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Fusion Protein:CERS6-GAD1

Fusion Gene and Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: CERS6-GAD1
	FusionPDB ID: 16000
	FusionGDB2.0 ID: 16000
		Hgene	Tgene
	Gene symbol	CERS6	GAD1
	Gene ID	253782	2571
	Gene name	ceramide synthase 6	glutamate decarboxylase 1
	Synonyms	CERS5\|LASS6	CPSQ1\|GAD\|SCP
	Cytomap	2q24.3	2q31.1
	Type of gene	protein-coding	protein-coding
	Description	ceramide synthase 6LAG1 homolog, ceramide synthase 6longevity assurance homolog 6	glutamate decarboxylase 167 kDa glutamic acid decarboxylaseGAD-67glutamate decarboxylase 1 (brain, 67kDa)glutamate decarboxylase 67 kDa isoform
	Modification date	20200313	20200315
	UniProtAcc	Q6ZMG9 Main function of 5'-partner protein: FUNCTION: Ceramide synthase that catalyzes formation of ceramide from sphinganine and acyl-CoA substrates, with high selectivity toward palmitoyl-CoA (hexadecanoyl-CoA; C16:0-CoA) as acyl donor (PubMed:17977534, PubMed:17609214, PubMed:23530041, PubMed:26887952, PubMed:31916624). Can use other acyl donors, but with less efficiency (By similarity). Ceramides generated by CERS6 play a role in inflammatory response (By similarity). Acts as a regulator of metabolism and hepatic lipid accumulation (By similarity). Under high fat diet, palmitoyl- (C16:0-) ceramides generated by CERS6 specifically bind the mitochondrial fission factor MFF, thereby promoting mitochondrial fragmentation and contributing to the development of obesity (By similarity). {ECO:0000250\|UniProtKB:Q8C172, ECO:0000269\|PubMed:17609214, ECO:0000269\|PubMed:17977534, ECO:0000269\|PubMed:23530041, ECO:0000269\|PubMed:26887952, ECO:0000269\|PubMed:31916624}.	Q99259 Main function of 5'-partner protein: FUNCTION: Catalyzes the production of GABA.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000305747, ENST00000392687,	ENST00000344257, ENST00000375272, ENST00000429023, ENST00000358196,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	18 X 12 X 8=1728	3 X 4 X 3=36
	# samples	22	3
	** MAII score	log2(22/1728*10)=-2.97352778863881 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(3/36*10)=-0.263034405833794 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Fusion gene context	PubMed: CERS6 [Title/Abstract] AND GAD1 [Title/Abstract] AND fusion [Title/Abstract]
Fusion neoantigen context	PubMed: CERS6 [Title/Abstract] AND GAD1 [Title/Abstract] AND neoantigen [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	CERS6(169487552)-GAD1(171715314), # samples:1
Anticipated loss of major functional domain due to fusion event.	CERS6-GAD1 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. CERS6-GAD1 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. CERS6-GAD1 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. CERS6-GAD1 seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame ORF.

* DoF score (Degree of Frequency) = # partners X # break points X # cancer types
** MAII score (Major Active Isofusion Index) = log2(# samples/DoF score*10)

Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez

Partner	Gene	GO ID	GO term	PubMed ID
Hgene	CERS6	GO:0046513	ceramide biosynthetic process	17609214\|17977534

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr2:169487552/chr2:171715314)
- 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 CERS6 (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 GAD1 (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)

ENST00000305747

CERS6

chr2

169487552

ENST00000358196

GAD1

chr2

171715314

2585

1052

287

1315

342

ENST00000392687

CERS6

chr2

169487552

ENST00000358196

GAD1

chr2

171715314

2198

665

140

928

262

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
ENST00000305747	ENST00000358196	CERS6	chr2	169487552	-	GAD1	chr2	171715314	+	0.00359103	0.996409
ENST00000392687	ENST00000358196	CERS6	chr2	169487552	-	GAD1	chr2	171715314	+	0.001711747	0.9982882

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 CERS6-GAD1

+/-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
CERS6	chr2	169487552	GAD1	chr2	171715314	1052	255	LYVFTYGVRFLKKPEHTNVCFWYIPQ
CERS6	chr2	169487552	GAD1	chr2	171715314	665	175	LYVFTYGVRFLKKPEHTNVCFWYIPQ

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Potential FusionNeoAntigen Information of CERS6-GAD1 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.

