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Fusion Protein:TMEM123-MMP20

Fusion Gene and Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: TMEM123-MMP20
	FusionPDB ID: 91599
	FusionGDB2.0 ID: 91599
		Hgene	Tgene
	Gene symbol	TMEM123	MMP20
	Gene ID	114908	64386
	Gene name	transmembrane protein 123	matrix metallopeptidase 25
	Synonyms	KCT3\|PORIMIN\|PORMIN	MMP-25\|MMP20\|MMP20A\|MMPL1\|MT-MMP 6\|MT-MMP6\|MT6-MMP\|MT6MMP\|MTMMP6
	Cytomap	11q22.2	16p13.3
	Type of gene	protein-coding	protein-coding
	Description	poriminKCT-3keratinocytes associated transmembrane protein 3pro-oncosis receptor inducing membrane injuryserine/threonine-rich receptor	matrix metalloproteinase-25leukolysinmatrix metallopeptidase-like 1matrix metalloproteinase 20matrix metalloproteinase-like 1membrane-type 6 matrix metalloproteinasemembrane-type matrix metalloproteinase 6
	Modification date	20200313	20200313
	UniProtAcc	.	.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000398136, ENST00000525577, ENST00000532161, ENST00000361236,	ENST00000544938, ENST00000260228,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	16 X 10 X 10=1600	2 X 5 X 5=50
	# samples	27	7
	** MAII score	log2(27/1600*10)=-2.56704059272389 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(7/50*10)=0.485426827170242 effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs). DoF>8 and MAII>0
Fusion gene context	PubMed: TMEM123 [Title/Abstract] AND MMP20 [Title/Abstract] AND fusion [Title/Abstract]
Fusion neoantigen context	PubMed: TMEM123 [Title/Abstract] AND MMP20 [Title/Abstract] AND neoantigen [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	TMEM123(102319543)-MMP20(102480761), # samples:4 TMEM123(102319543)-MMP20(102449873), # samples:4
Anticipated loss of major functional domain due to fusion event.	TMEM123-MMP20 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. TMEM123-MMP20 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. TMEM123-MMP20 seems lost the major protein functional domain in Tgene partner, which is a IUPHAR drug target 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
Hgene	TMEM123	GO:0070267	oncosis	9600958\|11481458

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr11:102319543/chr11:102480761)
- 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 TMEM123 (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 MMP20 (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)
ENST00000398136	TMEM123	chr11	102319542	-	ENST00000260228	MMP20	chr11	102464326	-	1431	578	85	939	284
ENST00000398136	TMEM123	chr11	102319543	-	ENST00000260228	MMP20	chr11	102464326	-	1431	578	85	939	284
ENST00000398136	TMEM123	chr11	102319543	-	ENST00000260228	MMP20	chr11	102480761	-	1998	578	85	1506	473

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
ENST00000398136	ENST00000260228	TMEM123	chr11	102319542	-	MMP20	chr11	102464326	-	0.002704016	0.99729604
ENST00000398136	ENST00000260228	TMEM123	chr11	102319543	-	MMP20	chr11	102464326	-	0.002704016	0.99729604
ENST00000398136	ENST00000260228	TMEM123	chr11	102319543	-	MMP20	chr11	102480761	-	0.000461714	0.9995383

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 TMEM123-MMP20

+/-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
TMEM123	chr11	102319542	MMP20	chr11	102464326	578	164	NSGLPHNSSANSTGPHYWITRGFQMQ
TMEM123	chr11	102319543	MMP20	chr11	102464326	578	164	NSGLPHNSSANSTGPHYWITRGFQMQ
TMEM123	chr11	102319543	MMP20	chr11	102480761	578	164	NSGLPHNSSANSTDHGDSYPFDGPRG

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Potential FusionNeoAntigen Information of TMEM123-MMP20 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.

