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	Fusion Gene Summary
	Fusion Gene Sample Information
	Fusion ORF Analysis
	Fusion Amino Acid Sequences
	Fusion Protein Functional Features
	Fusion Protein-Protein Interaction
	Related drugs with this fusion protein
	Related disease with this fusion protein

Fusion Protein:PCMTD1-WRN

Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: PCMTD1-WRN
	FusionPDB ID: 63385
	FusionGDB2.0 ID: 63385
		Hgene	Tgene
	Gene symbol	PCMTD1	WRN
	Gene ID	115294	7486
	Gene name	protein-L-isoaspartate (D-aspartate) O-methyltransferase domain containing 1	WRN RecQ like helicase
	Synonyms	-	RECQ3\|RECQL2\|RECQL3
	Cytomap	8q11.23	8p12
	Type of gene	protein-coding	protein-coding
	Description	protein-L-isoaspartate O-methyltransferase domain-containing protein 1	Werner syndrome ATP-dependent helicaseDNA helicase, RecQ-like type 3Werner syndrome RecQ like helicaseWerner syndrome, RecQ helicase-likeexonuclease WRNrecQ protein-like 2
	Modification date	20200313	20200320
	UniProtAcc	.	.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000360540, ENST00000519559, ENST00000521344, ENST00000522514, ENST00000544451,	ENST00000298139,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	27 X 12 X 15=4860	9 X 10 X 7=630
	# samples	40	11
	** MAII score	log2(40/4860*10)=-3.60288440871842 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(11/630*10)=-2.51784830486262 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)	PubMed: PCMTD1 [Title/Abstract] AND WRN [Title/Abstract] AND fusion [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	PCMTD1(52811490)-WRN(30998946), # samples:3
Anticipated loss of major functional domain due to fusion event.	PCMTD1-WRN 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. PCMTD1-WRN 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. PCMTD1-WRN 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. PCMTD1-WRN 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	WRN	GO:0000731	DNA synthesis involved in DNA repair	17563354
Tgene	WRN	GO:0006259	DNA metabolic process	16622405
Tgene	WRN	GO:0006284	base-excision repair	17611195
Tgene	WRN	GO:0006974	cellular response to DNA damage stimulus	18203716
Tgene	WRN	GO:0006979	response to oxidative stress	17611195
Tgene	WRN	GO:0009267	cellular response to starvation	11420665
Tgene	WRN	GO:0010225	response to UV-C	17563354
Tgene	WRN	GO:0031297	replication fork processing	17115688
Tgene	WRN	GO:0032508	DNA duplex unwinding	11735402\|26420422
Tgene	WRN	GO:0044806	G-quadruplex DNA unwinding	11735402
Tgene	WRN	GO:0051345	positive regulation of hydrolase activity	17611195
Tgene	WRN	GO:0061820	telomeric D-loop disassembly	15200954\|19734539\|26420422
Tgene	WRN	GO:0071480	cellular response to gamma radiation	21639834
Tgene	WRN	GO:0098530	positive regulation of strand invasion	26420422
Tgene	WRN	GO:1902570	protein localization to nucleolus	11420665

Fusion gene breakpoints across PCMTD1 (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 WRN (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	BRCA	TCGA-A8-A07P-01A	PCMTD1	chr8	52811490	-	WRN	chr8	30998946	+
ChimerDB4	BRCA	TCGA-A8-A07P	PCMTD1	chr8	52811489	-	WRN	chr8	30998945	+

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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)

ENST00000544451

PCMTD1

chr8

52811490

ENST00000298139

WRN

chr8

30998946

2245

246

216

1577

453

ENST00000544451

PCMTD1

chr8

52811489

ENST00000298139

WRN

chr8

30998945

2245

246

216

1577

453

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
ENST00000544451	ENST00000298139	PCMTD1	chr8	52811490	-	WRN	chr8	30998946	+	0.000304782	0.9996953
ENST00000544451	ENST00000298139	PCMTD1	chr8	52811489	-	WRN	chr8	30998945	+	0.000304782	0.9996953

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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

>63385_63385_1_PCMTD1-WRN_PCMTD1_chr8_52811489_ENST00000544451_WRN_chr8_30998945_ENST00000298139_length(amino acids)=453AA_BP=9
MACAPLPAPQNSQRLADQYRRHSLFGTGKDQTESWWKAFSRQLITEGFLVEVSRYNKFMKICALTKKGRNWLHKANTESQSLILQANEEL
CPKKLLLPSSKTVSSGTKEHCYNQVPVELSTEKKSNLEKLYSYKPCDKISSGSNISKKSIMVQSPEKAYSSSQPVISAQEQETQIVLYGK
LVEARQKHANKMDVPPAILATNKILVDMAKMRPTTVENVKRIDGVSEGKAAMLAPLLEVIKHFCQTNSVQTDLFSSTKPQEEQKTSLVAK
NKICTLSQSMAITYSLFQEKKMPLKSIAESRILPLMTIGMHLSQAVKAGCPLDLERAGLTPEVQKIIADVIRNPPVNSDMSKISLIRMLV
PENIDTYLIHMAIEILKHGPDSGLQPSCDVNKRRCFPGSEEICSSSKRSKEEVGINTETSSAERKRRLPVWFAKGSDTSKKLMDKTKRGG

