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Fusion Protein:MFSD6-PMS1

Fusion Gene and Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: MFSD6-PMS1
	FusionPDB ID: 53288
	FusionGDB2.0 ID: 53288
		Hgene	Tgene
	Gene symbol	MFSD6	PMS1
	Gene ID	54842	5378
	Gene name	major facilitator superfamily domain containing 6	PMS1 homolog 1, mismatch repair system component
	Synonyms	MMR2\|hMMR2	HNPCC3\|MLH2\|PMSL1\|hPMS1
	Cytomap	2q32.2	2q32.2
	Type of gene	protein-coding	protein-coding
	Description	major facilitator superfamily domain-containing protein 6macrophage MHC class I receptor 2 homologmacrophage MHC receptor 2	PMS1 protein homolog 1DNA mismatch repair protein PMS1PMS1 postmeiotic segregation increased 1human homolog of yeast mutLmismatch repair gene PMSL1rhabdomyosarcoma antigen MU-RMS-40.10Brhabdomyosarcoma antigen MU-RMS-40.10E
	Modification date	20200313	20200327
	UniProtAcc	Q6ZSS7 Main function of 5'-partner protein:	PMS1 Main function of 5'-partner protein: 932
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000281416, ENST00000392328, ENST00000489793, ENST00000535751,	ENST00000374826, ENST00000409985, ENST00000421722, ENST00000432292, ENST00000447232, ENST00000409823, ENST00000418224, ENST00000441310,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	8 X 3 X 5=120	11 X 6 X 7=462
	# samples	8	11
	** MAII score	log2(8/120*10)=-0.584962500721156 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(11/462*10)=-2.0703893278914 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Fusion gene context	PubMed: MFSD6 [Title/Abstract] AND PMS1 [Title/Abstract] AND fusion [Title/Abstract]
Fusion neoantigen context	PubMed: MFSD6 [Title/Abstract] AND PMS1 [Title/Abstract] AND neoantigen [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	MFSD6(191334581)-PMS1(190738222), # samples:2
Anticipated loss of major functional domain due to fusion event.	MFSD6-PMS1 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. MFSD6-PMS1 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. MFSD6-PMS1 seems lost the major protein functional domain in Tgene partner, which is a CGC 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

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr2:191334581/chr2:190738222)
- 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 MFSD6 (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 PMS1 (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)
ENST00000392328	MFSD6	chr2	191334581	+	ENST00000441310	PMS1	chr2	190738222	+	2473	1954	324	2279	651
ENST00000392328	MFSD6	chr2	191334581	+	ENST00000418224	PMS1	chr2	190738222	+	2471	1954	324	2279	651
ENST00000392328	MFSD6	chr2	191334581	+	ENST00000409823	PMS1	chr2	190738222	+	2280	1954	324	2279	651
ENST00000281416	MFSD6	chr2	191334581	+	ENST00000441310	PMS1	chr2	190738222	+	2284	1765	135	2090	651
ENST00000281416	MFSD6	chr2	191334581	+	ENST00000418224	PMS1	chr2	190738222	+	2282	1765	135	2090	651
ENST00000281416	MFSD6	chr2	191334581	+	ENST00000409823	PMS1	chr2	190738222	+	2091	1765	135	2090	651
ENST00000535751	MFSD6	chr2	191334581	+	ENST00000441310	PMS1	chr2	190738222	+	751	232	138	557	139
ENST00000535751	MFSD6	chr2	191334581	+	ENST00000418224	PMS1	chr2	190738222	+	749	232	138	557	139
ENST00000535751	MFSD6	chr2	191334581	+	ENST00000409823	PMS1	chr2	190738222	+	558	232	138	557	139

