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Fusion Protein:FAM117B-BMPR2

Fusion Gene and Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: FAM117B-BMPR2
	FusionPDB ID: 28375
	FusionGDB2.0 ID: 28375
		Hgene	Tgene
	Gene symbol	FAM117B	BMPR2
	Gene ID	150864	659
	Gene name	family with sequence similarity 117 member B	bone morphogenetic protein receptor type 2
	Synonyms	ALS2CR13	BMPR-II\|BMPR3\|BMR2\|BRK-3\|POVD1\|PPH1\|T-ALK
	Cytomap	2q33.2	2q33.1-q33.2
	Type of gene	protein-coding	protein-coding
	Description	protein FAM117Bamyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 13amyotrophic lateral sclerosis 2 chromosomal region candidate gene 13 protein	bone morphogenetic protein receptor type-2BMP type II receptorBMP type-2 receptorbone morphogenetic protein receptor type IIbone morphogenetic protein receptor, type II (serine/threonine kinase)type II activin receptor-like kinasetype II receptor fo
	Modification date	20200313	20200313
	UniProtAcc	Q6P1L5 Main function of 5'-partner protein:	Q13873 Main function of 5'-partner protein: FUNCTION: On ligand binding, forms a receptor complex consisting of two type II and two type I transmembrane serine/threonine kinases. Type II receptors phosphorylate and activate type I receptors which autophosphorylate, then bind and activate SMAD transcriptional regulators. Binds to BMP7, BMP2 and, less efficiently, BMP4. Binding is weak but enhanced by the presence of type I receptors for BMPs. Mediates induction of adipogenesis by GDF6. {ECO:0000250\|UniProtKB:O35607}.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000303116, ENST00000392238,	ENST00000479069, ENST00000374574, ENST00000374580,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	5 X 4 X 4=80	10 X 10 X 2=200
	# samples	5	10
	** MAII score	log2(5/80*10)=-0.678071905112638 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(10/200*10)=-1 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Fusion gene context	PubMed: FAM117B [Title/Abstract] AND BMPR2 [Title/Abstract] AND fusion [Title/Abstract]
Fusion neoantigen context	PubMed: FAM117B [Title/Abstract] AND BMPR2 [Title/Abstract] AND neoantigen [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	BMPR2(203242273)-FAM117B(203589640), # samples:1 FAM117B(203560755)-BMPR2(203417439), # samples:1
Anticipated loss of major functional domain due to fusion event.	FAM117B-BMPR2 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. FAM117B-BMPR2 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. FAM117B-BMPR2 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. FAM117B-BMPR2 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. BMPR2-FAM117B seems lost the major protein functional domain in Hgene partner, which is a IUPHAR drug target due to the frame-shifted ORF. BMPR2-FAM117B seems lost the major protein functional domain in Hgene partner, which is a kinase due to the frame-shifted ORF. BMPR2-FAM117B seems lost the major protein functional domain in Hgene partner, which is a tumor suppressor due to the frame-shifted 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
Tgene	BMPR2	GO:0007178	transmembrane receptor protein serine/threonine kinase signaling pathway	12045205
Tgene	BMPR2	GO:0010634	positive regulation of epithelial cell migration	12819188
Tgene	BMPR2	GO:0030308	negative regulation of cell growth	12819188
Tgene	BMPR2	GO:0030509	BMP signaling pathway	18436533

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr2:203242273/chr2:203589640)
- 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 FAM117B (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 BMPR2 (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)

ENST00000303116

FAM117B

chr2

203560755

ENST00000374580

BMPR2

chr2

203417439

10272

763

2466

818

ENST00000303116

FAM117B

chr2

203560755

ENST00000374574

BMPR2

chr2

203417439

8992

763

971

324

ENST00000392238

FAM117B

chr2

203560755

ENST00000374580

BMPR2

chr2

203417439

10262

753

2456

818

ENST00000392238

FAM117B

chr2

203560755

ENST00000374574

BMPR2

chr2

203417439

8982

753

961

320

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
ENST00000303116	ENST00000374580	FAM117B	chr2	203560755	+	BMPR2	chr2	203417439	+	0.000372423	0.9996276
ENST00000303116	ENST00000374574	FAM117B	chr2	203560755	+	BMPR2	chr2	203417439	+	0.1665361	0.83346397
ENST00000392238	ENST00000374580	FAM117B	chr2	203560755	+	BMPR2	chr2	203417439	+	0.000372215	0.9996277
ENST00000392238	ENST00000374574	FAM117B	chr2	203560755	+	BMPR2	chr2	203417439	+	0.16591752	0.8340825

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 FAM117B-BMPR2

+/-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
FAM117B	chr2	203560755	BMPR2	chr2	203417439	753	250	HGQAAPCMRDKATQAVRSLKETIEDC
FAM117B	chr2	203560755	BMPR2	chr2	203417439	763	250	HGQAAPCMRDKATQAVRSLKETIEDC

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Potential FusionNeoAntigen Information of FAM117B-BMPR2 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.

