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Fusion Protein:NFIX-GCDH

Fusion Gene and Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: NFIX-GCDH
	FusionPDB ID: 58947
	FusionGDB2.0 ID: 58947
		Hgene	Tgene
	Gene symbol	NFIX	GCDH
	Gene ID	4784	2639
	Gene name	nuclear factor I X	glutaryl-CoA dehydrogenase
	Synonyms	CTF\|MRSHSS\|NF-I/X\|NF1-X\|NF1A\|SOTOS2	ACAD5\|GCD
	Cytomap	19p13.13	19p13.13
	Type of gene	protein-coding	protein-coding
	Description	nuclear factor 1 X-typeCCAAT-box-binding transcription factorTGGCA-binding proteinnuclear factor 1/X	glutaryl-CoA dehydrogenase, mitochondrialglutaryl-Coenzyme A dehydrogenasetruncated GCDHtruncated glutaryl-CoA dehydrogenase
	Modification date	20200329	20200313
	UniProtAcc	Q14938 Main function of 5'-partner protein: FUNCTION: Recognizes and binds the palindromic sequence 5'-TTGGCNNNNNGCCAA-3' present in viral and cellular promoters and in the origin of replication of adenovirus type 2. These proteins are individually capable of activating transcription and replication.	Q92947 Main function of 5'-partner protein: FUNCTION: Catalyzes the oxidative decarboxylation of glutaryl-CoA to crotonyl-CoA and CO(2) in the degradative pathway of L-lysine, L-hydroxylysine, and L-tryptophan metabolism. It uses electron transfer flavoprotein as its electron acceptor. Isoform Short is inactive. {ECO:0000269\|PubMed:17176108, ECO:0000269\|PubMed:6423663, ECO:0000269\|PubMed:8541831}.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000358552, ENST00000360105, ENST00000397661, ENST00000585575, ENST00000587260, ENST00000587760, ENST00000588228, ENST00000592199, ENST00000588680,	ENST00000222214, ENST00000422947, ENST00000457854, ENST00000591470, ENST00000588242,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	27 X 14 X 16=6048	7 X 10 X 4=280
	# samples	42	9
	** MAII score	log2(42/6048*10)=-3.84799690655495 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(9/280*10)=-1.63742992061529 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Fusion gene context	PubMed: NFIX [Title/Abstract] AND GCDH [Title/Abstract] AND fusion [Title/Abstract]
Fusion neoantigen context	PubMed: NFIX [Title/Abstract] AND GCDH [Title/Abstract] AND neoantigen [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	NFIX(13136366)-GCDH(13002930), # samples:2
Anticipated loss of major functional domain due to fusion event.	NFIX-GCDH 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. NFIX-GCDH 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. NFIX-GCDH 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. NFIX-GCDH 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	NFIX	GO:0000122	negative regulation of transcription by RNA polymerase II	19706729
Hgene	NFIX	GO:0045944	positive regulation of transcription by RNA polymerase II	19706729
Tgene	GCDH	GO:0033539	fatty acid beta-oxidation using acyl-CoA dehydrogenase	25416781

