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Fusion Protein:GUK1-KDM5C

Fusion Gene and Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: GUK1-KDM5C
	FusionPDB ID: 35363
	FusionGDB2.0 ID: 35363
		Hgene	Tgene
	Gene symbol	GUK1	KDM5C
	Gene ID	2987	8242
	Gene name	guanylate kinase 1	lysine demethylase 5C
	Synonyms	GMK	DXS1272E\|JARID1C\|MRX13\|MRXJ\|MRXSCJ\|MRXSJ\|SMCX\|XE169
	Cytomap	1q42.13	Xp11.22
	Type of gene	protein-coding	protein-coding
	Description	guanylate kinaseATP:GMP phosphotransferaseGMP kinase	lysine-specific demethylase 5CJmjC domain-containing protein SMCXJumonji, AT rich interactive domain 1C (RBP2-like)Jumonji/ARID domain-containing protein 1CSmcx homolog, X chromosomeSmcy homolog, X-linkedhistone demethylase JARID1Clysine (K)-specif
	Modification date	20200320	20200313
	UniProtAcc	Q16774 Main function of 5'-partner protein: FUNCTION: Catalyzes the phosphorylation of GMP to GDP. Essential enzyme for recycling GMP and indirectly, cyclic GMP (cGMP) (PubMed:31201273). Involved in the cGMP metabolism in photoreceptors (By similarity). It may also have a role in the survival and growth progression of some tumors (PubMed:31201273). In addition to its physiological role, GUK1 is essential for convert prodrugs used for the treatment of cancers and viral infections into their pharmacologically active metabolites, most notably acyclovir, ganciclovir, and 6-thioguanine and its closely related analog 6-mercaptopurine (PubMed:197968, PubMed:6248551, PubMed:6306664). {ECO:0000250\|UniProtKB:P46195, ECO:0000269\|PubMed:197968, ECO:0000269\|PubMed:31201273, ECO:0000269\|PubMed:6248551, ECO:0000269\|PubMed:6306664}.	P41229 Main function of 5'-partner protein: FUNCTION: Histone demethylase that specifically demethylates 'Lys-4' of histone H3, thereby playing a central role in histone code (PubMed:28262558). Does not demethylate histone H3 'Lys-9', H3 'Lys-27', H3 'Lys-36', H3 'Lys-79' or H4 'Lys-20'. Demethylates trimethylated and dimethylated but not monomethylated H3 'Lys-4'. Participates in transcriptional repression of neuronal genes by recruiting histone deacetylases and REST at neuron-restrictive silencer elements. Represses the CLOCK-ARNTL/BMAL1 heterodimer-mediated transcriptional activation of the core clock component PER2 (By similarity). {ECO:0000250\|UniProtKB:P41230, ECO:0000269\|PubMed:17320160, ECO:0000269\|PubMed:17320161, ECO:0000269\|PubMed:17468742, ECO:0000269\|PubMed:26645689, ECO:0000269\|PubMed:28262558}.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000470040, ENST00000312726, ENST00000366716, ENST00000366718, ENST00000366721, ENST00000366722, ENST00000366723, ENST00000366726, ENST00000366730, ENST00000391865, ENST00000366728,	ENST00000375379, ENST00000375383, ENST00000375401, ENST00000404049, ENST00000452825, ENST00000465402,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	14 X 13 X 6=1092	4 X 5 X 1=20
	# samples	16	5
	** MAII score	log2(16/1092*10)=-2.77082904603249 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(5/20*10)=1.32192809488736 effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs). DoF>8 and MAII>0
Fusion gene context	PubMed: GUK1 [Title/Abstract] AND KDM5C [Title/Abstract] AND fusion [Title/Abstract]
Fusion neoantigen context	PubMed: GUK1 [Title/Abstract] AND KDM5C [Title/Abstract] AND neoantigen [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	GUK1(228336098)-KDM5C(53228198), # samples:1
Anticipated loss of major functional domain due to fusion event.	GUK1-KDM5C 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. GUK1-KDM5C 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. GUK1-KDM5C 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. GUK1-KDM5C 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. GUK1-KDM5C seems lost the major protein functional domain in Hgene partner, which is a cell metabolism gene due to the frame-shifted ORF. GUK1-KDM5C seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF. GUK1-KDM5C seems lost the major protein functional domain in Tgene partner, which is a CGC due to the frame-shifted ORF. GUK1-KDM5C seems lost the major protein functional domain in Tgene partner, which is a epigenetic factor due to the frame-shifted ORF. GUK1-KDM5C seems lost the major protein functional domain in Tgene partner, which is a essential gene due to the frame-shifted ORF. GUK1-KDM5C seems lost the major protein functional domain in Tgene partner, which is a IUPHAR drug target due to the frame-shifted ORF.

