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Fusion Protein:ABCC5-GCN1L1

Fusion Gene and Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: ABCC5-GCN1L1
	FusionPDB ID: 299
	FusionGDB2.0 ID: 299
		Hgene	Tgene
	Gene symbol	ABCC5	GCN1L1
	Gene ID	10057	10985
	Gene name	ATP binding cassette subfamily C member 5	GCN1 activator of EIF2AK4
	Synonyms	ABC33\|EST277145\|MOAT-C\|MOATC\|MRP5\|SMRP\|pABC11	GCN1L\|GCN1L1\|PRIC295
	Cytomap	3q27.1	12q24.23
	Type of gene	protein-coding	protein-coding
	Description	multidrug resistance-associated protein 5ATP-binding cassette, sub-family C (CFTR/MRP), member 5canalicular multispecific organic anion transporter Cmulti-specific organic anion transporter C	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
	Modification date	20200313	20200313
	UniProtAcc	O15440 Main function of 5'-partner protein: FUNCTION: Acts as a multispecific organic anion pump which can transport nucleotide analogs. Heme transporter required for the translocation of cytosolic heme to the secretory pathway (PubMed:24836561). {ECO:0000269\|PubMed:10840050, ECO:0000269\|PubMed:24836561}.	.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000334444, ENST00000382494, ENST00000392579, ENST00000265586, ENST00000427120, ENST00000446941, ENST00000492216,	ENST00000300648,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	16 X 12 X 9=1728	3 X 3 X 2=18
	# samples	15	3
	** MAII score	log2(15/1728*10)=-3.52606881166759 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(3/18*10)=0.736965594166206 effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs). DoF>8 and MAII>0
Fusion gene context	PubMed: ABCC5 [Title/Abstract] AND GCN1L1 [Title/Abstract] AND fusion [Title/Abstract]
Fusion neoantigen context	PubMed: ABCC5 [Title/Abstract] AND GCN1L1 [Title/Abstract] AND neoantigen [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	ABCC5(183705558)-GCN1L1(120599862), # samples:1
Anticipated loss of major functional domain due to fusion event.	ABCC5-GCN1L1 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. ABCC5-GCN1L1 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. ABCC5-GCN1L1 seems lost the major protein functional domain in Hgene partner, which is a cell metabolism gene due to the frame-shifted ORF. ABCC5-GCN1L1 seems lost the major protein functional domain in Hgene 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	ABCC5	GO:0042908	xenobiotic transport	10840050
Hgene	ABCC5	GO:0140115	export across plasma membrane	10840050

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr3:183705558/chr12:120599862)
- 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 ABCC5 (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 GCN1L1 (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)

ENST00000265586

ABCC5

chr3

183705558

ENST00000300648

GCN1L1

chr12

120599862

7102

603

6455

2147

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
ENST00000265586	ENST00000300648	ABCC5	chr3	183705558	-	GCN1L1	chr12	120599862	-	0.005454185	0.9945458

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 ABCC5-GCN1L1

+/-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
ABCC5	chr3	183705558	GCN1L1	chr12	120599862	603	197	CLMITQLAGFSGPSSMNAMGSLSVLS

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Potential FusionNeoAntigen Information of ABCC5-GCN1L1 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.