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr19:13136366/chr19:13002930)
- 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 NFIX (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 GCDH (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)
ENST00000397661	NFIX	chr19	13136366	+	ENST00000222214	GCDH	chr19	13002929	+	2263	789	173	1834	553
ENST00000397661	NFIX	chr19	13136366	+	ENST00000591470	GCDH	chr19	13002929	+	2240	789	173	1834	553
ENST00000397661	NFIX	chr19	13136366	+	ENST00000457854	GCDH	chr19	13002929	+	2030	789	173	1804	543
ENST00000592199	NFIX	chr19	13136366	+	ENST00000222214	GCDH	chr19	13002929	+	2033	559	0	1604	534
ENST00000592199	NFIX	chr19	13136366	+	ENST00000591470	GCDH	chr19	13002929	+	2010	559	0	1604	534
ENST00000592199	NFIX	chr19	13136366	+	ENST00000457854	GCDH	chr19	13002929	+	1800	559	0	1574	524
ENST00000587760	NFIX	chr19	13136366	+	ENST00000222214	GCDH	chr19	13002929	+	2050	576	14	1621	535
ENST00000587760	NFIX	chr19	13136366	+	ENST00000591470	GCDH	chr19	13002929	+	2027	576	14	1621	535
ENST00000587760	NFIX	chr19	13136366	+	ENST00000457854	GCDH	chr19	13002929	+	1817	576	14	1591	525
ENST00000585575	NFIX	chr19	13136366	+	ENST00000222214	GCDH	chr19	13002929	+	2009	535	0	1580	526
ENST00000585575	NFIX	chr19	13136366	+	ENST00000591470	GCDH	chr19	13002929	+	1986	535	0	1580	526
ENST00000585575	NFIX	chr19	13136366	+	ENST00000457854	GCDH	chr19	13002929	+	1776	535	0	1550	516
ENST00000360105	NFIX	chr19	13136366	+	ENST00000222214	GCDH	chr19	13002929	+	2107	633	65	1678	537
ENST00000360105	NFIX	chr19	13136366	+	ENST00000591470	GCDH	chr19	13002929	+	2084	633	65	1678	537
ENST00000360105	NFIX	chr19	13136366	+	ENST00000457854	GCDH	chr19	13002929	+	1874	633	65	1648	527
ENST00000588228	NFIX	chr19	13136366	+	ENST00000222214	GCDH	chr19	13002929	+	2110	636	53	1681	542
ENST00000588228	NFIX	chr19	13136366	+	ENST00000591470	GCDH	chr19	13002929	+	2087	636	53	1681	542
ENST00000588228	NFIX	chr19	13136366	+	ENST00000457854	GCDH	chr19	13002929	+	1877	636	53	1651	532
ENST00000587260	NFIX	chr19	13136366	+	ENST00000222214	GCDH	chr19	13002929	+	2088	614	58	1659	533
ENST00000587260	NFIX	chr19	13136366	+	ENST00000591470	GCDH	chr19	13002929	+	2065	614	58	1659	533
ENST00000587260	NFIX	chr19	13136366	+	ENST00000457854	GCDH	chr19	13002929	+	1855	614	58	1629	523
ENST00000358552	NFIX	chr19	13136366	+	ENST00000222214	GCDH	chr19	13002929	+	2030	556	0	1601	533
ENST00000358552	NFIX	chr19	13136366	+	ENST00000591470	GCDH	chr19	13002929	+	2007	556	0	1601	533
ENST00000358552	NFIX	chr19	13136366	+	ENST00000457854	GCDH	chr19	13002929	+	1797	556	0	1571	523
ENST00000397661	NFIX	chr19	13136366	+	ENST00000222214	GCDH	chr19	13002930	+	2263	789	173	1834	553
ENST00000397661	NFIX	chr19	13136366	+	ENST00000591470	GCDH	chr19	13002930	+	2240	789	173	1834	553
ENST00000397661	NFIX	chr19	13136366	+	ENST00000457854	GCDH	chr19	13002930	+	2030	789	173	1804	543
ENST00000592199	NFIX	chr19	13136366	+	ENST00000222214	GCDH	chr19	13002930	+	2033	559	0	1604	534
ENST00000592199	NFIX	chr19	13136366	+	ENST00000591470	GCDH	chr19	13002930	+	2010	559	0	1604	534
ENST00000592199	NFIX	chr19	13136366	+	ENST00000457854	GCDH	chr19	13002930	+	1800	559	0	1574	524
ENST00000587760	NFIX	chr19	13136366	+	ENST00000222214	GCDH	chr19	13002930	+	2050	576	14	1621	535
ENST00000587760	NFIX	chr19	13136366	+	ENST00000591470	GCDH	chr19	13002930	+	2027	576	14	1621	535
ENST00000587760	NFIX	chr19	13136366	+	ENST00000457854	GCDH	chr19	13002930	+	1817	576	14	1591	525
ENST00000585575	NFIX	chr19	13136366	+	ENST00000222214	GCDH	chr19	13002930	+	2009	535	0	1580	526
ENST00000585575	NFIX	chr19	13136366	+	ENST00000591470	GCDH	chr19	13002930	+	1986	535	0	1580	526
ENST00000585575	NFIX	chr19	13136366	+	ENST00000457854	GCDH	chr19	13002930	+	1776	535	0	1550	516
ENST00000360105	NFIX	chr19	13136366	+	ENST00000222214	GCDH	chr19	13002930	+	2107	633	65	1678	537
ENST00000360105	NFIX	chr19	13136366	+	ENST00000591470	GCDH	chr19	13002930	+	2084	633	65	1678	537
ENST00000360105	NFIX	chr19	13136366	+	ENST00000457854	GCDH	chr19	13002930	+	1874	633	65	1648	527