TMEM123-MMP20_102319542_102464326.msa
TMEM123-MMP20_102319543_102480761.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)
TMEM123-MMP20	chr11	102319542	chr11	102464326	578	HLA-B58:02	NSTGPHYW	0.9989	0.9558	10	18
TMEM123-MMP20	chr11	102319542	chr11	102464326	578	HLA-B58:01	NSTGPHYW	0.9985	0.9571	10	18
TMEM123-MMP20	chr11	102319542	chr11	102464326	578	HLA-B15:25	SANSTGPHY	0.9973	0.8996	8	17
TMEM123-MMP20	chr11	102319542	chr11	102464326	578	HLA-B35:08	SANSTGPHY	0.9942	0.8456	8	17
TMEM123-MMP20	chr11	102319542	chr11	102464326	578	HLA-B15:02	SANSTGPHY	0.9929	0.9088	8	17
TMEM123-MMP20	chr11	102319542	chr11	102464326	578	HLA-B58:01	ANSTGPHYW	0.9893	0.9853	9	18
TMEM123-MMP20	chr11	102319542	chr11	102464326	578	HLA-B58:02	ANSTGPHYW	0.9872	0.982	9	18
TMEM123-MMP20	chr11	102319542	chr11	102464326	578	HLA-B15:01	SANSTGPHY	0.9852	0.8773	8	17
TMEM123-MMP20	chr11	102319542	chr11	102464326	578	HLA-B35:01	SANSTGPHY	0.9839	0.8181	8	17
TMEM123-MMP20	chr11	102319542	chr11	102464326	578	HLA-B15:17	SANSTGPHY	0.9792	0.9006	8	17
TMEM123-MMP20	chr11	102319542	chr11	102464326	578	HLA-B15:16	SANSTGPHY	0.8733	0.5895	8	17
TMEM123-MMP20	chr11	102319542	chr11	102464326	578	HLA-B35:05	SANSTGPHY	0.8206	0.588	8	17
TMEM123-MMP20	chr11	102319542	chr11	102464326	578	HLA-B15:03	SANSTGPHY	0.788	0.741	8	17
TMEM123-MMP20	chr11	102319542	chr11	102464326	578	HLA-B15:18	SANSTGPHY	0.7185	0.6777	8	17
TMEM123-MMP20	chr11	102319542	chr11	102464326	578	HLA-B57:01	SANSTGPHYW	0.9997	0.9681	8	18
TMEM123-MMP20	chr11	102319542	chr11	102464326	578	HLA-B58:01	SANSTGPHYW	0.9993	0.9605	8	18
TMEM123-MMP20	chr11	102319542	chr11	102464326	578	HLA-B58:02	SANSTGPHYW	0.9992	0.9586	8	18
TMEM123-MMP20	chr11	102319542	chr11	102464326	578	HLA-B15:17	SANSTGPHYW	0.9978	0.9596	8	18
TMEM123-MMP20	chr11	102319542	chr11	102464326	578	HLA-B15:16	SANSTGPHYW	0.9929	0.8279	8	18
TMEM123-MMP20	chr11	102319542	chr11	102464326	578	HLA-B57:03	SANSTGPHYW	0.9927	0.9935	8	18
TMEM123-MMP20	chr11	102319542	chr11	102464326	578	HLA-A31:06	STGPHYWITR	0.975	0.6963	11	21
TMEM123-MMP20	chr11	102319542	chr11	102464326	578	HLA-A74:11	STGPHYWITR	0.9718	0.8213	11	21
TMEM123-MMP20	chr11	102319542	chr11	102464326	578	HLA-A74:09	STGPHYWITR	0.9718	0.8213	11	21
TMEM123-MMP20	chr11	102319542	chr11	102464326	578	HLA-A74:03	STGPHYWITR	0.9718	0.8213	11	21
TMEM123-MMP20	chr11	102319542	chr11	102464326	578	HLA-A31:02	STGPHYWITR	0.959	0.7775	11	21
TMEM123-MMP20	chr11	102319542	chr11	102464326	578	HLA-B57:01	SSANSTGPHYW	0.9999	0.9687	7	18
TMEM123-MMP20	chr11	102319542	chr11	102464326	578	HLA-B58:02	SSANSTGPHYW	0.9998	0.9533	7	18
TMEM123-MMP20	chr11	102319542	chr11	102464326	578	HLA-B58:01	SSANSTGPHYW	0.9997	0.9552	7	18
TMEM123-MMP20	chr11	102319542	chr11	102464326	578	HLA-B15:17	SSANSTGPHYW	0.9991	0.9424	7	18