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

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

Partner	Gene	GO ID	GO term	PubMed ID
Hgene	GUK1	GO:0006163	purine nucleotide metabolic process	8663313
Hgene	GUK1	GO:0006805	xenobiotic metabolic process	6306664
Tgene	KDM5C	GO:0034720	histone H3-K4 demethylation	17320160

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr1:228336098/chrX:53228198)
- 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 GUK1 (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 KDM5C (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)
ENST00000366730	GUK1	chr1	228336098	+	ENST00000452825	KDM5C	chrX	53228198	+	4295	734	2505	3404	299
ENST00000366730	GUK1	chr1	228336098	+	ENST00000375401	KDM5C	chrX	53228198	+	4029	734	2239	3138	299
ENST00000366730	GUK1	chr1	228336098	+	ENST00000404049	KDM5C	chrX	53228198	+	3924	734	2134	3033	299
ENST00000366730	GUK1	chr1	228336098	+	ENST00000375379	KDM5C	chrX	53228198	+	3243	734	1453	2352	299
ENST00000366730	GUK1	chr1	228336098	+	ENST00000375383	KDM5C	chrX	53228198	+	3243	734	1453	2352	299
ENST00000391865	GUK1	chr1	228336098	+	ENST00000452825	KDM5C	chrX	53228198	+	4233	672	2443	3342	299
ENST00000391865	GUK1	chr1	228336098	+	ENST00000375401	KDM5C	chrX	53228198	+	3967	672	36	1037	333
ENST00000391865	GUK1	chr1	228336098	+	ENST00000404049	KDM5C	chrX	53228198	+	3862	672	36	1037	333
ENST00000391865	GUK1	chr1	228336098	+	ENST00000375379	KDM5C	chrX	53228198	+	3181	672	36	1037	333
ENST00000391865	GUK1	chr1	228336098	+	ENST00000375383	KDM5C	chrX	53228198	+	3181	672	36	1037	333
ENST00000366726	GUK1	chr1	228336098	+	ENST00000452825	KDM5C	chrX	53228198	+	4191	630	2401	3300	299
ENST00000366726	GUK1	chr1	228336098	+	ENST00000375401	KDM5C	chrX	53228198	+	3925	630	42	995	317
ENST00000366726	GUK1	chr1	228336098	+	ENST00000404049	KDM5C	chrX	53228198	+	3820	630	42	995	317
ENST00000366726	GUK1	chr1	228336098	+	ENST00000375379	KDM5C	chrX	53228198	+	3139	630	42	995	317
ENST00000366726	GUK1	chr1	228336098	+	ENST00000375383	KDM5C	chrX	53228198	+	3139	630	42	995	317
ENST00000312726	GUK1	chr1	228336098	+	ENST00000452825	KDM5C	chrX	53228198	+	4336	775	2546	3445	299
ENST00000312726	GUK1	chr1	228336098	+	ENST00000375401	KDM5C	chrX	53228198	+	4070	775	205	1140	311
ENST00000312726	GUK1	chr1	228336098	+	ENST00000404049	KDM5C	chrX	53228198	+	3965	775	205	1140	311
ENST00000312726	GUK1	chr1	228336098	+	ENST00000375379	KDM5C	chrX	53228198	+	3284	775	205	1140	311
ENST00000312726	GUK1	chr1	228336098	+	ENST00000375383	KDM5C	chrX	53228198	+	3284	775	205	1140	311
ENST00000366721	GUK1	chr1	228336098	+	ENST00000452825	KDM5C	chrX	53228198	+	4135	574	2345	3244	299
ENST00000366721	GUK1	chr1	228336098	+	ENST00000375401	KDM5C	chrX	53228198	+	3869	574	10	939	309
ENST00000366721	GUK1	chr1	228336098	+	ENST00000404049	KDM5C	chrX	53228198	+	3764	574	10	939	309
ENST00000366721	GUK1	chr1	228336098	+	ENST00000375379	KDM5C	chrX	53228198	+	3083	574	10	939	309
ENST00000366721	GUK1	chr1	228336098	+	ENST00000375383	KDM5C	chrX	53228198	+	3083	574	10	939	309
ENST00000366718	GUK1	chr1	228336098	+	ENST00000452825	KDM5C	chrX	53228198	+	4522	961	2732	3631	299
ENST00000366718	GUK1	chr1	228336098	+	ENST00000375401	KDM5C	chrX	53228198	+	4256	961	394	1326	310
ENST00000366718	GUK1	chr1	228336098	+	ENST00000404049	KDM5C	chrX	53228198	+	4151	961	394	1326	310
ENST00000366718	GUK1	chr1	228336098	+	ENST00000375379	KDM5C	chrX	53228198	+	3470	961	394	1326	310
ENST00000366718	GUK1	chr1	228336098	+	ENST00000375383	KDM5C	chrX	53228198	+	3470	961	394	1326	310
ENST00000366716	GUK1	chr1	228336098	+	ENST00000452825	KDM5C	chrX	53228198	+	4154	593	2364	3263	299
ENST00000366716	GUK1	chr1	228336098	+	ENST00000375401	KDM5C	chrX	53228198	+	3888	593	2098	2997	299
ENST00000366716	GUK1	chr1	228336098	+	ENST00000404049	KDM5C	chrX	53228198	+	3783	593	1993	2892	299
ENST00000366716	GUK1	chr1	228336098	+	ENST00000375379	KDM5C	chrX	53228198	+	3102	593	1312	2211	299
ENST00000366716	GUK1	chr1	228336098	+	ENST00000375383	KDM5C	chrX	53228198	+	3102	593	1312	2211	299