ENST00000588228	NFIX	chr19	13136366	+	ENST00000222214	GCDH	chr19	13002930	+	2110	636	53	1681	542
ENST00000588228	NFIX	chr19	13136366	+	ENST00000591470	GCDH	chr19	13002930	+	2087	636	53	1681	542
ENST00000588228	NFIX	chr19	13136366	+	ENST00000457854	GCDH	chr19	13002930	+	1877	636	53	1651	532
ENST00000587260	NFIX	chr19	13136366	+	ENST00000222214	GCDH	chr19	13002930	+	2088	614	58	1659	533
ENST00000587260	NFIX	chr19	13136366	+	ENST00000591470	GCDH	chr19	13002930	+	2065	614	58	1659	533
ENST00000587260	NFIX	chr19	13136366	+	ENST00000457854	GCDH	chr19	13002930	+	1855	614	58	1629	523
ENST00000358552	NFIX	chr19	13136366	+	ENST00000222214	GCDH	chr19	13002930	+	2030	556	0	1601	533
ENST00000358552	NFIX	chr19	13136366	+	ENST00000591470	GCDH	chr19	13002930	+	2007	556	0	1601	533
ENST00000358552	NFIX	chr19	13136366	+	ENST00000457854	GCDH	chr19	13002930	+	1797	556	0	1571	523
ENST00000397661	NFIX	chr19	13136366	+	ENST00000222214	GCDH	chr19	13004297	+	2200	789	173	1771	532
ENST00000397661	NFIX	chr19	13136366	+	ENST00000591470	GCDH	chr19	13004297	+	2177	789	173	1771	532
ENST00000397661	NFIX	chr19	13136366	+	ENST00000457854	GCDH	chr19	13004297	+	1967	789	173	1741	522
ENST00000397661	NFIX	chr19	13136366	+	ENST00000422947	GCDH	chr19	13004297	+	2200	789	173	1771	532
ENST00000592199	NFIX	chr19	13136366	+	ENST00000222214	GCDH	chr19	13004297	+	1970	559	0	1541	513
ENST00000592199	NFIX	chr19	13136366	+	ENST00000591470	GCDH	chr19	13004297	+	1947	559	0	1541	513
ENST00000592199	NFIX	chr19	13136366	+	ENST00000457854	GCDH	chr19	13004297	+	1737	559	0	1511	503
ENST00000592199	NFIX	chr19	13136366	+	ENST00000422947	GCDH	chr19	13004297	+	1970	559	0	1541	513
ENST00000587760	NFIX	chr19	13136366	+	ENST00000222214	GCDH	chr19	13004297	+	1987	576	14	1558	514
ENST00000587760	NFIX	chr19	13136366	+	ENST00000591470	GCDH	chr19	13004297	+	1964	576	14	1558	514
ENST00000587760	NFIX	chr19	13136366	+	ENST00000457854	GCDH	chr19	13004297	+	1754	576	14	1528	504
ENST00000587760	NFIX	chr19	13136366	+	ENST00000422947	GCDH	chr19	13004297	+	1987	576	14	1558	514
ENST00000585575	NFIX	chr19	13136366	+	ENST00000222214	GCDH	chr19	13004297	+	1946	535	0	1517	505
ENST00000585575	NFIX	chr19	13136366	+	ENST00000591470	GCDH	chr19	13004297	+	1923	535	0	1517	505
ENST00000585575	NFIX	chr19	13136366	+	ENST00000457854	GCDH	chr19	13004297	+	1713	535	0	1487	495
ENST00000585575	NFIX	chr19	13136366	+	ENST00000422947	GCDH	chr19	13004297	+	1946	535	0	1517	505
ENST00000360105	NFIX	chr19	13136366	+	ENST00000222214	GCDH	chr19	13004297	+	2044	633	65	1615	516
ENST00000360105	NFIX	chr19	13136366	+	ENST00000591470	GCDH	chr19	13004297	+	2021	633	65	1615	516
ENST00000360105	NFIX	chr19	13136366	+	ENST00000457854	GCDH	chr19	13004297	+	1811	633	65	1585	506
ENST00000360105	NFIX	chr19	13136366	+	ENST00000422947	GCDH	chr19	13004297	+	2044	633	65	1615	516
ENST00000588228	NFIX	chr19	13136366	+	ENST00000222214	GCDH	chr19	13004297	+	2047	636	53	1618	521
ENST00000588228	NFIX	chr19	13136366	+	ENST00000591470	GCDH	chr19	13004297	+	2024	636	53	1618	521
ENST00000588228	NFIX	chr19	13136366	+	ENST00000457854	GCDH	chr19	13004297	+	1814	636	53	1588	511
ENST00000588228	NFIX	chr19	13136366	+	ENST00000422947	GCDH	chr19	13004297	+	2047	636	53	1618	521
ENST00000587260	NFIX	chr19	13136366	+	ENST00000222214	GCDH	chr19	13004297	+	2025	614	58	1596	512
ENST00000587260	NFIX	chr19	13136366	+	ENST00000591470	GCDH	chr19	13004297	+	2002	614	58	1596	512
ENST00000587260	NFIX	chr19	13136366	+	ENST00000457854	GCDH	chr19	13004297	+	1792	614	58	1566	502
ENST00000587260	NFIX	chr19	13136366	+	ENST00000422947	GCDH	chr19	13004297	+	2025	614	58	1596	512
ENST00000358552	NFIX	chr19	13136366	+	ENST00000222214	GCDH	chr19	13004297	+	1967	556	0	1538	512
ENST00000358552	NFIX	chr19	13136366	+	ENST00000591470	GCDH	chr19	13004297	+	1944	556	0	1538	512
ENST00000358552	NFIX	chr19	13136366	+	ENST00000457854	GCDH	chr19	13004297	+	1734	556	0	1508	502
ENST00000358552	NFIX	chr19	13136366	+	ENST00000422947	GCDH	chr19	13004297	+	1967	556	0	1538	512

