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Fusion Protein:SMPX-PDHA1

Fusion Gene and Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: SMPX-PDHA1
	FusionPDB ID: 84269
	FusionGDB2.0 ID: 84269
		Hgene	Tgene
	Gene symbol	SMPX	PDHA1
	Gene ID	23676	5160
	Gene name	small muscle protein X-linked	pyruvate dehydrogenase E1 subunit alpha 1
	Synonyms	Chisel\|Csl\|DFN6\|DFNX4	PDHA\|PDHAD\|PDHCE1A\|PHE1A
	Cytomap	Xp22.12	Xp22.12
	Type of gene	protein-coding	protein-coding
	Description	small muscular proteindeafness, X-linked 6, sensorineuralstretch-responsive skeletal muscle protein	pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrialPDHE1-A type Ipyruvate dehydrogenase (lipoamide) alpha 1pyruvate dehydrogenase E1 alpha 1 subunitpyruvate dehydrogenase E1 subunitpyruvate dehydrogenase alpha 1pyruvate de
	Modification date	20200313	20200313
	UniProtAcc	.	.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000379494, ENST00000494525,	ENST00000379804, ENST00000478795, ENST00000379805, ENST00000379806, ENST00000422285, ENST00000540249, ENST00000545074,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	2 X 2 X 2=8	8 X 8 X 4=256
	# samples	2	9
	** MAII score	log2(2/8*10)=1.32192809488736	log2(9/256*10)=-1.50814690367033 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Fusion gene context	PubMed: SMPX [Title/Abstract] AND PDHA1 [Title/Abstract] AND fusion [Title/Abstract]
Fusion neoantigen context	PubMed: SMPX [Title/Abstract] AND PDHA1 [Title/Abstract] AND neoantigen [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	SMPX(21761868)-PDHA1(19367430), # samples:3
Anticipated loss of major functional domain due to fusion event.

* 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	PDHA1	GO:0006086	acetyl-CoA biosynthetic process from pyruvate	19081061

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chrX:21761868/chrX:19367430)
- 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 SMPX (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 PDHA1 (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)
ENST00000379494	SMPX	chrX	21761868	-	ENST00000545074	PDHA1	chrX	19367430	+	3555	366	234	1502	422
ENST00000379494	SMPX	chrX	21761868	-	ENST00000540249	PDHA1	chrX	19367430	+	3441	366	234	1388	384
ENST00000379494	SMPX	chrX	21761868	-	ENST00000379806	PDHA1	chrX	19367430	+	3534	366	234	1481	415
ENST00000379494	SMPX	chrX	21761868	-	ENST00000422285	PDHA1	chrX	19367430	+	3514	366	234	1481	415
ENST00000379494	SMPX	chrX	21761868	-	ENST00000379805	PDHA1	chrX	19367430	+	973	366	818	120	232

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
ENST00000379494	ENST00000545074	SMPX	chrX	21761868	-	PDHA1	chrX	19367430	+	0.000567226	0.99943274
ENST00000379494	ENST00000540249	SMPX	chrX	21761868	-	PDHA1	chrX	19367430	+	0.000855438	0.99914455
ENST00000379494	ENST00000379806	SMPX	chrX	21761868	-	PDHA1	chrX	19367430	+	0.000431398	0.99956864
ENST00000379494	ENST00000422285	SMPX	chrX	21761868	-	PDHA1	chrX	19367430	+	0.000456556	0.99954337
ENST00000379494	ENST00000379805	SMPX	chrX	21761868	-	PDHA1	chrX	19367430	+	0.003348408	0.9966516

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 SMPX-PDHA1

+/-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
SMPX	chrX	21761868	PDHA1	chrX	19367430	366	44	PPRRKECTPEVEEASRVLVASRNFAN

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Potential FusionNeoAntigen Information of SMPX-PDHA1 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.

