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Fusion Protein:INADL-APITD1

Fusion Gene and Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: INADL-APITD1
	FusionPDB ID: 39706
	FusionGDB2.0 ID: 62902
		Hgene	Tgene
	Gene symbol	INADL	APITD1
	Gene ID	10207	100526739
	Gene name	PATJ crumbs cell polarity complex component	CENPS-CORT readthrough
	Synonyms	Cipp\|INADL\|InaD-like\|hINADL	APITD1\|APITD1-CORT\|CENP-S\|CENPS\|FAAP16\|MHF1
	Cytomap	1p31.3	1p36.22
	Type of gene	protein-coding	protein-coding
	Description	inaD-like proteinPALS1-associated tight junction proteinPDZ domain proteinchannel-interacting PDZ domain proteinchannel-interacting PDZ domain-containing proteininactivation no after-potential D-like proteininactivation-no-afterpotential D-likeprot	APITD1-CORT proteinAPITD1-CORT readthroughApoptosis-inducing TAF9-like domain-containing protein 1Centromere protein SFANCM-associated histone fold protein 1FANCM-interacting histone fold protein 1Fanconi anemia-associated polypeptide of 16 kDa
	Modification date	20200313	20200313
	UniProtAcc	.	.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000316485, ENST00000371158, ENST00000472512, ENST00000543708, ENST00000545929,	ENST00000462462, ENST00000309048, ENST00000602296, ENST00000602787,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	15 X 12 X 10=1800	3 X 4 X 3=36
	# samples	18	5
	** MAII score	log2(18/1800*10)=-3.32192809488736 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(5/36*10)=0.473931188332412 effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs). DoF>8 and MAII>0
Fusion gene context	PubMed: INADL [Title/Abstract] AND APITD1 [Title/Abstract] AND fusion [Title/Abstract]
Fusion neoantigen context	PubMed: INADL [Title/Abstract] AND APITD1 [Title/Abstract] AND neoantigen [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	INADL(62293255)-APITD1(10493898), # samples:1 INADL(62293255)-APITD1(10493899), # samples:1
Anticipated loss of major functional domain due to fusion event.	INADL-APITD1 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. INADL-APITD1 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. INADL-APITD1 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. INADL-APITD1 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

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr1:62293255/chr1:10493898)
- 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 INADL (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 APITD1 (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)
ENST00000316485	INADL	chr1	62293255	+	ENST00000602296	APITD1	chr1	10493898	+	3029	2094	114	2276	720
ENST00000316485	INADL	chr1	62293255	+	ENST00000602787	APITD1	chr1	10493898	+	3096	2094	114	2537	807
ENST00000316485	INADL	chr1	62293255	+	ENST00000309048	APITD1	chr1	10493898	+	2864	2094	114	2459	781
ENST00000371158	INADL	chr1	62293255	+	ENST00000602296	APITD1	chr1	10493898	+	3029	2094	114	2276	720
ENST00000371158	INADL	chr1	62293255	+	ENST00000602787	APITD1	chr1	10493898	+	3096	2094	114	2537	807
ENST00000371158	INADL	chr1	62293255	+	ENST00000309048	APITD1	chr1	10493898	+	2864	2094	114	2459	781
ENST00000316485	INADL	chr1	62293255	+	ENST00000602296	APITD1	chr1	10493899	+	3029	2094	114	2276	720
ENST00000316485	INADL	chr1	62293255	+	ENST00000602787	APITD1	chr1	10493899	+	3096	2094	114	2537	807
ENST00000316485	INADL	chr1	62293255	+	ENST00000309048	APITD1	chr1	10493899	+	2864	2094	114	2459	781
ENST00000371158	INADL	chr1	62293255	+	ENST00000602296	APITD1	chr1	10493899	+	3029	2094	114	2276	720
ENST00000371158	INADL	chr1	62293255	+	ENST00000602787	APITD1	chr1	10493899	+	3096	2094	114	2537	807
ENST00000371158	INADL	chr1	62293255	+	ENST00000309048	APITD1	chr1	10493899	+	2864	2094	114	2459	781

