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Fusion Protein:NF2-CABP7

Fusion Gene and Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: NF2-CABP7
	FusionPDB ID: 58718
	FusionGDB2.0 ID: 58718
		Hgene	Tgene
	Gene symbol	NF2	CABP7
	Gene ID	4771	164633
	Gene name	neurofibromin 2	calcium binding protein 7
	Synonyms	ACN\|BANF\|SCH	CALN2
	Cytomap	22q12.2	22q12.2
	Type of gene	protein-coding	protein-coding
	Description	merlinmoesin-ezrin-radixin likemoesin-ezrin-radixin-like proteinmoesin-ezrin-radizin-like proteinneurofibromin 2 (bilateral acoustic neuroma)schwannomerlinschwannomin	calcium-binding protein 7calneuron 2calneuron II
	Modification date	20200322	20200313
	UniProtAcc	P35240 Main function of 5'-partner protein: FUNCTION: Probable regulator of the Hippo/SWH (Sav/Wts/Hpo) signaling pathway, a signaling pathway that plays a pivotal role in tumor suppression by restricting proliferation and promoting apoptosis. Along with WWC1 can synergistically induce the phosphorylation of LATS1 and LATS2 and can probably function in the regulation of the Hippo/SWH (Sav/Wts/Hpo) signaling pathway. May act as a membrane stabilizing protein. May inhibit PI3 kinase by binding to AGAP2 and impairing its stimulating activity. Suppresses cell proliferation and tumorigenesis by inhibiting the CUL4A-RBX1-DDB1-VprBP/DCAF1 E3 ubiquitin-protein ligase complex. {ECO:0000269\|PubMed:20159598, ECO:0000269\|PubMed:20178741, ECO:0000269\|PubMed:21167305}.	Q86V35 Main function of 5'-partner protein: FUNCTION: Negatively regulates Golgi-to-plasma membrane trafficking by interacting with PI4KB and inhibiting its activity. {ECO:0000250}.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000334961, ENST00000338641, ENST00000347330, ENST00000353887, ENST00000361166, ENST00000361452, ENST00000361676, ENST00000397789, ENST00000403435, ENST00000403999, ENST00000413209,	ENST00000216144,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	15 X 11 X 7=1155	2 X 3 X 3=18
	# samples	18	3
	** MAII score	log2(18/1155*10)=-2.68182403997375 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: NF2 [Title/Abstract] AND CABP7 [Title/Abstract] AND fusion [Title/Abstract]
Fusion neoantigen context	PubMed: NF2 [Title/Abstract] AND CABP7 [Title/Abstract] AND neoantigen [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	NF2(30000101)-CABP7(30125044), # samples:2
Anticipated loss of major functional domain due to fusion event.	NF2-CABP7 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. NF2-CABP7 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. NF2-CABP7 seems lost the major protein functional domain in Hgene partner, which is a CGC due to the frame-shifted ORF. NF2-CABP7 seems lost the major protein functional domain in Hgene partner, which is a tumor suppressor due to the frame-shifted ORF. NF2-CABP7 seems lost the major protein functional domain in Tgene partner, which is a essential gene 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	NF2	GO:0008285	negative regulation of cell proliferation	12444102\|20178741
Hgene	NF2	GO:0022408	negative regulation of cell-cell adhesion	17210637
Hgene	NF2	GO:0042532	negative regulation of tyrosine phosphorylation of STAT protein	12444102
Hgene	NF2	GO:0046426	negative regulation of JAK-STAT cascade	12444102

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr22:30000101/chr22:30125044)
- 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 NF2 (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 CABP7 (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)
ENST00000347330	NF2	chr22	30000101	+	ENST00000216144	CABP7	chr22	30125044	+	3109	557	970	233	245
ENST00000413209	NF2	chr22	30000101	+	ENST00000216144	CABP7	chr22	30125044	+	3109	557	970	233	245
ENST00000338641	NF2	chr22	30000101	+	ENST00000216144	CABP7	chr22	30125044	+	3107	555	968	231	245
ENST00000403435	NF2	chr22	30000101	+	ENST00000216144	CABP7	chr22	30125044	+	3077	525	938	201	245
ENST00000361452	NF2	chr22	30000101	+	ENST00000216144	CABP7	chr22	30125044	+	3048	496	909	172	245
ENST00000403999	NF2	chr22	30000101	+	ENST00000216144	CABP7	chr22	30125044	+	3032	480	893	156	245
ENST00000334961	NF2	chr22	30000101	+	ENST00000216144	CABP7	chr22	30125044	+	2938	386	442	1089	215
ENST00000353887	NF2	chr22	30000101	+	ENST00000216144	CABP7	chr22	30125044	+	2918	366	422	1069	215
ENST00000361166	NF2	chr22	30000101	+	ENST00000216144	CABP7	chr22	30125044	+	2666	114	170	817	215
ENST00000397789	NF2	chr22	30000101	+	ENST00000216144	CABP7	chr22	30125044	+	2666	114	170	817	215
ENST00000361676	NF2	chr22	30000101	+	ENST00000216144	CABP7	chr22	30125044	+	2666	114	170	817	215

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
ENST00000347330	ENST00000216144	NF2	chr22	30000101	+	CABP7	chr22	30125044	+	0.57010704	0.42989296
ENST00000413209	ENST00000216144	NF2	chr22	30000101	+	CABP7	chr22	30125044	+	0.57010704	0.42989296
ENST00000338641	ENST00000216144	NF2	chr22	30000101	+	CABP7	chr22	30125044	+	0.5698568	0.43014315
ENST00000403435	ENST00000216144	NF2	chr22	30000101	+	CABP7	chr22	30125044	+	0.5513965	0.4486035
ENST00000361452	ENST00000216144	NF2	chr22	30000101	+	CABP7	chr22	30125044	+	0.53047794	0.4695221
ENST00000403999	ENST00000216144	NF2	chr22	30000101	+	CABP7	chr22	30125044	+	0.5425002	0.45749983
ENST00000334961	ENST00000216144	NF2	chr22	30000101	+	CABP7	chr22	30125044	+	0.41624498	0.58375496
ENST00000353887	ENST00000216144	NF2	chr22	30000101	+	CABP7	chr22	30125044	+	0.6214164	0.3785836
ENST00000361166	ENST00000216144	NF2	chr22	30000101	+	CABP7	chr22	30125044	+	0.7908434	0.2091566
ENST00000397789	ENST00000216144	NF2	chr22	30000101	+	CABP7	chr22	30125044	+	0.7908434	0.2091566
ENST00000361676	ENST00000216144	NF2	chr22	30000101	+	CABP7	chr22	30125044	+	0.7908434	0.2091566

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 NF2-CABP7

+/-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

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Potential FusionNeoAntigen Information of NF2-CABP7 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.

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)

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Potential FusionNeoAntigen Information of NF2-CABP7 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 NF2-CABP7

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.

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of NF2-CABP7

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

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Vaccine Design for the FusionNeoAntigens of NF2-CABP7

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

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 NF2-CABP7

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

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Potential target of CAR-T therapy development for NF2-CABP7

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

Tgene

CABP7

chr22:30000101

chr22:30125044

ENST00000216144

189_209

216.0

Transmembrane

Helical%3B Anchor for type IV membrane protein

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 NF2-CABP7

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 NF2-CABP7

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)