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
ENST00000392328	ENST00000441310	MFSD6	chr2	191334581	+	PMS1	chr2	190738222	+	0.000595692	0.9994043
ENST00000392328	ENST00000418224	MFSD6	chr2	191334581	+	PMS1	chr2	190738222	+	0.000587439	0.99941254
ENST00000392328	ENST00000409823	MFSD6	chr2	191334581	+	PMS1	chr2	190738222	+	0.001058201	0.99894184
ENST00000281416	ENST00000441310	MFSD6	chr2	191334581	+	PMS1	chr2	190738222	+	0.000274782	0.99972516
ENST00000281416	ENST00000418224	MFSD6	chr2	191334581	+	PMS1	chr2	190738222	+	0.000271981	0.999728
ENST00000281416	ENST00000409823	MFSD6	chr2	191334581	+	PMS1	chr2	190738222	+	0.000427141	0.9995728
ENST00000535751	ENST00000441310	MFSD6	chr2	191334581	+	PMS1	chr2	190738222	+	0.018855961	0.9811441
ENST00000535751	ENST00000418224	MFSD6	chr2	191334581	+	PMS1	chr2	190738222	+	0.0191697	0.9808303
ENST00000535751	ENST00000409823	MFSD6	chr2	191334581	+	PMS1	chr2	190738222	+	0.014137094	0.9858629

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 MFSD6-PMS1

+/-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
MFSD6	chr2	191334581	PMS1	chr2	190738222	1765	541	YLENAWTVLPMEVLQGVSITENYLEI
MFSD6	chr2	191334581	PMS1	chr2	190738222	1954	541	YLENAWTVLPMEVLQGVSITENYLEI
MFSD6	chr2	191334581	PMS1	chr2	190738222	232	29	YLENAWTVLPMEVLQGVSITENYLEI

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Potential FusionNeoAntigen Information of MFSD6-PMS1 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.

