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	Fusion Gene Summary
	Fusion Gene ORF analysis
	Fusion Genomic Features
	Fusion Protein Features
	Fusion Gene Sequence
	Fusion Gene PPI analysis
	Related Drugs
	Related Diseases

Fusion gene:PRKCSH-PGPEP1 (FusionGDB2 ID:68356)

Fusion Gene Summary for PRKCSH-PGPEP1

Fusion gene summary

Fusion gene information	Fusion gene name: PRKCSH-PGPEP1
	Fusion gene ID: 68356
		Hgene	Tgene
	Gene symbol	PRKCSH	PGPEP1
	Gene ID	5589	54858
	Gene name	protein kinase C substrate 80K-H	pyroglutamyl-peptidase I
	Synonyms	AGE-R2\|G19P1\|GIIB\|PCLD\|PCLD1\|PKCSH\|PLD1\|VASAP-60	PAP-I\|PGI\|PGP\|PGP-I\|PGPI\|Pcp
	Cytomap	19p13.2	19p13.11
	Type of gene	protein-coding	protein-coding
	Description	glucosidase 2 subunit betaAGE-binding receptor 2advanced glycation end-product receptor 2glucosidase II subunit betahepatocystinprotein kinase C substrate 60.1 kDa protein heavy chainprotein kinase C substrate, 80 Kda protein	pyroglutamyl-peptidase 15-oxoprolyl-peptidasepGlu-peptidase Ipyroglutamyl aminopeptidase Ipyrrolidone-carboxylate peptidase
	Modification date	20200313	20200313
	UniProtAcc	.	.
	Ensembl transtripts involved in fusion gene	ENST00000591462, ENST00000252455, ENST00000412601, ENST00000592741, ENST00000587327, ENST00000589838, ENST00000591510,	ENST00000269919, ENST00000604499, ENST00000595066, ENST00000252813, ENST00000597431,
Fusion gene scores	* DoF score	8 X 10 X 4=320	6 X 4 X 6=144
	# samples	10	6
	** MAII score	log2(10/320*10)=-1.67807190511264 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(6/144*10)=-1.26303440583379 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Context	PubMed: PRKCSH [Title/Abstract] AND PGPEP1 [Title/Abstract] AND fusion [Title/Abstract]
Most frequent breakpoint	PRKCSH(11556288)-PGPEP1(18466705), # samples:2
Anticipated loss of major functional domain due to fusion event.	PRKCSH-PGPEP1 seems lost the major protein functional domain in Hgene partner, which is a cell metabolism 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	PRKCSH	GO:0006491	N-glycan processing	10929008

Fusion gene breakpoints across PRKCSH (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 PGPEP1 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

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	SKCM	TCGA-ER-A19H-06A	PRKCSH	chr19	11556288	+	PGPEP1	chr19	18466705	+
ChimerDB4	SKCM	TCGA-ER-A19H-06A	PRKCSH	chr19	11556288	+	PGPEP1	chr19	18466705	+

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Fusion Gene ORF analysis for PRKCSH-PGPEP1

Open reading frame (ORF) analsis of fusion genes based on Ensembl gene isoform structure.
* Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser.