TMEM123-MMP20	chr11	102319542	chr11	102464326	578	HLA-B57:03	SSANSTGPHYW	0.9987	0.9908	7	18
TMEM123-MMP20	chr11	102319542	chr11	102464326	578	HLA-B15:16	SSANSTGPHYW	0.9977	0.7566	7	18
TMEM123-MMP20	chr11	102319542	chr11	102464326	578	HLA-B15:05	SANSTGPHY	0.9946	0.8094	8	17
TMEM123-MMP20	chr11	102319542	chr11	102464326	578	HLA-B15:21	SANSTGPHY	0.9937	0.8757	8	17
TMEM123-MMP20	chr11	102319542	chr11	102464326	578	HLA-B15:31	SANSTGPHY	0.9844	0.8203	8	17
TMEM123-MMP20	chr11	102319542	chr11	102464326	578	HLA-B15:07	SANSTGPHY	0.9587	0.6135	8	17
TMEM123-MMP20	chr11	102319542	chr11	102464326	578	HLA-C15:04	SANSTGPHY	0.6189	0.8239	8	17
TMEM123-MMP20	chr11	102319542	chr11	102464326	578	HLA-B15:04	SANSTGPHY	0.6091	0.9102	8	17
TMEM123-MMP20	chr11	102319542	chr11	102464326	578	HLA-C07:19	SANSTGPHY	0.6002	0.579	8	17
TMEM123-MMP20	chr11	102319542	chr11	102464326	578	HLA-C12:16	SANSTGPHY	0.5925	0.8933	8	17
TMEM123-MMP20	chr11	102319542	chr11	102464326	578	HLA-C07:95	SANSTGPHY	0.4803	0.6593	8	17
TMEM123-MMP20	chr11	102319542	chr11	102464326	578	HLA-B44:08	ANSTGPHYW	0.1787	0.6588	9	18
TMEM123-MMP20	chr11	102319542	chr11	102464326	578	HLA-C03:14	SANSTGPHY	0.1112	0.9542	8	17
TMEM123-MMP20	chr11	102319542	chr11	102464326	578	HLA-C12:04	SANSTGPHY	0.0336	0.9612	8	17
TMEM123-MMP20	chr11	102319542	chr11	102464326	578	HLA-C06:03	SANSTGPHY	0.0305	0.9537	8	17
TMEM123-MMP20	chr11	102319542	chr11	102464326	578	HLA-C12:12	SANSTGPHY	0.0144	0.8044	8	17
TMEM123-MMP20	chr11	102319542	chr11	102464326	578	HLA-A31:01	STGPHYWITR	0.9807	0.7612	11	21
TMEM123-MMP20	chr11	102319542	chr11	102464326	578	HLA-B44:08	SANSTGPHYW	0.8187	0.5957	8	18
TMEM123-MMP20	chr11	102319542	chr11	102464326	578	HLA-B15:39	SANSTGPHY	0.9969	0.8103	8	17
TMEM123-MMP20	chr11	102319542	chr11	102464326	578	HLA-B15:20	SANSTGPHY	0.9949	0.863	8	17
TMEM123-MMP20	chr11	102319542	chr11	102464326	578	HLA-B35:11	SANSTGPHY	0.9923	0.8653	8	17
TMEM123-MMP20	chr11	102319542	chr11	102464326	578	HLA-B35:28	SANSTGPHY	0.9914	0.8614	8	17
TMEM123-MMP20	chr11	102319542	chr11	102464326	578	HLA-B57:04	ANSTGPHYW	0.9867	0.8442	9	18
TMEM123-MMP20	chr11	102319542	chr11	102464326	578	HLA-B35:20	SANSTGPHY	0.9858	0.8676	8	17
TMEM123-MMP20	chr11	102319542	chr11	102464326	578	HLA-B15:34	SANSTGPHY	0.9852	0.8773	8	17
TMEM123-MMP20	chr11	102319542	chr11	102464326	578	HLA-B15:125	SANSTGPHY	0.9852	0.8773	8	17
TMEM123-MMP20	chr11	102319542	chr11	102464326	578	HLA-B15:33	SANSTGPHY	0.9852	0.8773	8	17
TMEM123-MMP20	chr11	102319542	chr11	102464326	578	HLA-B15:27	SANSTGPHY	0.9849	0.8756	8	17
TMEM123-MMP20	chr11	102319542	chr11	102464326	578	HLA-B35:77	SANSTGPHY	0.9839	0.8181	8	17
TMEM123-MMP20	chr11	102319542	chr11	102464326	578	HLA-B35:23	SANSTGPHY	0.9836	0.7705	8	17
TMEM123-MMP20	chr11	102319542	chr11	102464326	578	HLA-B15:135	SANSTGPHY	0.9827	0.8817	8	17
