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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:VKORC1L1-ACHE

Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: VKORC1L1-ACHE
	FusionPDB ID: 98171
	FusionGDB2.0 ID: 98171
		Hgene	Tgene
	Gene symbol	VKORC1L1	ACHE
	Gene ID	154807	43
	Gene name	vitamin K epoxide reductase complex subunit 1 like 1	acetylcholinesterase (Cartwright blood group)
	Synonyms	-	ACEE\|ARACHE\|N-ACHE\|YT
	Cytomap	7q11.21	7q22.1
	Type of gene	protein-coding	protein-coding
	Description	vitamin K epoxide reductase complex subunit 1-like protein 1VKORC1-like protein 1	acetylcholinesteraseYt blood groupacetylcholinesterase (Yt blood group)apoptosis-related acetylcholinesterase
	Modification date	20200313	20200313
	UniProtAcc	.	P22303
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000360768, ENST00000434382,	ENST00000497647, ENST00000241069, ENST00000302913, ENST00000411582, ENST00000412389, ENST00000419336, ENST00000428317,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	6 X 3 X 5=90	6 X 5 X 5=150
	# samples	7	6
	** MAII score	log2(7/90*10)=-0.362570079384708 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(6/150*10)=-1.32192809488736 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)	PubMed: VKORC1L1 [Title/Abstract] AND ACHE [Title/Abstract] AND fusion [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	VKORC1L1(65338552)-ACHE(100488959), # samples:3
Anticipated loss of major functional domain due to fusion event.	VKORC1L1-ACHE 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. VKORC1L1-ACHE 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	VKORC1L1	GO:0042373	vitamin K metabolic process	21367861
Tgene	ACHE	GO:0006581	acetylcholine catabolic process	1517212
Tgene	ACHE	GO:0007155	cell adhesion	15454088

Fusion gene breakpoints across VKORC1L1 (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 ACHE (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	READ	TCGA-CI-6621-01A	VKORC1L1	chr7	65338552	-	ACHE	chr7	100488959	-
ChimerDB4	READ	TCGA-CI-6621-01A	VKORC1L1	chr7	65338552	+	ACHE	chr7	100488959	-
ChimerDB4	READ	TCGA-CI-6621	VKORC1L1	chr7	65338552	+	ACHE	chr7	100488959	-

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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)
ENST00000360768	VKORC1L1	chr7	65338552	+	ENST00000419336	ACHE	chr7	100488959	-	811	299	105	590	161
ENST00000360768	VKORC1L1	chr7	65338552	+	ENST00000241069	ACHE	chr7	100488959	-	811	299	105	590	161
ENST00000360768	VKORC1L1	chr7	65338552	+	ENST00000428317	ACHE	chr7	100488959	-	811	299	105	590	161
ENST00000360768	VKORC1L1	chr7	65338552	+	ENST00000302913	ACHE	chr7	100488959	-	1563	299	289	846	185
ENST00000360768	VKORC1L1	chr7	65338552	+	ENST00000412389	ACHE	chr7	100488959	-	808	299	105	590	161
ENST00000360768	VKORC1L1	chr7	65338552	+	ENST00000411582	ACHE	chr7	100488959	-	842	299	289	840	184
ENST00000434382	VKORC1L1	chr7	65338552	+	ENST00000419336	ACHE	chr7	100488959	-	709	197	3	488	161
ENST00000434382	VKORC1L1	chr7	65338552	+	ENST00000241069	ACHE	chr7	100488959	-	709	197	3	488	161
ENST00000434382	VKORC1L1	chr7	65338552	+	ENST00000428317	ACHE	chr7	100488959	-	709	197	3	488	161
ENST00000434382	VKORC1L1	chr7	65338552	+	ENST00000302913	ACHE	chr7	100488959	-	1461	197	187	744	185
ENST00000434382	VKORC1L1	chr7	65338552	+	ENST00000412389	ACHE	chr7	100488959	-	706	197	3	488	161
ENST00000434382	VKORC1L1	chr7	65338552	+	ENST00000411582	ACHE	chr7	100488959	-	740	197	187	738	184