MFSD6-PMS1_191334581_190738222.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)
MFSD6-PMS1	chr2	191334581	chr2	190738222	1765	HLA-B51:01	LPMEVLQGV	0.9984	0.7576	8	17
MFSD6-PMS1	chr2	191334581	chr2	190738222	1765	HLA-B13:01	MEVLQGVSI	0.9976	0.9778	10	19
MFSD6-PMS1	chr2	191334581	chr2	190738222	1765	HLA-B50:02	MEVLQGVSI	0.9964	0.725	10	19
MFSD6-PMS1	chr2	191334581	chr2	190738222	1765	HLA-B51:02	LPMEVLQGV	0.9964	0.7964	8	17
MFSD6-PMS1	chr2	191334581	chr2	190738222	1765	HLA-B35:02	LPMEVLQGV	0.9931	0.9667	8	17
MFSD6-PMS1	chr2	191334581	chr2	190738222	1765	HLA-B35:04	LPMEVLQGV	0.9931	0.9667	8	17
MFSD6-PMS1	chr2	191334581	chr2	190738222	1765	HLA-B45:01	MEVLQGVSI	0.9824	0.9771	10	19
MFSD6-PMS1	chr2	191334581	chr2	190738222	1765	HLA-B44:05	MEVLQGVSI	0.9818	0.5163	10	19
MFSD6-PMS1	chr2	191334581	chr2	190738222	1765	HLA-B35:03	LPMEVLQGV	0.9812	0.8135	8	17
MFSD6-PMS1	chr2	191334581	chr2	190738222	1765	HLA-B47:01	MEVLQGVSI	0.9616	0.8064	10	19
MFSD6-PMS1	chr2	191334581	chr2	190738222	1765	HLA-B35:05	LPMEVLQGV	0.955	0.6773	8	17
MFSD6-PMS1	chr2	191334581	chr2	190738222	1765	HLA-B18:01	MEVLQGVSI	0.9286	0.9135	10	19
MFSD6-PMS1	chr2	191334581	chr2	190738222	1765	HLA-B53:01	LPMEVLQGV	0.9204	0.6016	8	17
MFSD6-PMS1	chr2	191334581	chr2	190738222	1765	HLA-B82:01	LPMEVLQGV	0.7161	0.732	8	17
MFSD6-PMS1	chr2	191334581	chr2	190738222	1765	HLA-B81:01	LPMEVLQGV	0.7055	0.5528	8	17
MFSD6-PMS1	chr2	191334581	chr2	190738222	1765	HLA-B41:01	MEVLQGVSI	0.5495	0.9809	10	19
MFSD6-PMS1	chr2	191334581	chr2	190738222	1765	HLA-B39:13	MEVLQGVSI	0.5366	0.9867	10	19
MFSD6-PMS1	chr2	191334581	chr2	190738222	1765	HLA-B50:01	MEVLQGVSI	0.3752	0.846	10	19
MFSD6-PMS1	chr2	191334581	chr2	190738222	1765	HLA-B52:01	MEVLQGVSI	0.1711	0.9881	10	19
MFSD6-PMS1	chr2	191334581	chr2	190738222	1765	HLA-A02:22	VLPMEVLQGV	0.9776	0.6215	7	17
MFSD6-PMS1	chr2	191334581	chr2	190738222	1765	HLA-A02:21	VLPMEVLQGV	0.9637	0.6352	7	17
MFSD6-PMS1	chr2	191334581	chr2	190738222	1765	HLA-A02:13	VLPMEVLQGV	0.9616	0.6213	7	17
MFSD6-PMS1	chr2	191334581	chr2	190738222	1765	HLA-A02:27	VLPMEVLQGV	0.9576	0.5339	7	17
MFSD6-PMS1	chr2	191334581	chr2	190738222	1765	HLA-A02:30	VLPMEVLQGV	0.9534	0.5221	7	17
MFSD6-PMS1	chr2	191334581	chr2	190738222	1765	HLA-A02:67	VLPMEVLQGV	0.9534	0.5221	7	17
MFSD6-PMS1	chr2	191334581	chr2	190738222	1765	HLA-A02:24	VLPMEVLQGV	0.9534	0.5221	7	17
MFSD6-PMS1	chr2	191334581	chr2	190738222	1765	HLA-A02:60	VLPMEVLQGV	0.9532	0.5471	7	17
MFSD6-PMS1	chr2	191334581	chr2	190738222	1765	HLA-A02:11	VLPMEVLQGV	0.9492	0.5526	7	17
MFSD6-PMS1	chr2	191334581	chr2	190738222	1765	HLA-A02:38	VLPMEVLQGV	0.9457	0.5323	7	17
MFSD6-PMS1	chr2	191334581	chr2	190738222	1765	HLA-A02:04	VLPMEVLQGV	0.9193	0.8322	7	17
MFSD6-PMS1	chr2	191334581	chr2	190738222	1765	HLA-A02:19	VLPMEVLQGV	0.916	0.5884	7	17
MFSD6-PMS1	chr2	191334581	chr2	190738222	1765	HLA-A02:35	VLPMEVLQGV	0.9008	0.5317	7	17
MFSD6-PMS1	chr2	191334581	chr2	190738222	1765	HLA-A02:29	VLPMEVLQGV	0.8923	0.5227	7	17
MFSD6-PMS1	chr2	191334581	chr2	190738222	1765	HLA-A02:17	VLPMEVLQGV	0.8781	0.8897	7	17
MFSD6-PMS1	chr2	191334581	chr2	190738222	1765	HLA-A02:20	VLPMEVLQGV	0.8746	0.5304	7	17
MFSD6-PMS1	chr2	191334581	chr2	190738222	1765	HLA-B51:02	VLPMEVLQGV	0.3802	0.8152	7	17
MFSD6-PMS1	chr2	191334581	chr2	190738222	1765	HLA-B35:03	LPMEVLQGVSI	0.9987	0.8449	8	19
MFSD6-PMS1	chr2	191334581	chr2	190738222	1765	HLA-B51:02	LPMEVLQGVSI	0.9983	0.7273	8	19