SMPX-PDHA1_21761868_19367430.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)
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	HLA-B39:13	VEEASRVL	0.9882	0.9761	10	18
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	HLA-B45:01	EEASRVLVA	0.9995	0.9242	11	20
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	HLA-B50:02	EEASRVLVA	0.9991	0.7887	11	20
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	HLA-B45:01	VEEASRVLV	0.9986	0.8424	10	19
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	HLA-B50:02	VEEASRVLV	0.9974	0.6785	10	19
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	HLA-B41:01	EEASRVLVA	0.9723	0.9682	11	20
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	HLA-B35:03	EVEEASRVL	0.8315	0.9126	9	18
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	HLA-B08:09	EEASRVLVA	0.8237	0.879	11	20
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	HLA-B18:01	EEASRVLVA	0.7869	0.8443	11	20
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	HLA-B41:01	VEEASRVLV	0.7469	0.9219	10	19
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	HLA-B35:04	EVEEASRVL	0.689	0.9603	9	18
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	HLA-B35:02	EVEEASRVL	0.689	0.9603	9	18
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	HLA-B50:01	VEEASRVLV	0.67	0.7801	10	19
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	HLA-B50:01	EEASRVLVA	0.6582	0.885	11	20
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	HLA-A68:24	EASRVLVASR	0.9988	0.6028	12	22
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	HLA-A68:03	EASRVLVASR	0.9985	0.5868	12	22
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	HLA-B45:01	VEEASRVLVA	0.9967	0.8984	10	20
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	HLA-A66:01	EASRVLVASR	0.9932	0.7973	12	22
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	HLA-B50:02	VEEASRVLVA	0.9849	0.7801	10	20
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	HLA-A33:05	EASRVLVASR	0.983	0.5274	12	22
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	HLA-A33:01	EASRVLVASR	0.983	0.5274	12	22
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	HLA-A68:05	EASRVLVASR	0.9732	0.589	12	22
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	HLA-B45:01	KECTPEVEEA	0.9709	0.8848	4	14
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	HLA-B41:01	VEEASRVLVA	0.9572	0.929	10	20
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	HLA-A68:08	EASRVLVASR	0.9369	0.685	12	22
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	HLA-B50:01	VEEASRVLVA	0.9115	0.8924	10	20
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	HLA-B50:01	KECTPEVEEA	0.786	0.8082	4	14
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	HLA-B41:01	KECTPEVEEA	0.766	0.891	4	14
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	HLA-B35:03	TPEVEEASRVL	0.9951	0.9397	7	18
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	HLA-B35:04	TPEVEEASRVL	0.9842	0.9897	7	18
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	HLA-B35:02	TPEVEEASRVL	0.9842	0.9897	7	18
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	HLA-B39:08	VEEASRVL	0.9977	0.8804	10	18
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	HLA-B40:06	VEEASRVLV	0.9992	0.6151	10	19
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	HLA-B40:06	EEASRVLVA	0.9973	0.7141	11	20
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	HLA-B35:12	EVEEASRVL	0.689	0.9603	9	18
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	HLA-B39:08	VEEASRVLV	0.5823	0.9004	10	19
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	HLA-A68:01	EASRVLVASR	0.9988	0.6028	12	22
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	HLA-B40:06	KECTPEVEEA	0.9858	0.7564	4	14
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	HLA-B35:12	TPEVEEASRVL	0.9842	0.9897	7	18
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	HLA-B39:10	TPEVEEASRVL	0.9807	0.9706	7	18
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	HLA-B40:04	VEEASRVL	0.9999	0.7327	10	18
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	HLA-B78:02	EASRVLVA	0.9992	0.891	12	20
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	HLA-B41:03	VEEASRVL	0.9893	0.5973	10	18
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	HLA-B40:04	VEEASRVLV	0.9933	0.7688	10	19
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	HLA-C03:06	EVEEASRVL	0.8533	0.9919	9	18
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	HLA-B18:06	EEASRVLVA	0.807	0.8861	11	20
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	HLA-B18:05	EEASRVLVA	0.7869	0.8443	11	20
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	HLA-B18:11	EEASRVLVA	0.7692	0.7769	11	20
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	HLA-B41:03	VEEASRVLV	0.7547	0.6348	10	19
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	HLA-B18:03	EEASRVLVA	0.7487	0.8318	11	20
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	HLA-B35:09	EVEEASRVL	0.689	0.9603	9	18
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	HLA-B50:05	VEEASRVLV	0.67	0.7801	10	19
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	HLA-B50:04	VEEASRVLV	0.67	0.7801	10	19
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	HLA-B50:04	EEASRVLVA	0.6582	0.885	11	20
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	HLA-B50:05	EEASRVLVA	0.6582	0.885	11	20
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	HLA-A68:02	EVEEASRVLV	0.9901	0.6253	9	19
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	HLA-A69:01	EVEEASRVLV	0.9468	0.6669	9	19
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	HLA-B50:05	VEEASRVLVA	0.9115	0.8924	10	20
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	HLA-B50:04	VEEASRVLVA	0.9115	0.8924	10	20
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	HLA-B50:05	KECTPEVEEA	0.786	0.8082	4	14
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	HLA-B50:04	KECTPEVEEA	0.786	0.8082	4	14
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	HLA-B51:05	TPEVEEASRV	0.6732	0.6666	7	17
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	HLA-B35:22	TPEVEEASRVL	0.9919	0.7102	7	18
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	HLA-B35:09	TPEVEEASRVL	0.9842	0.9897	7	18
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	HLA-B67:01	TPEVEEASRVL	0.9789	0.8826	7	18