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
ENST00000360768	ENST00000419336	VKORC1L1	chr7	65338552	+	ACHE	chr7	100488959	-	0.06579574	0.9342043
ENST00000360768	ENST00000241069	VKORC1L1	chr7	65338552	+	ACHE	chr7	100488959	-	0.06579574	0.9342043
ENST00000360768	ENST00000428317	VKORC1L1	chr7	65338552	+	ACHE	chr7	100488959	-	0.06579574	0.9342043
ENST00000360768	ENST00000302913	VKORC1L1	chr7	65338552	+	ACHE	chr7	100488959	-	0.5249885	0.4750115
ENST00000360768	ENST00000412389	VKORC1L1	chr7	65338552	+	ACHE	chr7	100488959	-	0.06643838	0.9335617
ENST00000360768	ENST00000411582	VKORC1L1	chr7	65338552	+	ACHE	chr7	100488959	-	0.1343309	0.8656691
ENST00000434382	ENST00000419336	VKORC1L1	chr7	65338552	+	ACHE	chr7	100488959	-	0.15447941	0.8455206
ENST00000434382	ENST00000241069	VKORC1L1	chr7	65338552	+	ACHE	chr7	100488959	-	0.15447941	0.8455206
ENST00000434382	ENST00000428317	VKORC1L1	chr7	65338552	+	ACHE	chr7	100488959	-	0.15447941	0.8455206
ENST00000434382	ENST00000302913	VKORC1L1	chr7	65338552	+	ACHE	chr7	100488959	-	0.76223665	0.2377633
ENST00000434382	ENST00000412389	VKORC1L1	chr7	65338552	+	ACHE	chr7	100488959	-	0.15629104	0.843709
ENST00000434382	ENST00000411582	VKORC1L1	chr7	65338552	+	ACHE	chr7	100488959	-	0.37531903	0.62468094

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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

>98171_98171_1_VKORC1L1-ACHE_VKORC1L1_chr7_65338552_ENST00000360768_ACHE_chr7_100488959_ENST00000241069_length(amino acids)=161AA_BP=64
MAAPVLLRVSVPRWERVARYAVCAAGILLSIYAYHVEREKERDPEHRALCDLGPWVKCSAALASRDPNEPRDPKAPQWPPYTAGAQQYVS

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

>98171_98171_2_VKORC1L1-ACHE_VKORC1L1_chr7_65338552_ENST00000360768_ACHE_chr7_100488959_ENST00000302913_length(amino acids)=185AA_BP=3
MPPGIPMSPETPRPHNGPRTRRGLSSTLVWTCGRWRCGGGCAPRPAPSGTASSPNCSAPPPRRLPAPAQASPMGRLLRGPASPCPSSSST
SFSSSSSPTSGGCEHGLFPYGHRGPSSNEWSDRGEGPHSGISDLVLPSSSNRETHTGQGRRRGPCLPPFSGTPTPLLFEWKWKSQYSFIK

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

>98171_98171_3_VKORC1L1-ACHE_VKORC1L1_chr7_65338552_ENST00000360768_ACHE_chr7_100488959_ENST00000411582_length(amino acids)=184AA_BP=3
MPPGIPMSPETPRPHNGPRTRRGLSSTLVWTCGRWRCGGGCAPRPAPSGTASSPNCSAPPPRRLPAPAQASPMGRLLRGPASPCPSSSST
SFSSSSSPTSGGCEHGLFPYGHRGPSSNEWSDRGEGPHSGISDLVLPSSSNRETHTGQGRRRGPCLPPFSGTPTPLLFEWKWKSQYSFIK

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

>98171_98171_4_VKORC1L1-ACHE_VKORC1L1_chr7_65338552_ENST00000360768_ACHE_chr7_100488959_ENST00000412389_length(amino acids)=161AA_BP=64
MAAPVLLRVSVPRWERVARYAVCAAGILLSIYAYHVEREKERDPEHRALCDLGPWVKCSAALASRDPNEPRDPKAPQWPPYTAGAQQYVS

