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	Fusion Gene Summary
	Fusion Gene Sample Information
	Fusion ORF Analysis
	Fusion Amino Acid Sequences
	Fusion Protein Functional Features
	Fusion Protein Structure
	pLDDT scores
	Ramachandran Plot of Fusion Protein Structure
	Fusion Protein-Protein Interaction
	Related drugs with this fusion protein
	Related disease with this fusion protein

Fusion Protein:CAP1-NARS2

Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: CAP1-NARS2
	FusionPDB ID: 12818
	FusionGDB2.0 ID: 12818
		Hgene	Tgene
	Gene symbol	CAP1	NARS2
	Gene ID	10487	79731
	Gene name	cyclase associated actin cytoskeleton regulatory protein 1	asparaginyl-tRNA synthetase 2, mitochondrial
	Synonyms	CAP\|CAP1-PEN	DFNB94\|SLM5\|asnRS
	Cytomap	1p34.2	11q14.1
	Type of gene	protein-coding	protein-coding
	Description	adenylyl cyclase-associated protein 1CAP, adenylate cyclase-associated protein 1adenylate cyclase associated protein 1testis secretory sperm-binding protein Li 218p	probable asparagine--tRNA ligase, mitochondrialasparagine tRNA ligase 2, mitochondrial (putative)asparaginyl-tRNA synthetase 2, mitochondrial (putative)deafness, autosomal recessive 94probable asparaginyl-tRNA synthetase, mitochondrial
	Modification date	20200313	20200313
	UniProtAcc	Q01518	Q96I59
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000340450, ENST00000372792, ENST00000372797, ENST00000372798, ENST00000372802, ENST00000372805, ENST00000479759,	ENST00000281038, ENST00000528850,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	16 X 13 X 7=1456	29 X 15 X 11=4785
	# samples	19	37
	** MAII score	log2(19/1456*10)=-2.93793903186775 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(37/4785*10)=-3.69292174885708 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)	PubMed: CAP1 [Title/Abstract] AND NARS2 [Title/Abstract] AND fusion [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	CAP1(40525842)-NARS2(78154804), # samples:2
Anticipated loss of major functional domain due to fusion event.	CAP1-NARS2 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. CAP1-NARS2 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

Fusion gene breakpoints across CAP1 (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 NARS2 (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 Gene Sample Information

Fusion gene information from FusionGDB2.0.

Fusion gene information from two resources (ChiTars 5.0 and ChimerDB 4.0)
* All genome coordinats were lifted-over on hg19.
* Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser.

Source	Disease	Sample	Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand
ChimerDB4	OV	TCGA-29-1778-01A	CAP1	chr1	40525842	+	NARS2	chr11	78154804	-
ChimerDB4	OV	TCGA-29-1778	CAP1	chr1	40525842	+	NARS2	chr11	78154804	-

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Fusion ORF Analysis

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)
ENST00000372797	CAP1	chr1	40525842	+	ENST00000281038	NARS2	chr11	78154804	-	1756	777	534	1046	170
ENST00000372797	CAP1	chr1	40525842	+	ENST00000528850	NARS2	chr11	78154804	-	1494	777	534	1046	170
ENST00000372802	CAP1	chr1	40525842	+	ENST00000281038	NARS2	chr11	78154804	-	1749	770	527	1039	170
ENST00000372802	CAP1	chr1	40525842	+	ENST00000528850	NARS2	chr11	78154804	-	1487	770	527	1039	170
ENST00000372792	CAP1	chr1	40525842	+	ENST00000281038	NARS2	chr11	78154804	-	1261	282	48	551	167
ENST00000372792	CAP1	chr1	40525842	+	ENST00000528850	NARS2	chr11	78154804	-	999	282	48	551	167
ENST00000372798	CAP1	chr1	40525842	+	ENST00000281038	NARS2	chr11	78154804	-	1255	276	45	545	166
ENST00000372798	CAP1	chr1	40525842	+	ENST00000528850	NARS2	chr11	78154804	-	993	276	45	545	166
ENST00000340450	CAP1	chr1	40525842	+	ENST00000281038	NARS2	chr11	78154804	-	1251	272	44	541	165
ENST00000340450	CAP1	chr1	40525842	+	ENST00000528850	NARS2	chr11	78154804	-	989	272	44	541	165
ENST00000372805	CAP1	chr1	40525842	+	ENST00000281038	NARS2	chr11	78154804	-	1246	267	36	536	166
ENST00000372805	CAP1	chr1	40525842	+	ENST00000528850	NARS2	chr11	78154804	-	984	267	36	536	166