TMEM123-MMP20	chr11	102319542	chr11	102464326	578	HLA-B15:11	SANSTGPHY	0.9781	0.8461	8	17
TMEM123-MMP20	chr11	102319542	chr11	102464326	578	HLA-B15:08	SANSTGPHY	0.9718	0.8253	8	17
TMEM123-MMP20	chr11	102319542	chr11	102464326	578	HLA-B15:50	SANSTGPHY	0.9712	0.8733	8	17
TMEM123-MMP20	chr11	102319542	chr11	102464326	578	HLA-B35:43	SANSTGPHY	0.9574	0.8328	8	17
TMEM123-MMP20	chr11	102319542	chr11	102464326	578	HLA-B15:35	SANSTGPHY	0.9515	0.7878	8	17
TMEM123-MMP20	chr11	102319542	chr11	102464326	578	HLA-B15:24	SANSTGPHY	0.9344	0.8647	8	17
TMEM123-MMP20	chr11	102319542	chr11	102464326	578	HLA-B35:30	SANSTGPHY	0.9326	0.6579	8	17
TMEM123-MMP20	chr11	102319542	chr11	102464326	578	HLA-B35:17	SANSTGPHY	0.9326	0.6579	8	17
TMEM123-MMP20	chr11	102319542	chr11	102464326	578	HLA-B15:12	SANSTGPHY	0.9013	0.8858	8	17
TMEM123-MMP20	chr11	102319542	chr11	102464326	578	HLA-B15:53	SANSTGPHY	0.8911	0.8388	8	17
TMEM123-MMP20	chr11	102319542	chr11	102464326	578	HLA-C03:02	SANSTGPHY	0.8584	0.9618	8	17
TMEM123-MMP20	chr11	102319542	chr11	102464326	578	HLA-B35:24	SANSTGPHY	0.8552	0.8385	8	17
TMEM123-MMP20	chr11	102319542	chr11	102464326	578	HLA-B57:02	ANSTGPHYW	0.8286	0.9773	9	18
TMEM123-MMP20	chr11	102319542	chr11	102464326	578	HLA-B58:06	SANSTGPHY	0.7239	0.6928	8	17
TMEM123-MMP20	chr11	102319542	chr11	102464326	578	HLA-B48:02	SANSTGPHY	0.7106	0.8514	8	17
TMEM123-MMP20	chr11	102319542	chr11	102464326	578	HLA-C07:22	SANSTGPHY	0.6627	0.6111	8	17
TMEM123-MMP20	chr11	102319542	chr11	102464326	578	HLA-C15:09	SANSTGPHY	0.6189	0.8239	8	17
TMEM123-MMP20	chr11	102319542	chr11	102464326	578	HLA-C07:17	SANSTGPHY	0.562	0.9269	8	17
TMEM123-MMP20	chr11	102319542	chr11	102464326	578	HLA-B15:54	SANSTGPHY	0.4894	0.8372	8	17
TMEM123-MMP20	chr11	102319542	chr11	102464326	578	HLA-C07:01	SANSTGPHY	0.4803	0.59	8	17
TMEM123-MMP20	chr11	102319542	chr11	102464326	578	HLA-C12:02	SANSTGPHY	0.3229	0.9076	8	17
TMEM123-MMP20	chr11	102319542	chr11	102464326	578	HLA-B18:04	SANSTGPHY	0.2128	0.8745	8	17
TMEM123-MMP20	chr11	102319542	chr11	102464326	578	HLA-C16:04	SANSTGPHY	0.1849	0.9324	8	17
TMEM123-MMP20	chr11	102319542	chr11	102464326	578	HLA-B15:68	SANSTGPHY	0.0751	0.5639	8	17
TMEM123-MMP20	chr11	102319542	chr11	102464326	578	HLA-C16:01	SANSTGPHY	0.0713	0.9387	8	17
TMEM123-MMP20	chr11	102319542	chr11	102464326	578	HLA-C12:03	SANSTGPHY	0.0489	0.9329	8	17
TMEM123-MMP20	chr11	102319542	chr11	102464326	578	HLA-B18:07	SANSTGPHY	0.0468	0.8219	8	17
TMEM123-MMP20	chr11	102319542	chr11	102464326	578	HLA-C16:02	SANSTGPHY	0.0209	0.9648	8	17
TMEM123-MMP20	chr11	102319542	chr11	102464326	578	HLA-C02:02	SANSTGPHY	0.0186	0.9752	8	17
TMEM123-MMP20	chr11	102319542	chr11	102464326	578	HLA-C02:10	SANSTGPHY	0.0186	0.9752	8	17
TMEM123-MMP20	chr11	102319542	chr11	102464326	578	HLA-B57:04	SANSTGPHYW	0.9997	0.7685	8	18