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

>98171_98171_5_VKORC1L1-ACHE_VKORC1L1_chr7_65338552_ENST00000360768_ACHE_chr7_100488959_ENST00000419336_length(amino acids)=161AA_BP=64
MAAPVLLRVSVPRWERVARYAVCAAGILLSIYAYHVEREKERDPEHRALCDLGPWVKCSAALASRDPNEPRDPKAPQWPPYTAGAQQYVS

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

>98171_98171_6_VKORC1L1-ACHE_VKORC1L1_chr7_65338552_ENST00000360768_ACHE_chr7_100488959_ENST00000428317_length(amino acids)=161AA_BP=64
MAAPVLLRVSVPRWERVARYAVCAAGILLSIYAYHVEREKERDPEHRALCDLGPWVKCSAALASRDPNEPRDPKAPQWPPYTAGAQQYVS

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

>98171_98171_7_VKORC1L1-ACHE_VKORC1L1_chr7_65338552_ENST00000434382_ACHE_chr7_100488959_ENST00000241069_length(amino acids)=161AA_BP=64
MAAPVLLRVSVPRWERVARYAVCAAGILLSIYAYHVEREKERDPEHRALCDLGPWVKCSAALASRDPNEPRDPKAPQWPPYTAGAQQYVS

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

>98171_98171_8_VKORC1L1-ACHE_VKORC1L1_chr7_65338552_ENST00000434382_ACHE_chr7_100488959_ENST00000302913_length(amino acids)=185AA_BP=3
MPPGIPMSPETPRPHNGPRTRRGLSSTLVWTCGRWRCGGGCAPRPAPSGTASSPNCSAPPPRRLPAPAQASPMGRLLRGPASPCPSSSST
SFSSSSSPTSGGCEHGLFPYGHRGPSSNEWSDRGEGPHSGISDLVLPSSSNRETHTGQGRRRGPCLPPFSGTPTPLLFEWKWKSQYSFIK

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

>98171_98171_9_VKORC1L1-ACHE_VKORC1L1_chr7_65338552_ENST00000434382_ACHE_chr7_100488959_ENST00000411582_length(amino acids)=184AA_BP=3
MPPGIPMSPETPRPHNGPRTRRGLSSTLVWTCGRWRCGGGCAPRPAPSGTASSPNCSAPPPRRLPAPAQASPMGRLLRGPASPCPSSSST
SFSSSSSPTSGGCEHGLFPYGHRGPSSNEWSDRGEGPHSGISDLVLPSSSNRETHTGQGRRRGPCLPPFSGTPTPLLFEWKWKSQYSFIK

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

>98171_98171_10_VKORC1L1-ACHE_VKORC1L1_chr7_65338552_ENST00000434382_ACHE_chr7_100488959_ENST00000412389_length(amino acids)=161AA_BP=64
MAAPVLLRVSVPRWERVARYAVCAAGILLSIYAYHVEREKERDPEHRALCDLGPWVKCSAALASRDPNEPRDPKAPQWPPYTAGAQQYVS

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

>98171_98171_11_VKORC1L1-ACHE_VKORC1L1_chr7_65338552_ENST00000434382_ACHE_chr7_100488959_ENST00000419336_length(amino acids)=161AA_BP=64
MAAPVLLRVSVPRWERVARYAVCAAGILLSIYAYHVEREKERDPEHRALCDLGPWVKCSAALASRDPNEPRDPKAPQWPPYTAGAQQYVS

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

>98171_98171_12_VKORC1L1-ACHE_VKORC1L1_chr7_65338552_ENST00000434382_ACHE_chr7_100488959_ENST00000428317_length(amino acids)=161AA_BP=64
MAAPVLLRVSVPRWERVARYAVCAAGILLSIYAYHVEREKERDPEHRALCDLGPWVKCSAALASRDPNEPRDPKAPQWPPYTAGAQQYVS

