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Center for Computational Systems Medicine
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Fusion Gene Summary

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Fusion Gene ORF analysis

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Fusion Genomic Features

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Fusion Protein Features

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Fusion Gene Sequence

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Fusion Gene PPI analysis

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Related Drugs

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Related Diseases

Fusion gene:PGAP3-MYOCD (FusionGDB2 ID:64148)

Fusion Gene Summary for PGAP3-MYOCD

check button Fusion gene summary
Fusion gene informationFusion gene name: PGAP3-MYOCD
Fusion gene ID: 64148
HgeneTgene
Gene symbol

PGAP3

MYOCD

Gene ID

93210

93649

Gene namepost-GPI attachment to proteins phospholipase 3myocardin
SynonymsAGLA546|CAB2|PERLD1|PP1498|hCOS16MGBL|MYCD
Cytomap

17q12

17p12

Type of geneprotein-codingprotein-coding
Descriptionpost-GPI attachment to proteins factor 3COS16 homologgene coamplified with ERBB2 proteinper1-like domain containing 1post-GPI attachment to proteins 3myocardin
Modification date2020032720200313
UniProtAcc.

Q8IZQ8

Ensembl transtripts involved in fusion geneENST00000579146, ENST00000300658, 
ENST00000378011, ENST00000429199, 
ENST00000425538, ENST00000343344, 
ENST00000395988, 
Fusion gene scores* DoF score18 X 8 X 9=12966 X 4 X 4=96
# samples 277
** MAII scorelog2(27/1296*10)=-2.26303440583379
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(7/96*10)=-0.45567948377619
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: PGAP3 [Title/Abstract] AND MYOCD [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointPGAP3(37840850)-MYOCD(12639478), # samples:3
Anticipated loss of major functional domain due to fusion event.
* DoF score (Degree of Frequency) = # partners X # break points X # cancer types
** MAII score (Major Active Isofusion Index) = log2(# samples/DoF score*10)

check button Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez
PartnerGeneGO IDGO termPubMed ID
TgeneMYOCD

GO:0003257

positive regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation

15907818

TgeneMYOCD

GO:0008285

negative regulation of cell proliferation

18451334

TgeneMYOCD

GO:0045736

negative regulation of cyclin-dependent protein serine/threonine kinase activity

18451334

TgeneMYOCD

GO:0045893

positive regulation of transcription, DNA-templated

19797053

TgeneMYOCD

GO:0045944

positive regulation of transcription by RNA polymerase II

14970199|17215356|19578358

TgeneMYOCD

GO:0045987

positive regulation of smooth muscle contraction

17215356

TgeneMYOCD

GO:0051091

positive regulation of DNA-binding transcription factor activity

19098903

TgeneMYOCD

GO:0051152

positive regulation of smooth muscle cell differentiation

18451334

TgeneMYOCD

GO:2000721

positive regulation of transcription from RNA polymerase II promoter involved in smooth muscle cell differentiation

15907818

TgeneMYOCD

GO:2000727

positive regulation of cardiac muscle cell differentiation

18451334

TgeneMYOCD

GO:2001015

negative regulation of skeletal muscle cell differentiation

18451334


check buttonFusion gene breakpoints across PGAP3 (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

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

check button 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.
SourceDiseaseSampleHgeneHchrHbpHstrandTgeneTchrTbpTstrand
ChimerDB4BLCATCGA-4Z-AA7S-01APGAP3chr17

37840850

-MYOCDchr17

12639478

+
ChimerDB4BLCATCGA-4Z-AA7SPGAP3chr17

37840850

-MYOCDchr17

12639478

+
ChimerDB4BLCATCGA-4Z-AA7SPGAP3chr17

37844087

-MYOCDchr17

12639478

+
ChimerDB4BLCATCGA-4Z-AA7S-01APGAP3chr17

37840850

-MYOCDchr17

12639478

+


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Fusion Gene ORF analysis for PGAP3-MYOCD

check button 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.
ORFHenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrand
Frame-shiftENST00000579146ENST00000425538PGAP3chr17

