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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:WBP1L-PTEN

Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: WBP1L-PTEN
	FusionPDB ID: 98789
	FusionGDB2.0 ID: 98789
		Hgene	Tgene
	Gene symbol	WBP1L	PTEN
	Gene ID	54838	5728
	Gene name	WW domain binding protein 1 like	phosphatase and tensin homolog
	Synonyms	C10orf26\|OPA1L\|OPAL1	10q23del\|BZS\|CWS1\|DEC\|GLM2\|MHAM\|MMAC1\|PTEN1\|PTENbeta\|TEP1
	Cytomap	10q24.32	10q23.31
	Type of gene	protein-coding	protein-coding
	Description	WW domain binding protein 1-likeoutcome predictor in acute leukemia 1	phosphatidylinositol 3,4,5-trisphosphate 3-phosphatase and dual-specificity protein phosphatase PTENMMAC1 phosphatase and tensin homolog deleted on chromosome 10PTENepsilonmitochondrial PTENalphamitochondrial phosphatase and tensin protein alphamutat
	Modification date	20200313	20200329
	UniProtAcc	Q9NX94	.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000369889, ENST00000448841,	ENST00000472832, ENST00000371953,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	14 X 11 X 10=1540	30 X 21 X 10=6300
	# samples	19	36
	** MAII score	log2(19/1540*10)=-3.01885902725132 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(36/6300*10)=-4.12928301694497 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)	PubMed: WBP1L [Title/Abstract] AND PTEN [Title/Abstract] AND fusion [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	WBP1L(104557852)-PTEN(89692770), # samples:2
Anticipated loss of major functional domain due to fusion event.	WBP1L-PTEN 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. WBP1L-PTEN 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. WBP1L-PTEN 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. WBP1L-PTEN 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
Tgene	PTEN	GO:0001933	negative regulation of protein phosphorylation	20123964
Tgene	PTEN	GO:0006470	protein dephosphorylation	9256433
Tgene	PTEN	GO:0008285	negative regulation of cell proliferation	19057511
Tgene	PTEN	GO:0045736	negative regulation of cyclin-dependent protein serine/threonine kinase activity	21241890
Tgene	PTEN	GO:0046855	inositol phosphate dephosphorylation	9593664
Tgene	PTEN	GO:0046856	phosphatidylinositol dephosphorylation	9593664\|9811831
Tgene	PTEN	GO:0050821	protein stabilization	20123964
Tgene	PTEN	GO:0060070	canonical Wnt signaling pathway	20123964
Tgene	PTEN	GO:1902807	negative regulation of cell cycle G1/S phase transition	10918569
Tgene	PTEN	GO:1904668	positive regulation of ubiquitin protein ligase activity	21241890
Tgene	PTEN	GO:2000060	positive regulation of ubiquitin-dependent protein catabolic process	21241890
Tgene	PTEN	GO:2000134	negative regulation of G1/S transition of mitotic cell cycle	21241890

Fusion gene breakpoints across WBP1L (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 PTEN (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	PRAD	TCGA-G9-6364-01A	WBP1L	chr10	104557852	+	PTEN	chr10	89692770	+
ChimerDB4	PRAD	TCGA-G9-6364	WBP1L	chr10	104557852	+	PTEN	chr10	89692770	+

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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)

ENST00000448841

WBP1L

chr10

104557852

ENST00000371953

PTEN

chr10

89692770

7694

277

1235

383

ENST00000369889

WBP1L

chr10

104557852

ENST00000371953

PTEN

chr10

89692770

7689

272

142

1230

362

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
ENST00000448841	ENST00000371953	WBP1L	chr10	104557852	+	PTEN	chr10	89692770	+	8.40E-05	0.99991596
ENST00000369889	ENST00000371953	WBP1L	chr10	104557852	+	PTEN	chr10	89692770	+	5.09E-05	0.9999491

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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

>98789_98789_1_WBP1L-PTEN_WBP1L_chr10_104557852_ENST00000369889_PTEN_chr10_89692770_ENST00000371953_length(amino acids)=362AA_BP=44
MPFLLGLRQDKEACVGTNNQSYICDTGHCCGQSQCCNYYYELWFAQYPFEDHNPPQLELIKPFCEDLDQWLSEDDNHVAAIHCKAGKGRT
GVMICAYLLHRGKFLKAQEALDFYGEVRTRDKKGVTIPSQRRYVYYYSYLLKNHLDYRPVALLFHKMMFETIPMFSGGTCNPQFVVCQLK
VKIYSSNSGPTRREDKFMYFEFPQPLPVCGDIKVEFFHKQNKMLKKDKMFHFWVNTFFIPGPEETSEKVENGSLCDQEIDSICSIERADN
DKEYLVLTLTKNDLDKANKDKANRYFSPNFKVKLYFTKTVEEPSNPEASSSTSVTPDVSDNEPDHYRYSDTTDSDPENEPFDEDQHTQIT

