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Fusion Protein:GCN1L1-CCND2

Fusion Gene and Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: GCN1L1-CCND2
	FusionPDB ID: 32771
	FusionGDB2.0 ID: 32771
		Hgene	Tgene
	Gene symbol	GCN1L1	CCND2
	Gene ID	10985	894
	Gene name	GCN1 activator of EIF2AK4	cyclin D2
	Synonyms	GCN1L\|GCN1L1\|PRIC295	KIAK0002\|MPPH3
	Cytomap	12q24.23	12p13.32
	Type of gene	protein-coding	protein-coding
	Description	eIF-2-alpha kinase activator GCN1GCN1 (general control of amino-acid synthesis 1, yeast)-like 1GCN1 eIF-2-alpha kinase activator homologGCN1 general control of amino-acid synthesis 1-like 1GCN1, eIF2 alpha kinase activator homologGCN1-like protein 1	G1/S-specific cyclin-D2
	Modification date	20200313	20200313
	UniProtAcc	.	P30279 Main function of 5'-partner protein: FUNCTION: Regulatory component of the cyclin D2-CDK4 (DC) complex that phosphorylates and inhibits members of the retinoblastoma (RB) protein family including RB1 and regulates the cell-cycle during G(1)/S transition. Phosphorylation of RB1 allows dissociation of the transcription factor E2F from the RB/E2F complex and the subsequent transcription of E2F target genes which are responsible for the progression through the G(1) phase. Hypophosphorylates RB1 in early G(1) phase. Cyclin D-CDK4 complexes are major integrators of various mitogenenic and antimitogenic signals. Also substrate for SMAD3, phosphorylating SMAD3 in a cell-cycle-dependent manner and repressing its transcriptional activity. Component of the ternary complex, cyclin D2/CDK4/CDKN1B, required for nuclear translocation and activity of the cyclin D-CDK4 complex (By similarity). {ECO:0000250}.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000300648,	ENST00000541542, ENST00000261254,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	8 X 15 X 8=960	4 X 6 X 3=72
	# samples	12	6
	** MAII score	log2(12/960*10)=-3 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(6/72*10)=-0.263034405833794 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Fusion gene context	PubMed: GCN1L1 [Title/Abstract] AND CCND2 [Title/Abstract] AND fusion [Title/Abstract]
Fusion neoantigen context	PubMed: GCN1L1 [Title/Abstract] AND CCND2 [Title/Abstract] AND neoantigen [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	GCN1L1(120600873)-CCND2(4398007), # samples:1 GCN1L1(120600874)-CCND2(4398008), # samples:1 GCN1L1(120600651)-CCND2(4398008), # samples:1
Anticipated loss of major functional domain due to fusion event.	GCN1L1-CCND2 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. GCN1L1-CCND2 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. GCN1L1-CCND2 seems lost the major protein functional domain in Tgene partner, which is a CGC due to the frame-shifted ORF.

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

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

Partner	Gene	GO ID	GO term	PubMed ID
Tgene	CCND2	GO:0001934	positive regulation of protein phosphorylation	8114739
Tgene	CCND2	GO:0045737	positive regulation of cyclin-dependent protein serine/threonine kinase activity	8114739

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr12:120600873/chr12:4398007)
- 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 GCN1L1 (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 CCND2 (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)

ENST00000300648

GCN1L1

chr12

120600873

ENST00000261254

CCND2

chr12

4398007

7691

2051

2349

778

ENST00000300648

GCN1L1

chr12

120600874

ENST00000261254

CCND2

chr12

4398008

7691

2051

2349

778

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
ENST00000300648	ENST00000261254	GCN1L1	chr12	120600873	-	CCND2	chr12	4398007	+	0.000715011	0.99928504
ENST00000300648	ENST00000261254	GCN1L1	chr12	120600874	-	CCND2	chr12	4398008	+	0.000715011	0.99928504

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 GCN1L1-CCND2

+/-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
GCN1L1	chr12	120600873	CCND2	chr12	4398007	2051	679	AQEMLIISHHPSLDFKFAMYPPSMIA
GCN1L1	chr12	120600874	CCND2	chr12	4398008	2051	679	AQEMLIISHHPSLDFKFAMYPPSMIA

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Potential FusionNeoAntigen Information of GCN1L1-CCND2 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.