FAM117B-BMPR2_203560755_203417439.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)
FAM117B-BMPR2	chr2	203560755	chr2	203417439	763	HLA-B39:06	MRDKATQAV	0.9966	0.8127	7	16
FAM117B-BMPR2	chr2	203560755	chr2	203417439	763	HLA-A30:08	ATQAVRSLK	0.9958	0.7312	11	20
FAM117B-BMPR2	chr2	203560755	chr2	203417439	763	HLA-B39:01	MRDKATQAV	0.9958	0.8681	7	16
FAM117B-BMPR2	chr2	203560755	chr2	203417439	763	HLA-B39:24	MRDKATQAV	0.9958	0.6481	7	16
FAM117B-BMPR2	chr2	203560755	chr2	203417439	763	HLA-B14:02	MRDKATQAV	0.9942	0.9065	7	16
FAM117B-BMPR2	chr2	203560755	chr2	203417439	763	HLA-B14:01	MRDKATQAV	0.9942	0.9065	7	16
FAM117B-BMPR2	chr2	203560755	chr2	203417439	763	HLA-B38:02	MRDKATQAV	0.9926	0.949	7	16
FAM117B-BMPR2	chr2	203560755	chr2	203417439	763	HLA-B38:01	MRDKATQAV	0.9923	0.9513	7	16
FAM117B-BMPR2	chr2	203560755	chr2	203417439	763	HLA-B27:07	MRDKATQAV	0.9877	0.5785	7	16
FAM117B-BMPR2	chr2	203560755	chr2	203417439	763	HLA-B15:17	KATQAVRSL	0.9869	0.8531	10	19
FAM117B-BMPR2	chr2	203560755	chr2	203417439	763	HLA-B15:16	KATQAVRSL	0.9825	0.7098	10	19
FAM117B-BMPR2	chr2	203560755	chr2	203417439	763	HLA-B08:09	CMRDKATQA	0.9675	0.6908	6	15
FAM117B-BMPR2	chr2	203560755	chr2	203417439	763	HLA-A74:09	ATQAVRSLK	0.9654	0.5217	11	20
FAM117B-BMPR2	chr2	203560755	chr2	203417439	763	HLA-A74:03	ATQAVRSLK	0.9654	0.5217	11	20
FAM117B-BMPR2	chr2	203560755	chr2	203417439	763	HLA-A74:11	ATQAVRSLK	0.9654	0.5217	11	20
FAM117B-BMPR2	chr2	203560755	chr2	203417439	763	HLA-B15:10	MRDKATQAV	0.9366	0.5014	7	16
FAM117B-BMPR2	chr2	203560755	chr2	203417439	763	HLA-B15:18	MRDKATQAV	0.6734	0.8056	7	16
FAM117B-BMPR2	chr2	203560755	chr2	203417439	763	HLA-B15:37	MRDKATQAV	0.5113	0.5657	7	16
FAM117B-BMPR2	chr2	203560755	chr2	203417439	763	HLA-A30:08	KATQAVRSLK	0.996	0.6231	10	20
FAM117B-BMPR2	chr2	203560755	chr2	203417439	763	HLA-C15:04	KATQAVRSL	0.9996	0.8034	10	19
FAM117B-BMPR2	chr2	203560755	chr2	203417439	763	HLA-C03:07	KATQAVRSL	0.9991	0.8998	10	19
FAM117B-BMPR2	chr2	203560755	chr2	203417439	763	HLA-C03:19	KATQAVRSL	0.9989	0.9737	10	19
FAM117B-BMPR2	chr2	203560755	chr2	203417439	763	HLA-C15:06	KATQAVRSL	0.9987	0.8166	10	19
FAM117B-BMPR2	chr2	203560755	chr2	203417439	763	HLA-C03:08	KATQAVRSL	0.9984	0.8801	10	19
FAM117B-BMPR2	chr2	203560755	chr2	203417439	763	HLA-B39:09	MRDKATQAV	0.9961	0.778	7	16
FAM117B-BMPR2	chr2	203560755	chr2	203417439	763	HLA-B39:12	MRDKATQAV	0.9955	0.8656	7	16
FAM117B-BMPR2	chr2	203560755	chr2	203417439	763	HLA-B39:05	MRDKATQAV	0.9931	0.8599	7	16
FAM117B-BMPR2	chr2	203560755	chr2	203417439	763	HLA-B73:01	MRDKATQAV	0.9784	0.9001	7	16
FAM117B-BMPR2	chr2	203560755	chr2	203417439	763	HLA-C04:06	KATQAVRSL	0.9772	0.8286	10	19
FAM117B-BMPR2	chr2	203560755	chr2	203417439	763	HLA-C02:06	KATQAVRSL	0.9671	0.8919	10	19
FAM117B-BMPR2	chr2	203560755	chr2	203417439	763	HLA-C01:17	KATQAVRSL	0.9536	0.9304	10	19
FAM117B-BMPR2	chr2	203560755	chr2	203417439	763	HLA-C07:05	MRDKATQAV	0.9495	0.9613	7	16