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
ENST00000316485	ENST00000602296	INADL	chr1	62293255	+	APITD1	chr1	10493898	+	0.00121393	0.99878603
ENST00000316485	ENST00000602787	INADL	chr1	62293255	+	APITD1	chr1	10493898	+	0.001032753	0.9989673
ENST00000316485	ENST00000309048	INADL	chr1	62293255	+	APITD1	chr1	10493898	+	0.001813014	0.998187
ENST00000371158	ENST00000602296	INADL	chr1	62293255	+	APITD1	chr1	10493898	+	0.00121393	0.99878603
ENST00000371158	ENST00000602787	INADL	chr1	62293255	+	APITD1	chr1	10493898	+	0.001032753	0.9989673
ENST00000371158	ENST00000309048	INADL	chr1	62293255	+	APITD1	chr1	10493898	+	0.001813014	0.998187
ENST00000316485	ENST00000602296	INADL	chr1	62293255	+	APITD1	chr1	10493899	+	0.00121393	0.99878603
ENST00000316485	ENST00000602787	INADL	chr1	62293255	+	APITD1	chr1	10493899	+	0.001032753	0.9989673
ENST00000316485	ENST00000309048	INADL	chr1	62293255	+	APITD1	chr1	10493899	+	0.001813014	0.998187
ENST00000371158	ENST00000602296	INADL	chr1	62293255	+	APITD1	chr1	10493899	+	0.00121393	0.99878603
ENST00000371158	ENST00000602787	INADL	chr1	62293255	+	APITD1	chr1	10493899	+	0.001032753	0.9989673
ENST00000371158	ENST00000309048	INADL	chr1	62293255	+	APITD1	chr1	10493899	+	0.001813014	0.998187

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 INADL-APITD1

+/-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
INADL	chr1	62293255	APITD1	chr1	10493898	2094	660	EPRRTETSLPETERLKAAVHYTVGCL
INADL	chr1	62293255	APITD1	chr1	10493899	2094	660	EPRRTETSLPETERLKAAVHYTVGCL

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Potential FusionNeoAntigen Information of INADL-APITD1 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.

