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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:NPM1-NPM1 (FusionGDB2 ID:59974)

Fusion Gene Summary for NPM1-NPM1

check button Fusion gene summary
Fusion gene informationFusion gene name: NPM1-NPM1
Fusion gene ID: 59974
HgeneTgene
Gene symbol

NPM1

NPM1

Gene ID

4869

4869

Gene namenucleophosmin 1nucleophosmin 1
SynonymsB23|NPMB23|NPM
Cytomap

5q35.1

5q35.1

Type of geneprotein-codingprotein-coding
Descriptionnucleophosminnucleolar protein NO38nucleophosmin (nucleolar phosphoprotein B23, numatrin)nucleophosmin/nucleoplasmin family, member 1testicular tissue protein Li 128nucleophosminnucleolar protein NO38nucleophosmin (nucleolar phosphoprotein B23, numatrin)nucleophosmin/nucleoplasmin family, member 1testicular tissue protein Li 128
Modification date2020032920200329
UniProtAcc

P06748

P06748

Ensembl transtripts involved in fusion geneENST00000296930, ENST00000351986, 
ENST00000517671, ENST00000393820, 
ENST00000296930, ENST00000351986, 
ENST00000517671, ENST00000393820, 
Fusion gene scores* DoF score21 X 25 X 6=315010 X 9 X 3=270
# samples 3211
** MAII scorelog2(32/3150*10)=-3.29920801838728
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(11/270*10)=-1.29545588352617
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: NPM1 [Title/Abstract] AND NPM1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointNPM1(170832389)-NPM1(170819948), # samples:1
NPM1(170837658)-NPM1(170837602), # 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
HgeneNPM1

GO:0006281

DNA repair

19188445

HgeneNPM1

GO:0006334

nucleosome assembly

11602260

HgeneNPM1

GO:0006913

nucleocytoplasmic transport

16041368

HgeneNPM1

GO:0008104

protein localization

18420587

HgeneNPM1

GO:0008284

positive regulation of cell proliferation

22528486

HgeneNPM1

GO:0032071

regulation of endodeoxyribonuclease activity

19188445

HgeneNPM1

GO:0034644

cellular response to UV

19160485

HgeneNPM1

GO:0043066

negative regulation of apoptotic process

12882984

HgeneNPM1

GO:0044387

negative regulation of protein kinase activity by regulation of protein phosphorylation

12882984

HgeneNPM1

GO:0045727

positive regulation of translation

12882984

HgeneNPM1

GO:0045893

positive regulation of transcription, DNA-templated

22528486

HgeneNPM1

GO:0045944

positive regulation of transcription by RNA polymerase II

19160485

HgeneNPM1

GO:0060699

regulation of endoribonuclease activity

19188445

HgeneNPM1

GO:0060735

regulation of eIF2 alpha phosphorylation by dsRNA

12882984

HgeneNPM1

GO:1902751

positive regulation of cell cycle G2/M phase transition

22528486

TgeneNPM1

GO:0006281

DNA repair

19188445

TgeneNPM1

GO:0006334

nucleosome assembly

11602260

TgeneNPM1

GO:0006913

nucleocytoplasmic transport

16041368

TgeneNPM1

GO:0008104

protein localization

18420587

TgeneNPM1

GO:0008284

positive regulation of cell proliferation

22528486

TgeneNPM1

GO:0032071

regulation of endodeoxyribonuclease activity

19188445

TgeneNPM1

GO:0034644

cellular response to UV

19160485

TgeneNPM1

GO:0043066

negative regulation of apoptotic process

12882984

TgeneNPM1

GO:0044387

negative regulation of protein kinase activity by regulation of protein phosphorylation

12882984

TgeneNPM1

GO:0045727

positive regulation of translation

12882984

TgeneNPM1

GO:0045893

positive regulation of transcription, DNA-templated

22528486

TgeneNPM1

GO:0045944

positive regulation of transcription by RNA polymerase II

19160485

TgeneNPM1

GO:0060699

regulation of endoribonuclease activity

19188445

TgeneNPM1

GO:0060735

regulation of eIF2 alpha phosphorylation by dsRNA

12882984

TgeneNPM1

GO:1902751

positive regulation of cell cycle G2/M phase transition

22528486


check buttonFusion gene breakpoints across NPM1 (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure

check buttonFusion gene breakpoints across NPM1 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure

