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Fusion Protein:CD40-LAMC3

Fusion Gene and Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: CD40-LAMC3
	FusionPDB ID: 14501
	FusionGDB2.0 ID: 14501
		Hgene	Tgene
	Gene symbol	CD40	LAMC3
	Gene ID	958	10319
	Gene name	CD40 molecule	laminin subunit gamma 3
	Synonyms	Bp50\|CDW40\|TNFRSF5\|p50	OCCM
	Cytomap	20q13.12	9q34.12
	Type of gene	protein-coding	protein-coding
	Description	tumor necrosis factor receptor superfamily member 5B cell surface antigen CD40B cell-associated moleculeCD40 molecule, TNF receptor superfamily member 5CD40L receptor	laminin subunit gamma-3laminin, gamma 3laminin-12 subunit gammalaminin-14 subunit gammalaminin-15 subunit gamma
	Modification date	20200327	20200313
	UniProtAcc	P25942 Main function of 5'-partner protein: FUNCTION: Receptor for TNFSF5/CD40LG (PubMed:31331973). Transduces TRAF6- and MAP3K8-mediated signals that activate ERK in macrophages and B cells, leading to induction of immunoglobulin secretion (By similarity). {ECO:0000250\|UniProtKB:P27512, ECO:0000269\|PubMed:31331973}.	Q9Y6N6 Main function of 5'-partner protein: FUNCTION: Binding to cells via a high affinity receptor, laminin is thought to mediate the attachment, migration and organization of cells into tissues during embryonic development by interacting with other extracellular matrix components.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000489304, ENST00000372276, ENST00000372285,	ENST00000361069, ENST00000480883,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	2 X 2 X 2=8	6 X 6 X 5=180
	# samples	2	6
	** MAII score	log2(2/8*10)=1.32192809488736	log2(6/180*10)=-1.58496250072116 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Fusion gene context	PubMed: CD40 [Title/Abstract] AND LAMC3 [Title/Abstract] AND fusion [Title/Abstract]
Fusion neoantigen context	PubMed: CD40 [Title/Abstract] AND LAMC3 [Title/Abstract] AND neoantigen [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	CD40(44751395)-LAMC3(133901672), # samples:1
Anticipated loss of major functional domain due to fusion event.	CD40-LAMC3 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. CD40-LAMC3 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. CD40-LAMC3 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. CD40-LAMC3 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	CD40	GO:0023035	CD40 signaling pathway	31331973
Hgene	CD40	GO:2000353	positive regulation of endothelial cell apoptotic process	12885753

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr20:44751395/chr9:133901672)
- 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 CD40 (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 LAMC3 (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)

ENST00000372285

CD40

chr20

44751395

ENST00000361069

LAMC3

chr9

133901672

6102

475

4829

1585

ENST00000372276

CD40

chr20

44751395

ENST00000361069

LAMC3

chr9

133901672

6058

431

4785

1585

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
ENST00000372285	ENST00000361069	CD40	chr20	44751395	+	LAMC3	chr9	133901672	+	0.007996205	0.99200374
ENST00000372276	ENST00000361069	CD40	chr20	44751395	+	LAMC3	chr9	133901672	+	0.007582798	0.9924172

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 CD40-LAMC3

+/-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
CD40	chr20	44751395	LAMC3	chr9	133901672	431	134	HRSCSPGFGVKQIGKAYEITYVRLKF
CD40	chr20	44751395	LAMC3	chr9	133901672	475	134	HRSCSPGFGVKQIGKAYEITYVRLKF

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Potential FusionNeoAntigen Information of CD40-LAMC3 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.