MFSD6-PMS1	chr2	191334581	chr2	190738222	1765	HLA-B51:01	LPMEVLQGVSI	0.9983	0.7624	8	19
MFSD6-PMS1	chr2	191334581	chr2	190738222	1765	HLA-B15:25	VLQGVSITENY	0.9965	0.9427	12	23
MFSD6-PMS1	chr2	191334581	chr2	190738222	1765	HLA-A02:21	TVLPMEVLQGV	0.964	0.6368	6	17
MFSD6-PMS1	chr2	191334581	chr2	190738222	1765	HLA-B81:01	LPMEVLQGVSI	0.9096	0.6114	8	19
MFSD6-PMS1	chr2	191334581	chr2	190738222	1765	HLA-B40:06	MEVLQGVSI	0.9997	0.7615	10	19
MFSD6-PMS1	chr2	191334581	chr2	190738222	1765	HLA-B54:01	LPMEVLQGV	0.9993	0.8064	8	17
MFSD6-PMS1	chr2	191334581	chr2	190738222	1765	HLA-B78:01	LPMEVLQGV	0.9986	0.7512	8	17
MFSD6-PMS1	chr2	191334581	chr2	190738222	1765	HLA-B51:07	LPMEVLQGV	0.9981	0.9744	8	17
MFSD6-PMS1	chr2	191334581	chr2	190738222	1765	HLA-B44:10	MEVLQGVSI	0.9967	0.6649	10	19
MFSD6-PMS1	chr2	191334581	chr2	190738222	1765	HLA-B51:08	LPMEVLQGV	0.9962	0.6057	8	17
MFSD6-PMS1	chr2	191334581	chr2	190738222	1765	HLA-B48:03	MEVLQGVSI	0.9957	0.5034	10	19
MFSD6-PMS1	chr2	191334581	chr2	190738222	1765	HLA-B35:12	LPMEVLQGV	0.9931	0.9667	8	17
MFSD6-PMS1	chr2	191334581	chr2	190738222	1765	HLA-B40:03	MEVLQGVSI	0.9816	0.6385	10	19
MFSD6-PMS1	chr2	191334581	chr2	190738222	1765	HLA-B56:04	LPMEVLQGV	0.9714	0.6572	8	17
MFSD6-PMS1	chr2	191334581	chr2	190738222	1765	HLA-B42:02	LPMEVLQGV	0.8644	0.8903	8	17
MFSD6-PMS1	chr2	191334581	chr2	190738222	1765	HLA-B42:01	LPMEVLQGV	0.804	0.8838	8	17
MFSD6-PMS1	chr2	191334581	chr2	190738222	1765	HLA-B39:10	LPMEVLQGV	0.6809	0.9838	8	17
MFSD6-PMS1	chr2	191334581	chr2	190738222	1765	HLA-B39:08	MEVLQGVSI	0.5846	0.9361	10	19
MFSD6-PMS1	chr2	191334581	chr2	190738222	1765	HLA-B51:07	MEVLQGVSI	0.0876	0.9729	10	19
MFSD6-PMS1	chr2	191334581	chr2	190738222	1765	HLA-A02:05	VLPMEVLQGV	0.9838	0.7121	7	17
MFSD6-PMS1	chr2	191334581	chr2	190738222	1765	HLA-A02:02	VLPMEVLQGV	0.9786	0.6202	7	17
MFSD6-PMS1	chr2	191334581	chr2	190738222	1765	HLA-A02:07	VLPMEVLQGV	0.9627	0.61	7	17
MFSD6-PMS1	chr2	191334581	chr2	190738222	1765	HLA-A02:01	VLPMEVLQGV	0.9534	0.5221	7	17
MFSD6-PMS1	chr2	191334581	chr2	190738222	1765	HLA-B78:01	LPMEVLQGVSI	0.9965	0.7616	8	19
MFSD6-PMS1	chr2	191334581	chr2	190738222	1765	HLA-B54:01	LPMEVLQGVSI	0.9953	0.5744	8	19
MFSD6-PMS1	chr2	191334581	chr2	190738222	1765	HLA-B56:04	LPMEVLQGVSI	0.9935	0.5235	8	19
MFSD6-PMS1	chr2	191334581	chr2	190738222	1765	HLA-B51:08	LPMEVLQGVSI	0.9929	0.5624	8	19
MFSD6-PMS1	chr2	191334581	chr2	190738222	1765	HLA-B15:05	VLQGVSITENY	0.9737	0.9175	12	23
MFSD6-PMS1	chr2	191334581	chr2	190738222	1765	HLA-B42:01	LPMEVLQGVSI	0.9294	0.9019	8	19
MFSD6-PMS1	chr2	191334581	chr2	190738222	1765	HLA-B40:04	MEVLQGVSI	0.9991	0.8189	10	19
MFSD6-PMS1	chr2	191334581	chr2	190738222	1765	HLA-B78:02	LPMEVLQGV	0.9987	0.7961	8	17
MFSD6-PMS1	chr2	191334581	chr2	190738222	1765	HLA-B51:14	LPMEVLQGV	0.9985	0.6736	8	17
MFSD6-PMS1	chr2	191334581	chr2	190738222	1765	HLA-B51:13	LPMEVLQGV	0.9983	0.6519	8	17
MFSD6-PMS1	chr2	191334581	chr2	190738222	1765	HLA-B51:09	LPMEVLQGV	0.9982	0.6806	8	17
MFSD6-PMS1	chr2	191334581	chr2	190738222	1765	HLA-B51:06	LPMEVLQGV	0.9977	0.7041	8	17
MFSD6-PMS1	chr2	191334581	chr2	190738222	1765	HLA-B51:21	LPMEVLQGV	0.9973	0.7386	8	17
MFSD6-PMS1	chr2	191334581	chr2	190738222	1765	HLA-B35:22	LPMEVLQGV	0.9973	0.5942	8	17
MFSD6-PMS1	chr2	191334581	chr2	190738222	1765	HLA-B40:12	MEVLQGVSI	0.9957	0.5034	10	19