CERS6-GAD1_169487552_171715314.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)
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	HLA-B27:04	VRFLKKPEH	0.9946	0.8398	7	16
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	HLA-B35:08	KPEHTNVCF	0.8619	0.77	12	21
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	HLA-B35:01	KPEHTNVCF	0.851	0.7914	12	21
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	HLA-B35:04	KPEHTNVCF	0.1873	0.8851	12	21
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	HLA-B35:02	KPEHTNVCF	0.1873	0.8851	12	21
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	HLA-A02:22	FLKKPEHTNV	0.978	0.8418	9	19
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	HLA-A02:13	FLKKPEHTNV	0.9338	0.8589	9	19
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	HLA-B27:14	VRFLKKPEH	0.9964	0.8975	7	16
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	HLA-C07:46	VRFLKKPEH	0.6269	0.8613	7	16
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	HLA-C04:10	KPEHTNVCF	0.38	0.7967	12	21
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	HLA-C04:07	KPEHTNVCF	0.3728	0.8329	12	21
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	HLA-B35:12	KPEHTNVCF	0.1873	0.8851	12	21
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	HLA-B39:10	KPEHTNVCF	0.0433	0.8508	12	21
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	HLA-A02:02	FLKKPEHTNV	0.9775	0.6208	9	19
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	HLA-B27:08	VRFLKKPEH	0.997	0.8862	7	16
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	HLA-B27:10	VRFLKKPEH	0.9944	0.915	7	16
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	HLA-B35:77	KPEHTNVCF	0.851	0.7914	12	21
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	HLA-B35:23	KPEHTNVCF	0.8288	0.7736	12	21
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	HLA-C04:01	KPEHTNVCF	0.3728	0.8329	12	21
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	HLA-B35:09	KPEHTNVCF	0.1873	0.8851	12	21
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	HLA-B67:01	KPEHTNVCF	0.0594	0.7552	12	21
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	HLA-A02:03	FLKKPEHTNV	0.9967	0.8985	9	19
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	HLA-B15:54	KKPEHTNVCF	0.9234	0.8894	11	21

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Potential FusionNeoAntigen Information of CERS6-GAD1 in HLA II