CD40-LAMC3_44751395_133901672.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)
CD40-LAMC3	chr20	44751395	chr9	133901672	431	HLA-B15:03	VKQIGKAY	0.9633	0.5844	9	17
CD40-LAMC3	chr20	44751395	chr9	133901672	431	HLA-B15:01	GVKQIGKAY	0.9986	0.7207	8	17
CD40-LAMC3	chr20	44751395	chr9	133901672	431	HLA-B15:25	GVKQIGKAY	0.987	0.7719	8	17
CD40-LAMC3	chr20	44751395	chr9	133901672	431	HLA-B13:02	KQIGKAYEI	0.9745	0.5618	10	19
CD40-LAMC3	chr20	44751395	chr9	133901672	431	HLA-B15:02	GVKQIGKAY	0.9696	0.8059	8	17
CD40-LAMC3	chr20	44751395	chr9	133901672	431	HLA-A32:13	KQIGKAYEI	0.9631	0.8448	10	19
CD40-LAMC3	chr20	44751395	chr9	133901672	431	HLA-B13:01	KQIGKAYEI	0.9059	0.8645	10	19
CD40-LAMC3	chr20	44751395	chr9	133901672	431	HLA-B47:01	KQIGKAYEI	0.8576	0.534	10	19
CD40-LAMC3	chr20	44751395	chr9	133901672	431	HLA-B38:01	KQIGKAYEI	0.6857	0.8227	10	19
CD40-LAMC3	chr20	44751395	chr9	133901672	431	HLA-B38:02	KQIGKAYEI	0.6633	0.8024	10	19
CD40-LAMC3	chr20	44751395	chr9	133901672	431	HLA-B39:13	KQIGKAYEI	0.6603	0.743	10	19
CD40-LAMC3	chr20	44751395	chr9	133901672	431	HLA-B15:03	GVKQIGKAY	0.57	0.5614	8	17
CD40-LAMC3	chr20	44751395	chr9	133901672	431	HLA-B52:01	KQIGKAYEI	0.1187	0.8373	10	19
CD40-LAMC3	chr20	44751395	chr9	133901672	431	HLA-B15:01	FGVKQIGKAY	0.9966	0.7069	7	17
CD40-LAMC3	chr20	44751395	chr9	133901672	431	HLA-B15:02	FGVKQIGKAY	0.9842	0.7826	7	17
CD40-LAMC3	chr20	44751395	chr9	133901672	431	HLA-B15:01	KQIGKAYEITY	1	0.7399	10	21
CD40-LAMC3	chr20	44751395	chr9	133901672	431	HLA-B15:25	KQIGKAYEITY	0.9984	0.7778	10	21
CD40-LAMC3	chr20	44751395	chr9	133901672	431	HLA-B15:03	KQIGKAYEITY	0.9689	0.5551	10	21
CD40-LAMC3	chr20	44751395	chr9	133901672	431	HLA-B15:07	GVKQIGKAY	0.9954	0.5013	8	17
CD40-LAMC3	chr20	44751395	chr9	133901672	431	HLA-B15:21	GVKQIGKAY	0.9717	0.7324	8	17
CD40-LAMC3	chr20	44751395	chr9	133901672	431	HLA-B15:04	KQIGKAYEI	0.9555	0.8263	10	19
CD40-LAMC3	chr20	44751395	chr9	133901672	431	HLA-C02:06	KQIGKAYEI	0.8772	0.9373	10	19
CD40-LAMC3	chr20	44751395	chr9	133901672	431	HLA-B15:04	GVKQIGKAY	0.8118	0.7819	8	17
CD40-LAMC3	chr20	44751395	chr9	133901672	431	HLA-B15:05	GVKQIGKAY	0.7655	0.6542	8	17
CD40-LAMC3	chr20	44751395	chr9	133901672	431	HLA-B39:08	KQIGKAYEI	0.7262	0.772	10	19
CD40-LAMC3	chr20	44751395	chr9	133901672	431	HLA-B15:31	GVKQIGKAY	0.6458	0.6808	8	17
CD40-LAMC3	chr20	44751395	chr9	133901672	431	HLA-B15:04	KQIGKAYEITY	0.9994	0.7656	10	21
CD40-LAMC3	chr20	44751395	chr9	133901672	431	HLA-B15:07	GFGVKQIGKAY	0.9965	0.6782	6	17
CD40-LAMC3	chr20	44751395	chr9	133901672	431	HLA-B15:05	KQIGKAYEITY	0.9919	0.7712	10	21