ABCC5-GCN1L1_183705558_120599862.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)
ABCC5-GCN1L1	chr3	183705558	chr12	120599862	603	HLA-B46:01	AGFSGPSSM	0.9835	0.8055	7	16
ABCC5-GCN1L1	chr3	183705558	chr12	120599862	603	HLA-B07:10	AGFSGPSSM	0.5998	0.6559	7	16
ABCC5-GCN1L1	chr3	183705558	chr12	120599862	603	HLA-B46:01	LAGFSGPSSM	0.9929	0.7924	6	16
ABCC5-GCN1L1	chr3	183705558	chr12	120599862	603	HLA-B07:05	GPSSMNAMGSL	0.9997	0.6063	11	22
ABCC5-GCN1L1	chr3	183705558	chr12	120599862	603	HLA-B07:02	GPSSMNAMGSL	0.9996	0.5299	11	22
ABCC5-GCN1L1	chr3	183705558	chr12	120599862	603	HLA-B81:01	GPSSMNAMGSL	0.8021	0.7956	11	22
ABCC5-GCN1L1	chr3	183705558	chr12	120599862	603	HLA-C03:19	AGFSGPSSM	0.9964	0.9971	7	16
ABCC5-GCN1L1	chr3	183705558	chr12	120599862	603	HLA-C03:08	AGFSGPSSM	0.9943	0.9783	7	16
ABCC5-GCN1L1	chr3	183705558	chr12	120599862	603	HLA-C03:07	AGFSGPSSM	0.9923	0.9918	7	16
ABCC5-GCN1L1	chr3	183705558	chr12	120599862	603	HLA-C12:12	AGFSGPSSM	0.9732	0.9864	7	16
ABCC5-GCN1L1	chr3	183705558	chr12	120599862	603	HLA-C03:14	AGFSGPSSM	0.827	0.9938	7	16
ABCC5-GCN1L1	chr3	183705558	chr12	120599862	603	HLA-C08:13	AGFSGPSSM	0.7735	0.9948	7	16
ABCC5-GCN1L1	chr3	183705558	chr12	120599862	603	HLA-C08:04	AGFSGPSSM	0.7735	0.9948	7	16
ABCC5-GCN1L1	chr3	183705558	chr12	120599862	603	HLA-C01:17	SGPSSMNAM	0.6989	0.9788	10	19
ABCC5-GCN1L1	chr3	183705558	chr12	120599862	603	HLA-C01:30	SGPSSMNAM	0.6564	0.9846	10	19
ABCC5-GCN1L1	chr3	183705558	chr12	120599862	603	HLA-C01:17	FSGPSSMNAM	0.9964	0.9795	9	19
ABCC5-GCN1L1	chr3	183705558	chr12	120599862	603	HLA-C03:19	LAGFSGPSSM	0.9956	0.997	6	16
ABCC5-GCN1L1	chr3	183705558	chr12	120599862	603	HLA-C03:08	LAGFSGPSSM	0.9951	0.9711	6	16
ABCC5-GCN1L1	chr3	183705558	chr12	120599862	603	HLA-C12:12	LAGFSGPSSM	0.9915	0.9886	6	16
ABCC5-GCN1L1	chr3	183705558	chr12	120599862	603	HLA-C01:30	FSGPSSMNAM	0.9881	0.9876	9	19
ABCC5-GCN1L1	chr3	183705558	chr12	120599862	603	HLA-B07:12	GPSSMNAMGSL	0.9984	0.6611	11	22
ABCC5-GCN1L1	chr3	183705558	chr12	120599862	603	HLA-C14:02	GFSGPSSM	0.9408	0.9921	8	16
ABCC5-GCN1L1	chr3	183705558	chr12	120599862	603	HLA-C14:03	GFSGPSSM	0.9408	0.9921	8	16
ABCC5-GCN1L1	chr3	183705558	chr12	120599862	603	HLA-C03:02	AGFSGPSSM	0.9968	0.9895	7	16
ABCC5-GCN1L1	chr3	183705558	chr12	120599862	603	HLA-C03:04	AGFSGPSSM	0.9967	0.9968	7	16
ABCC5-GCN1L1	chr3	183705558	chr12	120599862	603	HLA-C03:03	AGFSGPSSM	0.9967	0.9968	7	16
ABCC5-GCN1L1	chr3	183705558	chr12	120599862	603	HLA-C03:67	AGFSGPSSM	0.9948	0.9954	7	16
ABCC5-GCN1L1	chr3	183705558	chr12	120599862	603	HLA-C03:05	AGFSGPSSM	0.9942	0.9773	7	16
ABCC5-GCN1L1	chr3	183705558	chr12	120599862	603	HLA-C03:17	AGFSGPSSM	0.993	0.9891	7	16
ABCC5-GCN1L1	chr3	183705558	chr12	120599862	603	HLA-C12:02	AGFSGPSSM	0.985	0.99	7	16
ABCC5-GCN1L1	chr3	183705558	chr12	120599862	603	HLA-C12:03	AGFSGPSSM	0.9694	0.9934	7	16
ABCC5-GCN1L1	chr3	183705558	chr12	120599862	603	HLA-B15:73	AGFSGPSSM	0.8533	0.9932	7	16
ABCC5-GCN1L1	chr3	183705558	chr12	120599862	603	HLA-C03:06	AGFSGPSSM	0.8238	0.9969	7	16
ABCC5-GCN1L1	chr3	183705558	chr12	120599862	603	HLA-B35:13	AGFSGPSSM	0.8073	0.9474	7	16
ABCC5-GCN1L1	chr3	183705558	chr12	120599862	603	HLA-B15:30	AGFSGPSSM	0.7816	0.985	7	16
ABCC5-GCN1L1	chr3	183705558	chr12	120599862	603	HLA-C16:01	AGFSGPSSM	0.7772	0.9955	7	16
ABCC5-GCN1L1	chr3	183705558	chr12	120599862	603	HLA-C01:02	SGPSSMNAM	0.7102	0.9783	10	19
ABCC5-GCN1L1	chr3	183705558	chr12	120599862	603	HLA-B07:13	AGFSGPSSM	0.657	0.9088	7	16
ABCC5-GCN1L1	chr3	183705558	chr12	120599862	603	HLA-B48:05	AGFSGPSSM	0.6279	0.5747	7	16
ABCC5-GCN1L1	chr3	183705558	chr12	120599862	603	HLA-C01:03	SGPSSMNAM	0.5802	0.9758	10	19
ABCC5-GCN1L1	chr3	183705558	chr12	120599862	603	HLA-C01:03	FSGPSSMNAM	0.9975	0.9755	9	19
ABCC5-GCN1L1	chr3	183705558	chr12	120599862	603	HLA-C03:04	LAGFSGPSSM	0.9972	0.9963	6	16
ABCC5-GCN1L1	chr3	183705558	chr12	120599862	603	HLA-C03:03	LAGFSGPSSM	0.9972	0.9963	6	16
ABCC5-GCN1L1	chr3	183705558	chr12	120599862	603	HLA-C12:02	LAGFSGPSSM	0.997	0.9916	6	16
ABCC5-GCN1L1	chr3	183705558	chr12	120599862	603	HLA-C03:02	LAGFSGPSSM	0.9965	0.9889	6	16
ABCC5-GCN1L1	chr3	183705558	chr12	120599862	603	HLA-C01:02	FSGPSSMNAM	0.9947	0.9785	9	19
ABCC5-GCN1L1	chr3	183705558	chr12	120599862	603	HLA-C03:05	LAGFSGPSSM	0.9945	0.9678	6	16
ABCC5-GCN1L1	chr3	183705558	chr12	120599862	603	HLA-B35:43	LAGFSGPSSM	0.9863	0.9605	6	16
ABCC5-GCN1L1	chr3	183705558	chr12	120599862	603	HLA-B07:22	GPSSMNAMGSL	0.9996	0.5299	11	22