CERS6-GAD1_169487552_171715314.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)
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	DRB1-0802	TYGVRFLKKPEHTNV	4	19
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	DRB1-0804	TYGVRFLKKPEHTNV	4	19
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	DRB1-0804	FTYGVRFLKKPEHTN	3	18
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	DRB1-0806	TYGVRFLKKPEHTNV	4	19
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	DRB1-0806	FTYGVRFLKKPEHTN	3	18
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	DRB1-0809	TYGVRFLKKPEHTNV	4	19
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	DRB1-0810	TYGVRFLKKPEHTNV	4	19
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	DRB1-0810	FTYGVRFLKKPEHTN	3	18
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	DRB1-0812	TYGVRFLKKPEHTNV	4	19
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	DRB1-0812	FTYGVRFLKKPEHTN	3	18
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	DRB1-0820	TYGVRFLKKPEHTNV	4	19
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	DRB1-0820	FTYGVRFLKKPEHTN	3	18
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	DRB1-0821	TYGVRFLKKPEHTNV	4	19
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	DRB1-0822	TYGVRFLKKPEHTNV	4	19
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	DRB1-0822	FTYGVRFLKKPEHTN	3	18
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	DRB1-0828	TYGVRFLKKPEHTNV	4	19
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	DRB1-0828	FTYGVRFLKKPEHTN	3	18
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	DRB1-0831	TYGVRFLKKPEHTNV	4	19
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	DRB1-0831	FTYGVRFLKKPEHTN	3	18
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	DRB1-0831	VFTYGVRFLKKPEHT	2	17
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	DRB1-1103	TYGVRFLKKPEHTNV	4	19
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	DRB1-1103	FTYGVRFLKKPEHTN	3	18
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	DRB1-1104	TYGVRFLKKPEHTNV	4	19
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	DRB1-1104	FTYGVRFLKKPEHTN	3	18
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	DRB1-1105	TYGVRFLKKPEHTNV	4	19
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	DRB1-1105	FTYGVRFLKKPEHTN	3	18
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	DRB1-1106	TYGVRFLKKPEHTNV	4	19
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	DRB1-1106	FTYGVRFLKKPEHTN	3	18
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	DRB1-1118	TYGVRFLKKPEHTNV	4	19
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	DRB1-1118	FTYGVRFLKKPEHTN	3	18
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	DRB1-1125	TYGVRFLKKPEHTNV	4	19
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	DRB1-1125	FTYGVRFLKKPEHTN	3	18
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	DRB1-1132	TYGVRFLKKPEHTNV	4	19
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	DRB1-1134	TYGVRFLKKPEHTNV	4	19
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	DRB1-1134	FTYGVRFLKKPEHTN	3	18
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	DRB1-1135	TYGVRFLKKPEHTNV	4	19
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	DRB1-1135	FTYGVRFLKKPEHTN	3	18
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	DRB1-1138	TYGVRFLKKPEHTNV	4	19
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	DRB1-1138	FTYGVRFLKKPEHTN	3	18
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	DRB1-1141	TYGVRFLKKPEHTNV	4	19
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	DRB1-1141	FTYGVRFLKKPEHTN	3	18
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	DRB1-1142	TYGVRFLKKPEHTNV	4	19
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	DRB1-1142	FTYGVRFLKKPEHTN	3	18
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	DRB1-1143	TYGVRFLKKPEHTNV	4	19
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	DRB1-1143	FTYGVRFLKKPEHTN	3	18
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	DRB1-1144	TYGVRFLKKPEHTNV	4	19
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	DRB1-1144	FTYGVRFLKKPEHTN	3	18
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	DRB1-1146	TYGVRFLKKPEHTNV	4	19
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	DRB1-1146	FTYGVRFLKKPEHTN	3	18
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	DRB1-1147	TYGVRFLKKPEHTNV	4	19
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	DRB1-1147	FTYGVRFLKKPEHTN	3	18
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	DRB1-1150	TYGVRFLKKPEHTNV	4	19
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	DRB1-1150	FTYGVRFLKKPEHTN	3	18
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	DRB1-1154	TYGVRFLKKPEHTNV	4	19
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	DRB1-1154	FTYGVRFLKKPEHTN	3	18
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	DRB1-1156	TYGVRFLKKPEHTNV	4	19
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	DRB1-1156	FTYGVRFLKKPEHTN	3	18
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	DRB1-1157	TYGVRFLKKPEHTNV	4	19
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	DRB1-1157	FTYGVRFLKKPEHTN	3	18
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	DRB1-1158	TYGVRFLKKPEHTNV	4	19
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	DRB1-1158	FTYGVRFLKKPEHTN	3	18
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	DRB1-1159	TYGVRFLKKPEHTNV	4	19
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	DRB1-1159	FTYGVRFLKKPEHTN	3	18
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	DRB1-1160	TYGVRFLKKPEHTNV	4	19
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	DRB1-1160	FTYGVRFLKKPEHTN	3	18
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	DRB1-1163	TYGVRFLKKPEHTNV	4	19
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	DRB1-1163	FTYGVRFLKKPEHTN	3	18
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	DRB1-1167	TYGVRFLKKPEHTNV	4	19