GCN1L1-CCND2_120600873_4398007.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)
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	HLA-B15:10	SHHPSLDF	0.9956	0.6387	7	15
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	HLA-B35:05	HPSLDFKF	0.9945	0.5125	9	17
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	HLA-B35:01	HPSLDFKF	0.9933	0.7931	9	17
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	HLA-B35:08	HPSLDFKF	0.9931	0.7756	9	17
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	HLA-B15:18	SHHPSLDF	0.9909	0.7417	7	15
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	HLA-B38:02	SHHPSLDF	0.9897	0.9834	7	15
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	HLA-B38:01	SHHPSLDF	0.9867	0.9807	7	15
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	HLA-B15:37	SHHPSLDF	0.9826	0.7303	7	15
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	HLA-B15:17	ISHHPSLDF	0.9938	0.9194	6	15
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	HLA-B15:16	ISHHPSLDF	0.9907	0.6009	6	15
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	HLA-B58:02	ISHHPSLDF	0.9873	0.9151	6	15
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	HLA-B57:03	ISHHPSLDF	0.9864	0.9609	6	15
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	HLA-B58:01	ISHHPSLDF	0.9851	0.8839	6	15
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	HLA-B39:24	HHPSLDFKF	0.9804	0.5402	8	17
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	HLA-B39:01	HHPSLDFKF	0.9769	0.9543	8	17
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	HLA-B38:02	HHPSLDFKF	0.9554	0.9425	8	17
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	HLA-B38:01	HHPSLDFKF	0.9507	0.942	8	17
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	HLA-B15:25	SLDFKFAMY	0.9363	0.86	11	20
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	HLA-B15:02	SLDFKFAMY	0.8897	0.8864	11	20
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	HLA-B15:18	HHPSLDFKF	0.7558	0.6401	8	17
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	HLA-B15:10	HHPSLDFKF	0.7255	0.5179	8	17
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	HLA-A32:13	ISHHPSLDF	0.518	0.9616	6	15
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	HLA-B15:37	HHPSLDFKF	0.4973	0.5776	8	17
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	HLA-A24:14	HHPSLDFKF	0.4822	0.5535	8	17
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	HLA-B35:01	HPSLDFKFAM	0.996	0.8019	9	19
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	HLA-B39:01	SHHPSLDFKF	0.9954	0.9362	7	17
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	HLA-B15:18	SHHPSLDFKF	0.9954	0.6017	7	17
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	HLA-A30:08	ISHHPSLDFK	0.9946	0.6361	6	16
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	HLA-B35:08	HPSLDFKFAM	0.9945	0.7825	9	19
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	HLA-B38:01	SHHPSLDFKF	0.9943	0.96	7	17
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	HLA-B38:02	SHHPSLDFKF	0.9928	0.9641	7	17
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	HLA-B35:03	HPSLDFKFAM	0.9876	0.8665	9	19
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	HLA-B15:37	SHHPSLDFKF	0.962	0.5481	7	17
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	HLA-B35:02	HPSLDFKFAM	0.9069	0.8905	9	19
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	HLA-B35:04	HPSLDFKFAM	0.9069	0.8905	9	19
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	HLA-B57:01	ISHHPSLDFKF	1	0.9217	6	17
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	HLA-B57:03	ISHHPSLDFKF	0.9999	0.9155	6	17
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	HLA-B15:17	ISHHPSLDFKF	0.9998	0.8609	6	17
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	HLA-B39:24	HHPSLDFKFAM	0.9998	0.5911	8	19
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	HLA-B39:01	HHPSLDFKFAM	0.9997	0.9651	8	19
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	HLA-B38:02	HHPSLDFKFAM	0.9991	0.9818	8	19