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

>98789_98789_2_WBP1L-PTEN_WBP1L_chr10_104557852_ENST00000448841_PTEN_chr10_89692770_ENST00000371953_length(amino acids)=383AA_BP=65
MERRRLLGGMALLLLQALPSPLSARAEPPQDKEACVGTNNQSYICDTGHCCGQSQCCNYYYELWFAQYPFEDHNPPQLELIKPFCEDLDQ
WLSEDDNHVAAIHCKAGKGRTGVMICAYLLHRGKFLKAQEALDFYGEVRTRDKKGVTIPSQRRYVYYYSYLLKNHLDYRPVALLFHKMMF
ETIPMFSGGTCNPQFVVCQLKVKIYSSNSGPTRREDKFMYFEFPQPLPVCGDIKVEFFHKQNKMLKKDKMFHFWVNTFFIPGPEETSEKV
ENGSLCDQEIDSICSIERADNDKEYLVLTLTKNDLDKANKDKANRYFSPNFKVKLYFTKTVEEPSNPEASSSTSVTPDVSDNEPDHYRYS

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

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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/chr10:104557852/chr10:89692770)
- 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
WBP1L Q9NX94	.
	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.

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

WBP1L

chr10:104557852

chr10:89692770

ENST00000448841

42_62

64.33333333333333

364.0

Transmembrane

Helical

Tgene

PTEN

chr10:104557852

chr10:89692770

ENST00000371953

190_350

84.33333333333333

404.0

Domain

C2 tensin-type

Tgene

PTEN

chr10:104557852

chr10:89692770

ENST00000371953

401_403

84.33333333333333

404.0

Region

Note=PDZ domain-binding

- 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

WBP1L

chr10:104557852

chr10:89692770

ENST00000369889

101_183

43.333333333333336

343.0

Compositional bias

Note=Pro-rich

Hgene

WBP1L

chr10:104557852

chr10:89692770

ENST00000369889

335_342

43.333333333333336

343.0

Compositional bias

Note=Poly-Ser

Hgene

WBP1L

chr10:104557852

chr10:89692770

ENST00000448841

101_183

64.33333333333333

364.0

Compositional bias

Note=Pro-rich

Hgene

WBP1L

chr10:104557852

chr10:89692770

ENST00000448841

335_342

64.33333333333333

364.0

Compositional bias

Note=Poly-Ser

Hgene

WBP1L

chr10:104557852

chr10:89692770

ENST00000369889

42_62

43.333333333333336

343.0

Transmembrane

Helical

Tgene

PTEN

chr10:104557852

chr10:89692770

ENST00000371953

14_185

84.33333333333333

404.0

Domain

Phosphatase tensin-type

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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 >>>766_WBP1L_104557852_PTEN_89692770_ranked_0.pdb	WBP1L	104557852	104557852	ENST00000371953	PTEN	chr10	89692770	+	MERRRLLGGMALLLLQALPSPLSARAEPPQDKEACVGTNNQSYICDTGHCCGQSQCCNYYYELWFAQYPFEDHNPPQLELIKPFCEDLDQ WLSEDDNHVAAIHCKAGKGRTGVMICAYLLHRGKFLKAQEALDFYGEVRTRDKKGVTIPSQRRYVYYYSYLLKNHLDYRPVALLFHKMMF ETIPMFSGGTCNPQFVVCQLKVKIYSSNSGPTRREDKFMYFEFPQPLPVCGDIKVEFFHKQNKMLKKDKMFHFWVNTFFIPGPEETSEKV ENGSLCDQEIDSICSIERADNDKEYLVLTLTKNDLDKANKDKANRYFSPNFKVKLYFTKTVEEPSNPEASSSTSVTPDVSDNEPDHYRYS	383

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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.

WBP1L_pLDDT.png

PTEN_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
WBP1L
PTEN

- 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 WBP1L-PTEN

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 WBP1L-PTEN

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