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
ENST00000372797	ENST00000281038	CAP1	chr1	40525842	+	NARS2	chr11	78154804	-	0.004145061	0.9958549
ENST00000372797	ENST00000528850	CAP1	chr1	40525842	+	NARS2	chr11	78154804	-	0.004834065	0.99516594
ENST00000372802	ENST00000281038	CAP1	chr1	40525842	+	NARS2	chr11	78154804	-	0.004712747	0.9952872
ENST00000372802	ENST00000528850	CAP1	chr1	40525842	+	NARS2	chr11	78154804	-	0.006481415	0.99351853
ENST00000372792	ENST00000281038	CAP1	chr1	40525842	+	NARS2	chr11	78154804	-	0.003903204	0.9960968
ENST00000372792	ENST00000528850	CAP1	chr1	40525842	+	NARS2	chr11	78154804	-	0.004965011	0.99503505
ENST00000372798	ENST00000281038	CAP1	chr1	40525842	+	NARS2	chr11	78154804	-	0.003722312	0.99627763
ENST00000372798	ENST00000528850	CAP1	chr1	40525842	+	NARS2	chr11	78154804	-	0.005639523	0.9943605
ENST00000340450	ENST00000281038	CAP1	chr1	40525842	+	NARS2	chr11	78154804	-	0.003599255	0.9964007
ENST00000340450	ENST00000528850	CAP1	chr1	40525842	+	NARS2	chr11	78154804	-	0.005284438	0.9947155
ENST00000372805	ENST00000281038	CAP1	chr1	40525842	+	NARS2	chr11	78154804	-	0.004300237	0.99569976
ENST00000372805	ENST00000528850	CAP1	chr1	40525842	+	NARS2	chr11	78154804	-	0.005504046	0.9944959

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Fusion Amino Acid Sequences

For individual full-length fusion transcript sequence from FusionPDB, we ran ORFfinder and chose the longest ORF among the all predicted ones.

>FusionGDB ID_FusionGDB isoform ID_FGname_Hgene_Hchr_Hbp_Henst_Tgene_Tchr_Tbp_Tenst_length(fusion AA) seq_BP

>12818_12818_1_CAP1-NARS2_CAP1_chr1_40525842_ENST00000340450_NARS2_chr11_78154804_ENST00000281038_length(amino acids)=165AA_BP=76
MRWSIMADMQNLVERLERAVGRLEAVSHTSDMHRGYADSPSKGAAPYVQAFDSLLAGPVAEYLKISKEIGGDVQKHVAAVDLLVPGVGEL

--------------------------------------------------------------

>12818_12818_2_CAP1-NARS2_CAP1_chr1_40525842_ENST00000340450_NARS2_chr11_78154804_ENST00000528850_length(amino acids)=165AA_BP=76
MRWSIMADMQNLVERLERAVGRLEAVSHTSDMHRGYADSPSKGAAPYVQAFDSLLAGPVAEYLKISKEIGGDVQKHVAAVDLLVPGVGEL

--------------------------------------------------------------

>12818_12818_3_CAP1-NARS2_CAP1_chr1_40525842_ENST00000372792_NARS2_chr11_78154804_ENST00000281038_length(amino acids)=167AA_BP=78
MSRWSIMADMQNLVERLERAVGRLEAVSHTSDMHRGYADSPSKAGAAPYVQAFDSLLAGPVAEYLKISKEIGGDVQKHVAAVDLLVPGVG

--------------------------------------------------------------

>12818_12818_4_CAP1-NARS2_CAP1_chr1_40525842_ENST00000372792_NARS2_chr11_78154804_ENST00000528850_length(amino acids)=167AA_BP=78
MSRWSIMADMQNLVERLERAVGRLEAVSHTSDMHRGYADSPSKAGAAPYVQAFDSLLAGPVAEYLKISKEIGGDVQKHVAAVDLLVPGVG

--------------------------------------------------------------

>12818_12818_5_CAP1-NARS2_CAP1_chr1_40525842_ENST00000372797_NARS2_chr11_78154804_ENST00000281038_length(amino acids)=170AA_BP=81
MIAVRRWSIMADMQNLVERLERAVGRLEAVSHTSDMHRGYADSPSKAGAAPYVQAFDSLLAGPVAEYLKISKEIGGDVQKHVAAVDLLVP