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	HLA-B38:01	HHPSLDFKFAM	0.999	0.9801	8	19
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	HLA-B35:01	HPSLDFKFAMY	0.9989	0.7965	9	20
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	HLA-B35:08	HPSLDFKFAMY	0.9983	0.8308	9	20
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	HLA-C08:15	SLDFKFAM	0.9999	0.9585	11	19
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	HLA-B39:05	SHHPSLDF	0.9867	0.9526	7	15
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	HLA-C03:08	ISHHPSLDF	0.9835	0.9244	6	15
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	HLA-B39:09	HHPSLDFKF	0.9783	0.6847	8	17
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	HLA-B39:12	HHPSLDFKF	0.9752	0.9566	8	17
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	HLA-C15:04	ISHHPSLDF	0.9687	0.9455	6	15
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	HLA-B39:05	HHPSLDFKF	0.9421	0.945	8	17
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	HLA-C03:07	ISHHPSLDF	0.9419	0.9895	6	15
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	HLA-C15:06	ISHHPSLDF	0.8943	0.9559	6	15
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	HLA-B15:05	SLDFKFAMY	0.8817	0.8385	11	20
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	HLA-B15:31	SLDFKFAMY	0.8268	0.8448	11	20
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	HLA-C12:12	ISHHPSLDF	0.8095	0.9332	6	15
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	HLA-C07:95	HHPSLDFKF	0.7505	0.765	8	17
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	HLA-C03:14	ISHHPSLDF	0.706	0.9841	6	15
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	HLA-C07:27	HHPSLDFKF	0.6931	0.9478	8	17
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	HLA-C07:29	HHPSLDFKF	0.6346	0.9487	8	17
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	HLA-C07:13	HHPSLDFKF	0.5839	0.8717	8	17
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	HLA-C07:19	HHPSLDFKF	0.5231	0.7443	8	17
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	HLA-C07:46	HHPSLDFKF	0.51	0.8136	8	17
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	HLA-C07:80	HHPSLDFKF	0.5025	0.9005	8	17
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	HLA-C07:67	HHPSLDFKF	0.5025	0.9005	8	17
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	HLA-C07:10	HHPSLDFKF	0.4898	0.9397	8	17
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	HLA-B39:09	SHHPSLDFKF	0.9968	0.5642	7	17
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	HLA-B39:05	SHHPSLDFKF	0.9904	0.9149	7	17
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	HLA-B42:02	HPSLDFKFAM	0.9525	0.6388	9	19
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	HLA-B42:01	HPSLDFKFAM	0.9437	0.6337	9	19
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	HLA-B35:12	HPSLDFKFAM	0.9069	0.8905	9	19
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	HLA-B39:10	HPSLDFKFAM	0.8605	0.9547	9	19
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	HLA-B39:09	HHPSLDFKFAM	0.9998	0.7296	8	19
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	HLA-B39:05	HHPSLDFKFAM	0.9987	0.9591	8	19
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	HLA-C08:02	SLDFKFAM	0.9999	0.9585	11	19
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	HLA-B35:30	HPSLDFKF	0.9945	0.6553	9	17
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	HLA-B35:17	HPSLDFKF	0.9945	0.6553	9	17
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	HLA-B35:77	HPSLDFKF	0.9933	0.7931	9	17
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	HLA-B35:23	HPSLDFKF	0.9933	0.781	9	17
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	HLA-B38:05	SHHPSLDF	0.9867	0.9807	7	15
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	HLA-B35:24	HPSLDFKF	0.9762	0.8131	9	17
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	HLA-B15:09	SHHPSLDF	0.9695	0.5864	7	15
