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Fusion Protein:GIGYF2-CHRND

Fusion Gene and Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: GIGYF2-CHRND
	FusionPDB ID: 33092
	FusionGDB2.0 ID: 33092
		Hgene	Tgene
	Gene symbol	GIGYF2	CHRND
	Gene ID	26058	1144
	Gene name	GRB10 interacting GYF protein 2	cholinergic receptor nicotinic delta subunit
	Synonyms	GYF2\|PARK11\|PERQ2\|PERQ3\|TNRC15	ACHRD\|CMS2A\|CMS3A\|CMS3B\|CMS3C\|FCCMS\|SCCMS
	Cytomap	2q37.1	2q37.1
	Type of gene	protein-coding	protein-coding
	Description	GRB10-interacting GYF protein 2PERQ amino acid rich, with GYF domain 3PERQ amino acid-rich with GYF domain-containing protein 2Parkinson disease (autosomal recessive, early onset) 11trinucleotide repeat-containing gene 15 protein	acetylcholine receptor subunit deltaacetylcholine receptor, nicotinic, delta (muscle)cholinergic receptor, nicotinic deltacholinergic receptor, nicotinic, delta (muscle)cholinergic receptor, nicotinic, delta polypeptide
	Modification date	20200313	20200313
	UniProtAcc	Q6Y7W6 Main function of 5'-partner protein: FUNCTION: Key component of the 4EHP-GYF2 complex, a multiprotein complex that acts as a repressor of translation initiation (PubMed:22751931, PubMed:31439631). In the 4EHP-GYF2 complex, acts as a factor that bridges EIF4E2 to ZFP36/TTP, linking translation repression with mRNA decay (PubMed:31439631). Also recruits and bridges the association of the 4EHP complex with the decapping effector protein DDX6, which is required for the ZFP36/TTP-mediated down-regulation of AU-rich mRNA (PubMed:31439631). May act cooperatively with GRB10 to regulate tyrosine kinase receptor signaling, including IGF1 and insulin receptors (PubMed:12771153). {ECO:0000269\|PubMed:12771153, ECO:0000269\|PubMed:22751931, ECO:0000269\|PubMed:31439631}.	.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000373563, ENST00000373566, ENST00000409196, ENST00000409451, ENST00000409480, ENST00000409547, ENST00000452341, ENST00000482666,	ENST00000457943, ENST00000536614, ENST00000258385, ENST00000543200,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	24 X 20 X 15=7200	1 X 1 X 1=1
	# samples	34	1
	** MAII score	log2(34/7200*10)=-4.40439025507934 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(1/1*10)=3.32192809488736
Fusion gene context	PubMed: GIGYF2 [Title/Abstract] AND CHRND [Title/Abstract] AND fusion [Title/Abstract]
Fusion neoantigen context	PubMed: GIGYF2 [Title/Abstract] AND CHRND [Title/Abstract] AND neoantigen [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	GIGYF2(233613792)-CHRND(233398641), # samples:3
Anticipated loss of major functional domain due to fusion event.	GIGYF2-CHRND 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. GIGYF2-CHRND 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. GIGYF2-CHRND 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. GIGYF2-CHRND 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	GIGYF2	GO:0016441	posttranscriptional gene silencing	27157137
Hgene	GIGYF2	GO:0061157	mRNA destabilization	27157137

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr2:233613792/chr2:233398641)
- 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 GIGYF2 (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 CHRND (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)
ENST00000373566	GIGYF2	chr2	233613792	+	ENST00000543200	CHRND	chr2	233398641	+	1234	464	197	970	257
ENST00000373566	GIGYF2	chr2	233613792	+	ENST00000258385	CHRND	chr2	233398641	+	1497	464	197	970	257
ENST00000373563	GIGYF2	chr2	233613792	+	ENST00000543200	CHRND	chr2	233398641	+	1232	462	195	968	257
ENST00000373563	GIGYF2	chr2	233613792	+	ENST00000258385	CHRND	chr2	233398641	+	1495	462	195	968	257
ENST00000409480	GIGYF2	chr2	233613792	+	ENST00000543200	CHRND	chr2	233398641	+	1299	529	262	1035	257
ENST00000409480	GIGYF2	chr2	233613792	+	ENST00000258385	CHRND	chr2	233398641	+	1562	529	262	1035	257
ENST00000409547	GIGYF2	chr2	233613792	+	ENST00000543200	CHRND	chr2	233398641	+	1348	578	311	1084	257
ENST00000409547	GIGYF2	chr2	233613792	+	ENST00000258385	CHRND	chr2	233398641	+	1611	578	311	1084	257
ENST00000409196	GIGYF2	chr2	233613792	+	ENST00000543200	CHRND	chr2	233398641	+	1135	365	98	871	257
ENST00000409196	GIGYF2	chr2	233613792	+	ENST00000258385	CHRND	chr2	233398641	+	1398	365	98	871	257
ENST00000409451	GIGYF2	chr2	233613792	+	ENST00000543200	CHRND	chr2	233398641	+	1263	493	226	999	257
ENST00000409451	GIGYF2	chr2	233613792	+	ENST00000258385	CHRND	chr2	233398641	+	1526	493	226	999	257