MFSD6-PMS1	chr2	191334581	chr2	190738222	1765	HLA-B56:05	LPMEVLQGV	0.9944	0.6356	8	17
MFSD6-PMS1	chr2	191334581	chr2	190738222	1765	HLA-B51:29	LPMEVLQGV	0.9932	0.5071	8	17
MFSD6-PMS1	chr2	191334581	chr2	190738222	1765	HLA-B35:09	LPMEVLQGV	0.9931	0.9667	8	17
MFSD6-PMS1	chr2	191334581	chr2	190738222	1765	HLA-B55:02	LPMEVLQGV	0.9893	0.5885	8	17
MFSD6-PMS1	chr2	191334581	chr2	190738222	1765	HLA-B59:01	LPMEVLQGV	0.9848	0.7045	8	17
MFSD6-PMS1	chr2	191334581	chr2	190738222	1765	HLA-B55:04	LPMEVLQGV	0.9762	0.6761	8	17
MFSD6-PMS1	chr2	191334581	chr2	190738222	1765	HLA-B56:02	LPMEVLQGV	0.9714	0.6572	8	17
MFSD6-PMS1	chr2	191334581	chr2	190738222	1765	HLA-A69:01	LPMEVLQGV	0.9594	0.7043	8	17
MFSD6-PMS1	chr2	191334581	chr2	190738222	1765	HLA-B35:30	LPMEVLQGV	0.9506	0.7652	8	17
MFSD6-PMS1	chr2	191334581	chr2	190738222	1765	HLA-B35:17	LPMEVLQGV	0.9506	0.7652	8	17
MFSD6-PMS1	chr2	191334581	chr2	190738222	1765	HLA-B18:08	MEVLQGVSI	0.934	0.926	10	19
MFSD6-PMS1	chr2	191334581	chr2	190738222	1765	HLA-B18:05	MEVLQGVSI	0.9286	0.9135	10	19
MFSD6-PMS1	chr2	191334581	chr2	190738222	1765	HLA-B53:02	LPMEVLQGV	0.9117	0.5882	8	17
MFSD6-PMS1	chr2	191334581	chr2	190738222	1765	HLA-B18:03	MEVLQGVSI	0.8985	0.9068	10	19
MFSD6-PMS1	chr2	191334581	chr2	190738222	1765	HLA-B18:06	MEVLQGVSI	0.89	0.9248	10	19
MFSD6-PMS1	chr2	191334581	chr2	190738222	1765	HLA-B67:01	LPMEVLQGV	0.8086	0.9389	8	17
MFSD6-PMS1	chr2	191334581	chr2	190738222	1765	HLA-B41:03	MEVLQGVSI	0.7232	0.6887	10	19
MFSD6-PMS1	chr2	191334581	chr2	190738222	1765	HLA-B82:02	LPMEVLQGV	0.7161	0.732	8	17
MFSD6-PMS1	chr2	191334581	chr2	190738222	1765	HLA-B18:11	MEVLQGVSI	0.6857	0.9397	10	19
MFSD6-PMS1	chr2	191334581	chr2	190738222	1765	HLA-B39:02	MEVLQGVSI	0.5407	0.987	10	19
MFSD6-PMS1	chr2	191334581	chr2	190738222	1765	HLA-B50:04	MEVLQGVSI	0.3752	0.846	10	19
MFSD6-PMS1	chr2	191334581	chr2	190738222	1765	HLA-B50:05	MEVLQGVSI	0.3752	0.846	10	19
MFSD6-PMS1	chr2	191334581	chr2	190738222	1765	HLA-A02:03	VLPMEVLQGV	0.9862	0.6888	7	17
MFSD6-PMS1	chr2	191334581	chr2	190738222	1765	HLA-A02:14	VLPMEVLQGV	0.9648	0.6301	7	17
MFSD6-PMS1	chr2	191334581	chr2	190738222	1765	HLA-A02:06	VLPMEVLQGV	0.9637	0.6352	7	17
MFSD6-PMS1	chr2	191334581	chr2	190738222	1765	HLA-B59:01	VLPMEVLQGV	0.3088	0.8485	7	17
MFSD6-PMS1	chr2	191334581	chr2	190738222	1765	HLA-B51:14	LPMEVLQGVSI	0.9985	0.7185	8	19
MFSD6-PMS1	chr2	191334581	chr2	190738222	1765	HLA-B51:06	LPMEVLQGVSI	0.9981	0.6762	8	19
MFSD6-PMS1	chr2	191334581	chr2	190738222	1765	HLA-B51:09	LPMEVLQGVSI	0.9976	0.7049	8	19
MFSD6-PMS1	chr2	191334581	chr2	190738222	1765	HLA-B51:21	LPMEVLQGVSI	0.9975	0.679	8	19
MFSD6-PMS1	chr2	191334581	chr2	190738222	1765	HLA-B56:05	LPMEVLQGVSI	0.9967	0.5612	8	19
MFSD6-PMS1	chr2	191334581	chr2	190738222	1765	HLA-B15:39	VLQGVSITENY	0.9965	0.893	12	23
MFSD6-PMS1	chr2	191334581	chr2	190738222	1765	HLA-B55:04	LPMEVLQGVSI	0.9943	0.524	8	19
MFSD6-PMS1	chr2	191334581	chr2	190738222	1765	HLA-B56:02	LPMEVLQGVSI	0.9935	0.5235	8	19
MFSD6-PMS1	chr2	191334581	chr2	190738222	1765	HLA-A68:02	TVLPMEVLQGV	0.9821	0.8361	6	17
MFSD6-PMS1	chr2	191334581	chr2	190738222	1765	HLA-A69:01	TVLPMEVLQGV	0.9766	0.785	6	17
MFSD6-PMS1	chr2	191334581	chr2	190738222	1765	HLA-B15:20	VLQGVSITENY	0.9759	0.9458	12	23
MFSD6-PMS1	chr2	191334581	chr2	190738222	1765	HLA-B67:01	LPMEVLQGVSI	0.9701	0.9468	8	19
MFSD6-PMS1	chr2	191334581	chr2	190738222	1765	HLA-A02:06	TVLPMEVLQGV	0.964	0.6368	6	17