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	HLA-B39:11	SHHPSLDF	0.9418	0.8966	7	15
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	HLA-B18:07	HPSLDFKF	0.8528	0.8682	9	17
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	HLA-B57:04	ISHHPSLDF	0.9957	0.7338	6	15
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	HLA-C03:02	ISHHPSLDF	0.9927	0.9716	6	15
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	HLA-B58:06	ISHHPSLDF	0.9887	0.8055	6	15
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	HLA-B57:02	ISHHPSLDF	0.9753	0.9047	6	15
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	HLA-C15:09	ISHHPSLDF	0.9687	0.9455	6	15
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	HLA-B39:31	HHPSLDFKF	0.9658	0.9522	8	17
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	HLA-B38:05	HHPSLDFKF	0.9507	0.942	8	17
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	HLA-B15:39	SLDFKFAMY	0.9311	0.7388	11	20
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	HLA-C12:02	ISHHPSLDF	0.8314	0.9678	6	15
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	HLA-C07:22	HHPSLDFKF	0.7251	0.7471	8	17
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	HLA-C07:17	HHPSLDFKF	0.6608	0.9721	8	17
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	HLA-C16:01	ISHHPSLDF	0.5882	0.9872	6	15
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	HLA-C07:02	HHPSLDFKF	0.5025	0.9005	8	17
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	HLA-B39:11	HHPSLDFKF	0.3967	0.8108	8	17
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	HLA-C16:02	ISHHPSLDF	0.3278	0.9956	6	15
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	HLA-C02:10	ISHHPSLDF	0.0622	0.9765	6	15
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	HLA-C02:02	ISHHPSLDF	0.0622	0.9765	6	15
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	HLA-B35:77	HPSLDFKFAM	0.996	0.8019	9	19
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	HLA-B35:23	HPSLDFKFAM	0.9959	0.7694	9	19
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	HLA-B38:05	SHHPSLDFKF	0.9943	0.96	7	17
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	HLA-A30:01	ISHHPSLDFK	0.994	0.8304	6	16
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	HLA-B35:30	HPSLDFKFAM	0.9836	0.615	9	19
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	HLA-B35:17	HPSLDFKFAM	0.9836	0.615	9	19
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	HLA-B35:11	HPSLDFKFAM	0.9749	0.7907	9	19
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	HLA-B39:11	SHHPSLDFKF	0.9681	0.8132	7	17
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	HLA-B35:24	HPSLDFKFAM	0.9228	0.834	9	19
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	HLA-B35:09	HPSLDFKFAM	0.9069	0.8905	9	19
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	HLA-B67:01	HPSLDFKFAM	0.8327	0.7556	9	19
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	HLA-B35:43	HPSLDFKFAM	0.8301	0.7284	9	19
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	HLA-B57:10	ISHHPSLDFKF	1	0.9217	6	17
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	HLA-B57:02	ISHHPSLDFKF	0.9999	0.8288	6	17
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	HLA-B39:31	HHPSLDFKFAM	0.9997	0.965	8	19
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	HLA-B38:05	HHPSLDFKFAM	0.999	0.9801	8	19
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	HLA-B35:77	HPSLDFKFAMY	0.9989	0.7965	9	20
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	HLA-B35:23	HPSLDFKFAMY	0.9987	0.7756	9	20
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	HLA-B35:17	HPSLDFKFAMY	0.9962	0.6504	9	20
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	HLA-B35:30	HPSLDFKFAMY	0.9962	0.6504	9	20
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	HLA-B35:24	HPSLDFKFAMY	0.9845	0.8367	9	20
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	HLA-B15:11	HPSLDFKFAMY	0.9819	0.7375	9	20
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	HLA-B39:11	HHPSLDFKFAM	0.8776	0.8864	8	19