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
ENST00000366730	ENST00000452825	GUK1	chr1	228336098	+	KDM5C	chrX	53228198	+	0.010315264	0.9896847
ENST00000366730	ENST00000375401	GUK1	chr1	228336098	+	KDM5C	chrX	53228198	+	0.004822485	0.9951775
ENST00000366730	ENST00000404049	GUK1	chr1	228336098	+	KDM5C	chrX	53228198	+	0.004916173	0.99508375
ENST00000366730	ENST00000375379	GUK1	chr1	228336098	+	KDM5C	chrX	53228198	+	0.005024978	0.9949751
ENST00000366730	ENST00000375383	GUK1	chr1	228336098	+	KDM5C	chrX	53228198	+	0.005024978	0.9949751
ENST00000391865	ENST00000452825	GUK1	chr1	228336098	+	KDM5C	chrX	53228198	+	0.009946913	0.9900531
ENST00000391865	ENST00000375401	GUK1	chr1	228336098	+	KDM5C	chrX	53228198	+	0.006389135	0.9936108
ENST00000391865	ENST00000404049	GUK1	chr1	228336098	+	KDM5C	chrX	53228198	+	0.006663138	0.9933369
ENST00000391865	ENST00000375379	GUK1	chr1	228336098	+	KDM5C	chrX	53228198	+	0.00764333	0.99235666
ENST00000391865	ENST00000375383	GUK1	chr1	228336098	+	KDM5C	chrX	53228198	+	0.00764333	0.99235666
ENST00000366726	ENST00000452825	GUK1	chr1	228336098	+	KDM5C	chrX	53228198	+	0.010312284	0.98968774
ENST00000366726	ENST00000375401	GUK1	chr1	228336098	+	KDM5C	chrX	53228198	+	0.004891787	0.9951082
ENST00000366726	ENST00000404049	GUK1	chr1	228336098	+	KDM5C	chrX	53228198	+	0.004981254	0.9950187
ENST00000366726	ENST00000375379	GUK1	chr1	228336098	+	KDM5C	chrX	53228198	+	0.00504327	0.9949568
ENST00000366726	ENST00000375383	GUK1	chr1	228336098	+	KDM5C	chrX	53228198	+	0.00504327	0.9949568
ENST00000312726	ENST00000452825	GUK1	chr1	228336098	+	KDM5C	chrX	53228198	+	0.010179623	0.98982036
ENST00000312726	ENST00000375401	GUK1	chr1	228336098	+	KDM5C	chrX	53228198	+	0.00478188	0.9952181
ENST00000312726	ENST00000404049	GUK1	chr1	228336098	+	KDM5C	chrX	53228198	+	0.004890346	0.9951096
ENST00000312726	ENST00000375379	GUK1	chr1	228336098	+	KDM5C	chrX	53228198	+	0.004971488	0.99502856
ENST00000312726	ENST00000375383	GUK1	chr1	228336098	+	KDM5C	chrX	53228198	+	0.004971488	0.99502856
ENST00000366721	ENST00000452825	GUK1	chr1	228336098	+	KDM5C	chrX	53228198	+	0.010201464	0.98979855
ENST00000366721	ENST00000375401	GUK1	chr1	228336098	+	KDM5C	chrX	53228198	+	0.005142908	0.9948571
ENST00000366721	ENST00000404049	GUK1	chr1	228336098	+	KDM5C	chrX	53228198	+	0.005320458	0.9946795
ENST00000366721	ENST00000375379	GUK1	chr1	228336098	+	KDM5C	chrX	53228198	+	0.005570397	0.9944296
ENST00000366721	ENST00000375383	GUK1	chr1	228336098	+	KDM5C	chrX	53228198	+	0.005570397	0.9944296
ENST00000366718	ENST00000452825	GUK1	chr1	228336098	+	KDM5C	chrX	53228198	+	0.010859973	0.98914003
ENST00000366718	ENST00000375401	GUK1	chr1	228336098	+	KDM5C	chrX	53228198	+	0.00525299	0.994747
ENST00000366718	ENST00000404049	GUK1	chr1	228336098	+	KDM5C	chrX	53228198	+	0.005391444	0.9946085
ENST00000366718	ENST00000375379	GUK1	chr1	228336098	+	KDM5C	chrX	53228198	+	0.005575786	0.9944243
ENST00000366718	ENST00000375383	GUK1	chr1	228336098	+	KDM5C	chrX	53228198	+	0.005575786	0.9944243
ENST00000366716	ENST00000452825	GUK1	chr1	228336098	+	KDM5C	chrX	53228198	+	0.009893901	0.99010617
ENST00000366716	ENST00000375401	GUK1	chr1	228336098	+	KDM5C	chrX	53228198	+	0.004901583	0.9950984
ENST00000366716	ENST00000404049	GUK1	chr1	228336098	+	KDM5C	chrX	53228198	+	0.005030838	0.9949692
ENST00000366716	ENST00000375379	GUK1	chr1	228336098	+	KDM5C	chrX	53228198	+	0.004743964	0.995256
ENST00000366716	ENST00000375383	GUK1	chr1	228336098	+	KDM5C	chrX	53228198	+	0.004743964	0.995256