ORF	Henst	Tenst	Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand
Frame-shift	ENST00000591462	ENST00000269919	PRKCSH	chr19	11556288	+	PGPEP1	chr19	18466705	+
Frame-shift	ENST00000591462	ENST00000604499	PRKCSH	chr19	11556288	+	PGPEP1	chr19	18466705	+
Frame-shift	ENST00000591462	ENST00000595066	PRKCSH	chr19	11556288	+	PGPEP1	chr19	18466705	+
5CDS-5UTR	ENST00000591462	ENST00000252813	PRKCSH	chr19	11556288	+	PGPEP1	chr19	18466705	+
5CDS-5UTR	ENST00000591462	ENST00000597431	PRKCSH	chr19	11556288	+	PGPEP1	chr19	18466705	+
Frame-shift	ENST00000252455	ENST00000269919	PRKCSH	chr19	11556288	+	PGPEP1	chr19	18466705	+
Frame-shift	ENST00000252455	ENST00000604499	PRKCSH	chr19	11556288	+	PGPEP1	chr19	18466705	+
Frame-shift	ENST00000252455	ENST00000595066	PRKCSH	chr19	11556288	+	PGPEP1	chr19	18466705	+
5CDS-5UTR	ENST00000252455	ENST00000252813	PRKCSH	chr19	11556288	+	PGPEP1	chr19	18466705	+
5CDS-5UTR	ENST00000252455	ENST00000597431	PRKCSH	chr19	11556288	+	PGPEP1	chr19	18466705	+
Frame-shift	ENST00000412601	ENST00000269919	PRKCSH	chr19	11556288	+	PGPEP1	chr19	18466705	+
Frame-shift	ENST00000412601	ENST00000604499	PRKCSH	chr19	11556288	+	PGPEP1	chr19	18466705	+
Frame-shift	ENST00000412601	ENST00000595066	PRKCSH	chr19	11556288	+	PGPEP1	chr19	18466705	+
5CDS-5UTR	ENST00000412601	ENST00000252813	PRKCSH	chr19	11556288	+	PGPEP1	chr19	18466705	+
5CDS-5UTR	ENST00000412601	ENST00000597431	PRKCSH	chr19	11556288	+	PGPEP1	chr19	18466705	+
Frame-shift	ENST00000592741	ENST00000269919	PRKCSH	chr19	11556288	+	PGPEP1	chr19	18466705	+
Frame-shift	ENST00000592741	ENST00000604499	PRKCSH	chr19	11556288	+	PGPEP1	chr19	18466705	+
Frame-shift	ENST00000592741	ENST00000595066	PRKCSH	chr19	11556288	+	PGPEP1	chr19	18466705	+
5CDS-5UTR	ENST00000592741	ENST00000252813	PRKCSH	chr19	11556288	+	PGPEP1	chr19	18466705	+
5CDS-5UTR	ENST00000592741	ENST00000597431	PRKCSH	chr19	11556288	+	PGPEP1	chr19	18466705	+
Frame-shift	ENST00000587327	ENST00000269919	PRKCSH	chr19	11556288	+	PGPEP1	chr19	18466705	+
Frame-shift	ENST00000587327	ENST00000604499	PRKCSH	chr19	11556288	+	PGPEP1	chr19	18466705	+
Frame-shift	ENST00000587327	ENST00000595066	PRKCSH	chr19	11556288	+	PGPEP1	chr19	18466705	+
5CDS-5UTR	ENST00000587327	ENST00000252813	PRKCSH	chr19	11556288	+	PGPEP1	chr19	18466705	+
5CDS-5UTR	ENST00000587327	ENST00000597431	PRKCSH	chr19	11556288	+	PGPEP1	chr19	18466705	+
Frame-shift	ENST00000589838	ENST00000269919	PRKCSH	chr19	11556288	+	PGPEP1	chr19	18466705	+
Frame-shift	ENST00000589838	ENST00000604499	PRKCSH	chr19	11556288	+	PGPEP1	chr19	18466705	+
Frame-shift	ENST00000589838	ENST00000595066	PRKCSH	chr19	11556288	+	PGPEP1	chr19	18466705	+
5CDS-5UTR	ENST00000589838	ENST00000252813	PRKCSH	chr19	11556288	+	PGPEP1	chr19	18466705	+
5CDS-5UTR	ENST00000589838	ENST00000597431	PRKCSH	chr19	11556288	+	PGPEP1	chr19	18466705	+
intron-3CDS	ENST00000591510	ENST00000269919	PRKCSH	chr19	11556288	+	PGPEP1	chr19	18466705	+
intron-3CDS	ENST00000591510	ENST00000604499	PRKCSH	chr19	11556288	+	PGPEP1	chr19	18466705	+
intron-3CDS	ENST00000591510	ENST00000595066	PRKCSH	chr19	11556288	+	PGPEP1	chr19	18466705	+
intron-5UTR	ENST00000591510	ENST00000252813	PRKCSH	chr19	11556288	+	PGPEP1	chr19	18466705	+
intron-5UTR	ENST00000591510	ENST00000597431	PRKCSH	chr19	11556288	+	PGPEP1	chr19	18466705	+

ORFfinder result based on the fusion transcript sequence of in-frame fusion genes.

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)

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

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Fusion Genomic Features for PRKCSH-PGPEP1

FusionAI prediction of the potential fusion gene breakpoint based on the pre-mature RNA sequence context (+/- 5kb of individual partner genes, total 20kb length sequence). FusionAI is a fusion gene breakpoint classifier based on convolutional neural network by comparing the fusion positive and negative sequence context of ~ 20K fusion gene data. From here, we can have the relative potentency of the 20K genomic sequence how individual sequnce will be likely used as the gene fusion breakpoints.

Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand	1-p	p (fusion gene breakpoint)
PRKCSH	chr19	11556288	+	PGPEP1	chr19	18466704	+	1.44E-14	1
PRKCSH	chr19	11556288	+	PGPEP1	chr19	18466704	+	1.44E-14	1

Distribution of 44 human genomic features loci across 20kb length fusion breakpoint regions. We integrated a total of 44 different types of human genomic feature loci information across five big categories including virus integration sites, repeats, structural variants, chromatin states, and gene expression regulation. More details are in help page.

Distribution of 44 human genomic features loci across 20kb length fusion breakpoint regions that are ovelapped with the top 1% feature importance score regions. More details are in help page.

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Fusion Protein Features for PRKCSH-PGPEP1

Go to
FGviewer for the breakpoints of :-:
.
- FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels.

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.

- In-frame and 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

- In-frame and 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

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Fusion Gene Sequence for PRKCSH-PGPEP1

For in-frame fusion transcripts, we provide the fusion transcript sequences and fusion amino acid sequences. To have fusion amino acid sequence, we ran ORFfinder and chose the longest ORF among the all predicted ones.

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Fusion Gene PPI Analysis for PRKCSH-PGPEP1

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 (BIOGRID-3.4.160)

Hgene

Hgene's interactors

Tgene

Tgene's interactors

- Retained PPIs in in-frame fusion.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Still interaction with

- Lost PPIs in in-frame fusion.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Interaction lost with

- Retained PPIs, but lost function due to frame-shift fusion.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Interaction lost with

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Related Drugs for PRKCSH-PGPEP1

Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)

Partner

Gene

UniProtAcc

DrugBank ID

Drug name

Drug activity

Drug type

Drug status

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Related Diseases for PRKCSH-PGPEP1

Diseases associated with fusion partners.
(DisGeNet 4.0)

Partner	Gene	Disease ID	Disease name	# pubmeds	Source
Hgene	PRKCSH	C0158683	Polycystic liver disease	3	CTD_human;ORPHANET
Hgene	PRKCSH	C0022680	Polycystic Kidney Diseases	1	CTD_human
Hgene	PRKCSH	C0887850	Polycystic Kidney, Type 1 Autosomal Dominant Disease	1	GENOMICS_ENGLAND
Hgene	PRKCSH	C1567435	Polycystic Kidney - body part	1	CTD_human