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Potential FusionNeoAntigen Information of GCN1L1-CCND2 in HLA II

GCN1L1-CCND2_120600873_4398007.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)
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	DRB1-1117	QEMLIISHHPSLDFK	1	16
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	DRB1-1117	AQEMLIISHHPSLDF	0	15
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	DRB1-1152	QEMLIISHHPSLDFK	1	16
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	DRB1-1152	AQEMLIISHHPSLDF	0	15
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	DRB1-1401	QEMLIISHHPSLDFK	1	16
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	DRB1-1401	AQEMLIISHHPSLDF	0	15
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	DRB1-1404	QEMLIISHHPSLDFK	1	16
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	DRB1-1404	AQEMLIISHHPSLDF	0	15
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	DRB1-1405	QEMLIISHHPSLDFK	1	16
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	DRB1-1405	AQEMLIISHHPSLDF	0	15
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	DRB1-1407	QEMLIISHHPSLDFK	1	16
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	DRB1-1407	AQEMLIISHHPSLDF	0	15
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	DRB1-1408	QEMLIISHHPSLDFK	1	16
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	DRB1-1408	AQEMLIISHHPSLDF	0	15
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	DRB1-1411	QEMLIISHHPSLDFK	1	16
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	DRB1-1411	AQEMLIISHHPSLDF	0	15
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	DRB1-1418	QEMLIISHHPSLDFK	1	16
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	DRB1-1418	AQEMLIISHHPSLDF	0	15
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	DRB1-1423	QEMLIISHHPSLDFK	1	16
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	DRB1-1423	AQEMLIISHHPSLDF	0	15
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	DRB1-1426	QEMLIISHHPSLDFK	1	16
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	DRB1-1426	AQEMLIISHHPSLDF	0	15
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	DRB1-1428	QEMLIISHHPSLDFK	1	16
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	DRB1-1428	AQEMLIISHHPSLDF	0	15
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	DRB1-1431	QEMLIISHHPSLDFK	1	16
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	DRB1-1432	QEMLIISHHPSLDFK	1	16
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	DRB1-1435	QEMLIISHHPSLDFK	1	16
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	DRB1-1435	AQEMLIISHHPSLDF	0	15
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	DRB1-1438	QEMLIISHHPSLDFK	1	16
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	DRB1-1438	AQEMLIISHHPSLDF	0	15
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	DRB1-1439	QEMLIISHHPSLDFK	1	16
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	DRB1-1439	AQEMLIISHHPSLDF	0	15
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	DRB1-1443	QEMLIISHHPSLDFK	1	16
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	DRB1-1443	AQEMLIISHHPSLDF	0	15
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	DRB1-1445	QEMLIISHHPSLDFK	1	16
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	DRB1-1445	AQEMLIISHHPSLDF	0	15
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	DRB1-1448	QEMLIISHHPSLDFK	1	16
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	DRB1-1449	QEMLIISHHPSLDFK	1	16
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	DRB1-1450	QEMLIISHHPSLDFK	1	16
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	DRB1-1450	AQEMLIISHHPSLDF	0	15
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	DRB1-1454	QEMLIISHHPSLDFK	1	16
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	DRB1-1454	AQEMLIISHHPSLDF	0	15
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	DRB1-1455	QEMLIISHHPSLDFK	1	16
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	DRB1-1455	AQEMLIISHHPSLDF	0	15
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	DRB1-1456	QEMLIISHHPSLDFK	1	16
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	DRB1-1456	AQEMLIISHHPSLDF	0	15
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	DRB1-1458	QEMLIISHHPSLDFK	1	16
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	DRB1-1458	AQEMLIISHHPSLDF	0	15
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	DRB1-1459	QEMLIISHHPSLDFK	1	16
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	DRB1-1459	AQEMLIISHHPSLDF	0	15
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	DRB1-1460	QEMLIISHHPSLDFK	1	16
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	DRB1-1460	AQEMLIISHHPSLDF	0	15
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	DRB1-1461	QEMLIISHHPSLDFK	1	16
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	DRB1-1461	AQEMLIISHHPSLDF	0	15
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	DRB1-1462	QEMLIISHHPSLDFK	1	16
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	DRB1-1462	AQEMLIISHHPSLDF	0	15
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	DRB1-1464	QEMLIISHHPSLDFK	1	16
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	DRB1-1468	QEMLIISHHPSLDFK	1	16
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	DRB1-1470	QEMLIISHHPSLDFK	1	16
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	DRB1-1470	AQEMLIISHHPSLDF	0	15
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	DRB1-1471	QEMLIISHHPSLDFK	1	16
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	DRB1-1471	AQEMLIISHHPSLDF	0	15
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	DRB1-1472	QEMLIISHHPSLDFK	1	16
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	DRB1-1475	QEMLIISHHPSLDFK	1	16
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	DRB1-1475	AQEMLIISHHPSLDF	0	15
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	DRB1-1481	QEMLIISHHPSLDFK	1	16
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	DRB1-1482	QEMLIISHHPSLDFK	1	16
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	DRB1-1482	AQEMLIISHHPSLDF	0	15
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	DRB1-1486	QEMLIISHHPSLDFK	1	16
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	DRB1-1486	AQEMLIISHHPSLDF	0	15
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	DRB1-1487	QEMLIISHHPSLDFK	1	16
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	DRB1-1487	AQEMLIISHHPSLDF	0	15
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	DRB1-1488	QEMLIISHHPSLDFK	1	16
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	DRB1-1488	AQEMLIISHHPSLDF	0	15
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	DRB1-1490	QEMLIISHHPSLDFK	1	16
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	DRB1-1490	AQEMLIISHHPSLDF	0	15
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	DRB1-1491	QEMLIISHHPSLDFK	1	16
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	DRB1-1491	AQEMLIISHHPSLDF	0	15
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	DRB1-1493	QEMLIISHHPSLDFK	1	16
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	DRB1-1493	AQEMLIISHHPSLDF	0	15
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	DRB1-1495	QEMLIISHHPSLDFK	1	16
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	DRB1-1496	QEMLIISHHPSLDFK	1	16
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	DRB1-1496	AQEMLIISHHPSLDF	0	15
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	DRB1-1497	QEMLIISHHPSLDFK	1	16
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	DRB1-1497	AQEMLIISHHPSLDF	0	15
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	DRB1-1499	QEMLIISHHPSLDFK	1	16
GCN1L1-CCND2	chr12	120600873	chr12	4398007	2051	DRB1-1499	AQEMLIISHHPSLDF	0	15