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
ENST00000397661	ENST00000222214	NFIX	chr19	13136366	+	GCDH	chr19	13002929	+	0.01727589	0.98272413
ENST00000397661	ENST00000591470	NFIX	chr19	13136366	+	GCDH	chr19	13002929	+	0.01775126	0.9822488
ENST00000397661	ENST00000457854	NFIX	chr19	13136366	+	GCDH	chr19	13002929	+	0.018909436	0.9810906
ENST00000592199	ENST00000222214	NFIX	chr19	13136366	+	GCDH	chr19	13002929	+	0.014521918	0.98547804
ENST00000592199	ENST00000591470	NFIX	chr19	13136366	+	GCDH	chr19	13002929	+	0.015130046	0.98486996
ENST00000592199	ENST00000457854	NFIX	chr19	13136366	+	GCDH	chr19	13002929	+	0.016676608	0.9833234
ENST00000587760	ENST00000222214	NFIX	chr19	13136366	+	GCDH	chr19	13002929	+	0.007095414	0.9929046
ENST00000587760	ENST00000591470	NFIX	chr19	13136366	+	GCDH	chr19	13002929	+	0.007372593	0.99262744
ENST00000587760	ENST00000457854	NFIX	chr19	13136366	+	GCDH	chr19	13002929	+	0.008592823	0.99140716
ENST00000585575	ENST00000222214	NFIX	chr19	13136366	+	GCDH	chr19	13002929	+	0.007106633	0.9928934
ENST00000585575	ENST00000591470	NFIX	chr19	13136366	+	GCDH	chr19	13002929	+	0.007393658	0.9926064
ENST00000585575	ENST00000457854	NFIX	chr19	13136366	+	GCDH	chr19	13002929	+	0.008498183	0.9915018
ENST00000360105	ENST00000222214	NFIX	chr19	13136366	+	GCDH	chr19	13002929	+	0.01680802	0.983192
ENST00000360105	ENST00000591470	NFIX	chr19	13136366	+	GCDH	chr19	13002929	+	0.01746535	0.9825347
ENST00000360105	ENST00000457854	NFIX	chr19	13136366	+	GCDH	chr19	13002929	+	0.019884527	0.9801154
ENST00000588228	ENST00000222214	NFIX	chr19	13136366	+	GCDH	chr19	13002929	+	0.011206248	0.9887938
ENST00000588228	ENST00000591470	NFIX	chr19	13136366	+	GCDH	chr19	13002929	+	0.011748896	0.98825103
ENST00000588228	ENST00000457854	NFIX	chr19	13136366	+	GCDH	chr19	13002929	+	0.013882415	0.98611754
ENST00000587260	ENST00000222214	NFIX	chr19	13136366	+	GCDH	chr19	13002929	+	0.01642726	0.9835728
ENST00000587260	ENST00000591470	NFIX	chr19	13136366	+	GCDH	chr19	13002929	+	0.017017985	0.982982
ENST00000587260	ENST00000457854	NFIX	chr19	13136366	+	GCDH	chr19	13002929	+	0.017959185	0.98204076
ENST00000358552	ENST00000222214	NFIX	chr19	13136366	+	GCDH	chr19	13002929	+	0.014802735	0.98519725
ENST00000358552	ENST00000591470	NFIX	chr19	13136366	+	GCDH	chr19	13002929	+	0.01541255	0.98458743
ENST00000358552	ENST00000457854	NFIX	chr19	13136366	+	GCDH	chr19	13002929	+	0.016496373	0.9835036
ENST00000397661	ENST00000222214	NFIX	chr19	13136366	+	GCDH	chr19	13002930	+	0.01727589	0.98272413
ENST00000397661	ENST00000591470	NFIX	chr19	13136366	+	GCDH	chr19	13002930	+	0.01775126	0.9822488
ENST00000397661	ENST00000457854	NFIX	chr19	13136366	+	GCDH	chr19	13002930	+	0.018909436	0.9810906
ENST00000592199	ENST00000222214	NFIX	chr19	13136366	+	GCDH	chr19	13002930	+	0.014521918	0.98547804
ENST00000592199	ENST00000591470	NFIX	chr19	13136366	+	GCDH	chr19	13002930	+	0.015130046	0.98486996
ENST00000592199	ENST00000457854	NFIX	chr19	13136366	+	GCDH	chr19	13002930	+	0.016676608	0.9833234
ENST00000587760	ENST00000222214	NFIX	chr19	13136366	+	GCDH	chr19	13002930	+	0.007095414	0.9929046
ENST00000587760	ENST00000591470	NFIX	chr19	13136366	+	GCDH	chr19	13002930	+	0.007372593	0.99262744
ENST00000587760	ENST00000457854	NFIX	chr19	13136366	+	GCDH	chr19	13002930	+	0.008592823	0.99140716
ENST00000585575	ENST00000222214	NFIX	chr19	13136366	+	GCDH	chr19	13002930	+	0.007106633	0.9928934
ENST00000585575	ENST00000591470	NFIX	chr19	13136366	+	GCDH	chr19	13002930	+	0.007393658	0.9926064
ENST00000585575	ENST00000457854	NFIX	chr19	13136366	+	GCDH	chr19	13002930	+	0.008498183	0.9915018
ENST00000360105	ENST00000222214	NFIX	chr19	13136366	+	GCDH	chr19	13002930	+	0.01680802	0.983192
ENST00000360105	ENST00000591470	NFIX	chr19	13136366	+	GCDH	chr19	13002930	+	0.01746535	0.9825347
ENST00000360105	ENST00000457854	NFIX	chr19	13136366	+	GCDH	chr19	13002930	+	0.019884527	0.9801154
ENST00000588228	ENST00000222214	NFIX	chr19	13136366	+	GCDH	chr19	13002930	+	0.011206248	0.9887938
ENST00000588228	ENST00000591470	NFIX	chr19	13136366	+	GCDH	chr19	13002930	+	0.011748896	0.98825103
ENST00000588228	ENST00000457854	NFIX	chr19	13136366	+	GCDH	chr19	13002930	+	0.013882415	0.98611754
ENST00000587260	ENST00000222214	NFIX	chr19	13136366	+	GCDH	chr19	13002930	+	0.01642726	0.9835728
ENST00000587260	ENST00000591470	NFIX	chr19	13136366	+	GCDH	chr19	13002930	+	0.017017985	0.982982
ENST00000587260	ENST00000457854	NFIX	chr19	13136366	+	GCDH	chr19	13002930	+	0.017959185	0.98204076
ENST00000358552	ENST00000222214	NFIX	chr19	13136366	+	GCDH	chr19	13002930	+	0.014802735	0.98519725
ENST00000358552	ENST00000591470	NFIX	chr19	13136366	+	GCDH	chr19	13002930	+	0.01541255	0.98458743
ENST00000358552	ENST00000457854	NFIX	chr19	13136366	+	GCDH	chr19	13002930	+	0.016496373	0.9835036
ENST00000397661	ENST00000222214	NFIX	chr19	13136366	+	GCDH	chr19	13004297	+	0.015416038	0.984584
ENST00000397661	ENST00000591470	NFIX	chr19	13136366	+	GCDH	chr19	13004297	+	0.015825283	0.98417467
ENST00000397661	ENST00000457854	NFIX	chr19	13136366	+	GCDH	chr19	13004297	+	0.018492203	0.98150784
ENST00000397661	ENST00000422947	NFIX	chr19	13136366	+	GCDH	chr19	13004297	+	0.015416038	0.984584
ENST00000592199	ENST00000222214	NFIX	chr19	13136366	+	GCDH	chr19	13004297	+	0.013247496	0.9867525
ENST00000592199	ENST00000591470	NFIX	chr19	13136366	+	GCDH	chr19	13004297	+	0.013813113	0.98618686
ENST00000592199	ENST00000457854	NFIX	chr19	13136366	+	GCDH	chr19	13004297	+	0.016941322	0.9830587
ENST00000592199	ENST00000422947	NFIX	chr19	13136366	+	GCDH	chr19	13004297	+	0.013247496	0.9867525
ENST00000587760	ENST00000222214	NFIX	chr19	13136366	+	GCDH	chr19	13004297	+	0.004697594	0.99530244
ENST00000587760	ENST00000591470	NFIX	chr19	13136366	+	GCDH	chr19	13004297	+	0.004858353	0.9951416
ENST00000587760	ENST00000457854	NFIX	chr19	13136366	+	GCDH	chr19	13004297	+	0.00548903	0.994511
ENST00000587760	ENST00000422947	NFIX	chr19	13136366	+	GCDH	chr19	13004297	+	0.004697594	0.99530244
ENST00000585575	ENST00000222214	NFIX	chr19	13136366	+	GCDH	chr19	13004297	+	0.004729144	0.9952709
ENST00000585575	ENST00000591470	NFIX	chr19	13136366	+	GCDH	chr19	13004297	+	0.004881579	0.9951184
ENST00000585575	ENST00000457854	NFIX	chr19	13136366	+	GCDH	chr19	13004297	+	0.005500002	0.9944999
ENST00000585575	ENST00000422947	NFIX	chr19	13136366	+	GCDH	chr19	13004297	+	0.004729144	0.9952709
ENST00000360105	ENST00000222214	NFIX	chr19	13136366	+	GCDH	chr19	13004297	+	0.02096564	0.97903436
ENST00000360105	ENST00000591470	NFIX	chr19	13136366	+	GCDH	chr19	13004297	+	0.021784564	0.9782154
ENST00000360105	ENST00000457854	NFIX	chr19	13136366	+	GCDH	chr19	13004297	+	0.026114523	0.9738854
ENST00000360105	ENST00000422947	NFIX	chr19	13136366	+	GCDH	chr19	13004297	+	0.02096564	0.97903436
ENST00000588228	ENST00000222214	NFIX	chr19	13136366	+	GCDH	chr19	13004297	+	0.015774142	0.9842258
ENST00000588228	ENST00000591470	NFIX	chr19	13136366	+	GCDH	chr19	13004297	+	0.016454589	0.9835454
ENST00000588228	ENST00000457854	NFIX	chr19	13136366	+	GCDH	chr19	13004297	+	0.01867694	0.9813231
ENST00000588228	ENST00000422947	NFIX	chr19	13136366	+	GCDH	chr19	13004297	+	0.015774142	0.9842258
ENST00000587260	ENST00000222214	NFIX	chr19	13136366	+	GCDH	chr19	13004297	+	0.014136517	0.9858635
ENST00000587260	ENST00000591470	NFIX	chr19	13136366	+	GCDH	chr19	13004297	+	0.014627356	0.9853726
ENST00000587260	ENST00000457854	NFIX	chr19	13136366	+	GCDH	chr19	13004297	+	0.016353998	0.98364604
ENST00000587260	ENST00000422947	NFIX	chr19	13136366	+	GCDH	chr19	13004297	+	0.014136517	0.9858635
ENST00000358552	ENST00000222214	NFIX	chr19	13136366	+	GCDH	chr19	13004297	+	0.012885735	0.9871143
ENST00000358552	ENST00000591470	NFIX	chr19	13136366	+	GCDH	chr19	13004297	+	0.013368212	0.9866318
ENST00000358552	ENST00000457854	NFIX	chr19	13136366	+	GCDH	chr19	13004297	+	0.015303955	0.98469603
ENST00000358552	ENST00000422947	NFIX	chr19	13136366	+	GCDH	chr19	13004297	+	0.012885735	0.9871143