FAM117B-BMPR2	chr2	203560755	chr2	203417439	763	HLA-C12:12	KATQAVRSL	0.9303	0.9343	10	19
FAM117B-BMPR2	chr2	203560755	chr2	203417439	763	HLA-C08:04	KATQAVRSL	0.9289	0.9337	10	19
FAM117B-BMPR2	chr2	203560755	chr2	203417439	763	HLA-C08:13	KATQAVRSL	0.9289	0.9337	10	19
FAM117B-BMPR2	chr2	203560755	chr2	203417439	763	HLA-C03:14	KATQAVRSL	0.9272	0.9541	10	19
FAM117B-BMPR2	chr2	203560755	chr2	203417439	763	HLA-C06:03	KATQAVRSL	0.9162	0.987	10	19
FAM117B-BMPR2	chr2	203560755	chr2	203417439	763	HLA-C12:04	KATQAVRSL	0.9071	0.9855	10	19
FAM117B-BMPR2	chr2	203560755	chr2	203417439	763	HLA-C07:27	MRDKATQAV	0.8822	0.9497	7	16
FAM117B-BMPR2	chr2	203560755	chr2	203417439	763	HLA-C07:95	MRDKATQAV	0.8717	0.7876	7	16
FAM117B-BMPR2	chr2	203560755	chr2	203417439	763	HLA-C07:46	MRDKATQAV	0.8496	0.9203	7	16
FAM117B-BMPR2	chr2	203560755	chr2	203417439	763	HLA-C07:67	MRDKATQAV	0.8023	0.9593	7	16
FAM117B-BMPR2	chr2	203560755	chr2	203417439	763	HLA-C07:80	MRDKATQAV	0.8023	0.9593	7	16
FAM117B-BMPR2	chr2	203560755	chr2	203417439	763	HLA-C07:10	MRDKATQAV	0.8001	0.9654	7	16
FAM117B-BMPR2	chr2	203560755	chr2	203417439	763	HLA-C07:13	MRDKATQAV	0.7783	0.9049	7	16
FAM117B-BMPR2	chr2	203560755	chr2	203417439	763	HLA-C07:29	MRDKATQAV	0.7428	0.9204	7	16
FAM117B-BMPR2	chr2	203560755	chr2	203417439	763	HLA-B14:03	MRDKATQAV	0.7274	0.7443	7	16
FAM117B-BMPR2	chr2	203560755	chr2	203417439	763	HLA-C08:03	KATQAVRSL	0.7008	0.9763	10	19
FAM117B-BMPR2	chr2	203560755	chr2	203417439	763	HLA-C01:30	KATQAVRSL	0.5059	0.922	10	19
FAM117B-BMPR2	chr2	203560755	chr2	203417439	763	HLA-C12:16	MRDKATQAV	0.0109	0.9652	7	16
FAM117B-BMPR2	chr2	203560755	chr2	203417439	763	HLA-C15:09	KATQAVRSL	0.9996	0.8034	10	19
FAM117B-BMPR2	chr2	203560755	chr2	203417439	763	HLA-C03:17	KATQAVRSL	0.9984	0.9722	10	19
FAM117B-BMPR2	chr2	203560755	chr2	203417439	763	HLA-C15:02	KATQAVRSL	0.9983	0.7704	10	19
FAM117B-BMPR2	chr2	203560755	chr2	203417439	763	HLA-C15:05	KATQAVRSL	0.9981	0.8329	10	19
FAM117B-BMPR2	chr2	203560755	chr2	203417439	763	HLA-C03:03	KATQAVRSL	0.9979	0.9773	10	19
FAM117B-BMPR2	chr2	203560755	chr2	203417439	763	HLA-C03:04	KATQAVRSL	0.9979	0.9773	10	19
FAM117B-BMPR2	chr2	203560755	chr2	203417439	763	HLA-C03:05	KATQAVRSL	0.9977	0.9348	10	19
FAM117B-BMPR2	chr2	203560755	chr2	203417439	763	HLA-C03:67	KATQAVRSL	0.997	0.9689	10	19
FAM117B-BMPR2	chr2	203560755	chr2	203417439	763	HLA-B39:31	MRDKATQAV	0.9963	0.8677	7	16
FAM117B-BMPR2	chr2	203560755	chr2	203417439	763	HLA-C03:02	KATQAVRSL	0.9957	0.9656	10	19
FAM117B-BMPR2	chr2	203560755	chr2	203417439	763	HLA-A30:01	ATQAVRSLK	0.9953	0.8845	11	20
FAM117B-BMPR2	chr2	203560755	chr2	203417439	763	HLA-B38:05	MRDKATQAV	0.9923	0.9513	7	16
FAM117B-BMPR2	chr2	203560755	chr2	203417439	763	HLA-C06:06	KATQAVRSL	0.9889	0.976	10	19
FAM117B-BMPR2	chr2	203560755	chr2	203417439	763	HLA-B27:06	MRDKATQAV	0.9884	0.5689	7	16