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Fusion breakpoint peptide structures of GCN1L1-CCND2

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
3988	ISHHPSLDFKFAMY	GCN1L1	CCND2	chr12	120600873	chr12	4398007	2051

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of GCN1L1-CCND2

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	3988	ISHHPSLDFKFAMY	-7.15543	-7.26883
HLA-B14:02	3BVN	3988	ISHHPSLDFKFAMY	-4.77435	-5.80965
HLA-B52:01	3W39	3988	ISHHPSLDFKFAMY	-6.80875	-6.92215
HLA-B52:01	3W39	3988	ISHHPSLDFKFAMY	-4.20386	-5.23916
HLA-A11:01	4UQ2	3988	ISHHPSLDFKFAMY	-7.5194	-8.5547
HLA-A11:01	4UQ2	3988	ISHHPSLDFKFAMY	-6.9601	-7.0735
HLA-A24:02	5HGA	3988	ISHHPSLDFKFAMY	-7.52403	-7.63743
HLA-A24:02	5HGA	3988	ISHHPSLDFKFAMY	-5.82433	-6.85963
HLA-B27:05	6PYJ	3988	ISHHPSLDFKFAMY	-3.28285	-4.31815
HLA-B44:05	3DX8	3988	ISHHPSLDFKFAMY	-5.91172	-6.94702
HLA-B44:05	3DX8	3988	ISHHPSLDFKFAMY	-4.24346	-4.35686

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Vaccine Design for the FusionNeoAntigens of GCN1L1-CCND2

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
GCN1L1-CCND2	chr12	120600873	chr12	4398007	11	19	SLDFKFAM	CCTTAGACTTTAAGTTTGCCATGT
GCN1L1-CCND2	chr12	120600873	chr12	4398007	11	20	SLDFKFAMY	CCTTAGACTTTAAGTTTGCCATGTACC
GCN1L1-CCND2	chr12	120600873	chr12	4398007	6	15	ISHHPSLDF	TCTCCCACCACCCATCCTTAGACTTTA
GCN1L1-CCND2	chr12	120600873	chr12	4398007	6	16	ISHHPSLDFK	TCTCCCACCACCCATCCTTAGACTTTAAGT
GCN1L1-CCND2	chr12	120600873	chr12	4398007	6	17	ISHHPSLDFKF	TCTCCCACCACCCATCCTTAGACTTTAAGTTTG
GCN1L1-CCND2	chr12	120600873	chr12	4398007	7	15	SHHPSLDF	CCCACCACCCATCCTTAGACTTTA
GCN1L1-CCND2	chr12	120600873	chr12	4398007	7	17	SHHPSLDFKF	CCCACCACCCATCCTTAGACTTTAAGTTTG
GCN1L1-CCND2	chr12	120600873	chr12	4398007	8	17	HHPSLDFKF	ACCACCCATCCTTAGACTTTAAGTTTG
GCN1L1-CCND2	chr12	120600873	chr12	4398007	8	19	HHPSLDFKFAM	ACCACCCATCCTTAGACTTTAAGTTTGCCATGT
GCN1L1-CCND2	chr12	120600873	chr12	4398007	9	17	HPSLDFKF	ACCCATCCTTAGACTTTAAGTTTG
GCN1L1-CCND2	chr12	120600873	chr12	4398007	9	19	HPSLDFKFAM	ACCCATCCTTAGACTTTAAGTTTGCCATGT
GCN1L1-CCND2	chr12	120600873	chr12	4398007	9	20	HPSLDFKFAMY	ACCCATCCTTAGACTTTAAGTTTGCCATGTACC

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
GCN1L1-CCND2	chr12	120600873	chr12	4398007	0	15	AQEMLIISHHPSLDF	CCCAGGAAATGCTGATCATCTCCCACCACCCATCCTTAGACTTTA
GCN1L1-CCND2	chr12	120600873	chr12	4398007	1	16	QEMLIISHHPSLDFK	AGGAAATGCTGATCATCTCCCACCACCCATCCTTAGACTTTAAGT

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Information of the samples that have these potential fusion neoantigens of GCN1L1-CCND2

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
LUSC	GCN1L1-CCND2	chr12	120600873	ENST00000300648	chr12	4398007	ENST00000261254	TCGA-22-1017

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Potential target of CAR-T therapy development for GCN1L1-CCND2

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 GCN1L1-CCND2

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 GCN1L1-CCND2

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)