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 NFIX-GCDH

+/-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
NFIX	chr19	13136366	GCDH	chr19	13002929	535	178	ELDLYLAYFVHTPVFHREIISEMGEL
NFIX	chr19	13136366	GCDH	chr19	13002929	556	185	ELDLYLAYFVHTPVFHREIISEMGEL
NFIX	chr19	13136366	GCDH	chr19	13002929	559	186	ELDLYLAYFVHTPVFHREIISEMGEL
NFIX	chr19	13136366	GCDH	chr19	13002929	576	187	ELDLYLAYFVHTPVFHREIISEMGEL
NFIX	chr19	13136366	GCDH	chr19	13002929	614	185	ELDLYLAYFVHTPVFHREIISEMGEL
NFIX	chr19	13136366	GCDH	chr19	13002929	633	189	ELDLYLAYFVHTPVFHREIISEMGEL
NFIX	chr19	13136366	GCDH	chr19	13002929	636	194	ELDLYLAYFVHTPVFHREIISEMGEL
NFIX	chr19	13136366	GCDH	chr19	13002929	789	205	ELDLYLAYFVHTPVFHREIISEMGEL
NFIX	chr19	13136366	GCDH	chr19	13002930	535	178	ELDLYLAYFVHTPVFHREIISEMGEL
NFIX	chr19	13136366	GCDH	chr19	13002930	556	185	ELDLYLAYFVHTPVFHREIISEMGEL
NFIX	chr19	13136366	GCDH	chr19	13002930	559	186	ELDLYLAYFVHTPVFHREIISEMGEL
NFIX	chr19	13136366	GCDH	chr19	13002930	576	187	ELDLYLAYFVHTPVFHREIISEMGEL
NFIX	chr19	13136366	GCDH	chr19	13002930	614	185	ELDLYLAYFVHTPVFHREIISEMGEL
NFIX	chr19	13136366	GCDH	chr19	13002930	633	189	ELDLYLAYFVHTPVFHREIISEMGEL
NFIX	chr19	13136366	GCDH	chr19	13002930	636	194	ELDLYLAYFVHTPVFHREIISEMGEL
NFIX	chr19	13136366	GCDH	chr19	13002930	789	205	ELDLYLAYFVHTPVFHREIISEMGEL
NFIX	chr19	13136366	GCDH	chr19	13004297	535	177	KELDLYLAYFVHTPGYGCAGVSSVAY
NFIX	chr19	13136366	GCDH	chr19	13004297	556	184	KELDLYLAYFVHTPGYGCAGVSSVAY
NFIX	chr19	13136366	GCDH	chr19	13004297	559	185	KELDLYLAYFVHTPGYGCAGVSSVAY
NFIX	chr19	13136366	GCDH	chr19	13004297	576	186	KELDLYLAYFVHTPGYGCAGVSSVAY
NFIX	chr19	13136366	GCDH	chr19	13004297	614	184	KELDLYLAYFVHTPGYGCAGVSSVAY
NFIX	chr19	13136366	GCDH	chr19	13004297	633	188	KELDLYLAYFVHTPGYGCAGVSSVAY
NFIX	chr19	13136366	GCDH	chr19	13004297	636	193	KELDLYLAYFVHTPGYGCAGVSSVAY
NFIX	chr19	13136366	GCDH	chr19	13004297	789	204	KELDLYLAYFVHTPGYGCAGVSSVAY

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Potential FusionNeoAntigen Information of NFIX-GCDH 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.