CD40-LAMC3	chr20	44751395	chr9	133901672	431	HLA-B15:125	GVKQIGKAY	0.9986	0.7207	8	17
CD40-LAMC3	chr20	44751395	chr9	133901672	431	HLA-B15:33	GVKQIGKAY	0.9986	0.7207	8	17
CD40-LAMC3	chr20	44751395	chr9	133901672	431	HLA-B15:34	GVKQIGKAY	0.9986	0.7207	8	17
CD40-LAMC3	chr20	44751395	chr9	133901672	431	HLA-B15:27	GVKQIGKAY	0.9985	0.7638	8	17
CD40-LAMC3	chr20	44751395	chr9	133901672	431	HLA-B15:135	GVKQIGKAY	0.9983	0.7512	8	17
CD40-LAMC3	chr20	44751395	chr9	133901672	431	HLA-B27:06	KQIGKAYEI	0.9976	0.6226	10	19
CD40-LAMC3	chr20	44751395	chr9	133901672	431	HLA-B15:50	GVKQIGKAY	0.9964	0.6808	8	17
CD40-LAMC3	chr20	44751395	chr9	133901672	431	HLA-B15:11	GVKQIGKAY	0.9964	0.6624	8	17
CD40-LAMC3	chr20	44751395	chr9	133901672	431	HLA-B15:08	GVKQIGKAY	0.9961	0.6587	8	17
CD40-LAMC3	chr20	44751395	chr9	133901672	431	HLA-B15:24	KQIGKAYEI	0.9958	0.8447	10	19
CD40-LAMC3	chr20	44751395	chr9	133901672	431	HLA-B15:35	GVKQIGKAY	0.9953	0.7594	8	17
CD40-LAMC3	chr20	44751395	chr9	133901672	431	HLA-A32:01	KQIGKAYEI	0.995	0.8258	10	19
CD40-LAMC3	chr20	44751395	chr9	133901672	431	HLA-B35:43	GVKQIGKAY	0.9943	0.6565	8	17
CD40-LAMC3	chr20	44751395	chr9	133901672	431	HLA-B15:24	GVKQIGKAY	0.993	0.784	8	17
CD40-LAMC3	chr20	44751395	chr9	133901672	431	HLA-B15:39	GVKQIGKAY	0.9866	0.6492	8	17
CD40-LAMC3	chr20	44751395	chr9	133901672	431	HLA-B15:73	KQIGKAYEI	0.9855	0.8589	10	19
CD40-LAMC3	chr20	44751395	chr9	133901672	431	HLA-B15:35	IGKAYEITY	0.9847	0.7072	12	21
CD40-LAMC3	chr20	44751395	chr9	133901672	431	HLA-C06:08	KQIGKAYEI	0.9798	0.9844	10	19
CD40-LAMC3	chr20	44751395	chr9	133901672	431	HLA-C06:06	KQIGKAYEI	0.9787	0.9779	10	19
CD40-LAMC3	chr20	44751395	chr9	133901672	431	HLA-C06:02	KQIGKAYEI	0.9715	0.9847	10	19
CD40-LAMC3	chr20	44751395	chr9	133901672	431	HLA-C06:17	KQIGKAYEI	0.9715	0.9847	10	19
CD40-LAMC3	chr20	44751395	chr9	133901672	431	HLA-B15:30	KQIGKAYEI	0.9601	0.8183	10	19
CD40-LAMC3	chr20	44751395	chr9	133901672	431	HLA-B15:53	GVKQIGKAY	0.96	0.6857	8	17
CD40-LAMC3	chr20	44751395	chr9	133901672	431	HLA-B15:12	GVKQIGKAY	0.9531	0.7422	8	17
CD40-LAMC3	chr20	44751395	chr9	133901672	431	HLA-C07:04	KQIGKAYEI	0.9225	0.9153	10	19
CD40-LAMC3	chr20	44751395	chr9	133901672	431	HLA-B15:20	GVKQIGKAY	0.7913	0.7714	8	17
CD40-LAMC3	chr20	44751395	chr9	133901672	431	HLA-B39:02	KQIGKAYEI	0.7853	0.738	10	19
CD40-LAMC3	chr20	44751395	chr9	133901672	431	HLA-B15:54	GVKQIGKAY	0.7577	0.6306	8	17
CD40-LAMC3	chr20	44751395	chr9	133901672	431	HLA-B38:05	KQIGKAYEI	0.6857	0.8227	10	19
CD40-LAMC3	chr20	44751395	chr9	133901672	431	HLA-B35:28	GVKQIGKAY	0.6819	0.7826	8	17