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

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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/chr7:65338552/chr7:100488959)
- 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
.	ACHE P22303
FUNCTION: Might normally function as a transcriptional repressor. EWS-fusion-proteins (EFPS) may play a role in the tumorigenic process. They may disturb gene expression by mimicking, or interfering with the normal function of CTD-POLII within the transcription initiation complex. They may also contribute to an aberrant activation of the fusion protein target genes.	FUNCTION: Terminates signal transduction at the neuromuscular junction by rapid hydrolysis of the acetylcholine released into the synaptic cleft. Role in neuronal apoptosis. {ECO:0000269\|PubMed:11985878, ECO:0000269\|PubMed:1517212, ECO:0000269\|PubMed:1748670, ECO:0000269\|PubMed:2714437}.

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

Hgene

VKORC1L1

chr7:65338552

chr7:100488959

ENST00000360768

1_16

64.66666666666667

177.0

Topological domain

Cytoplasmic

Hgene

VKORC1L1

chr7:65338552

chr7:100488959

ENST00000360768

17_37

64.66666666666667

177.0

Transmembrane

Helical

- 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

VKORC1L1

chr7:65338552

chr7:100488959

ENST00000360768

113_113

64.66666666666667

177.0

Topological domain

Cytoplasmic

Hgene

VKORC1L1

chr7:65338552

chr7:100488959

ENST00000360768

156_176

64.66666666666667

177.0

Topological domain

Cytoplasmic

Hgene

VKORC1L1

chr7:65338552

chr7:100488959

ENST00000360768

38_91

64.66666666666667

177.0

Topological domain

Lumenal

Hgene

VKORC1L1

chr7:65338552

chr7:100488959

ENST00000360768

114_134

64.66666666666667

177.0

Transmembrane

Helical

Hgene

VKORC1L1

chr7:65338552

chr7:100488959

ENST00000360768

135_155

64.66666666666667

177.0

Transmembrane

Helical

Hgene

VKORC1L1

chr7:65338552

chr7:100488959

ENST00000360768

92_112

64.66666666666667

177.0

Transmembrane

Helical

Tgene

ACHE

chr7:65338552

chr7:100488959

ENST00000241069

233_234

517.6666666666666

615.0

Region

Galanthamine binding

Tgene

ACHE

chr7:65338552

chr7:100488959

ENST00000302913

233_234

517.6666666666666

618.0

Region

Galanthamine binding

Tgene

ACHE

chr7:65338552

chr7:100488959

ENST00000411582

233_234

517.6666666666666

618.0

Region

Galanthamine binding

Tgene

ACHE

chr7:65338552

chr7:100488959

ENST00000412389

233_234

517.6666666666666

615.0

Region

Galanthamine binding

Tgene

ACHE

chr7:65338552

chr7:100488959

ENST00000419336

233_234

429.6666666666667

527.0

Region

Galanthamine binding

Tgene

ACHE

chr7:65338552

chr7:100488959

ENST00000428317

233_234

517.6666666666666

615.0

Region

Galanthamine binding

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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 >>>221_VKORC1L1_65338552_ACHE_100488959_ranked_0.pdb	VKORC1L1	65338552	65338552	ENST00000411582	ACHE	chr7	100488959	-	MPPGIPMSPETPRPHNGPRTRRGLSSTLVWTCGRWRCGGGCAPRPAPSGTASSPNCSAPPPRRLPAPAQASPMGRLLRGPASPCPSSSST SFSSSSSPTSGGCEHGLFPYGHRGPSSNEWSDRGEGPHSGISDLVLPSSSNRETHTGQGRRRGPCLPPFSGTPTPLLFEWKWKSQYSFIK	185

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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.

VKORC1L1_pLDDT.png

ACHE_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
VKORC1L1
ACHE

- 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 VKORC1L1-ACHE

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 VKORC1L1-ACHE

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