NFIX-GCDH_13136366_13002929.msa
NFIX-GCDH_13136366_13004297.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)
NFIX-GCDH	chr19	13136366	chr19	13002929	556	HLA-B51:01	LAYFVHTPV	0.9967	0.6555	5	14
NFIX-GCDH	chr19	13136366	chr19	13002929	556	HLA-A74:09	FVHTPVFHR	0.9309	0.6002	8	17
NFIX-GCDH	chr19	13136366	chr19	13002929	556	HLA-A74:03	FVHTPVFHR	0.9309	0.6002	8	17
NFIX-GCDH	chr19	13136366	chr19	13002929	556	HLA-A74:11	FVHTPVFHR	0.9309	0.6002	8	17
NFIX-GCDH	chr19	13136366	chr19	13002929	556	HLA-A32:13	AYFVHTPVF	0.9082	0.7669	6	15
NFIX-GCDH	chr19	13136366	chr19	13002929	556	HLA-A31:02	FVHTPVFHR	0.8976	0.5153	8	17
NFIX-GCDH	chr19	13136366	chr19	13002929	556	HLA-B15:03	AYFVHTPVF	0.357	0.6552	6	15
NFIX-GCDH	chr19	13136366	chr19	13002929	556	HLA-B15:18	AYFVHTPVF	0.2978	0.5616	6	15
NFIX-GCDH	chr19	13136366	chr19	13002929	556	HLA-B38:01	VHTPVFHREI	0.9565	0.9405	9	19
NFIX-GCDH	chr19	13136366	chr19	13002929	556	HLA-B38:02	VHTPVFHREI	0.9484	0.947	9	19
NFIX-GCDH	chr19	13136366	chr19	13002929	556	HLA-A31:02	AYFVHTPVFHR	0.9896	0.5452	6	17
NFIX-GCDH	chr19	13136366	chr19	13002929	556	HLA-A74:03	AYFVHTPVFHR	0.9845	0.6391	6	17
NFIX-GCDH	chr19	13136366	chr19	13002929	556	HLA-A74:09	AYFVHTPVFHR	0.9845	0.6391	6	17
NFIX-GCDH	chr19	13136366	chr19	13002929	556	HLA-A74:11	AYFVHTPVFHR	0.9845	0.6391	6	17
NFIX-GCDH	chr19	13136366	chr19	13002929	556	HLA-C07:80	YFVHTPVF	0.9912	0.8491	7	15
NFIX-GCDH	chr19	13136366	chr19	13002929	556	HLA-C07:67	YFVHTPVF	0.9912	0.8491	7	15
NFIX-GCDH	chr19	13136366	chr19	13002929	556	HLA-C07:10	YFVHTPVF	0.9893	0.8741	7	15
NFIX-GCDH	chr19	13136366	chr19	13002929	556	HLA-B78:01	LAYFVHTPV	0.9985	0.7246	5	14
NFIX-GCDH	chr19	13136366	chr19	13002929	556	HLA-C15:06	HTPVFHREI	0.9868	0.8953	10	19
NFIX-GCDH	chr19	13136366	chr19	13002929	556	HLA-B15:21	AYFVHTPVF	0.797	0.8359	6	15
NFIX-GCDH	chr19	13136366	chr19	13002929	556	HLA-C01:17	HTPVFHREI	0.5952	0.9468	10	19
NFIX-GCDH	chr19	13136366	chr19	13002929	556	HLA-C12:04	HTPVFHREI	0.5755	0.9874	10	19
NFIX-GCDH	chr19	13136366	chr19	13002929	556	HLA-C06:03	HTPVFHREI	0.5653	0.9864	10	19
NFIX-GCDH	chr19	13136366	chr19	13002929	556	HLA-C07:19	AYFVHTPVF	0.5085	0.6703	6	15
NFIX-GCDH	chr19	13136366	chr19	13002929	556	HLA-C07:05	AYFVHTPVF	0.4937	0.9059	6	15
NFIX-GCDH	chr19	13136366	chr19	13002929	556	HLA-C07:95	AYFVHTPVF	0.4861	0.5831	6	15
NFIX-GCDH	chr19	13136366	chr19	13002929	556	HLA-C07:27	AYFVHTPVF	0.4808	0.9125	6	15
NFIX-GCDH	chr19	13136366	chr19	13002929	556	HLA-C07:67	AYFVHTPVF	0.4732	0.9095	6	15
NFIX-GCDH	chr19	13136366	chr19	13002929	556	HLA-C07:80	AYFVHTPVF	0.4732	0.9095	6	15
NFIX-GCDH	chr19	13136366	chr19	13002929	556	HLA-C07:10	AYFVHTPVF	0.4549	0.9306	6	15
NFIX-GCDH	chr19	13136366	chr19	13002929	556	HLA-C12:12	HTPVFHREI	0.4532	0.8993	10	19
NFIX-GCDH	chr19	13136366	chr19	13002929	556	HLA-C07:29	AYFVHTPVF	0.4356	0.8645	6	15
NFIX-GCDH	chr19	13136366	chr19	13002929	556	HLA-C12:16	AYFVHTPVF	0.4267	0.9355	6	15
NFIX-GCDH	chr19	13136366	chr19	13002929	556	HLA-C07:46	AYFVHTPVF	0.4259	0.8316	6	15
NFIX-GCDH	chr19	13136366	chr19	13002929	556	HLA-C07:13	AYFVHTPVF	0.391	0.8486	6	15
NFIX-GCDH	chr19	13136366	chr19	13002929	556	HLA-C01:30	HTPVFHREI	0.2664	0.9534	10	19
NFIX-GCDH	chr19	13136366	chr19	13002929	556	HLA-B39:10	TPVFHREII	0.2332	0.8624	11	20
NFIX-GCDH	chr19	13136366	chr19	13002929	556	HLA-C04:14	AYFVHTPVF	0.0743	0.6974	6	15
NFIX-GCDH	chr19	13136366	chr19	13002929	556	HLA-A31:01	AYFVHTPVFHR	0.9921	0.5361	6	17
NFIX-GCDH	chr19	13136366	chr19	13002929	556	HLA-B78:02	TPVFHREI	0.9959	0.5017	11	19
NFIX-GCDH	chr19	13136366	chr19	13002929	556	HLA-C03:67	YFVHTPVF	0.9945	0.9592	7	15
NFIX-GCDH	chr19	13136366	chr19	13002929	556	HLA-C07:02	YFVHTPVF	0.9912	0.8491	7	15
NFIX-GCDH	chr19	13136366	chr19	13002929	556	HLA-C07:17	YFVHTPVF	0.9898	0.8982	7	15
NFIX-GCDH	chr19	13136366	chr19	13002929	556	HLA-C04:04	YFVHTPVF	0.9614	0.5289	7	15
NFIX-GCDH	chr19	13136366	chr19	13002929	556	HLA-C14:02	YFVHTPVF	0.9297	0.8391	7	15
NFIX-GCDH	chr19	13136366	chr19	13002929	556	HLA-C14:03	YFVHTPVF	0.9297	0.8391	7	15
NFIX-GCDH	chr19	13136366	chr19	13002929	556	HLA-B78:02	LAYFVHTPV	0.9978	0.8561	5	14
NFIX-GCDH	chr19	13136366	chr19	13002929	556	HLA-B51:14	LAYFVHTPV	0.997	0.5269	5	14