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Potential FusionNeoAntigen Information of SMPX-PDHA1 in HLA II

SMPX-PDHA1_21761868_19367430.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)
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	DRB1-1113	TPEVEEASRVLVASR	7	22
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	DRB1-1117	TPEVEEASRVLVASR	7	22
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	DRB1-1117	CTPEVEEASRVLVAS	6	21
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	DRB1-1152	TPEVEEASRVLVASR	7	22
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	DRB1-1152	CTPEVEEASRVLVAS	6	21
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	DRB1-1189	TPEVEEASRVLVASR	7	22
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	DRB1-1189	CTPEVEEASRVLVAS	6	21
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	DRB1-1401	TPEVEEASRVLVASR	7	22
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	DRB1-1401	CTPEVEEASRVLVAS	6	21
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	DRB1-1401	ECTPEVEEASRVLVA	5	20
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	DRB1-1401	PEVEEASRVLVASRN	8	23
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	DRB1-1404	TPEVEEASRVLVASR	7	22
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	DRB1-1404	CTPEVEEASRVLVAS	6	21
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	DRB1-1404	ECTPEVEEASRVLVA	5	20
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	DRB1-1405	TPEVEEASRVLVASR	7	22
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	DRB1-1405	CTPEVEEASRVLVAS	6	21
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	DRB1-1407	TPEVEEASRVLVASR	7	22
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	DRB1-1407	CTPEVEEASRVLVAS	6	21
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	DRB1-1408	TPEVEEASRVLVASR	7	22
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	DRB1-1408	CTPEVEEASRVLVAS	6	21
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	DRB1-1411	TPEVEEASRVLVASR	7	22
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	DRB1-1411	CTPEVEEASRVLVAS	6	21
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	DRB1-1414	TPEVEEASRVLVASR	7	22
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	DRB1-1418	TPEVEEASRVLVASR	7	22
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	DRB1-1418	CTPEVEEASRVLVAS	6	21
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	DRB1-1423	TPEVEEASRVLVASR	7	22
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	DRB1-1423	CTPEVEEASRVLVAS	6	21
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	DRB1-1426	TPEVEEASRVLVASR	7	22
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	DRB1-1426	CTPEVEEASRVLVAS	6	21
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	DRB1-1426	ECTPEVEEASRVLVA	5	20
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	DRB1-1426	PEVEEASRVLVASRN	8	23
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	DRB1-1428	TPEVEEASRVLVASR	7	22
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	DRB1-1428	CTPEVEEASRVLVAS	6	21
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	DRB1-1428	ECTPEVEEASRVLVA	5	20
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	DRB1-1431	TPEVEEASRVLVASR	7	22
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	DRB1-1432	TPEVEEASRVLVASR	7	22
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	DRB1-1432	CTPEVEEASRVLVAS	6	21
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	DRB1-1434	TPEVEEASRVLVASR	7	22
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	DRB1-1435	TPEVEEASRVLVASR	7	22
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	DRB1-1435	CTPEVEEASRVLVAS	6	21
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	DRB1-1435	ECTPEVEEASRVLVA	5	20
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	DRB1-1435	PEVEEASRVLVASRN	8	23
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	DRB1-1436	TPEVEEASRVLVASR	7	22
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	DRB1-1438	TPEVEEASRVLVASR	7	22
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	DRB1-1438	CTPEVEEASRVLVAS	6	21
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	DRB1-1438	ECTPEVEEASRVLVA	5	20
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	DRB1-1438	PEVEEASRVLVASRN	8	23
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	DRB1-1439	TPEVEEASRVLVASR	7	22
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	DRB1-1439	CTPEVEEASRVLVAS	6	21
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	DRB1-1442	TPEVEEASRVLVASR	7	22
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	DRB1-1443	TPEVEEASRVLVASR	7	22
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	DRB1-1443	CTPEVEEASRVLVAS	6	21
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	DRB1-1444	TPEVEEASRVLVASR	7	22
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	DRB1-1445	TPEVEEASRVLVASR	7	22
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	DRB1-1445	CTPEVEEASRVLVAS	6	21
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	DRB1-1445	EEASRVLVASRNFAN	11	26
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	DRB1-1450	TPEVEEASRVLVASR	7	22
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	DRB1-1450	CTPEVEEASRVLVAS	6	21
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	DRB1-1450	ECTPEVEEASRVLVA	5	20
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	DRB1-1454	TPEVEEASRVLVASR	7	22
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	DRB1-1454	CTPEVEEASRVLVAS	6	21
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	DRB1-1454	ECTPEVEEASRVLVA	5	20
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	DRB1-1454	PEVEEASRVLVASRN	8	23