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 GUK1-KDM5C

+/-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
GUK1	chr1	228336098	KDM5C	chrX	53228198	574	212	RSRWMEKELGLYKSDTELLGLSAQDL
GUK1	chr1	228336098	KDM5C	chrX	53228198	593	212	RSRWMEKELGLYKSDTELLGLSAQDL
GUK1	chr1	228336098	KDM5C	chrX	53228198	630	212	RSRWMEKELGLYKSDTELLGLSAQDL
GUK1	chr1	228336098	KDM5C	chrX	53228198	672	212	RSRWMEKELGLYKSDTELLGLSAQDL
GUK1	chr1	228336098	KDM5C	chrX	53228198	734	212	RSRWMEKELGLYKSDTELLGLSAQDL
GUK1	chr1	228336098	KDM5C	chrX	53228198	775	212	RSRWMEKELGLYKSDTELLGLSAQDL
GUK1	chr1	228336098	KDM5C	chrX	53228198	961	212	RSRWMEKELGLYKSDTELLGLSAQDL

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Potential FusionNeoAntigen Information of GUK1-KDM5C 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.

GUK1-KDM5C_228336098_53228198.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)
GUK1-KDM5C	chr1	228336098	chrX	53228198	775	HLA-A02:22	GLYKSDTEL	0.987	0.5336	9	18
GUK1-KDM5C	chr1	228336098	chrX	53228198	775	HLA-A02:13	GLYKSDTEL	0.972	0.7568	9	18
GUK1-KDM5C	chr1	228336098	chrX	53228198	775	HLA-A02:27	GLYKSDTEL	0.9717	0.6273	9	18
GUK1-KDM5C	chr1	228336098	chrX	53228198	775	HLA-A02:16	GLYKSDTEL	0.9491	0.6307	9	18
GUK1-KDM5C	chr1	228336098	chrX	53228198	775	HLA-A02:11	GLYKSDTEL	0.944	0.7508	9	18
GUK1-KDM5C	chr1	228336098	chrX	53228198	775	HLA-A02:60	GLYKSDTEL	0.9439	0.6455	9	18
GUK1-KDM5C	chr1	228336098	chrX	53228198	775	HLA-A02:67	GLYKSDTEL	0.9437	0.7099	9	18
GUK1-KDM5C	chr1	228336098	chrX	53228198	775	HLA-A02:30	GLYKSDTEL	0.9437	0.7099	9	18
GUK1-KDM5C	chr1	228336098	chrX	53228198	775	HLA-A02:24	GLYKSDTEL	0.9437	0.7099	9	18
GUK1-KDM5C	chr1	228336098	chrX	53228198	775	HLA-A02:38	GLYKSDTEL	0.9144	0.6802	9	18
GUK1-KDM5C	chr1	228336098	chrX	53228198	775	HLA-A02:04	GLYKSDTEL	0.8563	0.6477	9	18
GUK1-KDM5C	chr1	228336098	chrX	53228198	775	HLA-A02:29	GLYKSDTEL	0.7712	0.7111	9	18
GUK1-KDM5C	chr1	228336098	chrX	53228198	775	HLA-A02:20	GLYKSDTEL	0.769	0.7189	9	18
GUK1-KDM5C	chr1	228336098	chrX	53228198	775	HLA-A02:35	GLYKSDTEL	0.7539	0.7276	9	18
GUK1-KDM5C	chr1	228336098	chrX	53228198	775	HLA-B13:01	GLYKSDTEL	0.0531	0.9312	9	18
GUK1-KDM5C	chr1	228336098	chrX	53228198	775	HLA-B13:02	GLYKSDTEL	0.0487	0.6235	9	18
GUK1-KDM5C	chr1	228336098	chrX	53228198	775	HLA-A02:22	GLYKSDTELL	0.9661	0.5397	9	19
GUK1-KDM5C	chr1	228336098	chrX	53228198	775	HLA-A02:16	GLYKSDTELL	0.9049	0.6484	9	19
GUK1-KDM5C	chr1	228336098	chrX	53228198	775	HLA-C05:09	KSDTELLGL	0.9999	0.8962	12	21