NFIX-GCDH	chr19	13136366	chr19	13002929	556	HLA-B51:21	LAYFVHTPV	0.9935	0.5777	5	14
NFIX-GCDH	chr19	13136366	chr19	13002929	556	HLA-C12:03	LAYFVHTPV	0.9913	0.9664	5	14
NFIX-GCDH	chr19	13136366	chr19	13002929	556	HLA-C15:05	HTPVFHREI	0.9876	0.8821	10	19
NFIX-GCDH	chr19	13136366	chr19	13002929	556	HLA-C15:02	HTPVFHREI	0.9848	0.8528	10	19
NFIX-GCDH	chr19	13136366	chr19	13002929	556	HLA-C03:17	HTPVFHREI	0.9539	0.9595	10	19
NFIX-GCDH	chr19	13136366	chr19	13002929	556	HLA-A74:01	FVHTPVFHR	0.9309	0.6002	8	17
NFIX-GCDH	chr19	13136366	chr19	13002929	556	HLA-C16:02	HTPVFHREI	0.7952	0.9859	10	19
NFIX-GCDH	chr19	13136366	chr19	13002929	556	HLA-C16:04	HTPVFHREI	0.73	0.9662	10	19
NFIX-GCDH	chr19	13136366	chr19	13002929	556	HLA-C01:03	HTPVFHREI	0.5922	0.9493	10	19
NFIX-GCDH	chr19	13136366	chr19	13002929	556	HLA-C01:02	HTPVFHREI	0.5783	0.9463	10	19
NFIX-GCDH	chr19	13136366	chr19	13002929	556	HLA-C06:17	HTPVFHREI	0.5601	0.9866	10	19
NFIX-GCDH	chr19	13136366	chr19	13002929	556	HLA-C06:02	HTPVFHREI	0.5601	0.9866	10	19
NFIX-GCDH	chr19	13136366	chr19	13002929	556	HLA-C07:22	AYFVHTPVF	0.5045	0.6183	6	15
NFIX-GCDH	chr19	13136366	chr19	13002929	556	HLA-C07:01	AYFVHTPVF	0.5036	0.549	6	15
NFIX-GCDH	chr19	13136366	chr19	13002929	556	HLA-C07:17	AYFVHTPVF	0.4765	0.928	6	15
NFIX-GCDH	chr19	13136366	chr19	13002929	556	HLA-C07:02	AYFVHTPVF	0.4732	0.9095	6	15
NFIX-GCDH	chr19	13136366	chr19	13002929	556	HLA-C06:08	HTPVFHREI	0.4055	0.9842	10	19
NFIX-GCDH	chr19	13136366	chr19	13002929	556	HLA-B67:01	TPVFHREII	0.3937	0.7955	11	20
NFIX-GCDH	chr19	13136366	chr19	13002929	556	HLA-C12:03	HTPVFHREI	0.3283	0.9656	10	19
NFIX-GCDH	chr19	13136366	chr19	13002929	556	HLA-C03:67	AYFVHTPVF	0.2714	0.9715	6	15
NFIX-GCDH	chr19	13136366	chr19	13002929	556	HLA-C07:04	AYFVHTPVF	0.2394	0.852	6	15
NFIX-GCDH	chr19	13136366	chr19	13002929	556	HLA-C06:17	AYFVHTPVF	0.1228	0.9884	6	15
NFIX-GCDH	chr19	13136366	chr19	13002929	556	HLA-C06:02	AYFVHTPVF	0.1228	0.9884	6	15
NFIX-GCDH	chr19	13136366	chr19	13002929	556	HLA-C06:08	AYFVHTPVF	0.0381	0.9842	6	15
NFIX-GCDH	chr19	13136366	chr19	13002929	556	HLA-C14:02	AYFVHTPVF	0.0246	0.9148	6	15
NFIX-GCDH	chr19	13136366	chr19	13002929	556	HLA-C14:03	AYFVHTPVF	0.0246	0.9148	6	15
NFIX-GCDH	chr19	13136366	chr19	13002929	556	HLA-C06:06	AYFVHTPVF	0.02	0.975	6	15
NFIX-GCDH	chr19	13136366	chr19	13002929	556	HLA-C04:04	AYFVHTPVF	0.0153	0.8476	6	15
NFIX-GCDH	chr19	13136366	chr19	13002929	556	HLA-A02:03	YLAYFVHTPV	0.9989	0.5822	4	14
NFIX-GCDH	chr19	13136366	chr19	13002929	556	HLA-B38:05	VHTPVFHREI	0.9565	0.9405	9	19
NFIX-GCDH	chr19	13136366	chr19	13002929	556	HLA-A74:01	AYFVHTPVFHR	0.9845	0.6391	6	17
NFIX-GCDH	chr19	13136366	chr19	13004297	556	HLA-B39:06	VHTPGYGCA	0.9163	0.9396	10	19
NFIX-GCDH	chr19	13136366	chr19	13004297	556	HLA-B15:18	AYFVHTPGY	0.1813	0.6305	7	16
NFIX-GCDH	chr19	13136366	chr19	13004297	556	HLA-B15:21	AYFVHTPGY	0.731	0.8196	7	16
NFIX-GCDH	chr19	13136366	chr19	13004297	556	HLA-C07:19	AYFVHTPGY	0.4686	0.5503	7	16
NFIX-GCDH	chr19	13136366	chr19	13004297	556	HLA-C07:80	AYFVHTPGY	0.417	0.8032	7	16
NFIX-GCDH	chr19	13136366	chr19	13004297	556	HLA-C07:67	AYFVHTPGY	0.417	0.8032	7	16
NFIX-GCDH	chr19	13136366	chr19	13004297	556	HLA-C07:46	AYFVHTPGY	0.3798	0.6797	7	16
NFIX-GCDH	chr19	13136366	chr19	13004297	556	HLA-C07:10	AYFVHTPGY	0.3742	0.8563	7	16
NFIX-GCDH	chr19	13136366	chr19	13004297	556	HLA-C07:27	AYFVHTPGY	0.2813	0.8815	7	16
NFIX-GCDH	chr19	13136366	chr19	13004297	556	HLA-C12:16	AYFVHTPGY	0.1924	0.9193	7	16
NFIX-GCDH	chr19	13136366	chr19	13004297	556	HLA-C07:05	AYFVHTPGY	0.1482	0.8825	7	16
NFIX-GCDH	chr19	13136366	chr19	13004297	556	HLA-C14:02	YFVHTPGY	0.6424	0.7716	8	16
NFIX-GCDH	chr19	13136366	chr19	13004297	556	HLA-C14:03	YFVHTPGY	0.6424	0.7716	8	16
NFIX-GCDH	chr19	13136366	chr19	13004297	556	HLA-C07:02	AYFVHTPGY	0.417	0.8032	7	16
NFIX-GCDH	chr19	13136366	chr19	13004297	556	HLA-C07:17	AYFVHTPGY	0.3887	0.882	7	16
NFIX-GCDH	chr19	13136366	chr19	13004297	556	HLA-C06:06	AYFVHTPGY	0.0018	0.9677	7	16
NFIX-GCDH	chr19	13136366	chr19	13004297	556	HLA-C14:03	AYFVHTPGY	0.0012	0.8543	7	16
NFIX-GCDH	chr19	13136366	chr19	13004297	556	HLA-C14:02	AYFVHTPGY	0.0012	0.8543	7	16