--------------------------------------------------------------

>12818_12818_6_CAP1-NARS2_CAP1_chr1_40525842_ENST00000372797_NARS2_chr11_78154804_ENST00000528850_length(amino acids)=170AA_BP=81
MIAVRRWSIMADMQNLVERLERAVGRLEAVSHTSDMHRGYADSPSKAGAAPYVQAFDSLLAGPVAEYLKISKEIGGDVQKHVAAVDLLVP

--------------------------------------------------------------

>12818_12818_7_CAP1-NARS2_CAP1_chr1_40525842_ENST00000372798_NARS2_chr11_78154804_ENST00000281038_length(amino acids)=166AA_BP=77
MSRWSIMADMQNLVERLERAVGRLEAVSHTSDMHRGYADSPSKGAAPYVQAFDSLLAGPVAEYLKISKEIGGDVQKHVAAVDLLVPGVGE

--------------------------------------------------------------

>12818_12818_8_CAP1-NARS2_CAP1_chr1_40525842_ENST00000372798_NARS2_chr11_78154804_ENST00000528850_length(amino acids)=166AA_BP=77
MSRWSIMADMQNLVERLERAVGRLEAVSHTSDMHRGYADSPSKGAAPYVQAFDSLLAGPVAEYLKISKEIGGDVQKHVAAVDLLVPGVGE

--------------------------------------------------------------

>12818_12818_9_CAP1-NARS2_CAP1_chr1_40525842_ENST00000372802_NARS2_chr11_78154804_ENST00000281038_length(amino acids)=170AA_BP=81
MIAVRSRWSIMADMQNLVERLERAVGRLEAVSHTSDMHRGYADSPSKGAAPYVQAFDSLLAGPVAEYLKISKEIGGDVQKHVAAVDLLVP

--------------------------------------------------------------

>12818_12818_10_CAP1-NARS2_CAP1_chr1_40525842_ENST00000372802_NARS2_chr11_78154804_ENST00000528850_length(amino acids)=170AA_BP=81
MIAVRSRWSIMADMQNLVERLERAVGRLEAVSHTSDMHRGYADSPSKGAAPYVQAFDSLLAGPVAEYLKISKEIGGDVQKHVAAVDLLVP

--------------------------------------------------------------

>12818_12818_11_CAP1-NARS2_CAP1_chr1_40525842_ENST00000372805_NARS2_chr11_78154804_ENST00000281038_length(amino acids)=166AA_BP=77
MRWSIMADMQNLVERLERAVGRLEAVSHTSDMHRGYADSPSKAGAAPYVQAFDSLLAGPVAEYLKISKEIGGDVQKHVAAVDLLVPGVGE

--------------------------------------------------------------

>12818_12818_12_CAP1-NARS2_CAP1_chr1_40525842_ENST00000372805_NARS2_chr11_78154804_ENST00000528850_length(amino acids)=166AA_BP=77
MRWSIMADMQNLVERLERAVGRLEAVSHTSDMHRGYADSPSKAGAAPYVQAFDSLLAGPVAEYLKISKEIGGDVQKHVAAVDLLVPGVGE

--------------------------------------------------------------

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Fusion Protein Functional Features

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr1:40525842/chr11:78154804)
- 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.

Main function of each fusion partner protein. (from UniProt)

Hgene	Tgene
CAP1 Q01518	NARS2 Q96I59
FUNCTION: Directly regulates filament dynamics and has been implicated in a number of complex developmental and morphological processes, including mRNA localization and the establishment of cell polarity.

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, because of limited space for viewing, we only show the protein feature retention information belong to the 13 regional features. All retention annotation result can be downloaded at
download page
* Minus value of BPloci means that the break pointn is located before the CDS.

- Retained protein feature among the 13 regional features.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Protein feature

Protein feature note

- Not-retained protein feature among the 13 regional features.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Protein feature