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

>63385_63385_2_PCMTD1-WRN_PCMTD1_chr8_52811490_ENST00000544451_WRN_chr8_30998946_ENST00000298139_length(amino acids)=453AA_BP=9
MACAPLPAPQNSQRLADQYRRHSLFGTGKDQTESWWKAFSRQLITEGFLVEVSRYNKFMKICALTKKGRNWLHKANTESQSLILQANEEL
CPKKLLLPSSKTVSSGTKEHCYNQVPVELSTEKKSNLEKLYSYKPCDKISSGSNISKKSIMVQSPEKAYSSSQPVISAQEQETQIVLYGK
LVEARQKHANKMDVPPAILATNKILVDMAKMRPTTVENVKRIDGVSEGKAAMLAPLLEVIKHFCQTNSVQTDLFSSTKPQEEQKTSLVAK
NKICTLSQSMAITYSLFQEKKMPLKSIAESRILPLMTIGMHLSQAVKAGCPLDLERAGLTPEVQKIIADVIRNPPVNSDMSKISLIRMLV
PENIDTYLIHMAIEILKHGPDSGLQPSCDVNKRRCFPGSEEICSSSKRSKEEVGINTETSSAERKRRLPVWFAKGSDTSKKLMDKTKRGG

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

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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/chr8:52811490/chr8:30998946)
- 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
.	.
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: 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

Tgene

WRN

chr8:52811489

chr8:30998945

ENST00000298139

1150_1229

989.0

1433.0

Domain

HRDC

Tgene

WRN

chr8:52811490

chr8:30998946

ENST00000298139

1150_1229

989.0

1433.0

Domain

HRDC

- 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

Tgene

WRN

chr8:52811489

chr8:30998945

ENST00000298139

507_510

989.0

1433.0

Compositional bias

Note=Poly-Glu

Tgene

WRN

chr8:52811490

chr8:30998946

ENST00000298139

507_510

989.0

1433.0

Compositional bias

Note=Poly-Glu

Tgene

WRN

chr8:52811489

chr8:30998945

ENST00000298139

558_724

989.0

1433.0

Domain

Helicase ATP-binding

Tgene

WRN

chr8:52811489

chr8:30998945

ENST00000298139

60_228

989.0

1433.0

Domain

Note=3'-5' exonuclease

Tgene

WRN

chr8:52811489

chr8:30998945

ENST00000298139

749_899

989.0

1433.0

Domain

Helicase C-terminal

Tgene

WRN

chr8:52811490

chr8:30998946

ENST00000298139

558_724

989.0

1433.0

Domain

Helicase ATP-binding

Tgene

WRN

chr8:52811490

chr8:30998946

ENST00000298139

60_228

989.0

1433.0

Domain

Note=3'-5' exonuclease

Tgene

WRN

chr8:52811490

chr8:30998946

ENST00000298139

749_899

989.0

1433.0

Domain

Helicase C-terminal

Tgene

WRN

chr8:52811489

chr8:30998945

ENST00000298139

668_671

989.0

1433.0

Motif

Note=DEAH box

Tgene

WRN

chr8:52811490

chr8:30998946

ENST00000298139

668_671

989.0

1433.0

Motif

Note=DEAH box

Tgene

WRN

chr8:52811489

chr8:30998945

ENST00000298139

571_578

989.0

1433.0

Nucleotide binding

ATP

Tgene

WRN

chr8:52811490

chr8:30998946

ENST00000298139

571_578

989.0

1433.0

Nucleotide binding

ATP

Tgene

WRN

chr8:52811489

chr8:30998945

ENST00000298139

424_477

989.0

1433.0

Region

Note=2 X 27 AA tandem repeats of H-L-S-P-N-D-N-E-N-D-T-S-Y-V-I-E-S-D-E-D-L-E-M-E-M-L-K

Tgene

WRN

chr8:52811490

chr8:30998946

ENST00000298139

424_477

989.0

1433.0

Region

Note=2 X 27 AA tandem repeats of H-L-S-P-N-D-N-E-N-D-T-S-Y-V-I-E-S-D-E-D-L-E-M-E-M-L-K

Tgene

WRN

chr8:52811489

chr8:30998945

ENST00000298139

424_450

989.0

1433.0

Repeat

Tgene

WRN

chr8:52811489

chr8:30998945

ENST00000298139

451_477

989.0

1433.0

Repeat

Tgene

WRN

chr8:52811490

chr8:30998946

ENST00000298139

424_450

989.0

1433.0

Repeat

Tgene

WRN

chr8:52811490

chr8:30998946

ENST00000298139

451_477

989.0

1433.0

Repeat

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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
PCMTD1
WRN

- 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
Tgene	WRN	chr8:52811489	chr8:30998945	ENST00000298139		23	35	2_277	989.0	1433.0	WRNIP1
Tgene	WRN	chr8:52811490	chr8:30998946	ENST00000298139		23	35	2_277	989.0	1433.0	WRNIP1

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Related Drugs to PCMTD1-WRN

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 PCMTD1-WRN

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