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
ENST00000373566	ENST00000543200	GIGYF2	chr2	233613792	+	CHRND	chr2	233398641	+	0.009049302	0.9909507
ENST00000373566	ENST00000258385	GIGYF2	chr2	233613792	+	CHRND	chr2	233398641	+	0.009965301	0.99003476
ENST00000373563	ENST00000543200	GIGYF2	chr2	233613792	+	CHRND	chr2	233398641	+	0.008527317	0.9914726
ENST00000373563	ENST00000258385	GIGYF2	chr2	233613792	+	CHRND	chr2	233398641	+	0.009336025	0.990664
ENST00000409480	ENST00000543200	GIGYF2	chr2	233613792	+	CHRND	chr2	233398641	+	0.009113809	0.9908862
ENST00000409480	ENST00000258385	GIGYF2	chr2	233613792	+	CHRND	chr2	233398641	+	0.009315604	0.9906844
ENST00000409547	ENST00000543200	GIGYF2	chr2	233613792	+	CHRND	chr2	233398641	+	0.011164399	0.98883563
ENST00000409547	ENST00000258385	GIGYF2	chr2	233613792	+	CHRND	chr2	233398641	+	0.012551562	0.9874485
ENST00000409196	ENST00000543200	GIGYF2	chr2	233613792	+	CHRND	chr2	233398641	+	0.010746304	0.9892537
ENST00000409196	ENST00000258385	GIGYF2	chr2	233613792	+	CHRND	chr2	233398641	+	0.011715596	0.98828435
ENST00000409451	ENST00000543200	GIGYF2	chr2	233613792	+	CHRND	chr2	233398641	+	0.010011775	0.98998827
ENST00000409451	ENST00000258385	GIGYF2	chr2	233613792	+	CHRND	chr2	233398641	+	0.010019056	0.9899809

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 GIGYF2-CHRND

+/-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
GIGYF2	chr2	233613792	CHRND	chr2	233398641	365	88	LPPLALVPFTEEEQLFLETLPELLHM
GIGYF2	chr2	233613792	CHRND	chr2	233398641	462	88	LPPLALVPFTEEEQLFLETLPELLHM
GIGYF2	chr2	233613792	CHRND	chr2	233398641	464	88	LPPLALVPFTEEEQLFLETLPELLHM
GIGYF2	chr2	233613792	CHRND	chr2	233398641	493	88	LPPLALVPFTEEEQLFLETLPELLHM
GIGYF2	chr2	233613792	CHRND	chr2	233398641	529	88	LPPLALVPFTEEEQLFLETLPELLHM
GIGYF2	chr2	233613792	CHRND	chr2	233398641	578	88	LPPLALVPFTEEEQLFLETLPELLHM

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Potential FusionNeoAntigen Information of GIGYF2-CHRND 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.