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/AAW601664NPM1chr5

170832389

+NPM1chr5

170819948

+
ChiTaRS5.0N/AN67581NPM1chr5

170837658

-NPM1chr5

170837602

+


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Fusion Gene ORF analysis for NPM1-NPM1

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-3UTRENST00000296930ENST00000296930NPM1chr5

170837658

-NPM1chr5

170837602

+
3UTR-3UTRENST00000296930ENST00000351986NPM1chr5

170837658

-NPM1chr5

170837602

+
3UTR-3UTRENST00000296930ENST00000517671NPM1chr5

170837658

-NPM1chr5

170837602

+
3UTR-3UTRENST00000351986ENST00000296930NPM1chr5

170837658

-NPM1chr5

170837602

+
3UTR-3UTRENST00000351986ENST00000351986NPM1chr5

170837658

-NPM1chr5

170837602

+
3UTR-3UTRENST00000351986ENST00000517671NPM1chr5

170837658

-NPM1chr5

170837602

+
3UTR-3UTRENST00000517671ENST00000296930NPM1chr5

170837658

-NPM1chr5

170837602

+
3UTR-3UTRENST00000517671ENST00000351986NPM1chr5

170837658

-NPM1chr5

170837602

+
3UTR-3UTRENST00000517671ENST00000517671NPM1chr5

170837658

-NPM1chr5

170837602

+
3UTR-intronENST00000296930ENST00000393820NPM1chr5

170837658

-NPM1chr5

170837602

+
3UTR-intronENST00000351986ENST00000393820NPM1chr5

170837658

-NPM1chr5

170837602

+
3UTR-intronENST00000517671ENST00000393820NPM1chr5

170837658

-NPM1chr5

170837602

+
In-frameENST00000296930ENST00000296930NPM1chr5

170832389

+NPM1chr5

170819948

+
In-frameENST00000296930ENST00000351986NPM1chr5

170832389

+NPM1chr5

170819948

+
In-frameENST00000296930ENST00000393820NPM1chr5

170832389

+NPM1chr5

170819948

+
In-frameENST00000296930ENST00000517671NPM1chr5

170832389

+NPM1chr5

170819948

+
In-frameENST00000351986ENST00000296930NPM1chr5

170832389

+NPM1chr5

170819948

+
In-frameENST00000351986ENST00000351986NPM1chr5

170832389

+NPM1chr5

170819948

+
In-frameENST00000351986ENST00000393820NPM1chr5

170832389

+NPM1chr5

170819948

+
In-frameENST00000351986ENST00000517671NPM1chr5

170832389

+NPM1chr5

170819948

+
In-frameENST00000393820ENST00000296930NPM1chr5

170832389

+NPM1chr5

170819948

+
In-frameENST00000393820ENST00000351986NPM1chr5

170832389

+NPM1chr5

170819948

+
In-frameENST00000393820ENST00000393820NPM1chr5

170832389

+NPM1chr5

170819948

+
In-frameENST00000393820ENST00000517671NPM1chr5

170832389

+NPM1chr5

170819948

+
In-frameENST00000517671ENST00000296930NPM1chr5

170832389

+NPM1chr5

170819948

+
In-frameENST00000517671ENST00000351986NPM1chr5

170832389

+NPM1chr5

170819948

+
In-frameENST00000517671ENST00000393820NPM1chr5

170832389

+NPM1chr5

170819948

+
In-frameENST00000517671ENST00000517671NPM1chr5

170832389

+NPM1chr5

170819948

+
intron-3UTRENST00000393820ENST00000296930NPM1chr5

170837658

-NPM1chr5

170837602

+
intron-3UTRENST00000393820ENST00000351986NPM1chr5

170837658

-NPM1chr5

170837602

+
intron-3UTRENST00000393820ENST00000517671NPM1chr5

170837658

-NPM1chr5

170837602

+
intron-intronENST00000393820ENST00000393820NPM1chr5

170837658

-NPM1chr5

170837602

+

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 NPM1-NPM1


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)