GUK1-KDM5C	chr1	228336098	chrX	53228198	775	HLA-C08:15	KSDTELLGL	0.9998	0.9678	12	21
GUK1-KDM5C	chr1	228336098	chrX	53228198	775	HLA-C04:06	KSDTELLGL	0.9889	0.8525	12	21
GUK1-KDM5C	chr1	228336098	chrX	53228198	775	HLA-A02:01	GLYKSDTEL	0.9437	0.7099	9	18
GUK1-KDM5C	chr1	228336098	chrX	53228198	775	HLA-B15:04	GLYKSDTEL	0.9207	0.912	9	18
GUK1-KDM5C	chr1	228336098	chrX	53228198	775	HLA-C08:13	KSDTELLGL	0.8647	0.9472	12	21
GUK1-KDM5C	chr1	228336098	chrX	53228198	775	HLA-C08:04	KSDTELLGL	0.8647	0.9472	12	21
GUK1-KDM5C	chr1	228336098	chrX	53228198	775	HLA-C08:03	KSDTELLGL	0.5067	0.986	12	21
GUK1-KDM5C	chr1	228336098	chrX	53228198	775	HLA-C07:29	LYKSDTELL	0.2293	0.9798	10	19
GUK1-KDM5C	chr1	228336098	chrX	53228198	775	HLA-C07:13	LYKSDTELL	0.1916	0.9516	10	19
GUK1-KDM5C	chr1	228336098	chrX	53228198	775	HLA-C07:67	LYKSDTELL	0.158	0.9658	10	19
GUK1-KDM5C	chr1	228336098	chrX	53228198	775	HLA-C07:80	LYKSDTELL	0.158	0.9658	10	19
GUK1-KDM5C	chr1	228336098	chrX	53228198	775	HLA-C07:10	LYKSDTELL	0.1487	0.9798	10	19
GUK1-KDM5C	chr1	228336098	chrX	53228198	775	HLA-C05:09	YKSDTELLGL	0.9997	0.8953	11	21
GUK1-KDM5C	chr1	228336098	chrX	53228198	775	HLA-C14:03	LYKSDTEL	0.8158	0.968	10	18
GUK1-KDM5C	chr1	228336098	chrX	53228198	775	HLA-C14:02	LYKSDTEL	0.8158	0.968	10	18
GUK1-KDM5C	chr1	228336098	chrX	53228198	775	HLA-C05:01	KSDTELLGL	0.9999	0.8962	12	21
GUK1-KDM5C	chr1	228336098	chrX	53228198	775	HLA-C04:03	KSDTELLGL	0.9999	0.8192	12	21
GUK1-KDM5C	chr1	228336098	chrX	53228198	775	HLA-C08:02	KSDTELLGL	0.9998	0.9678	12	21
GUK1-KDM5C	chr1	228336098	chrX	53228198	775	HLA-A02:03	GLYKSDTEL	0.9879	0.7321	9	18
GUK1-KDM5C	chr1	228336098	chrX	53228198	775	HLA-C15:05	KSDTELLGL	0.9869	0.8708	12	21
GUK1-KDM5C	chr1	228336098	chrX	53228198	775	HLA-C15:02	KSDTELLGL	0.9857	0.8638	12	21
GUK1-KDM5C	chr1	228336098	chrX	53228198	775	HLA-A02:14	GLYKSDTEL	0.9151	0.7029	9	18
GUK1-KDM5C	chr1	228336098	chrX	53228198	775	HLA-B15:73	GLYKSDTEL	0.9122	0.9062	9	18
GUK1-KDM5C	chr1	228336098	chrX	53228198	775	HLA-B15:30	GLYKSDTEL	0.6795	0.8132	9	18
GUK1-KDM5C	chr1	228336098	chrX	53228198	775	HLA-C08:01	KSDTELLGL	0.5067	0.986	12	21
GUK1-KDM5C	chr1	228336098	chrX	53228198	775	HLA-C14:02	LYKSDTELL	0.2331	0.973	10	19
GUK1-KDM5C	chr1	228336098	chrX	53228198	775	HLA-C14:03	LYKSDTELL	0.2331	0.973	10	19
GUK1-KDM5C	chr1	228336098	chrX	53228198	775	HLA-C06:06	LYKSDTELL	0.2274	0.992	10	19
GUK1-KDM5C	chr1	228336098	chrX	53228198	775	HLA-C07:02	LYKSDTELL	0.158	0.9658	10	19
GUK1-KDM5C	chr1	228336098	chrX	53228198	775	HLA-C05:01	YKSDTELLGL	0.9997	0.8953	11	21