TMEM123-MMP20	chr11	102319542	chr11	102464326	578	HLA-B57:10	SANSTGPHYW	0.9997	0.9681	8	18
TMEM123-MMP20	chr11	102319542	chr11	102464326	578	HLA-B58:06	SANSTGPHYW	0.9992	0.8957	8	18
TMEM123-MMP20	chr11	102319542	chr11	102464326	578	HLA-B57:02	SANSTGPHYW	0.997	0.9567	8	18
TMEM123-MMP20	chr11	102319542	chr11	102464326	578	HLA-B15:13	SANSTGPHYW	0.9912	0.838	8	18
TMEM123-MMP20	chr11	102319542	chr11	102464326	578	HLA-A74:01	STGPHYWITR	0.9718	0.8213	11	21
TMEM123-MMP20	chr11	102319542	chr11	102464326	578	HLA-B15:24	SANSTGPHYW	0.9294	0.9702	8	18
TMEM123-MMP20	chr11	102319542	chr11	102464326	578	HLA-B57:04	SSANSTGPHYW	0.9999	0.7817	7	18
TMEM123-MMP20	chr11	102319542	chr11	102464326	578	HLA-B57:10	SSANSTGPHYW	0.9999	0.9687	7	18
TMEM123-MMP20	chr11	102319542	chr11	102464326	578	HLA-B58:06	SSANSTGPHYW	0.9997	0.8882	7	18
TMEM123-MMP20	chr11	102319542	chr11	102464326	578	HLA-B57:02	SSANSTGPHYW	0.9993	0.9549	7	18
TMEM123-MMP20	chr11	102319543	chr11	102480761	578	HLA-B35:08	NSTDHGDSY	0.8947	0.5624	10	19
TMEM123-MMP20	chr11	102319543	chr11	102480761	578	HLA-B35:01	NSTDHGDSY	0.7513	0.6339	10	19
TMEM123-MMP20	chr11	102319543	chr11	102480761	578	HLA-B35:08	SANSTDHGDSY	0.9966	0.7476	8	19
TMEM123-MMP20	chr11	102319543	chr11	102480761	578	HLA-B15:31	NSTDHGDSY	0.7614	0.5899	10	19
TMEM123-MMP20	chr11	102319543	chr11	102480761	578	HLA-C03:14	NSTDHGDSY	0.0054	0.884	10	19
TMEM123-MMP20	chr11	102319543	chr11	102480761	578	HLA-C05:09	STDHGDSYPF	0.9999	0.8309	11	21
TMEM123-MMP20	chr11	102319543	chr11	102480761	578	HLA-B35:11	NSTDHGDSY	0.8242	0.6759	10	19
TMEM123-MMP20	chr11	102319543	chr11	102480761	578	HLA-B35:77	NSTDHGDSY	0.7513	0.6339	10	19
TMEM123-MMP20	chr11	102319543	chr11	102480761	578	HLA-B35:20	NSTDHGDSY	0.7438	0.7099	10	19
TMEM123-MMP20	chr11	102319543	chr11	102480761	578	HLA-B35:23	NSTDHGDSY	0.741	0.6325	10	19
TMEM123-MMP20	chr11	102319543	chr11	102480761	578	HLA-B35:24	NSTDHGDSY	0.5169	0.7414	10	19
TMEM123-MMP20	chr11	102319543	chr11	102480761	578	HLA-B15:11	NSTDHGDSY	0.4589	0.5106	10	19
TMEM123-MMP20	chr11	102319543	chr11	102480761	578	HLA-B15:08	NSTDHGDSY	0.4558	0.5338	10	19
TMEM123-MMP20	chr11	102319543	chr11	102480761	578	HLA-B35:43	NSTDHGDSY	0.3852	0.5268	10	19
TMEM123-MMP20	chr11	102319543	chr11	102480761	578	HLA-C03:02	NSTDHGDSY	0.3479	0.8094	10	19
TMEM123-MMP20	chr11	102319543	chr11	102480761	578	HLA-C12:02	NSTDHGDSY	0.0268	0.7556	10	19
TMEM123-MMP20	chr11	102319543	chr11	102480761	578	HLA-C16:01	NSTDHGDSY	0.002	0.8763	10	19
TMEM123-MMP20	chr11	102319543	chr11	102480761	578	HLA-C04:03	STDHGDSYPF	0.9999	0.6717	11	21
TMEM123-MMP20	chr11	102319543	chr11	102480761	578	HLA-C05:01	STDHGDSYPF	0.9999	0.8309	11	21
TMEM123-MMP20	chr11	102319543	chr11	102480761	578	HLA-B57:02	STDHGDSYPF	0.9819	0.8573	11	21