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	DRB1-1455	TPEVEEASRVLVASR	7	22
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	DRB1-1455	CTPEVEEASRVLVAS	6	21
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	DRB1-1456	TPEVEEASRVLVASR	7	22
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	DRB1-1456	CTPEVEEASRVLVAS	6	21
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	DRB1-1458	TPEVEEASRVLVASR	7	22
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	DRB1-1458	CTPEVEEASRVLVAS	6	21
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	DRB1-1458	ECTPEVEEASRVLVA	5	20
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	DRB1-1458	PEVEEASRVLVASRN	8	23
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	DRB1-1459	TPEVEEASRVLVASR	7	22
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	DRB1-1459	CTPEVEEASRVLVAS	6	21
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	DRB1-1460	TPEVEEASRVLVASR	7	22
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	DRB1-1460	CTPEVEEASRVLVAS	6	21
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	DRB1-1460	ECTPEVEEASRVLVA	5	20
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	DRB1-1460	PEVEEASRVLVASRN	8	23
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	DRB1-1461	TPEVEEASRVLVASR	7	22
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	DRB1-1461	CTPEVEEASRVLVAS	6	21
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	DRB1-1461	ECTPEVEEASRVLVA	5	20
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	DRB1-1462	TPEVEEASRVLVASR	7	22
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	DRB1-1462	CTPEVEEASRVLVAS	6	21
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	DRB1-1462	ECTPEVEEASRVLVA	5	20
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	DRB1-1464	TPEVEEASRVLVASR	7	22
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	DRB1-1464	CTPEVEEASRVLVAS	6	21
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	DRB1-1470	TPEVEEASRVLVASR	7	22
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	DRB1-1470	CTPEVEEASRVLVAS	6	21
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	DRB1-1470	ECTPEVEEASRVLVA	5	20
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	DRB1-1471	TPEVEEASRVLVASR	7	22
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	DRB1-1471	CTPEVEEASRVLVAS	6	21
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	DRB1-1471	ECTPEVEEASRVLVA	5	20
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	DRB1-1472	TPEVEEASRVLVASR	7	22
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	DRB1-1472	CTPEVEEASRVLVAS	6	21
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	DRB1-1475	TPEVEEASRVLVASR	7	22
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	DRB1-1475	CTPEVEEASRVLVAS	6	21
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	DRB1-1475	ECTPEVEEASRVLVA	5	20
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	DRB1-1481	TPEVEEASRVLVASR	7	22
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	DRB1-1482	TPEVEEASRVLVASR	7	22
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	DRB1-1482	CTPEVEEASRVLVAS	6	21
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	DRB1-1482	ECTPEVEEASRVLVA	5	20
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	DRB1-1486	TPEVEEASRVLVASR	7	22
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	DRB1-1486	CTPEVEEASRVLVAS	6	21
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	DRB1-1486	ECTPEVEEASRVLVA	5	20
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	DRB1-1486	PEVEEASRVLVASRN	8	23
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	DRB1-1487	TPEVEEASRVLVASR	7	22
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	DRB1-1487	CTPEVEEASRVLVAS	6	21
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	DRB1-1487	ECTPEVEEASRVLVA	5	20
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	DRB1-1487	PEVEEASRVLVASRN	8	23
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	DRB1-1488	TPEVEEASRVLVASR	7	22
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	DRB1-1488	CTPEVEEASRVLVAS	6	21
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	DRB1-1488	ECTPEVEEASRVLVA	5	20
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	DRB1-1488	PEVEEASRVLVASRN	8	23
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	DRB1-1490	TPEVEEASRVLVASR	7	22
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	DRB1-1490	CTPEVEEASRVLVAS	6	21
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	DRB1-1490	ECTPEVEEASRVLVA	5	20
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	DRB1-1490	PEVEEASRVLVASRN	8	23
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	DRB1-1491	TPEVEEASRVLVASR	7	22
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	DRB1-1491	CTPEVEEASRVLVAS	6	21
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	DRB1-1495	TPEVEEASRVLVASR	7	22
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	DRB1-1495	CTPEVEEASRVLVAS	6	21
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	DRB1-1496	TPEVEEASRVLVASR	7	22
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	DRB1-1496	CTPEVEEASRVLVAS	6	21
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	DRB1-1497	TPEVEEASRVLVASR	7	22
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	DRB1-1497	CTPEVEEASRVLVAS	6	21
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	DRB1-1497	ECTPEVEEASRVLVA	5	20
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	DRB1-1497	PEVEEASRVLVASRN	8	23
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	DRB1-1499	TPEVEEASRVLVASR	7	22
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	DRB1-1499	CTPEVEEASRVLVAS	6	21
SMPX-PDHA1	chrX	21761868	chrX	19367430	366	DRB1-1499	ECTPEVEEASRVLVA	5	20