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Potential FusionNeoAntigen Information of MFSD6-PMS1 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 MFSD6-PMS1

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
9727	TVLPMEVLQGVSIT	MFSD6	PMS1	chr2	191334581	chr2	190738222	1765

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of MFSD6-PMS1

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	9727	TVLPMEVLQGVSIT	-7.9962	-8.1096
HLA-B14:02	3BVN	9727	TVLPMEVLQGVSIT	-5.70842	-6.74372
HLA-B52:01	3W39	9727	TVLPMEVLQGVSIT	-6.83737	-6.95077
HLA-B52:01	3W39	9727	TVLPMEVLQGVSIT	-4.4836	-5.5189
HLA-A11:01	4UQ2	9727	TVLPMEVLQGVSIT	-10.0067	-10.1201
HLA-A11:01	4UQ2	9727	TVLPMEVLQGVSIT	-9.03915	-10.0745
HLA-A24:02	5HGA	9727	TVLPMEVLQGVSIT	-6.56204	-6.67544
HLA-A24:02	5HGA	9727	TVLPMEVLQGVSIT	-5.42271	-6.45801
HLA-B44:05	3DX8	9727	TVLPMEVLQGVSIT	-7.85648	-8.89178
HLA-B44:05	3DX8	9727	TVLPMEVLQGVSIT	-5.3978	-5.5112
HLA-A02:01	6TDR	9727	TVLPMEVLQGVSIT	-3.37154	-4.40684

