B67:01	IGPDGEAVRL	0.6789	0.7779	7	17
SMARCA4-SMIM7	chr19	11107220	chr19	16758072	2017	HLA-B35:09	IGPDGEAVRL	0.6681	0.9673	7	17
SMARCA4-SMIM7	chr19	11107220	chr19	16758072	2017	HLA-B35:09	GPDGEAVRLL	0.3311	0.9576	8	18
SMARCA4-SMIM7	chr19	11107220	chr19	16758072	2017	HLA-B51:05	TPAIGPDGEAV	0.9948	0.5475	4	15
SMARCA4-SMIM7	chr19	11107220	chr19	16758072	2017	HLA-B67:01	TPAIGPDGEAV	0.9649	0.9272	4	15

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Potential FusionNeoAntigen Information of SMARCA4-SMIM7 in HLA II

SMARCA4-SMIM7_11107220_16758072.msa

Potential FusionNeoAntigen Information
* We used NetMHCIIpan v4.1 (%rank<0.5).

Fusion gene	Hchr	Hbp	Tgene	Tchr	Tbp	HLA II	FusionNeoAntigen peptide	Neoantigen start (at BP 13)	Neoantigen end (at BP 13)
SMARCA4-SMIM7	chr19	11107220	chr19	16758072	2017	DRB1-0301	TPAIGPDGEAVRLLN	4	19
SMARCA4-SMIM7	chr19	11107220	chr19	16758072	2017	DRB1-0301	QTPAIGPDGEAVRLL	3	18
SMARCA4-SMIM7	chr19	11107220	chr19	16758072	2017	DRB1-0313	TPAIGPDGEAVRLLN	4	19
SMARCA4-SMIM7	chr19	11107220	chr19	16758072	2017	DRB1-0313	QTPAIGPDGEAVRLL	3	18
SMARCA4-SMIM7	chr19	11107220	chr19	16758072	2017	DRB1-0315	TPAIGPDGEAVRLLN	4	19
SMARCA4-SMIM7	chr19	11107220	chr19	16758072	2017	DRB1-0318	TPAIGPDGEAVRLLN	4	19
SMARCA4-SMIM7	chr19	11107220	chr19	16758072	2017	DRB1-0318	QTPAIGPDGEAVRLL	3	18
SMARCA4-SMIM7	chr19	11107220	chr19	16758072	2017	DRB1-0320	TPAIGPDGEAVRLLN	4	19
SMARCA4-SMIM7	chr19	11107220	chr19	16758072	2017	DRB1-0322	TPAIGPDGEAVRLLN	4	19
SMARCA4-SMIM7	chr19	11107220	chr19	16758072	2017	DRB1-0322	QTPAIGPDGEAVRLL	3	18
SMARCA4-SMIM7	chr19	11107220	chr19	16758072	2017	DRB1-0326	TPAIGPDGEAVRLLN	4	19
SMARCA4-SMIM7	chr19	11107220	chr19	16758072	2017	DRB1-0328	TPAIGPDGEAVRLLN	4	19
SMARCA4-SMIM7	chr19	11107220	chr19	16758072	2017	DRB1-0328	QTPAIGPDGEAVRLL	3	18
SMARCA4-SMIM7	chr19	11107220	chr19	16758072	2017	DRB1-0330	TPAIGPDGEAVRLLN	4	19
SMARCA4-SMIM7	chr19	11107220	chr19	16758072	2017	DRB1-0330	QTPAIGPDGEAVRLL	3	18
SMARCA4-SMIM7	chr19	11107220	chr19	16758072	2017	DRB1-0332	TPAIGPDGEAVRLLN	4	19
SMARCA4-SMIM7	chr19	11107220	chr19	16758072	2017	DRB1-0332	QTPAIGPDGEAVRLL	3	18
SMARCA4-SMIM7	chr19	11107220	chr19	16758072	2017	DRB1-0334	TPAIGPDGEAVRLLN	4	19
SMARCA4-SMIM7	chr19	11107220	chr19	16758072	2017	DRB1-0334	QTPAIGPDGEAVRLL	3	18
SMARCA4-SMIM7	chr19	11107220	chr19	16758072	2017	DRB1-0336	TPAIGPDGEAVRLLN	4	19
SMARCA4-SMIM7	chr19	11107220	chr19	16758072	2017	DRB1-0336	QTPAIGPDGEAVRLL	3	18
SMARCA4-SMIM7	chr19	11107220	chr19	16758072	2017	DRB1-0344	TPAIGPDGEAVRLLN	4	19
SMARCA4-SMIM7	chr19	11107220	chr19	16758072	2017	DRB1-0344	QTPAIGPDGEAVRLL	3	18
SMARCA4-SMIM7	chr19	11107220	chr19	16758072	2017	DRB1-0346	TPAIGPDGEAVRLLN	4	19
SMARCA4-SMIM7	chr19	11107220	chr19	16758072	2017	DRB1-0346	QTPAIGPDGEAVRLL	3	18
SMARCA4-SMIM7	chr19	11107220	chr19	16758072	2017	DRB1-0348	TPAIGPDGEAVRLLN	4	19
SMARCA4-SMIM7	chr19	11107220	chr19	16758072	2017	DRB1-0350	TPAIGPDGEAVRLLN	4	19
SMARCA4-SMIM7	chr19	11107220	chr19	16758072	2017	DRB1-0350	QTPAIGPDGEAVRLL	3	18
SMARCA4-SMIM7	chr19	11107220	chr19	16758072	2017	DRB1-0352	TPAIGPDGEAVRLLN	4	19
SMARCA4-SMIM7	chr19	11107220	chr19	16758072	2017	DRB1-0352	QTPAIGPDGEAVRLL	3	18
SMARCA4-SMIM7	chr19	11107220	chr19	16758072	2017	DRB1-0354	TPAIGPDGEAVRLLN	4	19
SMARCA4-SMIM7	chr19	11107220	chr19	16758072	2017	DRB1-0354	QTPAIGPDGEAVRLL	3	18

