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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:RUNX2-PGK1 (FusionGDB2 ID:HG860TG5230)

Fusion Gene Summary for RUNX2-PGK1

check button Fusion gene summary
Fusion gene informationFusion gene name: RUNX2-PGK1
Fusion gene ID: hg860tg5230
HgeneTgene
Gene symbol

RUNX2

PGK1

Gene ID

860

5230

Gene nameRUNX family transcription factor 2phosphoglycerate kinase 1
SynonymsAML3|CBF-alpha-1|CBFA1|CCD|CCD1|CLCD|OSF-2|OSF2|PEA2aA|PEBP2aAHEL-S-68p|MIG10|PGKA
Cytomap('RUNX2')('PGK1')

6p21.1

Xq21.1

Type of geneprotein-codingprotein-coding
Descriptionrunt-related transcription factor 2PEA2-alpha APEBP2-alpha ASL3-3 enhancer factor 1 alpha A subunitSL3/AKV core-binding factor alpha A subunitacute myeloid leukemia 3 proteincore-binding factor, runt domain, alpha subunit 1oncogene AML-3osteoblastphosphoglycerate kinase 1PRP 2cell migration-inducing gene 10 proteinepididymis secretory sperm binding protein Li 68pprimer recognition protein 2
Modification date2020032220200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000352853, ENST00000359524, 
ENST00000371432, ENST00000371436, 
ENST00000371438, ENST00000465038, 
ENST00000483243, ENST00000541979, 
ENST00000576263, 
Fusion gene scores* DoF score8 X 8 X 5=32013 X 12 X 6=936
# samples 914
** MAII scorelog2(9/320*10)=-1.83007499855769
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(14/936*10)=-2.74108170263844
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: RUNX2 [Title/Abstract] AND PGK1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointRUNX2(45500668)-PGK1(77381770), # samples:1
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
HgeneRUNX2

GO:0045892

negative regulation of transcription, DNA-templated

11965546

HgeneRUNX2

GO:0045893

positive regulation of transcription, DNA-templated

11965546

TgenePGK1

GO:0071456

cellular response to hypoxia

11130727



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
ChiTaRS5.0N/AAA165201RUNX2chr6

45500668

+PGK1chrX

77381770

-


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Fusion Gene ORF analysis for RUNX2-PGK1

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
intron-3UTRENST00000352853ENST00000373316RUNX2chr6