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	DRB1-1167	FTYGVRFLKKPEHTN	3	18
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	DRB1-1172	TYGVRFLKKPEHTNV	4	19
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	DRB1-1176	TYGVRFLKKPEHTNV	4	19
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	DRB1-1176	FTYGVRFLKKPEHTN	3	18
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	DRB1-1177	TYGVRFLKKPEHTNV	4	19
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	DRB1-1177	FTYGVRFLKKPEHTN	3	18
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	DRB1-1178	TYGVRFLKKPEHTNV	4	19
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	DRB1-1178	FTYGVRFLKKPEHTN	3	18
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	DRB1-1180	TYGVRFLKKPEHTNV	4	19
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	DRB1-1183	TYGVRFLKKPEHTNV	4	19
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	DRB1-1183	FTYGVRFLKKPEHTN	3	18
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	DRB1-1184	TYGVRFLKKPEHTNV	4	19
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	DRB1-1184	FTYGVRFLKKPEHTN	3	18
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	DRB1-1185	TYGVRFLKKPEHTNV	4	19
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	DRB1-1185	FTYGVRFLKKPEHTN	3	18
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	DRB1-1187	TYGVRFLKKPEHTNV	4	19
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	DRB1-1188	TYGVRFLKKPEHTNV	4	19
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	DRB1-1188	FTYGVRFLKKPEHTN	3	18
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	DRB1-1192	TYGVRFLKKPEHTNV	4	19
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	DRB1-1192	FTYGVRFLKKPEHTN	3	18
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	DRB1-1204	TYGVRFLKKPEHTNV	4	19
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	DRB1-1204	FTYGVRFLKKPEHTN	3	18
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	DRB1-1204	VFTYGVRFLKKPEHT	2	17
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	DRB1-1209	TYGVRFLKKPEHTNV	4	19
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	DRB1-1209	FTYGVRFLKKPEHTN	3	18
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	DRB1-1209	VFTYGVRFLKKPEHT	2	17
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	DRB1-1220	TYGVRFLKKPEHTNV	4	19
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	DRB1-1220	FTYGVRFLKKPEHTN	3	18
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	DRB1-1306	TYGVRFLKKPEHTNV	4	19
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	DRB1-1306	FTYGVRFLKKPEHTN	3	18
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	DRB1-1311	TYGVRFLKKPEHTNV	4	19
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	DRB1-1311	FTYGVRFLKKPEHTN	3	18
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	DRB1-1318	TYGVRFLKKPEHTNV	4	19
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	DRB1-1318	FTYGVRFLKKPEHTN	3	18
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	DRB1-1324	TYGVRFLKKPEHTNV	4	19
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	DRB1-1324	FTYGVRFLKKPEHTN	3	18
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	DRB1-1326	TYGVRFLKKPEHTNV	4	19
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	DRB1-1326	FTYGVRFLKKPEHTN	3	18
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	DRB1-1342	TYGVRFLKKPEHTNV	4	19
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	DRB1-1342	FTYGVRFLKKPEHTN	3	18
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	DRB1-1344	TYGVRFLKKPEHTNV	4	19
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	DRB1-1344	FTYGVRFLKKPEHTN	3	18
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	DRB1-1358	TYGVRFLKKPEHTNV	4	19
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	DRB1-1358	FTYGVRFLKKPEHTN	3	18
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	DRB1-1406	TYGVRFLKKPEHTNV	4	19
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	DRB1-1406	FTYGVRFLKKPEHTN	3	18
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	DRB1-1412	TYGVRFLKKPEHTNV	4	19
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	DRB1-1412	FTYGVRFLKKPEHTN	3	18
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	DRB1-1415	TYGVRFLKKPEHTNV	4	19
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	DRB1-1415	FTYGVRFLKKPEHTN	3	18
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	DRB1-1417	TYGVRFLKKPEHTNV	4	19
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	DRB1-1417	FTYGVRFLKKPEHTN	3	18
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	DRB1-1420	TYGVRFLKKPEHTNV	4	19
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	DRB1-1420	FTYGVRFLKKPEHTN	3	18
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	DRB1-1427	TYGVRFLKKPEHTNV	4	19
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	DRB1-1429	TYGVRFLKKPEHTNV	4	19
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	DRB1-1429	FTYGVRFLKKPEHTN	3	18
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	DRB1-1437	TYGVRFLKKPEHTNV	4	19
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	DRB1-1452	TYGVRFLKKPEHTNV	4	19
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	DRB1-1452	FTYGVRFLKKPEHTN	3	18
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	DRB1-1478	TYGVRFLKKPEHTNV	4	19
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	DRB1-1478	FTYGVRFLKKPEHTN	3	18
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	DRB1-1480	TYGVRFLKKPEHTNV	4	19
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	DRB1-1480	FTYGVRFLKKPEHTN	3	18
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	DRB1-1481	TYGVRFLKKPEHTNV	4	19
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	DRB1-1483	TYGVRFLKKPEHTNV	4	19
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	DRB1-1483	FTYGVRFLKKPEHTN	3	18
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	DRB1-1484	TYGVRFLKKPEHTNV	4	19
CERS6-GAD1	chr2	169487552	chr2	171715314	1052	DRB1-1484	FTYGVRFLKKPEHTN	3	18