GIGYF2-CHRND_233613792_233398641.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)
GIGYF2-CHRND	chr2	233613792	chr2	233398641	462	HLA-B44:03	EEQLFLETL	0.9915	0.9416	11	20
GIGYF2-CHRND	chr2	233613792	chr2	233398641	462	HLA-B50:02	EEQLFLETL	0.9912	0.6083	11	20
GIGYF2-CHRND	chr2	233613792	chr2	233398641	462	HLA-B45:01	EEEQLFLET	0.9835	0.7967	10	19
GIGYF2-CHRND	chr2	233613792	chr2	233398641	462	HLA-B18:01	EEQLFLETL	0.9756	0.8527	11	20
GIGYF2-CHRND	chr2	233613792	chr2	233398641	462	HLA-B35:03	VPFTEEEQL	0.972	0.8836	6	15
GIGYF2-CHRND	chr2	233613792	chr2	233398641	462	HLA-B45:01	EEQLFLETL	0.968	0.8757	11	20
GIGYF2-CHRND	chr2	233613792	chr2	233398641	462	HLA-B35:01	VPFTEEEQL	0.9599	0.9063	6	15
GIGYF2-CHRND	chr2	233613792	chr2	233398641	462	HLA-B50:02	EEEQLFLET	0.9556	0.6072	10	19
GIGYF2-CHRND	chr2	233613792	chr2	233398641	462	HLA-B35:08	VPFTEEEQL	0.9352	0.6825	6	15
GIGYF2-CHRND	chr2	233613792	chr2	233398641	462	HLA-B35:05	VPFTEEEQL	0.9064	0.5661	6	15
GIGYF2-CHRND	chr2	233613792	chr2	233398641	462	HLA-B35:02	VPFTEEEQL	0.8774	0.9487	6	15
GIGYF2-CHRND	chr2	233613792	chr2	233398641	462	HLA-B35:04	VPFTEEEQL	0.8774	0.9487	6	15
GIGYF2-CHRND	chr2	233613792	chr2	233398641	462	HLA-B39:13	EEQLFLETL	0.7291	0.913	11	20
GIGYF2-CHRND	chr2	233613792	chr2	233398641	462	HLA-B41:01	EEQLFLETL	0.543	0.8848	11	20
GIGYF2-CHRND	chr2	233613792	chr2	233398641	462	HLA-B35:01	VPFTEEEQLF	0.9909	0.9545	6	16
GIGYF2-CHRND	chr2	233613792	chr2	233398641	462	HLA-B35:08	VPFTEEEQLF	0.9852	0.9039	6	16
GIGYF2-CHRND	chr2	233613792	chr2	233398641	462	HLA-B35:05	VPFTEEEQLF	0.9841	0.7455	6	16
GIGYF2-CHRND	chr2	233613792	chr2	233398641	462	HLA-B35:03	VPFTEEEQLF	0.9751	0.9353	6	16
GIGYF2-CHRND	chr2	233613792	chr2	233398641	462	HLA-B35:04	VPFTEEEQLF	0.9086	0.9727	6	16
GIGYF2-CHRND	chr2	233613792	chr2	233398641	462	HLA-B35:02	VPFTEEEQLF	0.9086	0.9727	6	16
GIGYF2-CHRND	chr2	233613792	chr2	233398641	462	HLA-B35:03	LVPFTEEEQL	0.704	0.8955	5	15
GIGYF2-CHRND	chr2	233613792	chr2	233398641	462	HLA-B35:04	LVPFTEEEQL	0.5882	0.9649	5	15
GIGYF2-CHRND	chr2	233613792	chr2	233398641	462	HLA-B35:02	LVPFTEEEQL	0.5882	0.9649	5	15
GIGYF2-CHRND	chr2	233613792	chr2	233398641	462	HLA-B35:03	VPFTEEEQLFL	0.9639	0.9026	6	17
GIGYF2-CHRND	chr2	233613792	chr2	233398641	462	HLA-B35:04	VPFTEEEQLFL	0.9457	0.9522	6	17
GIGYF2-CHRND	chr2	233613792	chr2	233398641	462	HLA-B35:02	VPFTEEEQLFL	0.9457	0.9522	6	17
GIGYF2-CHRND	chr2	233613792	chr2	233398641	462	HLA-A02:22	ALVPFTEEEQL	0.9423	0.5977	4	15
