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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:C11orf54-PGM1 (FusionGDB2 ID:HG28970TG5236)

Fusion Gene Summary for C11orf54-PGM1

check button Fusion gene summary
Fusion gene informationFusion gene name: C11orf54-PGM1
Fusion gene ID: hg28970tg5236
HgeneTgene
Gene symbol

C11orf54

PGM1

Gene ID

28970

5236

Gene namechromosome 11 open reading frame 54phosphoglucomutase 1
SynonymsPTD012|PTOD012CDG1T|GSD14
Cytomap('C11orf54')('PGM1')

11q21

1p31.3

Type of geneprotein-codingprotein-coding
Descriptionester hydrolase C11orf54epididymis secretory sperm binding proteinphosphoglucomutase-1PGM 1glucose phosphomutase 1
Modification date2020032720200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000531516, ENST00000331239, 
ENST00000354421, ENST00000528099, 
ENST00000528288, ENST00000540113, 
Fusion gene scores* DoF score5 X 4 X 3=608 X 7 X 6=336
# samples 49
** MAII scorelog2(4/60*10)=-0.584962500721156
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(9/336*10)=-1.90046432644909
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: C11orf54 [Title/Abstract] AND PGM1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointC11orf54(93474894)-PGM1(64125257), # 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
TgenePGM1

GO:0006006

glucose metabolic process

25288802



check button Fusion gene information
* 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
ChimerDB4GBMTCGA-06-5415-01AC11orf54chr11

93474894

+PGM1chr1

64125257

+


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Fusion Gene ORF analysis for C11orf54-PGM1

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
3UTR-3CDSENST00000531516ENST00000371083C11orf54chr11

93474894

+PGM1chr1

64125257

+
3UTR-3CDSENST00000531516ENST00000371084C11orf54chr11

93474894

+PGM1chr1

64125257

+
3UTR-3CDSENST00000531516ENST00000540265C11orf54chr11

93474894

+PGM1chr1

64125257

+
3UTR-intronENST00000531516ENST00000483707C11orf54chr11

93474894

+PGM1chr1

64125257

+
5UTR-3CDSENST00000331239ENST00000371083C11orf54chr11

93474894

+PGM1chr1

64125257

+
5UTR-3CDSENST00000331239ENST00000371084C11orf54chr11

93474894

+PGM1chr1

64125257

+
5UTR-3CDSENST00000331239ENST00000540265C11orf54chr11

93474894

+PGM1chr1

64125257

+
5UTR-3CDSENST00000354421ENST00000371083C11orf54chr11

93474894

+PGM1chr1

64125257

+
5UTR-3CDSENST00000354421ENST00000371084C11orf54chr11

93474894

+PGM1chr1

64125257

+
5UTR-3CDSENST00000354421ENST00000540265C11orf54chr11

93474894

+PGM1chr1

64125257

+
5UTR-3CDSENST00000528099ENST00000371083C11orf54chr11

93474894

+PGM1chr1

64125257

+
5UTR-3CDSENST00000528099ENST00000371084C11orf54chr11

93474894

+PGM1chr1

64125257

+
5UTR-3CDSENST00000528099ENST00000540265C11orf54chr11

93474894

+PGM1chr1

64125257

+
5UTR-3CDSENST00000528288ENST00000371083C11orf54chr11

93474894

+PGM1chr1

64125257

+
5UTR-3CDSENST00000528288ENST00000371084C11orf54chr11

93474894

+PGM1chr1

64125257

+
5UTR-3CDSENST00000528288ENST00000540265C11orf54chr11

93474894

+PGM1chr1

64125257

+
5UTR-3CDSENST00000540113ENST00000371083C11orf54chr11

93474894

+PGM1chr1

64125257

+
5UTR-3CDSENST00000540113ENST00000371084C11orf54chr11

93474894

+PGM1chr1

64125257

+
5UTR-3CDSENST00000540113ENST00000540265C11orf54chr11

93474894

+PGM1chr1

64125257

+
5UTR-intronENST00000331239ENST00000483707C11orf54chr11

93474894

+PGM1chr1

64125257

+
5UTR-intronENST00000354421ENST00000483707C11orf54chr11

93474894

+PGM1chr1

64125257

+
5UTR-intronENST00000528099ENST00000483707C11orf54chr11

93474894

+PGM1chr1

64125257

+
5UTR-intronENST00000528288ENST00000483707C11orf54chr11

93474894

+PGM1chr1

64125257

+
5UTR-intronENST00000540113ENST00000483707C11orf54chr11

93474894

+PGM1chr1

64125257

+

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 C11orf54-PGM1


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)
C11orf54chr1193474894+PGM1chr164125256+0.043256310.95674366
C11orf54chr1193474894+PGM1chr164125256+0.043256310.95674366


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.
genomic feature of top 1%

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Fusion Protein Features for C11orf54-PGM1


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/:93474894/:64125257)
- 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 C11orf54-PGM1


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 C11orf54-PGM1


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 C11orf54-PGM1


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 C11orf54-PGM1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneC2752015Glycogen Storage Disease XIV8CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
TgeneC0017919Glycogen Storage Disease2GENOMICS_ENGLAND
TgeneC3808991NGLY1 deficiency2GENOMICS_ENGLAND
TgeneC0009402Colorectal Carcinoma1CTD_human
TgeneC0009404Colorectal Neoplasms1CTD_human
TgeneC0019193Hepatitis, Toxic1CTD_human
TgeneC0151744Myocardial Ischemia1CTD_human
TgeneC0860207Drug-Induced Liver Disease1CTD_human
TgeneC1262760Hepatitis, Drug-Induced1CTD_human
TgeneC3658290Drug-Induced Acute Liver Injury1CTD_human
TgeneC4277682Chemical and Drug Induced Liver Injury1CTD_human
TgeneC4279912Chemically-Induced Liver Toxicity1CTD_human