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Fusion breakpoint peptide structures of SMPX-PDHA1

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
951	CTPEVEEASRVLVA	SMPX	PDHA1	chrX	21761868	chrX	19367430	366

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of SMPX-PDHA1

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	951	CTPEVEEASRVLVA	-7.15543	-7.26883
HLA-B14:02	3BVN	951	CTPEVEEASRVLVA	-4.77435	-5.80965
HLA-B52:01	3W39	951	CTPEVEEASRVLVA	-6.80875	-6.92215
HLA-B52:01	3W39	951	CTPEVEEASRVLVA	-4.20386	-5.23916
HLA-A11:01	4UQ2	951	CTPEVEEASRVLVA	-7.5194	-8.5547
HLA-A11:01	4UQ2	951	CTPEVEEASRVLVA	-6.9601	-7.0735
HLA-A24:02	5HGA	951	CTPEVEEASRVLVA	-7.52403	-7.63743
HLA-A24:02	5HGA	951	CTPEVEEASRVLVA	-5.82433	-6.85963
HLA-B27:05	6PYJ	951	CTPEVEEASRVLVA	-3.28285	-4.31815
HLA-B44:05	3DX8	951	CTPEVEEASRVLVA	-5.91172	-6.94702
HLA-B44:05	3DX8	951	CTPEVEEASRVLVA	-4.24346	-4.35686