GIGYF2-CHRND	chr2	233613792	chr2	233398641	462	HLA-A02:30	ALVPFTEEEQL	0.942	0.5756	4	15
GIGYF2-CHRND	chr2	233613792	chr2	233398641	462	HLA-A02:24	ALVPFTEEEQL	0.942	0.5756	4	15
GIGYF2-CHRND	chr2	233613792	chr2	233398641	462	HLA-A02:67	ALVPFTEEEQL	0.942	0.5756	4	15
GIGYF2-CHRND	chr2	233613792	chr2	233398641	462	HLA-B39:08	TEEEQLFL	0.9696	0.8703	9	17
GIGYF2-CHRND	chr2	233613792	chr2	233398641	462	HLA-B51:07	EQLFLETL	0.8792	0.7298	12	20
GIGYF2-CHRND	chr2	233613792	chr2	233398641	462	HLA-C05:09	FTEEEQLFL	0.9999	0.9748	8	17
GIGYF2-CHRND	chr2	233613792	chr2	233398641	462	HLA-C04:10	FTEEEQLFL	0.9998	0.913	8	17
GIGYF2-CHRND	chr2	233613792	chr2	233398641	462	HLA-C08:15	FTEEEQLFL	0.9998	0.9858	8	17
GIGYF2-CHRND	chr2	233613792	chr2	233398641	462	HLA-C04:07	FTEEEQLFL	0.9998	0.8978	8	17
GIGYF2-CHRND	chr2	233613792	chr2	233398641	462	HLA-C03:07	FTEEEQLFL	0.996	0.9917	8	17
GIGYF2-CHRND	chr2	233613792	chr2	233398641	462	HLA-C04:06	FTEEEQLFL	0.9918	0.9593	8	17
GIGYF2-CHRND	chr2	233613792	chr2	233398641	462	HLA-C15:06	FTEEEQLFL	0.9912	0.9627	8	17
GIGYF2-CHRND	chr2	233613792	chr2	233398641	462	HLA-C03:19	FTEEEQLFL	0.9901	0.9943	8	17
GIGYF2-CHRND	chr2	233613792	chr2	233398641	462	HLA-C03:08	FTEEEQLFL	0.9827	0.9366	8	17
GIGYF2-CHRND	chr2	233613792	chr2	233398641	462	HLA-C08:04	FTEEEQLFL	0.9677	0.9827	8	17
GIGYF2-CHRND	chr2	233613792	chr2	233398641	462	HLA-C08:13	FTEEEQLFL	0.9677	0.9827	8	17
GIGYF2-CHRND	chr2	233613792	chr2	233398641	462	HLA-A02:07	FTEEEQLFL	0.9322	0.5567	8	17
GIGYF2-CHRND	chr2	233613792	chr2	233398641	462	HLA-C04:14	FTEEEQLFL	0.9218	0.9314	8	17
GIGYF2-CHRND	chr2	233613792	chr2	233398641	462	HLA-B51:07	VPFTEEEQL	0.9058	0.8147	6	15
GIGYF2-CHRND	chr2	233613792	chr2	233398641	462	HLA-B35:12	VPFTEEEQL	0.8774	0.9487	6	15
GIGYF2-CHRND	chr2	233613792	chr2	233398641	462	HLA-C08:03	FTEEEQLFL	0.8258	0.9927	8	17
GIGYF2-CHRND	chr2	233613792	chr2	233398641	462	HLA-B39:08	EEQLFLETL	0.7821	0.819	11	20
GIGYF2-CHRND	chr2	233613792	chr2	233398641	462	HLA-C02:06	FTEEEQLFL	0.5825	0.9857	8	17
GIGYF2-CHRND	chr2	233613792	chr2	233398641	462	HLA-B39:10	VPFTEEEQL	0.5779	0.8921	6	15
GIGYF2-CHRND	chr2	233613792	chr2	233398641	462	HLA-B42:02	VPFTEEEQL	0.3781	0.575	6	15
GIGYF2-CHRND	chr2	233613792	chr2	233398641	462	HLA-B42:01	VPFTEEEQL	0.2766	0.5657	6	15
GIGYF2-CHRND	chr2	233613792	chr2	233398641	462	HLA-B51:07	EEQLFLETL	0.1739	0.7428	11	20
GIGYF2-CHRND	chr2	233613792	chr2	233398641	462	HLA-B35:12	VPFTEEEQLF	0.9086	0.9727	6	16
GIGYF2-CHRND	chr2	233613792	chr2	233398641	462	HLA-B35:12	LVPFTEEEQL	0.5882	0.9649	5	15