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Potential FusionNeoAntigen Information of TMEM123-MMP20 in HLA II

TMEM123-MMP20_102319542_102464326.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)
TMEM123-MMP20	chr11	102319542	chr11	102464326	578	DRB1-0701	STGPHYWITRGFQMQ	11	26
TMEM123-MMP20	chr11	102319542	chr11	102464326	578	DRB1-0703	STGPHYWITRGFQMQ	11	26
TMEM123-MMP20	chr11	102319542	chr11	102464326	578	DRB1-0704	STGPHYWITRGFQMQ	11	26
TMEM123-MMP20	chr11	102319542	chr11	102464326	578	DRB1-0705	STGPHYWITRGFQMQ	11	26
TMEM123-MMP20	chr11	102319542	chr11	102464326	578	DRB1-0706	STGPHYWITRGFQMQ	11	26
TMEM123-MMP20	chr11	102319542	chr11	102464326	578	DRB1-0707	STGPHYWITRGFQMQ	11	26
TMEM123-MMP20	chr11	102319542	chr11	102464326	578	DRB1-0708	STGPHYWITRGFQMQ	11	26
TMEM123-MMP20	chr11	102319542	chr11	102464326	578	DRB1-0709	STGPHYWITRGFQMQ	11	26
TMEM123-MMP20	chr11	102319542	chr11	102464326	578	DRB1-0711	STGPHYWITRGFQMQ	11	26
TMEM123-MMP20	chr11	102319542	chr11	102464326	578	DRB1-0712	STGPHYWITRGFQMQ	11	26
TMEM123-MMP20	chr11	102319542	chr11	102464326	578	DRB1-0713	STGPHYWITRGFQMQ	11	26
TMEM123-MMP20	chr11	102319542	chr11	102464326	578	DRB1-0714	STGPHYWITRGFQMQ	11	26
TMEM123-MMP20	chr11	102319542	chr11	102464326	578	DRB1-0715	STGPHYWITRGFQMQ	11	26
TMEM123-MMP20	chr11	102319542	chr11	102464326	578	DRB1-0716	STGPHYWITRGFQMQ	11	26
TMEM123-MMP20	chr11	102319542	chr11	102464326	578	DRB1-0717	STGPHYWITRGFQMQ	11	26
TMEM123-MMP20	chr11	102319542	chr11	102464326	578	DRB1-0719	STGPHYWITRGFQMQ	11	26