45500668

+PGK1chrX

77381770

-
intron-3UTRENST00000359524ENST00000373316RUNX2chr6

45500668

+PGK1chrX

77381770

-
intron-3UTRENST00000371432ENST00000373316RUNX2chr6

45500668

+PGK1chrX

77381770

-
intron-3UTRENST00000371436ENST00000373316RUNX2chr6

45500668

+PGK1chrX

77381770

-
intron-3UTRENST00000371438ENST00000373316RUNX2chr6

45500668

+PGK1chrX

77381770

-
intron-3UTRENST00000465038ENST00000373316RUNX2chr6

45500668

+PGK1chrX

77381770

-
intron-3UTRENST00000483243ENST00000373316RUNX2chr6

45500668

+PGK1chrX

77381770

-
intron-3UTRENST00000541979ENST00000373316RUNX2chr6

45500668

+PGK1chrX

77381770

-
intron-3UTRENST00000576263ENST00000373316RUNX2chr6

45500668

+PGK1chrX

77381770

-
intron-intronENST00000352853ENST00000442431RUNX2chr6

45500668

+PGK1chrX

77381770

-
intron-intronENST00000352853ENST00000476531RUNX2chr6

45500668

+PGK1chrX

77381770

-
intron-intronENST00000352853ENST00000537456RUNX2chr6

45500668

+PGK1chrX

77381770

-
intron-intronENST00000359524ENST00000442431RUNX2chr6

45500668

+PGK1chrX

77381770

-
intron-intronENST00000359524ENST00000476531RUNX2chr6

45500668

+PGK1chrX

77381770

-
intron-intronENST00000359524ENST00000537456RUNX2chr6

45500668

+PGK1chrX

77381770

-
intron-intronENST00000371432ENST00000442431RUNX2chr6

45500668

+PGK1chrX

77381770

-
intron-intronENST00000371432ENST00000476531RUNX2chr6

45500668

+PGK1chrX

77381770

-
intron-intronENST00000371432ENST00000537456RUNX2chr6

45500668

+PGK1chrX

77381770

-
intron-intronENST00000371436ENST00000442431RUNX2chr6

45500668

+PGK1chrX

77381770

-
intron-intronENST00000371436ENST00000476531RUNX2chr6

45500668

+PGK1chrX

77381770

-
intron-intronENST00000371436ENST00000537456RUNX2chr6

45500668

+PGK1chrX

77381770

-
intron-intronENST00000371438ENST00000442431RUNX2chr6

45500668

+PGK1chrX

77381770

-
intron-intronENST00000371438ENST00000476531RUNX2chr6

45500668

+PGK1chrX

77381770

-
intron-intronENST00000371438ENST00000537456RUNX2chr6

45500668

+PGK1chrX

77381770

-
intron-intronENST00000465038ENST00000442431RUNX2chr6

45500668

+PGK1chrX

77381770

-
intron-intronENST00000465038ENST00000476531RUNX2chr6

45500668

+PGK1chrX

77381770

-
intron-intronENST00000465038ENST00000537456RUNX2chr6

45500668

+PGK1chrX

77381770

-
intron-intronENST00000483243ENST00000442431RUNX2chr6

45500668

+PGK1chrX

77381770

-
intron-intronENST00000483243ENST00000476531RUNX2chr6

45500668

+PGK1chrX

77381770

-
intron-intronENST00000483243ENST00000537456RUNX2chr6

45500668

+PGK1chrX

77381770

-
intron-intronENST00000541979ENST00000442431RUNX2chr6

45500668

+PGK1chrX

77381770

-
intron-intronENST00000541979ENST00000476531RUNX2chr6

45500668

+PGK1chrX

77381770

-
intron-intronENST00000541979ENST00000537456RUNX2chr6

45500668

+PGK1chrX

77381770

-
intron-intronENST00000576263ENST00000442431RUNX2chr6

45500668

+PGK1chrX

77381770

-
intron-intronENST00000576263ENST00000476531RUNX2chr6

45500668

+PGK1chrX

77381770

-
intron-intronENST00000576263ENST00000537456RUNX2chr6

45500668

+PGK1chrX

77381770

-

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 RUNX2-PGK1


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)


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Fusion Protein Features for RUNX2-PGK1


check button Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/:45500668/:77381770)
- 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.
FGviewer

check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
..
FUNCTION: Transcriptional activator which is required for calcium-dependent dendritic growth and branching in cortical neurons. Recruits CREB-binding protein (CREBBP) to nuclear bodies. Component of the CREST-BRG1 complex, a multiprotein complex that regulates promoter activation by orchestrating a calcium-dependent release of a repressor complex and a recruitment of an activator complex. In resting neurons, transcription of the c-FOS promoter is inhibited by BRG1-dependent recruitment of a phospho-RB1-HDAC1 repressor complex. Upon calcium influx, RB1 is dephosphorylated by calcineurin, which leads to release of the repressor complex. At the same time, there is increased recruitment of CREBBP to the promoter by a CREST-dependent mechanism, which leads to transcriptional activation. The CREST-BRG1 complex also binds to the NR2B promoter, and activity-dependent induction of NR2B expression involves a release of HDAC1 and recruitment of CREBBP (By similarity). {ECO:0000250}.FUNCTION: Transcriptional activator which is required for calcium-dependent dendritic growth and branching in cortical neurons. Recruits CREB-binding protein (CREBBP) to nuclear bodies. Component of the CREST-BRG1 complex, a multiprotein complex that regulates promoter activation by orchestrating a calcium-dependent release of a repressor complex and a recruitment of an activator complex. In resting neurons, transcription of the c-FOS promoter is inhibited by BRG1-dependent recruitment of a phospho-RB1-HDAC1 repressor complex. Upon calcium influx, RB1 is dephosphorylated by calcineurin, which leads to release of the repressor complex. At the same time, there is increased recruitment of CREBBP to the promoter by a CREST-dependent mechanism, which leads to transcriptional activation. The CREST-BRG1 complex also binds to the NR2B promoter, and activity-dependent induction of NR2B expression involves a release of HDAC1 and recruitment of CREBBP (By similarity). {ECO:0000250}.

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 RUNX2-PGK1


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 RUNX2-PGK1


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 RUNX2-PGK1


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 RUNX2-PGK1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneRUNX2C0008928Cleidocranial Dysplasia21CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
HgeneRUNX2C0029463Osteosarcoma2CTD_human
HgeneRUNX2C3549874METAPHYSEAL DYSPLASIA WITH MAXILLARY HYPOPLASIA WITH OR WITHOUT BRACHYDACTYLY2GENOMICS_ENGLAND;ORPHANET
HgeneRUNX2C0003872Arthritis, Psoriatic1CTD_human
HgeneRUNX2C0003873Rheumatoid Arthritis1CTD_human
HgeneRUNX2C0009171Cocaine Abuse1CTD_human
HgeneRUNX2C0010278Craniosynostosis1GENOMICS_ENGLAND
HgeneRUNX2C0029408Degenerative polyarthritis1CTD_human
HgeneRUNX2C0029410Osteoarthritis of hip1CTD_human
HgeneRUNX2C0038587Substance Withdrawal Syndrome1CTD_human
HgeneRUNX2C0040427Tooth Abnormalities1CTD_human
HgeneRUNX2C0041948Uremia1CTD_human
HgeneRUNX2C0086189Drug Withdrawal Symptoms1CTD_human
HgeneRUNX2C0086743Osteoarthrosis Deformans1CTD_human
HgeneRUNX2C0087169Withdrawal Symptoms1CTD_human
HgeneRUNX2C0236736Cocaine-Related Disorders1CTD_human
HgeneRUNX2C0243057Stomatognathic System Abnormalities1CTD_human
HgeneRUNX2C0376634Craniofacial Abnormalities1CTD_human
HgeneRUNX2C0524730Odontome1CTD_human
HgeneRUNX2C0600427Cocaine Dependence1CTD_human
HgeneRUNX2C0949690Spondylarthritis1CTD_human
TgeneC1970848Phosphoglycerate Kinase 1 Deficiency11CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
TgeneC0007134Renal Cell Carcinoma1CTD_human
TgeneC0279702Conventional (Clear Cell) Renal Cell Carcinoma1CTD_human
TgeneC0684324Deficiency of phosphoglycerate kinase1ORPHANET
TgeneC1266042Chromophobe Renal Cell Carcinoma1CTD_human
TgeneC1266043Sarcomatoid Renal Cell Carcinoma1CTD_human
TgeneC1266044Collecting Duct Carcinoma of the Kidney1CTD_human
TgeneC1306837Papillary Renal Cell Carcinoma1CTD_human
TgeneC2239176Liver carcinoma1CTD_human