GIGYF2-CHRND	chr2	233613792	chr2	233398641	462	HLA-B35:12	VPFTEEEQLFL	0.9457	0.9522	6	17
GIGYF2-CHRND	chr2	233613792	chr2	233398641	462	HLA-A02:01	ALVPFTEEEQL	0.942	0.5756	4	15
GIGYF2-CHRND	chr2	233613792	chr2	233398641	462	HLA-B41:03	TEEEQLFL	0.9105	0.5502	9	17
GIGYF2-CHRND	chr2	233613792	chr2	233398641	462	HLA-C04:03	FTEEEQLFL	0.9999	0.9079	8	17
GIGYF2-CHRND	chr2	233613792	chr2	233398641	462	HLA-C05:01	FTEEEQLFL	0.9999	0.9748	8	17
GIGYF2-CHRND	chr2	233613792	chr2	233398641	462	HLA-C04:01	FTEEEQLFL	0.9998	0.8978	8	17
GIGYF2-CHRND	chr2	233613792	chr2	233398641	462	HLA-C18:01	FTEEEQLFL	0.9998	0.9059	8	17
GIGYF2-CHRND	chr2	233613792	chr2	233398641	462	HLA-C08:02	FTEEEQLFL	0.9998	0.9858	8	17
GIGYF2-CHRND	chr2	233613792	chr2	233398641	462	HLA-C01:03	FTEEEQLFL	0.9997	0.9546	8	17
GIGYF2-CHRND	chr2	233613792	chr2	233398641	462	HLA-B40:04	EEQLFLETL	0.9969	0.7098	11	20
GIGYF2-CHRND	chr2	233613792	chr2	233398641	462	HLA-B44:07	EEQLFLETL	0.9915	0.9416	11	20
GIGYF2-CHRND	chr2	233613792	chr2	233398641	462	HLA-B44:13	EEQLFLETL	0.9915	0.9416	11	20
GIGYF2-CHRND	chr2	233613792	chr2	233398641	462	HLA-B44:26	EEQLFLETL	0.9915	0.9416	11	20
GIGYF2-CHRND	chr2	233613792	chr2	233398641	462	HLA-C15:05	FTEEEQLFL	0.991	0.9541	8	17
GIGYF2-CHRND	chr2	233613792	chr2	233398641	462	HLA-C03:03	FTEEEQLFL	0.9909	0.9938	8	17
GIGYF2-CHRND	chr2	233613792	chr2	233398641	462	HLA-C03:04	FTEEEQLFL	0.9909	0.9938	8	17
GIGYF2-CHRND	chr2	233613792	chr2	233398641	462	HLA-C15:02	FTEEEQLFL	0.9885	0.9513	8	17
GIGYF2-CHRND	chr2	233613792	chr2	233398641	462	HLA-B18:04	EEQLFLETL	0.9832	0.8661	11	20
GIGYF2-CHRND	chr2	233613792	chr2	233398641	462	HLA-C04:04	FTEEEQLFL	0.9785	0.9542	8	17
GIGYF2-CHRND	chr2	233613792	chr2	233398641	462	HLA-B18:07	EEQLFLETL	0.9764	0.8124	11	20
GIGYF2-CHRND	chr2	233613792	chr2	233398641	462	HLA-B18:05	EEQLFLETL	0.9756	0.8527	11	20
GIGYF2-CHRND	chr2	233613792	chr2	233398641	462	HLA-B18:08	EEQLFLETL	0.9753	0.85	11	20
GIGYF2-CHRND	chr2	233613792	chr2	233398641	462	HLA-B35:13	VPFTEEEQL	0.9683	0.8873	6	15
GIGYF2-CHRND	chr2	233613792	chr2	233398641	462	HLA-B18:06	EEQLFLETL	0.9663	0.8645	11	20
GIGYF2-CHRND	chr2	233613792	chr2	233398641	462	HLA-B35:23	VPFTEEEQL	0.9612	0.8829	6	15
GIGYF2-CHRND	chr2	233613792	chr2	233398641	462	HLA-B18:03	EEQLFLETL	0.9605	0.8368	11	20
GIGYF2-CHRND	chr2	233613792	chr2	233398641	462	HLA-B35:77	VPFTEEEQL	0.9599	0.9063	6	15
GIGYF2-CHRND	chr2	233613792	chr2	233398641	462	HLA-B18:11	EEQLFLETL	0.9361	0.7931	11	20