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Potential FusionNeoAntigen Information of NFIX-GCDH 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 NFIX-GCDH

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
743	AYFVHTPVFHREII	NFIX	GCDH	chr19	13136366	chr19	13002929	556

File name	BPseq	Hgene	Tgene	Hchr	Hbp	Tchr	Tbp	AAlen
4806	LAYFVHTPGYGCAG	NFIX	GCDH	chr19	13136366	chr19	13004297	556

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of NFIX-GCDH

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	743	AYFVHTPVFHREII	-8.68237	-8.68847
HLA-B52:01	3W39	743	AYFVHTPVFHREII	-6.07055	-6.07665
HLA-A24:02	5HGA	743	AYFVHTPVFHREII	-7.76531	-7.77141
HLA-B44:05	3DX8	743	AYFVHTPVFHREII	-5.76313	-5.76923
HLA-B14:02	3BVN	4806	LAYFVHTPGYGCAG	-7.9962	-8.1096
HLA-B14:02	3BVN	4806	LAYFVHTPGYGCAG	-5.70842	-6.74372
HLA-B52:01	3W39	4806	LAYFVHTPGYGCAG	-6.83737	-6.95077
HLA-B52:01	3W39	4806	LAYFVHTPGYGCAG	-4.4836	-5.5189
HLA-A11:01	4UQ2	4806	LAYFVHTPGYGCAG	-10.0067	-10.1201
HLA-A11:01	4UQ2	4806	LAYFVHTPGYGCAG	-9.03915	-10.0745
HLA-A24:02	5HGA	4806	LAYFVHTPGYGCAG	-6.56204	-6.67544
HLA-A24:02	5HGA	4806	LAYFVHTPGYGCAG	-5.42271	-6.45801
HLA-B44:05	3DX8	4806	LAYFVHTPGYGCAG	-7.85648	-8.89178
HLA-B44:05	3DX8	4806	LAYFVHTPGYGCAG	-5.3978	-5.5112
HLA-A02:01	6TDR	4806	LAYFVHTPGYGCAG	-3.37154	-4.40684

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Vaccine Design for the FusionNeoAntigens of NFIX-GCDH

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
NFIX-GCDH	chr19	13136366	chr19	13002929	10	19	HTPVFHREI	ACACTCCGGTTTTTCATCGGGAGATCA
NFIX-GCDH	chr19	13136366	chr19	13002929	11	19	TPVFHREI	CTCCGGTTTTTCATCGGGAGATCA
NFIX-GCDH	chr19	13136366	chr19	13002929	11	20	TPVFHREII	CTCCGGTTTTTCATCGGGAGATCATTT
NFIX-GCDH	chr19	13136366	chr19	13002929	4	14	YLAYFVHTPV	ATCTGGCTTACTTTGTCCACACTCCGGTTT
NFIX-GCDH	chr19	13136366	chr19	13002929	5	14	LAYFVHTPV	TGGCTTACTTTGTCCACACTCCGGTTT
NFIX-GCDH	chr19	13136366	chr19	13002929	6	15	AYFVHTPVF	CTTACTTTGTCCACACTCCGGTTTTTC
NFIX-GCDH	chr19	13136366	chr19	13002929	6	17	AYFVHTPVFHR	CTTACTTTGTCCACACTCCGGTTTTTCATCGGG
NFIX-GCDH	chr19	13136366	chr19	13002929	7	15	YFVHTPVF	ACTTTGTCCACACTCCGGTTTTTC
NFIX-GCDH	chr19	13136366	chr19	13002929	8	17	FVHTPVFHR	TTGTCCACACTCCGGTTTTTCATCGGG
NFIX-GCDH	chr19	13136366	chr19	13002929	9	19	VHTPVFHREI	TCCACACTCCGGTTTTTCATCGGGAGATCA
NFIX-GCDH	chr19	13136366	chr19	13004297	10	19	VHTPGYGCA	ACACTCCGGGATATGGCTGTGCTGGGG
NFIX-GCDH	chr19	13136366	chr19	13004297	7	16	AYFVHTPGY	ACTTTGTCCACACTCCGGGATATGGCT
NFIX-GCDH	chr19	13136366	chr19	13004297	8	16	YFVHTPGY	TTGTCCACACTCCGGGATATGGCT

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 NFIX-GCDH

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
LUAD	NFIX-GCDH	chr19	13136366	ENST00000358552	chr19	13004297	ENST00000222214	TCGA-55-8506-01A
LUAD	NFIX-GCDH	chr19	13136366	ENST00000358552	chr19	13002929	ENST00000222214	TCGA-55-8506

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Potential target of CAR-T therapy development for NFIX-GCDH

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 NFIX-GCDH

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 NFIX-GCDH

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)