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Fusion breakpoint peptide structures of SMARCA4-SMIM7

3D 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 name	BPseq	Hgene	Tgene	Hchr	Hbp	Tchr	Tbp	AAlen
281	AIGPDGEAVRLLNP	SMARCA4	SMIM7	chr19	11107220	chr19	16758072	2017

File name	BPseq	Hgene	Tgene	Hchr	Hbp	Tchr	Tbp	AAlen
8408	SAPGPARRGGGGAG	SMARCA4	SMIM7	chr19	11107220	chr19	16758072	2093

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of SMARCA4-SMIM7

Virtual screening between 25 HLAs (from PDB) and FusionNeoAntigens
* We used Glide to predict the interaction between HLAs and neoantigens.

HLA allele	PDB ID	File name	BPseq	Docking score	Glide score
HLA-B14:02	3BVN	281	AIGPDGEAVRLLNP	-7.9962	-8.1096
HLA-B14:02	3BVN	281	AIGPDGEAVRLLNP	-5.70842	-6.74372
HLA-B52:01	3W39	281	AIGPDGEAVRLLNP	-6.83737	-6.95077
HLA-B52:01	3W39	281	AIGPDGEAVRLLNP	-4.4836	-5.5189
HLA-A11:01	4UQ2	281	AIGPDGEAVRLLNP	-10.0067	-10.1201
HLA-A11:01	4UQ2	281	AIGPDGEAVRLLNP	-9.03915	-10.0745
HLA-A24:02	5HGA	281	AIGPDGEAVRLLNP	-6.56204	-6.67544
HLA-A24:02	5HGA	281	AIGPDGEAVRLLNP	-5.42271	-6.45801
HLA-B44:05	3DX8	281	AIGPDGEAVRLLNP	-7.85648	-8.89178
HLA-B44:05	3DX8	281	AIGPDGEAVRLLNP	-5.3978	-5.5112
HLA-A02:01	6TDR	281	AIGPDGEAVRLLNP	-3.37154	-4.40684
HLA-B14:02	3BVN	8408	SAPGPARRGGGGAG	-6.60553	-6.71893
HLA-B14:02	3BVN	8408	SAPGPARRGGGGAG	-3.25382	-4.28912
HLA-B52:01	3W39	8408	SAPGPARRGGGGAG	-5.90011	-6.01351
HLA-B52:01	3W39	8408	SAPGPARRGGGGAG	-5.4415	-6.4768
HLA-B18:01	4JQV	8408	SAPGPARRGGGGAG	-2.23313	-2.34653
HLA-A11:01	4UQ2	8408	SAPGPARRGGGGAG	-6.31705	-6.43045
HLA-A11:01	4UQ2	8408	SAPGPARRGGGGAG	-4.25402	-5.28932
HLA-A24:02	5HGA	8408	SAPGPARRGGGGAG	-7.95591	-8.06931
HLA-A24:02	5HGA	8408	SAPGPARRGGGGAG	-6.24522	-7.28052
HLA-B27:05	6PYJ	8408	SAPGPARRGGGGAG	-3.83335	-4.86865
HLA-B44:05	3DX8	8408	SAPGPARRGGGGAG	-6.2025	-6.3159
HLA-B44:05	3DX8	8408	SAPGPARRGGGGAG	-5.27651	-6.31181
HLA-A02:01	6TDR	8408	SAPGPARRGGGGAG	-6.48102	-6.59442

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Vaccine Design for the FusionNeoAntigens of SMARCA4-SMIM7

mRNA and peptide sequences of FusionNeoAntigens that have potential interaction with HLA-Is.