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Potential FusionNeoAntigen Information of ABCC5-GCN1L1 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 ABCC5-GCN1L1

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
4741	LAGFSGPSSMNAMG	ABCC5	GCN1L1	chr3	183705558	chr12	120599862	603

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of ABCC5-GCN1L1

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	4741	LAGFSGPSSMNAMG	-7.75776	-7.86956
HLA-B14:02	3BVN	4741	LAGFSGPSSMNAMG	-4.52646	-5.56956
HLA-B52:01	3W39	4741	LAGFSGPSSMNAMG	-7.1873	-7.2991
HLA-B52:01	3W39	4741	LAGFSGPSSMNAMG	-2.81174	-3.85484
HLA-A11:01	4UQ2	4741	LAGFSGPSSMNAMG	-5.13576	-5.24756
HLA-A24:02	5HGA	4741	LAGFSGPSSMNAMG	-8.42076	-8.53256
HLA-A24:02	5HGA	4741	LAGFSGPSSMNAMG	-7.10496	-8.14806
HLA-B27:05	6PYJ	4741	LAGFSGPSSMNAMG	-9.28296	-9.39476
HLA-B44:05	3DX8	4741	LAGFSGPSSMNAMG	-6.88262	-6.99442
HLA-B44:05	3DX8	4741	LAGFSGPSSMNAMG	-5.46822	-6.51132

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Vaccine Design for the FusionNeoAntigens of ABCC5-GCN1L1

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
ABCC5-GCN1L1	chr3	183705558	chr12	120599862	10	19	SGPSSMNAM	AGTGGACCATCCTCCATGAATGCCATG
ABCC5-GCN1L1	chr3	183705558	chr12	120599862	11	22	GPSSMNAMGSL	GGACCATCCTCCATGAATGCCATGGGCTCCCTT
ABCC5-GCN1L1	chr3	183705558	chr12	120599862	6	16	LAGFSGPSSM	CTGGCTGGCTTCAGTGGACCATCCTCCATG
ABCC5-GCN1L1	chr3	183705558	chr12	120599862	7	16	AGFSGPSSM	GCTGGCTTCAGTGGACCATCCTCCATG
ABCC5-GCN1L1	chr3	183705558	chr12	120599862	8	16	GFSGPSSM	GGCTTCAGTGGACCATCCTCCATG
ABCC5-GCN1L1	chr3	183705558	chr12	120599862	9	19	FSGPSSMNAM	TTCAGTGGACCATCCTCCATGAATGCCATG

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 ABCC5-GCN1L1

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
STAD	ABCC5-GCN1L1	chr3	183705558	ENST00000265586	chr12	120599862	ENST00000300648	TCGA-BR-8284-01A

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Potential target of CAR-T therapy development for ABCC5-GCN1L1

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

ABCC5

chr3:183705558

chr12:120599862

ENST00000334444

179_199

197

1438.0

Transmembrane

Helical

Hgene

ABCC5

chr3:183705558

chr12:120599862

ENST00000382494

179_199

197

533.3333333333334

Transmembrane

Helical

Hgene

ABCC5

chr3:183705558

chr12:120599862

ENST00000392579

179_199

197

226.0

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 ABCC5-GCN1L1

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 ABCC5-GCN1L1

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)