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Potential FusionNeoAntigen Information of GUK1-KDM5C in HLA II

GUK1-KDM5C_228336098_53228198.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)
GUK1-KDM5C	chr1	228336098	chrX	53228198	775	DRB1-0466	LGLYKSDTELLGLSA	8	23

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Fusion breakpoint peptide structures of GUK1-KDM5C

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
4205	KELGLYKSDTELLG	GUK1	KDM5C	chr1	228336098	chrX	53228198	775

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of GUK1-KDM5C

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	4205	KELGLYKSDTELLG	-7.20958	-7.40908
HLA-B14:02	3BVN	4205	KELGLYKSDTELLG	-7.20354	-7.40304
HLA-B14:02	3BVN	4205	KELGLYKSDTELLG	-6.53966	-7.66106
HLA-B14:02	3BVN	4205	KELGLYKSDTELLG	-6.07079	-7.44279
HLA-B14:02	3BVN	4205	KELGLYKSDTELLG	-5.7628	-8.0567
HLA-B14:02	3BVN	4205	KELGLYKSDTELLG	-5.74878	-7.12078
HLA-B14:02	3BVN	4205	KELGLYKSDTELLG	-5.42361	-6.54501
HLA-B14:02	3BVN	4205	KELGLYKSDTELLG	-5.23518	-7.52908
HLA-B14:02	3BVN	4205	KELGLYKSDTELLG	-3.35465	-5.81645
HLA-B14:02	3BVN	4205	KELGLYKSDTELLG	-2.73695	-5.19875
HLA-B52:01	3W39	4205	KELGLYKSDTELLG	-6.24948	-6.44898
HLA-B52:01	3W39	4205	KELGLYKSDTELLG	-6.19528	-6.39478
HLA-B52:01	3W39	4205	KELGLYKSDTELLG	-5.84699	-6.96839
HLA-B52:01	3W39	4205	KELGLYKSDTELLG	-5.71707	-8.01097
HLA-B52:01	3W39	4205	KELGLYKSDTELLG	-5.65619	-7.02819
HLA-B52:01	3W39	4205	KELGLYKSDTELLG	-5.53945	-6.66085
HLA-B52:01	3W39	4205	KELGLYKSDTELLG	-5.50774	-6.62914
HLA-B52:01	3W39	4205	KELGLYKSDTELLG	-5.28389	-6.65589
HLA-B52:01	3W39	4205	KELGLYKSDTELLG	-5.23646	-7.69826
HLA-B52:01	3W39	4205	KELGLYKSDTELLG	-4.52568	-6.81958
HLA-B52:01	3W39	4205	KELGLYKSDTELLG	-4.09311	-6.55491
HLA-B52:01	3W39	4205	KELGLYKSDTELLG	-4.01895	-4.21845
HLA-B52:01	3W39	4205	KELGLYKSDTELLG	-3.55077	-6.01257
HLA-B52:01	3W39	4205	KELGLYKSDTELLG	-3.40657	-5.70047
HLA-B52:01	3W39	4205	KELGLYKSDTELLG	-3.13498	-4.50698
HLA-A11:01	4UQ2	4205	KELGLYKSDTELLG	-9.73183	-10.8532