Protein feature note

Hgene

CAP1

chr1:40525842

chr11:78154804

ENST00000340450

218_256

71.0

475.0

Compositional bias

Note=Ala/Pro/Ser-rich

Hgene

CAP1

chr1:40525842

chr11:78154804

ENST00000340450

230_241

71.0

475.0

Compositional bias

Note=Poly-Pro

Hgene

CAP1

chr1:40525842

chr11:78154804

ENST00000372792

218_256

72.0

476.0

Compositional bias

Note=Ala/Pro/Ser-rich

Hgene

CAP1

chr1:40525842

chr11:78154804

ENST00000372792

230_241

72.0

476.0

Compositional bias

Note=Poly-Pro

Hgene

CAP1

chr1:40525842

chr11:78154804

ENST00000372797

218_256

72.0

476.0

Compositional bias

Note=Ala/Pro/Ser-rich

Hgene

CAP1

chr1:40525842

chr11:78154804

ENST00000372797

230_241

72.0

476.0

Compositional bias

Note=Poly-Pro

Hgene

CAP1

chr1:40525842

chr11:78154804

ENST00000372798

218_256

71.0

475.0

Compositional bias

Note=Ala/Pro/Ser-rich

Hgene

CAP1

chr1:40525842

chr11:78154804

ENST00000372798

230_241

71.0

475.0

Compositional bias

Note=Poly-Pro

Hgene

CAP1

chr1:40525842

chr11:78154804

ENST00000372802

218_256

71.0

475.0

Compositional bias

Note=Ala/Pro/Ser-rich

Hgene

CAP1

chr1:40525842

chr11:78154804

ENST00000372802

230_241

71.0

475.0

Compositional bias

Note=Poly-Pro

Hgene

CAP1

chr1:40525842

chr11:78154804

ENST00000372805

218_256

72.0

476.0

Compositional bias

Note=Ala/Pro/Ser-rich

Hgene

CAP1

chr1:40525842

chr11:78154804

ENST00000372805

230_241

72.0

476.0

Compositional bias

Note=Poly-Pro

Hgene

CAP1

chr1:40525842

chr11:78154804

ENST00000340450

319_453

71.0

475.0

Domain

C-CAP/cofactor C-like

Hgene

CAP1

chr1:40525842

chr11:78154804

ENST00000372792

319_453

72.0

476.0

Domain

C-CAP/cofactor C-like

Hgene

CAP1

chr1:40525842

chr11:78154804

ENST00000372797

319_453

72.0

476.0

Domain

C-CAP/cofactor C-like

Hgene

CAP1

chr1:40525842

chr11:78154804

ENST00000372798

319_453

71.0

475.0

Domain

C-CAP/cofactor C-like

Hgene

CAP1

chr1:40525842

chr11:78154804

ENST00000372802

319_453

71.0

475.0

Domain

C-CAP/cofactor C-like

Hgene

CAP1

chr1:40525842

chr11:78154804

ENST00000372805

319_453

72.0

476.0

Domain

C-CAP/cofactor C-like

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Fusion Protein Structures

PDB and CIF files of the predicted fusion proteins
* Here we show the 3D structure of the fusion proteins using Mol*. AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. Model confidence is shown from the pLDDT values per residue. pLDDT corresponds to the model’s prediction of its score on the local Distance Difference Test. It is a measure of local accuracy (from AlphfaFold website). To color code individual residues, we transformed individual PDB files into CIF format.

Fusion protein PDB link (fusion AA seq ID in FusionPDB)	Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand	AA seq	Len(AA seq)
PDB file >>>180_CAP1_40525842_NARS2_78154804_ranked_0.pdb	CAP1	40525842	40525842	ENST00000528850	NARS2	chr11	78154804	-	MIAVRRWSIMADMQNLVERLERAVGRLEAVSHTSDMHRGYADSPSKAGAAPYVQAFDSLLAGPVAEYLKISKEIGGDVQKHVAAVDLLVP	170

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pLDDT score distribution

pLDDT score distribution of the predicted wild-type structures of two partner proteins from AlphaFold2
* AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100.

CAP1_pLDDT.png

NARS2_pLDDT.png

pLDDT score distribution of the predicted fusion protein structures from AlphaFold2
* AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100.

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Ramachandran Plot of Fusion Protein Structure

Ramachandran plot of the torsional angles - phi (φ)and psi (ψ) - of the residues (amino acids) contained in this fusion protein peptide.

Fusion AA seq ID in FusionPDB and their Ramachandran plots

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Fusion Protein-Protein Interaction

Go to ChiPPI (Chimeric Protein-Protein interactions) to see the chimeric PPI interaction in
ChiPPI page.

Protein-protein interactors with each fusion partner protein in wild-type from validated records (BIOGRID-3.4.160)

Gene

PPI interactors

Protein-protein interactors based on sequence similarity (STRING)

Gene	STRING network
CAP1
NARS2

- Retained interactions in fusion protein (protein functional feature from UniProt).

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Still interaction with

- Lost interactions due to fusion (protein functional feature from UniProt).

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Interaction lost with

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Related Drugs to CAP1-NARS2

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 CAP1-NARS2

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