INADL-APITD1_62293255_10493898.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)
INADL-APITD1	chr1	62293255	chr1	10493898	2094	HLA-B27:05	ERLKAAVHY	0.9981	0.7534	12	21
INADL-APITD1	chr1	62293255	chr1	10493898	2094	HLA-B27:04	ERLKAAVHY	0.9979	0.6522	12	21
INADL-APITD1	chr1	62293255	chr1	10493898	2094	HLA-A66:01	ETSLPETER	0.9971	0.5716	5	14
INADL-APITD1	chr1	62293255	chr1	10493898	2094	HLA-A26:03	ETSLPETER	0.99	0.6048	5	14
INADL-APITD1	chr1	62293255	chr1	10493898	2094	HLA-B57:03	TSLPETERL	0.9196	0.9959	6	15
INADL-APITD1	chr1	62293255	chr1	10493898	2094	HLA-B44:03	TERLKAAVHY	0.9979	0.8844	11	21
INADL-APITD1	chr1	62293255	chr1	10493898	2094	HLA-B27:04	TERLKAAVHY	0.9654	0.6099	11	21
INADL-APITD1	chr1	62293255	chr1	10493898	2094	HLA-B18:01	TERLKAAVHY	0.957	0.768	11	21
INADL-APITD1	chr1	62293255	chr1	10493898	2094	HLA-C01:17	SLPETERL	0.9865	0.9569	7	15
INADL-APITD1	chr1	62293255	chr1	10493898	2094	HLA-C01:30	SLPETERL	0.931	0.9696	7	15
INADL-APITD1	chr1	62293255	chr1	10493898	2094	HLA-C03:07	TSLPETERL	0.9996	0.9899	6	15
INADL-APITD1	chr1	62293255	chr1	10493898	2094	HLA-C03:08	TSLPETERL	0.9995	0.9593	6	15
INADL-APITD1	chr1	62293255	chr1	10493898	2094	HLA-C15:06	TSLPETERL	0.9994	0.96	6	15
INADL-APITD1	chr1	62293255	chr1	10493898	2094	HLA-B27:14	ERLKAAVHY	0.9927	0.6772	12	21
INADL-APITD1	chr1	62293255	chr1	10493898	2094	HLA-B27:03	ERLKAAVHY	0.978	0.7783	12	21
INADL-APITD1	chr1	62293255	chr1	10493898	2094	HLA-C07:27	ERLKAAVHY	0.9511	0.8829	12	21
INADL-APITD1	chr1	62293255	chr1	10493898	2094	HLA-C07:05	ERLKAAVHY	0.8246	0.779	12	21
INADL-APITD1	chr1	62293255	chr1	10493898	2094	HLA-C07:46	ERLKAAVHY	0.7678	0.7587	12	21
INADL-APITD1	chr1	62293255	chr1	10493898	2094	HLA-C07:10	ERLKAAVHY	0.7355	0.9095	12	21
INADL-APITD1	chr1	62293255	chr1	10493898	2094	HLA-C07:67	ERLKAAVHY	0.7351	0.8949	12	21
INADL-APITD1	chr1	62293255	chr1	10493898	2094	HLA-C07:80	ERLKAAVHY	0.7351	0.8949	12	21
INADL-APITD1	chr1	62293255	chr1	10493898	2094	HLA-C12:16	ERLKAAVHY	0.0254	0.899	12	21
INADL-APITD1	chr1	62293255	chr1	10493898	2094	HLA-B54:01	LPETERLKAA	0.9862	0.635	8	18
INADL-APITD1	chr1	62293255	chr1	10493898	2094	HLA-B27:03	TERLKAAVHY	0.6366	0.7576	11	21
INADL-APITD1	chr1	62293255	chr1	10493898	2094	HLA-C01:03	SLPETERL	0.9964	0.92	7	15
INADL-APITD1	chr1	62293255	chr1	10493898	2094	HLA-C01:02	SLPETERL	0.9961	0.954	7	15
INADL-APITD1	chr1	62293255	chr1	10493898	2094	HLA-C15:05	TSLPETERL	0.9994	0.9381	6	15
INADL-APITD1	chr1	62293255	chr1	10493898	2094	HLA-B27:08	ERLKAAVHY	0.9982	0.6307	12	21
INADL-APITD1	chr1	62293255	chr1	10493898	2094	HLA-B27:10	ERLKAAVHY	0.9978	0.7979	12	21
INADL-APITD1	chr1	62293255	chr1	10493898	2094	HLA-C03:06	TSLPETERL	0.9823	0.9952	6	15
INADL-APITD1	chr1	62293255	chr1	10493898	2094	HLA-B57:02	TSLPETERL	0.9564	0.9578	6	15
INADL-APITD1	chr1	62293255	chr1	10493898	2094	HLA-A69:01	ETERLKAAV	0.881	0.6173	10	19
INADL-APITD1	chr1	62293255	chr1	10493898	2094	HLA-B35:13	TSLPETERL	0.8622	0.9699	6	15
INADL-APITD1	chr1	62293255	chr1	10493898	2094	HLA-C07:17	ERLKAAVHY	0.8064	0.912	12	21
INADL-APITD1	chr1	62293255	chr1	10493898	2094	HLA-C07:02	ERLKAAVHY	0.7351	0.8949	12	21
INADL-APITD1	chr1	62293255	chr1	10493898	2094	HLA-C17:01	TSLPETERL	0.4897	0.9612	6	15
INADL-APITD1	chr1	62293255	chr1	10493898	2094	HLA-B44:26	TERLKAAVHY	0.9979	0.8844	11	21
INADL-APITD1	chr1	62293255	chr1	10493898	2094	HLA-B44:13	TERLKAAVHY	0.9979	0.8844	11	21
INADL-APITD1	chr1	62293255	chr1	10493898	2094	HLA-B44:07	TERLKAAVHY	0.9979	0.8844	11	21
INADL-APITD1	chr1	62293255	chr1	10493898	2094	HLA-A68:02	ETSLPETERL	0.9799	0.5363	5	15
INADL-APITD1	chr1	62293255	chr1	10493898	2094	HLA-B18:05	TERLKAAVHY	0.957	0.768	11	21
INADL-APITD1	chr1	62293255	chr1	10493898	2094	HLA-B15:53	TERLKAAVHY	0.9554	0.6874	11	21
INADL-APITD1	chr1	62293255	chr1	10493898	2094	HLA-B18:08	TERLKAAVHY	0.9549	0.5867	11	21
INADL-APITD1	chr1	62293255	chr1	10493898	2094	HLA-B18:11	TERLKAAVHY	0.9027	0.7937	11	21
INADL-APITD1	chr1	62293255	chr1	10493898	2094	HLA-B56:05	LPETERLKAA	0.741	0.5095	8	18
INADL-APITD1	chr1	62293255	chr1	10493898	2094	HLA-B40:04	TETSLPETERL	0.9979	0.7319	4	15