HLA-A11:01	4UQ2	4205	KELGLYKSDTELLG	-7.85048	-9.22248
HLA-A11:01	4UQ2	4205	KELGLYKSDTELLG	-7.56644	-8.93844
HLA-A11:01	4UQ2	4205	KELGLYKSDTELLG	-7.45167	-8.57307
HLA-A11:01	4UQ2	4205	KELGLYKSDTELLG	-7.24892	-9.71072
HLA-A11:01	4UQ2	4205	KELGLYKSDTELLG	-2.82047	-5.28227
HLA-A24:02	5HGA	4205	KELGLYKSDTELLG	-7.81624	-8.01574
HLA-A24:02	5HGA	4205	KELGLYKSDTELLG	-7.6578	-7.8573
HLA-A24:02	5HGA	4205	KELGLYKSDTELLG	-5.64627	-7.01827
HLA-A24:02	5HGA	4205	KELGLYKSDTELLG	-5.59563	-8.05743
HLA-A24:02	5HGA	4205	KELGLYKSDTELLG	-5.37647	-6.74847
HLA-A24:02	5HGA	4205	KELGLYKSDTELLG	-5.33518	-6.45658
HLA-A24:02	5HGA	4205	KELGLYKSDTELLG	-4.91729	-7.37909
HLA-A24:02	5HGA	4205	KELGLYKSDTELLG	-4.42617	-5.54757
HLA-A24:02	5HGA	4205	KELGLYKSDTELLG	-3.95805	-6.25195
HLA-A24:02	5HGA	4205	KELGLYKSDTELLG	-3.81749	-6.11139
HLA-B27:05	6PYJ	4205	KELGLYKSDTELLG	-5.70885	-5.90835
HLA-B27:05	6PYJ	4205	KELGLYKSDTELLG	-5.03282	-7.49462
HLA-B27:05	6PYJ	4205	KELGLYKSDTELLG	-2.40586	-4.69976
HLA-B27:05	6PYJ	4205	KELGLYKSDTELLG	-1.70032	-3.99422
HLA-B27:05	6PYJ	4205	KELGLYKSDTELLG	-0.200707	-1.32211
HLA-B44:05	3DX8	4205	KELGLYKSDTELLG	-6.17504	-7.54704
HLA-B44:05	3DX8	4205	KELGLYKSDTELLG	-6.03938	-7.41138
HLA-B44:05	3DX8	4205	KELGLYKSDTELLG	-5.94458	-7.06598
HLA-B44:05	3DX8	4205	KELGLYKSDTELLG	-5.57593	-8.03773
HLA-B44:05	3DX8	4205	KELGLYKSDTELLG	-5.47451	-5.67401
HLA-B44:05	3DX8	4205	KELGLYKSDTELLG	-5.33866	-5.53816
HLA-B44:05	3DX8	4205	KELGLYKSDTELLG	-4.93454	-6.05594
HLA-B44:05	3DX8	4205	KELGLYKSDTELLG	-4.90645	-6.27845
HLA-B44:05	3DX8	4205	KELGLYKSDTELLG	-4.77431	-4.97381
HLA-B44:05	3DX8	4205	KELGLYKSDTELLG	-4.49756	-6.79146
HLA-B44:05	3DX8	4205	KELGLYKSDTELLG	-4.33503	-5.45643
HLA-B44:05	3DX8	4205	KELGLYKSDTELLG	-3.63441	-6.09621
HLA-B44:05	3DX8	4205	KELGLYKSDTELLG	-3.3323	-5.6262
HLA-B44:05	3DX8	4205	KELGLYKSDTELLG	-2.60783	-4.90173
HLA-B44:05	3DX8	4205	KELGLYKSDTELLG	-1.65363	-4.11543
HLA-A02:01	6TDR	4205	KELGLYKSDTELLG	-4.85416	-7.31596
HLA-A02:01	6TDR	4205	KELGLYKSDTELLG	-2.30987	-4.77167