GIGYF2-CHRND	chr2	233613792	chr2	233398641	462	HLA-C03:06	FTEEEQLFL	0.9333	0.9942	8	17
GIGYF2-CHRND	chr2	233613792	chr2	233398641	462	HLA-A02:14	FTEEEQLFL	0.9247	0.5923	8	17
GIGYF2-CHRND	chr2	233613792	chr2	233398641	462	HLA-B78:02	VPFTEEEQL	0.9225	0.6017	6	15
GIGYF2-CHRND	chr2	233613792	chr2	233398641	462	HLA-B35:30	VPFTEEEQL	0.9101	0.7625	6	15
GIGYF2-CHRND	chr2	233613792	chr2	233398641	462	HLA-B35:17	VPFTEEEQL	0.9101	0.7625	6	15
GIGYF2-CHRND	chr2	233613792	chr2	233398641	462	HLA-B35:24	VPFTEEEQL	0.8848	0.9225	6	15
GIGYF2-CHRND	chr2	233613792	chr2	233398641	462	HLA-B35:09	VPFTEEEQL	0.8774	0.9487	6	15
GIGYF2-CHRND	chr2	233613792	chr2	233398641	462	HLA-C08:01	FTEEEQLFL	0.8258	0.9927	8	17
GIGYF2-CHRND	chr2	233613792	chr2	233398641	462	HLA-B39:11	EEQLFLETL	0.7762	0.7727	11	20
GIGYF2-CHRND	chr2	233613792	chr2	233398641	462	HLA-B39:02	EEQLFLETL	0.7401	0.9162	11	20
GIGYF2-CHRND	chr2	233613792	chr2	233398641	462	HLA-B39:31	EEQLFLETL	0.7384	0.8789	11	20
GIGYF2-CHRND	chr2	233613792	chr2	233398641	462	HLA-B41:03	EEQLFLETL	0.7347	0.6022	11	20
GIGYF2-CHRND	chr2	233613792	chr2	233398641	462	HLA-C17:01	FTEEEQLFL	0.6125	0.8554	8	17
GIGYF2-CHRND	chr2	233613792	chr2	233398641	462	HLA-B67:01	VPFTEEEQL	0.5914	0.7477	6	15
GIGYF2-CHRND	chr2	233613792	chr2	233398641	462	HLA-B18:07	VPFTEEEQL	0.0895	0.8525	6	15
GIGYF2-CHRND	chr2	233613792	chr2	233398641	462	HLA-B07:13	FTEEEQLFL	0.0212	0.8134	8	17
GIGYF2-CHRND	chr2	233613792	chr2	233398641	462	HLA-B35:77	VPFTEEEQLF	0.9909	0.9545	6	16
GIGYF2-CHRND	chr2	233613792	chr2	233398641	462	HLA-B35:23	VPFTEEEQLF	0.9908	0.953	6	16
GIGYF2-CHRND	chr2	233613792	chr2	233398641	462	HLA-B35:30	VPFTEEEQLF	0.9865	0.8915	6	16
GIGYF2-CHRND	chr2	233613792	chr2	233398641	462	HLA-B35:17	VPFTEEEQLF	0.9865	0.8915	6	16
GIGYF2-CHRND	chr2	233613792	chr2	233398641	462	HLA-B35:24	VPFTEEEQLF	0.9739	0.965	6	16
GIGYF2-CHRND	chr2	233613792	chr2	233398641	462	HLA-B35:11	VPFTEEEQLF	0.9692	0.9624	6	16
GIGYF2-CHRND	chr2	233613792	chr2	233398641	462	HLA-B35:09	VPFTEEEQLF	0.9086	0.9727	6	16
GIGYF2-CHRND	chr2	233613792	chr2	233398641	462	HLA-B35:43	VPFTEEEQLF	0.8858	0.9421	6	16
GIGYF2-CHRND	chr2	233613792	chr2	233398641	462	HLA-B35:13	LVPFTEEEQL	0.6733	0.8993	5	15
GIGYF2-CHRND	chr2	233613792	chr2	233398641	462	HLA-B35:09	LVPFTEEEQL	0.5882	0.9649	5	15
GIGYF2-CHRND	chr2	233613792	chr2	233398641	462	HLA-B35:13	VPFTEEEQLFL	0.9518	0.9059	6	17
GIGYF2-CHRND	chr2	233613792	chr2	233398641	462	HLA-B35:09	VPFTEEEQLFL	0.9457	0.9522	6	17