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Fusion breakpoint peptide structures of CERS6-GAD1

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
3219	GVRFLKKPEHTNVC	CERS6	GAD1	chr2	169487552	chr2	171715314	1052

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of CERS6-GAD1

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	3219	GVRFLKKPEHTNVC	-6.07233	-6.07953
HLA-B52:01	3W39	3219	GVRFLKKPEHTNVC	-5.45645	-5.46365
HLA-A24:02	5HGA	3219	GVRFLKKPEHTNVC	-3.85827	-3.86547
HLA-B44:05	3DX8	3219	GVRFLKKPEHTNVC	-4.76301	-4.77021

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Vaccine Design for the FusionNeoAntigens of CERS6-GAD1

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
CERS6-GAD1	chr2	169487552	chr2	171715314	11	21	KKPEHTNVCF	AAAAAGCCTGAGCACACAAACGTCTGTTTT
CERS6-GAD1	chr2	169487552	chr2	171715314	12	21	KPEHTNVCF	AAGCCTGAGCACACAAACGTCTGTTTT
CERS6-GAD1	chr2	169487552	chr2	171715314	7	16	VRFLKKPEH	GTCAGATTCCTGAAAAAGCCTGAGCAC
CERS6-GAD1	chr2	169487552	chr2	171715314	9	19	FLKKPEHTNV	TTCCTGAAAAAGCCTGAGCACACAAACGTC

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
CERS6-GAD1	chr2	169487552	chr2	171715314	2	17	VFTYGVRFLKKPEHT	GTATTTACCTACGGAGTCAGATTCCTGAAAAAGCCTGAGCACACA
CERS6-GAD1	chr2	169487552	chr2	171715314	3	18	FTYGVRFLKKPEHTN	TTTACCTACGGAGTCAGATTCCTGAAAAAGCCTGAGCACACAAAC
CERS6-GAD1	chr2	169487552	chr2	171715314	4	19	TYGVRFLKKPEHTNV	ACCTACGGAGTCAGATTCCTGAAAAAGCCTGAGCACACAAACGTC

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Information of the samples that have these potential fusion neoantigens of CERS6-GAD1

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
LIHC	CERS6-GAD1	chr2	169487552	ENST00000305747	chr2	171715314	ENST00000358196	TCGA-XR-A8TG-01A

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Potential target of CAR-T therapy development for CERS6-GAD1

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

CERS6

chr2:169487552

chr2:171715314

ENST00000305747

35_55

155

385.0

Transmembrane

Helical

Hgene

CERS6

chr2:169487552

chr2:171715314

ENST00000392687

35_55

155

393.0

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 CERS6-GAD1

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 CERS6-GAD1

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)