Fusion gene	Hchr	Hbp	Tchr	Tbp	Start in +/-13AA	End in +/-13AA	FusionNeoAntigen peptide sequence	FusionNeoAntigen RNA sequence
SMARCA4-SMIM7	chr19	11107220	chr19	16758072	11	20	GEAVRLLNP	GGCGAGGCTGTTCGGCTCTTGAATCCC
SMARCA4-SMIM7	chr19	11107220	chr19	16758072	12	21	RRGGGGAGK	GAGGCTGTTCGGCTCTTGAATCCCAGC
SMARCA4-SMIM7	chr19	11107220	chr19	16758072	3	14	DAHSAPGPARR	CAGACGCCTGCCATTGGGCCGGATGGCGAGGCT
SMARCA4-SMIM7	chr19	11107220	chr19	16758072	4	14	AHSAPGPARR	ACGCCTGCCATTGGGCCGGATGGCGAGGCT
SMARCA4-SMIM7	chr19	11107220	chr19	16758072	4	15	TPAIGPDGEAV	ACGCCTGCCATTGGGCCGGATGGCGAGGCTGTT
SMARCA4-SMIM7	chr19	11107220	chr19	16758072	5	14	HSAPGPARR	CCTGCCATTGGGCCGGATGGCGAGGCT
SMARCA4-SMIM7	chr19	11107220	chr19	16758072	7	17	IGPDGEAVRL	ATTGGGCCGGATGGCGAGGCTGTTCGGCTC
SMARCA4-SMIM7	chr19	11107220	chr19	16758072	8	17	GPDGEAVRL	GGGCCGGATGGCGAGGCTGTTCGGCTC
SMARCA4-SMIM7	chr19	11107220	chr19	16758072	8	18	GPDGEAVRLL	GGGCCGGATGGCGAGGCTGTTCGGCTCTTG

mRNA and peptide sequences of FusionNeoAntigens that have potential interaction with HLA-IIs.

Fusion gene	Hchr	Hbp	Tchr	Tbp	Start in +/-13AA	End in +/-13AA	FusionNeoAntigen peptide	FusionNEoAntigen RNA sequence
SMARCA4-SMIM7	chr19	11107220	chr19	16758072	3	18	QTPAIGPDGEAVRLL	CAGACGCCTGCCATTGGGCCGGATGGCGAGGCTGTTCGGCTCTTG
SMARCA4-SMIM7	chr19	11107220	chr19	16758072	4	19	TPAIGPDGEAVRLLN	ACGCCTGCCATTGGGCCGGATGGCGAGGCTGTTCGGCTCTTGAAT

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Information of the samples that have these potential fusion neoantigens of SMARCA4-SMIM7

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 type	Fusion gene	Hchr	Hbp	Henst	Tchr	Tbp	Tenst	Sample
LGG	SMARCA4-SMIM7	chr19	11107220	ENST00000344626	chr19	16758072	ENST00000487416	TCGA-TM-A7CF-01A
LGG	SMARCA4-SMIM7	chr19	11107220	ENST00000429416	chr19	16758072	ENST00000487416	TCGA-TM-A7CF-01A

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Potential target of CAR-T therapy development for SMARCA4-SMIM7

Predicted 3D structure. We used RoseTTAFold.

Retention 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'.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Protein feature

Protein feature note

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.

Hgene

Hchr

Hbp

Henst

Tgene

Tchr

Tbp

Tenst

DeepLoc result

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Related Drugs to SMARCA4-SMIM7

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

Hgene

Tgene

Drug

Source

PMID

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Related Diseases to SMARCA4-SMIM7

Diseases that have this fusion gene.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)

Hgene

Tgene

Disease

Source

PMID

Diseases associated with fusion partners.
(DisGeNet 4.0)

Partner

Gene

Disease ID

Disease name

# pubmeds

Source

	Fusion Gene and Fusion Protein Summary
	Fusion Amino Acid Sequences (multiple BPs and multiple gene isoforms)
	Fusion Protein Breakpoint Sequences - (for the Screening of the FusionNeoAntigens)
	Potential FusionNeoAntigens in HLA I - (netMHCpan v4.1 + deepHLApan v1.1)
	Potential FusionNeoAntigens in HLA II - (netMHCIIpan v4.1)
	Fusion Breakpoint 14 AA Peptide Structure - (RoseTTAFold)
	Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D - (Glide)
	Vaccine Design for the FusionNeoAntigens (RNA/protein sequences)
	Potential target of CAR-T therapy development
	Information on the samples that have these potential fusion neoantigens
	Fusion Protein Targeting Drugs - (Manual Curation)
	Fusion Protein Related diseases - (Manual Curation)