CD40-LAMC3	chr20	44751395	chr9	133901672	431	HLA-C12:02	GVKQIGKAY	0.4569	0.9079	8	17
CD40-LAMC3	chr20	44751395	chr9	133901672	431	HLA-C02:10	GVKQIGKAY	0.0793	0.9618	8	17
CD40-LAMC3	chr20	44751395	chr9	133901672	431	HLA-C02:02	GVKQIGKAY	0.0793	0.9618	8	17
CD40-LAMC3	chr20	44751395	chr9	133901672	431	HLA-B15:125	FGVKQIGKAY	0.9966	0.7069	7	17
CD40-LAMC3	chr20	44751395	chr9	133901672	431	HLA-B15:27	FGVKQIGKAY	0.9966	0.7402	7	17
CD40-LAMC3	chr20	44751395	chr9	133901672	431	HLA-B15:33	FGVKQIGKAY	0.9966	0.7069	7	17
CD40-LAMC3	chr20	44751395	chr9	133901672	431	HLA-B15:34	FGVKQIGKAY	0.9966	0.7069	7	17
CD40-LAMC3	chr20	44751395	chr9	133901672	431	HLA-B15:135	FGVKQIGKAY	0.996	0.7601	7	17
CD40-LAMC3	chr20	44751395	chr9	133901672	431	HLA-B15:50	FGVKQIGKAY	0.9951	0.7349	7	17
CD40-LAMC3	chr20	44751395	chr9	133901672	431	HLA-B15:11	FGVKQIGKAY	0.995	0.6538	7	17
CD40-LAMC3	chr20	44751395	chr9	133901672	431	HLA-B15:08	FGVKQIGKAY	0.9948	0.6556	7	17
CD40-LAMC3	chr20	44751395	chr9	133901672	431	HLA-B15:35	FGVKQIGKAY	0.9931	0.7358	7	17
CD40-LAMC3	chr20	44751395	chr9	133901672	431	HLA-B15:12	FGVKQIGKAY	0.9733	0.7884	7	17
CD40-LAMC3	chr20	44751395	chr9	133901672	431	HLA-B15:34	KQIGKAYEITY	1	0.7399	10	21
CD40-LAMC3	chr20	44751395	chr9	133901672	431	HLA-B15:27	KQIGKAYEITY	1	0.7738	10	21
CD40-LAMC3	chr20	44751395	chr9	133901672	431	HLA-B15:135	KQIGKAYEITY	1	0.7622	10	21
CD40-LAMC3	chr20	44751395	chr9	133901672	431	HLA-B15:24	KQIGKAYEITY	1	0.7929	10	21
CD40-LAMC3	chr20	44751395	chr9	133901672	431	HLA-B15:50	KQIGKAYEITY	1	0.7338	10	21
CD40-LAMC3	chr20	44751395	chr9	133901672	431	HLA-B15:125	KQIGKAYEITY	1	0.7399	10	21
CD40-LAMC3	chr20	44751395	chr9	133901672	431	HLA-B15:33	KQIGKAYEITY	1	0.7399	10	21
CD40-LAMC3	chr20	44751395	chr9	133901672	431	HLA-B15:12	KQIGKAYEITY	0.9999	0.6498	10	21
CD40-LAMC3	chr20	44751395	chr9	133901672	431	HLA-B15:53	KQIGKAYEITY	0.9996	0.701	10	21
CD40-LAMC3	chr20	44751395	chr9	133901672	431	HLA-B15:54	KQIGKAYEITY	0.9995	0.6512	10	21
CD40-LAMC3	chr20	44751395	chr9	133901672	431	HLA-B15:35	KQIGKAYEITY	0.9994	0.7548	10	21
CD40-LAMC3	chr20	44751395	chr9	133901672	431	HLA-B15:39	KQIGKAYEITY	0.9985	0.6492	10	21
CD40-LAMC3	chr20	44751395	chr9	133901672	431	HLA-B15:35	GFGVKQIGKAY	0.9954	0.8725	6	17
CD40-LAMC3	chr20	44751395	chr9	133901672	431	HLA-B15:20	KQIGKAYEITY	0.9925	0.845	10	21
CD40-LAMC3	chr20	44751395	chr9	133901672	431	HLA-B35:28	KQIGKAYEITY	0.9892	0.858	10	21
CD40-LAMC3	chr20	44751395	chr9	133901672	431	HLA-A32:01	KQIGKAYEITY	0.9765	0.7995	10	21
CD40-LAMC3	chr20	44751395	chr9	133901672	431	HLA-B48:02	KQIGKAYEITY	0.9317	0.828	10	21