FAM117B-BMPR2	chr2	203560755	chr2	203417439	763	HLA-C18:01	MRDKATQAV	0.9884	0.9253	7	16
FAM117B-BMPR2	chr2	203560755	chr2	203417439	763	HLA-B27:09	MRDKATQAV	0.9854	0.572	7	16
FAM117B-BMPR2	chr2	203560755	chr2	203417439	763	HLA-C16:02	KATQAVRSL	0.9852	0.9658	10	19
FAM117B-BMPR2	chr2	203560755	chr2	203417439	763	HLA-B58:06	KATQAVRSL	0.981	0.8119	10	19
FAM117B-BMPR2	chr2	203560755	chr2	203417439	763	HLA-C16:01	KATQAVRSL	0.9781	0.9423	10	19
FAM117B-BMPR2	chr2	203560755	chr2	203417439	763	HLA-A74:01	ATQAVRSLK	0.9654	0.5217	11	20
FAM117B-BMPR2	chr2	203560755	chr2	203417439	763	HLA-C02:02	KATQAVRSL	0.9636	0.9681	10	19
FAM117B-BMPR2	chr2	203560755	chr2	203417439	763	HLA-C02:10	KATQAVRSL	0.9636	0.9681	10	19
FAM117B-BMPR2	chr2	203560755	chr2	203417439	763	HLA-B07:13	KATQAVRSL	0.9586	0.8307	10	19
FAM117B-BMPR2	chr2	203560755	chr2	203417439	763	HLA-C06:08	KATQAVRSL	0.9457	0.9868	10	19
FAM117B-BMPR2	chr2	203560755	chr2	203417439	763	HLA-C01:02	KATQAVRSL	0.9422	0.9249	10	19
FAM117B-BMPR2	chr2	203560755	chr2	203417439	763	HLA-C01:03	KATQAVRSL	0.9416	0.9395	10	19
FAM117B-BMPR2	chr2	203560755	chr2	203417439	763	HLA-C12:03	KATQAVRSL	0.9159	0.9727	10	19
FAM117B-BMPR2	chr2	203560755	chr2	203417439	763	HLA-C06:02	KATQAVRSL	0.9149	0.9854	10	19
FAM117B-BMPR2	chr2	203560755	chr2	203417439	763	HLA-C06:17	KATQAVRSL	0.9149	0.9854	10	19
FAM117B-BMPR2	chr2	203560755	chr2	203417439	763	HLA-B15:09	MRDKATQAV	0.9054	0.8757	7	16
FAM117B-BMPR2	chr2	203560755	chr2	203417439	763	HLA-C16:04	KATQAVRSL	0.9006	0.9544	10	19
FAM117B-BMPR2	chr2	203560755	chr2	203417439	763	HLA-C07:01	MRDKATQAV	0.8888	0.7076	7	16
FAM117B-BMPR2	chr2	203560755	chr2	203417439	763	HLA-C07:17	MRDKATQAV	0.8596	0.9576	7	16
FAM117B-BMPR2	chr2	203560755	chr2	203417439	763	HLA-C03:06	KATQAVRSL	0.8556	0.9795	10	19
FAM117B-BMPR2	chr2	203560755	chr2	203417439	763	HLA-C06:08	MRDKATQAV	0.8421	0.9926	7	16
FAM117B-BMPR2	chr2	203560755	chr2	203417439	763	HLA-B39:11	MRDKATQAV	0.8204	0.7101	7	16
FAM117B-BMPR2	chr2	203560755	chr2	203417439	763	HLA-C07:02	MRDKATQAV	0.8023	0.9593	7	16
FAM117B-BMPR2	chr2	203560755	chr2	203417439	763	HLA-C07:04	MRDKATQAV	0.7837	0.8858	7	16
FAM117B-BMPR2	chr2	203560755	chr2	203417439	763	HLA-C06:06	MRDKATQAV	0.7536	0.9893	7	16
FAM117B-BMPR2	chr2	203560755	chr2	203417439	763	HLA-C08:01	KATQAVRSL	0.7008	0.9763	10	19
FAM117B-BMPR2	chr2	203560755	chr2	203417439	763	HLA-C12:02	KATQAVRSL	0.6842	0.9664	10	19
FAM117B-BMPR2	chr2	203560755	chr2	203417439	763	HLA-C07:22	MRDKATQAV	0.6725	0.7442	7	16
FAM117B-BMPR2	chr2	203560755	chr2	203417439	763	HLA-B35:13	KATQAVRSL	0.5917	0.8754	10	19
FAM117B-BMPR2	chr2	203560755	chr2	203417439	763	HLA-C17:01	KATQAVRSL	0.5108	0.8491	10	19
FAM117B-BMPR2	chr2	203560755	chr2	203417439	763	HLA-C06:17	MRDKATQAV	0.1385	0.9936	7	16
FAM117B-BMPR2	chr2	203560755	chr2	203417439	763	HLA-C06:02	MRDKATQAV	0.1385	0.9936	7	16
FAM117B-BMPR2	chr2	203560755	chr2	203417439	763	HLA-A30:01	KATQAVRSLK	0.9963	0.8194	10	20