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Vaccine Design for the FusionNeoAntigens of MFSD6-PMS1

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
MFSD6-PMS1	chr2	191334581	chr2	190738222	10	19	MEVLQGVSI	TTCTTCAAGGAGTTTCAATTACTGAAA
MFSD6-PMS1	chr2	191334581	chr2	190738222	12	23	VLQGVSITENY	AAGGAGTTTCAATTACTGAAAATTACTTGGAAA
MFSD6-PMS1	chr2	191334581	chr2	190738222	6	17	TVLPMEVLQGV	TCCCCATGGAAGTTCTTCAAGGAGTTTCAATTA
MFSD6-PMS1	chr2	191334581	chr2	190738222	7	17	VLPMEVLQGV	CCATGGAAGTTCTTCAAGGAGTTTCAATTA
MFSD6-PMS1	chr2	191334581	chr2	190738222	8	17	LPMEVLQGV	TGGAAGTTCTTCAAGGAGTTTCAATTA
MFSD6-PMS1	chr2	191334581	chr2	190738222	8	19	LPMEVLQGVSI	TGGAAGTTCTTCAAGGAGTTTCAATTACTGAAA

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 MFSD6-PMS1

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
OV	MFSD6-PMS1	chr2	191334581	ENST00000281416	chr2	190738222	ENST00000409823	TCGA-24-1417-01A

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Potential target of CAR-T therapy development for MFSD6-PMS1

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

Hgene

MFSD6

chr2:191334581

chr2:190738222

ENST00000281416

105_125

543

792.0

Transmembrane

Helical

Hgene

MFSD6

chr2:191334581

chr2:190738222

ENST00000281416

132_152

543

792.0

Transmembrane

Helical

Hgene

MFSD6

chr2:191334581

chr2:190738222

ENST00000281416

286_306

543

792.0

Transmembrane

Helical

Hgene

MFSD6

chr2:191334581

chr2:190738222

ENST00000281416

335_355

543

792.0

Transmembrane

Helical

Hgene

MFSD6

chr2:191334581

chr2:190738222

ENST00000281416

369_389

543

792.0

Transmembrane

Helical

Hgene

MFSD6

chr2:191334581

chr2:190738222

ENST00000281416

450_470

543

792.0

Transmembrane

Helical

Hgene

MFSD6

chr2:191334581

chr2:190738222

ENST00000281416

479_499

543

792.0

Transmembrane

Helical

Hgene

MFSD6

chr2:191334581

chr2:190738222

ENST00000281416

507_527

543

792.0

Transmembrane

Helical

Hgene

MFSD6

chr2:191334581

chr2:190738222

ENST00000281416

73_93

543

792.0

Transmembrane

Helical

Hgene

MFSD6

chr2:191334581

chr2:190738222

ENST00000392328

105_125

543

792.0

Transmembrane

Helical

Hgene

MFSD6

chr2:191334581

chr2:190738222

ENST00000392328

132_152

543

792.0

Transmembrane

Helical

Hgene

MFSD6

chr2:191334581

chr2:190738222

ENST00000392328

286_306

543

792.0

Transmembrane

Helical

Hgene

MFSD6

chr2:191334581

chr2:190738222

ENST00000392328

335_355

543

792.0

Transmembrane

Helical

Hgene

MFSD6

chr2:191334581

chr2:190738222

ENST00000392328

369_389

543

792.0

Transmembrane

Helical

Hgene

MFSD6

chr2:191334581

chr2:190738222

ENST00000392328

450_470

543

792.0

Transmembrane

Helical

Hgene

MFSD6

chr2:191334581

chr2:190738222

ENST00000392328

479_499

543

792.0

Transmembrane

Helical

Hgene

MFSD6

chr2:191334581

chr2:190738222

ENST00000392328

507_527

543

792.0

Transmembrane

Helical

Hgene

MFSD6

chr2:191334581

chr2:190738222

ENST00000392328

73_93

543

792.0

Transmembrane

Helical

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 MFSD6-PMS1

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 MFSD6-PMS1

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)