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Potential FusionNeoAntigen Information of CD40-LAMC3 in HLA II

CD40-LAMC3_44751395_133901672.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)
CD40-LAMC3	chr20	44751395	chr9	133901672	431	DRB1-0802	SPGFGVKQIGKAYEI	4	19
CD40-LAMC3	chr20	44751395	chr9	133901672	431	DRB1-0802	CSPGFGVKQIGKAYE	3	18
CD40-LAMC3	chr20	44751395	chr9	133901672	431	DRB1-0806	GFGVKQIGKAYEITY	6	21
CD40-LAMC3	chr20	44751395	chr9	133901672	431	DRB1-0806	PGFGVKQIGKAYEIT	5	20
CD40-LAMC3	chr20	44751395	chr9	133901672	431	DRB1-0809	SPGFGVKQIGKAYEI	4	19
CD40-LAMC3	chr20	44751395	chr9	133901672	431	DRB1-0809	CSPGFGVKQIGKAYE	3	18
CD40-LAMC3	chr20	44751395	chr9	133901672	431	DRB1-0810	GFGVKQIGKAYEITY	6	21
CD40-LAMC3	chr20	44751395	chr9	133901672	431	DRB1-0810	PGFGVKQIGKAYEIT	5	20
CD40-LAMC3	chr20	44751395	chr9	133901672	431	DRB1-0812	GFGVKQIGKAYEITY	6	21
CD40-LAMC3	chr20	44751395	chr9	133901672	431	DRB1-0812	PGFGVKQIGKAYEIT	5	20
CD40-LAMC3	chr20	44751395	chr9	133901672	431	DRB1-0821	SPGFGVKQIGKAYEI	4	19
CD40-LAMC3	chr20	44751395	chr9	133901672	431	DRB1-0821	CSPGFGVKQIGKAYE	3	18
CD40-LAMC3	chr20	44751395	chr9	133901672	431	DRB1-0822	GFGVKQIGKAYEITY	6	21
CD40-LAMC3	chr20	44751395	chr9	133901672	431	DRB1-0822	PGFGVKQIGKAYEIT	5	20
CD40-LAMC3	chr20	44751395	chr9	133901672	431	DRB1-0822	SPGFGVKQIGKAYEI	4	19
CD40-LAMC3	chr20	44751395	chr9	133901672	431	DRB1-1358	GFGVKQIGKAYEITY	6	21
CD40-LAMC3	chr20	44751395	chr9	133901672	431	DRB1-1358	PGFGVKQIGKAYEIT	5	20
CD40-LAMC3	chr20	44751395	chr9	133901672	431	DRB1-1381	GFGVKQIGKAYEITY	6	21
CD40-LAMC3	chr20	44751395	chr9	133901672	431	DRB1-1381	PGFGVKQIGKAYEIT	5	20
CD40-LAMC3	chr20	44751395	chr9	133901672	431	DRB1-1389	PGFGVKQIGKAYEIT	5	20
CD40-LAMC3	chr20	44751395	chr9	133901672	431	DRB1-1389	GFGVKQIGKAYEITY	6	21
CD40-LAMC3	chr20	44751395	chr9	133901672	431	DRB1-1427	SPGFGVKQIGKAYEI	4	19