37840850

-MYOCDchr17

12639478

+
Frame-shiftENST00000579146ENST00000343344PGAP3chr17

37840850

-MYOCDchr17

12639478

+
5CDS-3UTRENST00000579146ENST00000395988PGAP3chr17

37840850

-MYOCDchr17

12639478

+
Frame-shiftENST00000300658ENST00000425538PGAP3chr17

37840850

-MYOCDchr17

12639478

+
Frame-shiftENST00000300658ENST00000343344PGAP3chr17

37840850

-MYOCDchr17

12639478

+
5CDS-3UTRENST00000300658ENST00000395988PGAP3chr17

37840850

-MYOCDchr17

12639478

+
intron-3CDSENST00000378011ENST00000425538PGAP3chr17

37840850

-MYOCDchr17

12639478

+
intron-3CDSENST00000378011ENST00000343344PGAP3chr17

37840850

-MYOCDchr17

12639478

+
intron-3UTRENST00000378011ENST00000395988PGAP3chr17

37840850

-MYOCDchr17

12639478

+
Frame-shiftENST00000429199ENST00000425538PGAP3chr17

37840850

-MYOCDchr17

12639478

+
Frame-shiftENST00000429199ENST00000343344PGAP3chr17

37840850

-MYOCDchr17

12639478

+
5CDS-3UTRENST00000429199ENST00000395988PGAP3chr17

37840850

-MYOCDchr17

12639478

+
Frame-shiftENST00000579146ENST00000425538PGAP3chr17

37844087

-MYOCDchr17

12639478

+
Frame-shiftENST00000579146ENST00000343344PGAP3chr17

37844087

-MYOCDchr17

12639478

+
5CDS-3UTRENST00000579146ENST00000395988PGAP3chr17

37844087

-MYOCDchr17

12639478

+
Frame-shiftENST00000300658ENST00000425538PGAP3chr17

37844087

-MYOCDchr17

12639478

+
Frame-shiftENST00000300658ENST00000343344PGAP3chr17

37844087

-MYOCDchr17

12639478

+
5CDS-3UTRENST00000300658ENST00000395988PGAP3chr17

37844087

-MYOCDchr17

12639478

+
Frame-shiftENST00000378011ENST00000425538PGAP3chr17

37844087

-MYOCDchr17

12639478

+
Frame-shiftENST00000378011ENST00000343344PGAP3chr17

37844087

-MYOCDchr17

12639478

+
5CDS-3UTRENST00000378011ENST00000395988PGAP3chr17

37844087

-MYOCDchr17

12639478

+
Frame-shiftENST00000429199ENST00000425538PGAP3chr17

37844087

-MYOCDchr17

12639478

+
Frame-shiftENST00000429199ENST00000343344PGAP3chr17

37844087

-MYOCDchr17

12639478

+
5CDS-3UTRENST00000429199ENST00000395988PGAP3chr17

37844087

-MYOCDchr17

12639478

+

check buttonORFfinder result based on the fusion transcript sequence of in-frame fusion genes.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandSeq length
(transcript)		BP loci
(transcript)		Predicted start
(transcript)		Predicted stop
(transcript)		Seq length
(amino acids)

check buttonDeepORF 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.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandNo-coding scoreCoding score

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Fusion Genomic Features for PGAP3-MYOCD


check buttonFusionAI 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.
HgeneHchrHbpHstrandTgeneTchrTbpTstrand1-pp (fusion gene breakpoint)
PGAP3chr1737840849-MYOCDchr1712639477+6.66E-070.9999993
PGAP3chr1737840849-MYOCDchr1712639477+6.66E-070.9999993
PGAP3chr1737844086-MYOCDchr1712639477+1.56E-070.9999999
PGAP3chr1737840849-MYOCDchr1712639477+6.66E-070.9999993
PGAP3chr1737840849-MYOCDchr1712639477+6.66E-070.9999993
PGAP3chr1737844086-MYOCDchr1712639477+1.56E-070.9999999

check buttonDistribution 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.

check buttonDistribution 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 PGAP3-MYOCD


check button 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.
FGviewer

check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
.MYOCD

Q8IZQ8

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: Smooth muscle cells (SM) and cardiac muscle cells-specific transcriptional factor which uses the canonical single or multiple CArG boxes DNA sequence. Acts as a cofactor of serum response factor (SRF) with the potential to modulate SRF-target genes. Plays a crucial role in cardiogenesis, urinary bladder development, and differentiation of the smooth muscle cell lineage (myogenesis) (By similarity). {ECO:0000250, ECO:0000269|PubMed:12640126, ECO:0000269|PubMed:31513549}.

check buttonRetention 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.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note


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Fusion Gene Sequence for PGAP3-MYOCD


check button 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 PGAP3-MYOCD


check button Go to ChiPPI (Chimeric Protein-Protein interactions) to see the chimeric PPI interaction in

ChiPPI page.


check button Protein-protein interactors with each fusion partner protein in wild-type (BIOGRID-3.4.160)
HgeneHgene's interactorsTgeneTgene's interactors


check button - Retained PPIs in in-frame fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenStill interaction with


check button - Lost PPIs in in-frame fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


check button - Retained PPIs, but lost function due to frame-shift fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


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Related Drugs for PGAP3-MYOCD


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

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Related Diseases for PGAP3-MYOCD


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgenePGAP3C1855923Hyperphosphatasia with Mental Retardation1CTD_human;ORPHANET
HgenePGAP3C3810354HYPERPHOSPHATASIA WITH MENTAL RETARDATION SYNDROME 41GENOMICS_ENGLAND;UNIPROT
TgeneMYOCDC0004238Atrial Fibrillation2CTD_human
TgeneMYOCDC0235480Paroxysmal atrial fibrillation2CTD_human
TgeneMYOCDC2585653Persistent atrial fibrillation2CTD_human
TgeneMYOCDC3468561familial atrial fibrillation2CTD_human
TgeneMYOCDC0018800Cardiomegaly1CTD_human
TgeneMYOCDC0152021Congenital heart disease1GENOMICS_ENGLAND
TgeneMYOCDC0549253Dilatation of the bladder1GENOMICS_ENGLAND
TgeneMYOCDC0878544Cardiomyopathies1GENOMICS_ENGLAND
TgeneMYOCDC1383860Cardiac Hypertrophy1CTD_human