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Vaccine Design for the FusionNeoAntigens of GUK1-KDM5C

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
GUK1-KDM5C	chr1	228336098	chrX	53228198	10	18	LYKSDTEL	CTCTCTGAGCCCTGAGTCCCTTGA
GUK1-KDM5C	chr1	228336098	chrX	53228198	10	19	LYKSDTELL	CTCTCTGAGCCCTGAGTCCCTTGACTT
GUK1-KDM5C	chr1	228336098	chrX	53228198	11	21	YKSDTELLGL	TCTGAGCCCTGAGTCCCTTGACTTTTGTAT
GUK1-KDM5C	chr1	228336098	chrX	53228198	12	21	KSDTELLGL	GAGCCCTGAGTCCCTTGACTTTTGTAT
GUK1-KDM5C	chr1	228336098	chrX	53228198	9	18	GLYKSDTEL	GCGCTCTCTGAGCCCTGAGTCCCTTGA
GUK1-KDM5C	chr1	228336098	chrX	53228198	9	19	GLYKSDTELL	GCGCTCTCTGAGCCCTGAGTCCCTTGACTT

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
GUK1-KDM5C	chr1	228336098	chrX	53228198	8	23	LGLYKSDTELLGLSA	GAGGCGCTCTCTGAGCCCTGAGTCCCTTGACTTTTGTATTCTGAC

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Information of the samples that have these potential fusion neoantigens of GUK1-KDM5C

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
N/A	GUK1-KDM5C	chr1	228336098	ENST00000312726	chrX	53228198	ENST00000452825	BE939838

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Potential target of CAR-T therapy development for GUK1-KDM5C

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 GUK1-KDM5C

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 GUK1-KDM5C

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)