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Potential FusionNeoAntigen Information of INADL-APITD1 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 INADL-APITD1

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
9649	TSLPETERLKAAVH	INADL	APITD1	chr1	62293255	chr1	10493898	2094

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of INADL-APITD1

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	9649	TSLPETERLKAAVH	-6.8019	-6.809
HLA-B52:01	3W39	9649	TSLPETERLKAAVH	-7.25721	-7.26431
HLA-A24:02	5HGA	9649	TSLPETERLKAAVH	-6.75938	-6.76648
HLA-B44:05	3DX8	9649	TSLPETERLKAAVH	-5.08187	-5.08897

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Vaccine Design for the FusionNeoAntigens of INADL-APITD1

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
INADL-APITD1	chr1	62293255	chr1	10493898	10	19	ETERLKAAV	GAGACAGAGAGGCTAAAGGCAGCAGTT
INADL-APITD1	chr1	62293255	chr1	10493898	11	21	TERLKAAVHY	ACAGAGAGGCTAAAGGCAGCAGTTCACTAT
INADL-APITD1	chr1	62293255	chr1	10493898	12	21	ERLKAAVHY	GAGAGGCTAAAGGCAGCAGTTCACTAT
INADL-APITD1	chr1	62293255	chr1	10493898	4	15	TETSLPETERL	ACTGAAACCTCTCTTCCTGAGACAGAGAGGCTA
INADL-APITD1	chr1	62293255	chr1	10493898	5	14	ETSLPETER	GAAACCTCTCTTCCTGAGACAGAGAGG
INADL-APITD1	chr1	62293255	chr1	10493898	5	15	ETSLPETERL	GAAACCTCTCTTCCTGAGACAGAGAGGCTA
INADL-APITD1	chr1	62293255	chr1	10493898	6	15	TSLPETERL	ACCTCTCTTCCTGAGACAGAGAGGCTA
INADL-APITD1	chr1	62293255	chr1	10493898	7	15	SLPETERL	TCTCTTCCTGAGACAGAGAGGCTA
INADL-APITD1	chr1	62293255	chr1	10493898	8	18	LPETERLKAA	CTTCCTGAGACAGAGAGGCTAAAGGCAGCA

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 INADL-APITD1

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
CESC	INADL-APITD1	chr1	62293255	ENST00000316485	chr1	10493898	ENST00000309048	TCGA-C5-A8YQ

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Potential target of CAR-T therapy development for INADL-APITD1

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 INADL-APITD1

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 INADL-APITD1

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)