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Potential FusionNeoAntigen Information of FAM117B-BMPR2 in HLA II

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)

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Fusion breakpoint peptide structures of FAM117B-BMPR2

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
883	CMRDKATQAVRSLK	FAM117B	BMPR2	chr2	203560755	chr2	203417439	763

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of FAM117B-BMPR2

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	883	CMRDKATQAVRSLK	-7.15543	-7.26883
HLA-B14:02	3BVN	883	CMRDKATQAVRSLK	-4.77435	-5.80965
HLA-B52:01	3W39	883	CMRDKATQAVRSLK	-6.80875	-6.92215
HLA-B52:01	3W39	883	CMRDKATQAVRSLK	-4.20386	-5.23916
HLA-A11:01	4UQ2	883	CMRDKATQAVRSLK	-7.5194	-8.5547
HLA-A11:01	4UQ2	883	CMRDKATQAVRSLK	-6.9601	-7.0735
HLA-A24:02	5HGA	883	CMRDKATQAVRSLK	-7.52403	-7.63743
HLA-A24:02	5HGA	883	CMRDKATQAVRSLK	-5.82433	-6.85963
HLA-B27:05	6PYJ	883	CMRDKATQAVRSLK	-3.28285	-4.31815
HLA-B44:05	3DX8	883	CMRDKATQAVRSLK	-5.91172	-6.94702
HLA-B44:05	3DX8	883	CMRDKATQAVRSLK	-4.24346	-4.35686

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Vaccine Design for the FusionNeoAntigens of FAM117B-BMPR2

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
FAM117B-BMPR2	chr2	203560755	chr2	203417439	10	19	KATQAVRSL	GCTACACAGGCAGTGAGGTCACTCAAG
FAM117B-BMPR2	chr2	203560755	chr2	203417439	10	20	KATQAVRSLK	GCTACACAGGCAGTGAGGTCACTCAAGGAG
FAM117B-BMPR2	chr2	203560755	chr2	203417439	11	20	ATQAVRSLK	ACACAGGCAGTGAGGTCACTCAAGGAG
FAM117B-BMPR2	chr2	203560755	chr2	203417439	6	15	CMRDKATQA	ATGAGGGACAAAGCTACACAGGCAGTG
FAM117B-BMPR2	chr2	203560755	chr2	203417439	7	16	MRDKATQAV	AGGGACAAAGCTACACAGGCAGTGAGG

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

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Information of the samples that have these potential fusion neoantigens of FAM117B-BMPR2

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
LUSC	FAM117B-BMPR2	chr2	203560755	ENST00000303116	chr2	203417439	ENST00000374580	TCGA-21-1081

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Potential target of CAR-T therapy development for FAM117B-BMPR2

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 FAM117B-BMPR2

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 FAM117B-BMPR2

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)