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Fusion breakpoint peptide structures of CD40-LAMC3

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
2773	GFGVKQIGKAYEIT	CD40	LAMC3	chr20	44751395	chr9	133901672	431

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of CD40-LAMC3

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	2773	GFGVKQIGKAYEIT	-7.9962	-8.1096
HLA-B14:02	3BVN	2773	GFGVKQIGKAYEIT	-5.70842	-6.74372
HLA-B52:01	3W39	2773	GFGVKQIGKAYEIT	-6.83737	-6.95077
HLA-B52:01	3W39	2773	GFGVKQIGKAYEIT	-4.4836	-5.5189
HLA-A11:01	4UQ2	2773	GFGVKQIGKAYEIT	-10.0067	-10.1201
HLA-A11:01	4UQ2	2773	GFGVKQIGKAYEIT	-9.03915	-10.0745
HLA-A24:02	5HGA	2773	GFGVKQIGKAYEIT	-6.56204	-6.67544
HLA-A24:02	5HGA	2773	GFGVKQIGKAYEIT	-5.42271	-6.45801
HLA-B44:05	3DX8	2773	GFGVKQIGKAYEIT	-7.85648	-8.89178
HLA-B44:05	3DX8	2773	GFGVKQIGKAYEIT	-5.3978	-5.5112
HLA-A02:01	6TDR	2773	GFGVKQIGKAYEIT	-3.37154	-4.40684

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Vaccine Design for the FusionNeoAntigens of CD40-LAMC3

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
CD40-LAMC3	chr20	44751395	chr9	133901672	10	19	KQIGKAYEI	AGCAGATTGGGAAGGCTTATGAGATCA
CD40-LAMC3	chr20	44751395	chr9	133901672	10	21	KQIGKAYEITY	AGCAGATTGGGAAGGCTTATGAGATCACGTATG
CD40-LAMC3	chr20	44751395	chr9	133901672	12	21	IGKAYEITY	TTGGGAAGGCTTATGAGATCACGTATG
CD40-LAMC3	chr20	44751395	chr9	133901672	6	17	GFGVKQIGKAY	GCTTTGGGGTCAAGCAGATTGGGAAGGCTTATG
CD40-LAMC3	chr20	44751395	chr9	133901672	7	17	FGVKQIGKAY	TTGGGGTCAAGCAGATTGGGAAGGCTTATG
CD40-LAMC3	chr20	44751395	chr9	133901672	8	17	GVKQIGKAY	GGGTCAAGCAGATTGGGAAGGCTTATG
CD40-LAMC3	chr20	44751395	chr9	133901672	9	17	VKQIGKAY	TCAAGCAGATTGGGAAGGCTTATG

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
CD40-LAMC3	chr20	44751395	chr9	133901672	3	18	CSPGFGVKQIGKAYE	GCTCGCCCGGCTTTGGGGTCAAGCAGATTGGGAAGGCTTATGAGA
CD40-LAMC3	chr20	44751395	chr9	133901672	4	19	SPGFGVKQIGKAYEI	CGCCCGGCTTTGGGGTCAAGCAGATTGGGAAGGCTTATGAGATCA
CD40-LAMC3	chr20	44751395	chr9	133901672	5	20	PGFGVKQIGKAYEIT	CCGGCTTTGGGGTCAAGCAGATTGGGAAGGCTTATGAGATCACGT
CD40-LAMC3	chr20	44751395	chr9	133901672	6	21	GFGVKQIGKAYEITY	GCTTTGGGGTCAAGCAGATTGGGAAGGCTTATGAGATCACGTATG

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Information of the samples that have these potential fusion neoantigens of CD40-LAMC3

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
GBM	CD40-LAMC3	chr20	44751395	ENST00000372276	chr9	133901672	ENST00000361069	TCGA-28-5215-01A

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Potential target of CAR-T therapy development for CD40-LAMC3

Predicted 3D structure. We used RoseTTAFold.

89_CD40-LAMC3_t000_.e2e.pdb

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
CD40	chr20	44751395	ENST00000372276	LAMC3	chr9	133901672	ENST00000361069

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Related Drugs to CD40-LAMC3

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 CD40-LAMC3

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)