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Potential FusionNeoAntigen Information of GIGYF2-CHRND 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 GIGYF2-CHRND

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
10167	VPFTEEEQLFLETL	GIGYF2	CHRND	chr2	233613792	chr2	233398641	462

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of GIGYF2-CHRND

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	10167	VPFTEEEQLFLETL	-6.28603	-6.40253
HLA-B14:02	3BVN	10167	VPFTEEEQLFLETL	-4.00651	-5.04491
HLA-B52:01	3W39	10167	VPFTEEEQLFLETL	-5.96786	-6.08436
HLA-B52:01	3W39	10167	VPFTEEEQLFLETL	-3.2333	-4.2717
HLA-A11:01	4UQ2	10167	VPFTEEEQLFLETL	-6.26032	-7.29872
HLA-A24:02	5HGA	10167	VPFTEEEQLFLETL	-7.13569	-7.25219
HLA-A24:02	5HGA	10167	VPFTEEEQLFLETL	-3.37303	-4.41143
HLA-B27:05	6PYJ	10167	VPFTEEEQLFLETL	-7.5142	-7.6307
HLA-B44:05	3DX8	10167	VPFTEEEQLFLETL	-5.00131	-5.11781
HLA-B44:05	3DX8	10167	VPFTEEEQLFLETL	-4.2623	-5.3007
HLA-B35:01	1A1N	10167	VPFTEEEQLFLETL	-7.34436	-8.38276
HLA-B35:01	1A1N	10167	VPFTEEEQLFLETL	-5.21806	-5.33456
HLA-A02:01	6TDR	10167	VPFTEEEQLFLETL	-4.54115	-4.65765

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Vaccine Design for the FusionNeoAntigens of GIGYF2-CHRND

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
GIGYF2-CHRND	chr2	233613792	chr2	233398641	10	19	EEEQLFLET	GAAGAACAGCTCTTCCTGGAGACCCTG
GIGYF2-CHRND	chr2	233613792	chr2	233398641	11	20	EEQLFLETL	GAACAGCTCTTCCTGGAGACCCTGCCG
GIGYF2-CHRND	chr2	233613792	chr2	233398641	12	20	EQLFLETL	CAGCTCTTCCTGGAGACCCTGCCG
GIGYF2-CHRND	chr2	233613792	chr2	233398641	4	15	ALVPFTEEEQL	CTGGTACCCTTTACAGAAGAAGAACAGCTCTTC
GIGYF2-CHRND	chr2	233613792	chr2	233398641	5	15	LVPFTEEEQL	GTACCCTTTACAGAAGAAGAACAGCTCTTC
GIGYF2-CHRND	chr2	233613792	chr2	233398641	6	15	VPFTEEEQL	CCCTTTACAGAAGAAGAACAGCTCTTC
GIGYF2-CHRND	chr2	233613792	chr2	233398641	6	16	VPFTEEEQLF	CCCTTTACAGAAGAAGAACAGCTCTTCCTG
GIGYF2-CHRND	chr2	233613792	chr2	233398641	6	17	VPFTEEEQLFL	CCCTTTACAGAAGAAGAACAGCTCTTCCTGGAG
GIGYF2-CHRND	chr2	233613792	chr2	233398641	8	17	FTEEEQLFL	ACAGAAGAAGAACAGCTCTTCCTGGAG
GIGYF2-CHRND	chr2	233613792	chr2	233398641	9	17	TEEEQLFL	GAAGAAGAACAGCTCTTCCTGGAG

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 GIGYF2-CHRND

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
BRCA	GIGYF2-CHRND	chr2	233613792	ENST00000373563	chr2	233398641	ENST00000258385	TCGA-AR-A256-01A

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Potential target of CAR-T therapy development for GIGYF2-CHRND

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

Tgene

CHRND

chr2:233613792

chr2:233398641

ENST00000258385

472_490

518.0

Transmembrane

Helical

Tgene

CHRND

chr2:233613792

chr2:233398641

ENST00000543200

472_490

503.0

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 GIGYF2-CHRND

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 GIGYF2-CHRND

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)