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Fusion breakpoint peptide structures of TMEM123-MMP20

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
6394	NSSANSTDHGDSYP	TMEM123	MMP20	chr11	102319543	chr11	102480761	578

File name	BPseq	Hgene	Tgene	Hchr	Hbp	Tchr	Tbp	AAlen
6396	NSSANSTGPHYWIT	TMEM123	MMP20	chr11	102319542	chr11	102464326	578

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of TMEM123-MMP20

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	6394	NSSANSTDHGDSYP	-7.10743	-7.22083
HLA-B14:02	3BVN	6394	NSSANSTDHGDSYP	-3.79488	-4.83018
HLA-B52:01	3W39	6394	NSSANSTDHGDSYP	-6.78681	-6.90021
HLA-B52:01	3W39	6394	NSSANSTDHGDSYP	-3.75119	-4.78649
HLA-A11:01	4UQ2	6394	NSSANSTDHGDSYP	-10.1888	-11.2241
HLA-A11:01	4UQ2	6394	NSSANSTDHGDSYP	-6.59241	-6.70581
HLA-A24:02	5HGA	6394	NSSANSTDHGDSYP	-8.29771	-9.33301
HLA-A24:02	5HGA	6394	NSSANSTDHGDSYP	-8.23185	-8.34525
HLA-B44:05	3DX8	6394	NSSANSTDHGDSYP	-7.25218	-7.36558
HLA-B44:05	3DX8	6394	NSSANSTDHGDSYP	-3.76181	-4.79711
HLA-A02:01	6TDR	6394	NSSANSTDHGDSYP	-2.73959	-3.77489
HLA-B14:02	3BVN	6396	NSSANSTGPHYWIT	-7.15543	-7.26883
HLA-B14:02	3BVN	6396	NSSANSTGPHYWIT	-4.77435	-5.80965
HLA-B52:01	3W39	6396	NSSANSTGPHYWIT	-6.80875	-6.92215
HLA-B52:01	3W39	6396	NSSANSTGPHYWIT	-4.20386	-5.23916
HLA-A11:01	4UQ2	6396	NSSANSTGPHYWIT	-7.5194	-8.5547
HLA-A11:01	4UQ2	6396	NSSANSTGPHYWIT	-6.9601	-7.0735
HLA-A24:02	5HGA	6396	NSSANSTGPHYWIT	-7.52403	-7.63743
HLA-A24:02	5HGA	6396	NSSANSTGPHYWIT	-5.82433	-6.85963
HLA-B27:05	6PYJ	6396	NSSANSTGPHYWIT	-3.28285	-4.31815
HLA-B44:05	3DX8	6396	NSSANSTGPHYWIT	-5.91172	-6.94702
HLA-B44:05	3DX8	6396	NSSANSTGPHYWIT	-4.24346	-4.35686

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Vaccine Design for the FusionNeoAntigens of TMEM123-MMP20

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
TMEM123-MMP20	chr11	102319542	chr11	102464326	10	18	NSTGPHYW	ACTCAACAGGTCCCCACTACTGGA
TMEM123-MMP20	chr11	102319542	chr11	102464326	11	21	STGPHYWITR	CAACAGGTCCCCACTACTGGATAACAAGAG
TMEM123-MMP20	chr11	102319542	chr11	102464326	7	18	SSANSTGPHYW	CCAGTGCTAACTCAACAGGTCCCCACTACTGGA
TMEM123-MMP20	chr11	102319542	chr11	102464326	8	17	SANSTGPHY	GTGCTAACTCAACAGGTCCCCACTACT
TMEM123-MMP20	chr11	102319542	chr11	102464326	8	18	SANSTGPHYW	GTGCTAACTCAACAGGTCCCCACTACTGGA
TMEM123-MMP20	chr11	102319542	chr11	102464326	9	18	ANSTGPHYW	CTAACTCAACAGGTCCCCACTACTGGA
TMEM123-MMP20	chr11	102319543	chr11	102480761	10	19	NSTDHGDSY	ACTCAACAGATCACGGGGATTCCTATC
TMEM123-MMP20	chr11	102319543	chr11	102480761	11	21	STDHGDSYPF	CAACAGATCACGGGGATTCCTATCCATTCG
TMEM123-MMP20	chr11	102319543	chr11	102480761	8	19	SANSTDHGDSY	GTGCTAACTCAACAGATCACGGGGATTCCTATC

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
TMEM123-MMP20	chr11	102319542	chr11	102464326	11	26	STGPHYWITRGFQMQ	CAACAGGTCCCCACTACTGGATAACAAGAGGATTCCAAATGCAAG

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Information of the samples that have these potential fusion neoantigens of TMEM123-MMP20

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
COAD	TMEM123-MMP20	chr11	102319542	ENST00000398136	chr11	102464326	ENST00000260228	TCGA-CA-5254
LUAD	TMEM123-MMP20	chr11	102319543	ENST00000398136	chr11	102480761	ENST00000260228	TCGA-35-4122-01A

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Potential target of CAR-T therapy development for TMEM123-MMP20

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 TMEM123-MMP20

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 TMEM123-MMP20

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)