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Vaccine Design for the FusionNeoAntigens of SMPX-PDHA1

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
SMPX-PDHA1	chrX	21761868	chrX	19367430	10	18	VEEASRVL	GTGGAGGAGGCAAGCAGAGTGCTG
SMPX-PDHA1	chrX	21761868	chrX	19367430	10	19	VEEASRVLV	GTGGAGGAGGCAAGCAGAGTGCTGGTA
SMPX-PDHA1	chrX	21761868	chrX	19367430	10	20	VEEASRVLVA	GTGGAGGAGGCAAGCAGAGTGCTGGTAGCA
SMPX-PDHA1	chrX	21761868	chrX	19367430	11	20	EEASRVLVA	GAGGAGGCAAGCAGAGTGCTGGTAGCA
SMPX-PDHA1	chrX	21761868	chrX	19367430	12	20	EASRVLVA	GAGGCAAGCAGAGTGCTGGTAGCA
SMPX-PDHA1	chrX	21761868	chrX	19367430	12	22	EASRVLVASR	GAGGCAAGCAGAGTGCTGGTAGCATCCCGT
SMPX-PDHA1	chrX	21761868	chrX	19367430	4	14	KECTPEVEEA	AAAGAATGTACTCCTGAAGTGGAGGAGGCA
SMPX-PDHA1	chrX	21761868	chrX	19367430	7	17	TPEVEEASRV	ACTCCTGAAGTGGAGGAGGCAAGCAGAGTG
SMPX-PDHA1	chrX	21761868	chrX	19367430	7	18	TPEVEEASRVL	ACTCCTGAAGTGGAGGAGGCAAGCAGAGTGCTG
SMPX-PDHA1	chrX	21761868	chrX	19367430	9	18	EVEEASRVL	GAAGTGGAGGAGGCAAGCAGAGTGCTG
SMPX-PDHA1	chrX	21761868	chrX	19367430	9	19	EVEEASRVLV	GAAGTGGAGGAGGCAAGCAGAGTGCTGGTA

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
SMPX-PDHA1	chrX	21761868	chrX	19367430	11	26	EEASRVLVASRNFAN	GAGGAGGCAAGCAGAGTGCTGGTAGCATCCCGTAATTTTGCAAAT
SMPX-PDHA1	chrX	21761868	chrX	19367430	5	20	ECTPEVEEASRVLVA	GAATGTACTCCTGAAGTGGAGGAGGCAAGCAGAGTGCTGGTAGCA
SMPX-PDHA1	chrX	21761868	chrX	19367430	6	21	CTPEVEEASRVLVAS	TGTACTCCTGAAGTGGAGGAGGCAAGCAGAGTGCTGGTAGCATCC
SMPX-PDHA1	chrX	21761868	chrX	19367430	7	22	TPEVEEASRVLVASR	ACTCCTGAAGTGGAGGAGGCAAGCAGAGTGCTGGTAGCATCCCGT
SMPX-PDHA1	chrX	21761868	chrX	19367430	8	23	PEVEEASRVLVASRN	CCTGAAGTGGAGGAGGCAAGCAGAGTGCTGGTAGCATCCCGTAAT

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Information of the samples that have these potential fusion neoantigens of SMPX-PDHA1

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
SARC	SMPX-PDHA1	chrX	21761868	ENST00000379494	chrX	19367430	ENST00000379806	TCGA-QQ-A5VA-01A

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Potential target of CAR-T therapy development for SMPX-PDHA1

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 SMPX-PDHA1

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 SMPX-PDHA1

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)