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.
genomic feature

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 NPM1-NPM1


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/chr5:170832389/chr5:170819948)
- 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
NPM1

P06748

NPM1

P06748

FUNCTION: Involved in diverse cellular processes such as ribosome biogenesis, centrosome duplication, protein chaperoning, histone assembly, cell proliferation, and regulation of tumor suppressors p53/TP53 and ARF. Binds ribosome presumably to drive ribosome nuclear export. Associated with nucleolar ribonucleoprotein structures and bind single-stranded nucleic acids. Acts as a chaperonin for the core histones H3, H2B and H4. Stimulates APEX1 endonuclease activity on apurinic/apyrimidinic (AP) double-stranded DNA but inhibits APEX1 endonuclease activity on AP single-stranded RNA. May exert a control of APEX1 endonuclease activity within nucleoli devoted to repair AP on rDNA and the removal of oxidized rRNA molecules. In concert with BRCA2, regulates centrosome duplication. Regulates centriole duplication: phosphorylation by PLK2 is able to trigger centriole replication. Negatively regulates the activation of EIF2AK2/PKR and suppresses apoptosis through inhibition of EIF2AK2/PKR autophosphorylation. Antagonizes the inhibitory effect of ATF5 on cell proliferation and relieves ATF5-induced G2/M blockade (PubMed:22528486). In complex with MYC enhances the transcription of MYC target genes (PubMed:25956029). {ECO:0000269|PubMed:12882984, ECO:0000269|PubMed:16107701, ECO:0000269|PubMed:17015463, ECO:0000269|PubMed:18809582, ECO:0000269|PubMed:19188445, ECO:0000269|PubMed:20352051, ECO:0000269|PubMed:21084279, ECO:0000269|PubMed:22002061, ECO:0000269|PubMed:22528486, ECO:0000269|PubMed:25956029}.FUNCTION: Involved in diverse cellular processes such as ribosome biogenesis, centrosome duplication, protein chaperoning, histone assembly, cell proliferation, and regulation of tumor suppressors p53/TP53 and ARF. Binds ribosome presumably to drive ribosome nuclear export. Associated with nucleolar ribonucleoprotein structures and bind single-stranded nucleic acids. Acts as a chaperonin for the core histones H3, H2B and H4. Stimulates APEX1 endonuclease activity on apurinic/apyrimidinic (AP) double-stranded DNA but inhibits APEX1 endonuclease activity on AP single-stranded RNA. May exert a control of APEX1 endonuclease activity within nucleoli devoted to repair AP on rDNA and the removal of oxidized rRNA molecules. In concert with BRCA2, regulates centrosome duplication. Regulates centriole duplication: phosphorylation by PLK2 is able to trigger centriole replication. Negatively regulates the activation of EIF2AK2/PKR and suppresses apoptosis through inhibition of EIF2AK2/PKR autophosphorylation. Antagonizes the inhibitory effect of ATF5 on cell proliferation and relieves ATF5-induced G2/M blockade (PubMed:22528486). In complex with MYC enhances the transcription of MYC target genes (PubMed:25956029). {ECO:0000269|PubMed:12882984, ECO:0000269|PubMed:16107701, ECO:0000269|PubMed:17015463, ECO:0000269|PubMed:18809582, ECO:0000269|PubMed:19188445, ECO:0000269|PubMed:20352051, ECO:0000269|PubMed:21084279, ECO:0000269|PubMed:22002061, ECO:0000269|PubMed:22528486, ECO:0000269|PubMed:25956029}.

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
TgeneNPM1chr5:170832389chr5:170819948ENST00000296930011120_1320295.0Compositional biasNote=Asp/Glu-rich (acidic)
TgeneNPM1chr5:170832389chr5:170819948ENST00000296930011161_1880295.0Compositional biasNote=Asp/Glu-rich (highly acidic)
TgeneNPM1chr5:170832389chr5:170819948ENST000002969300111_90295.0Compositional biasNote=Met-rich
TgeneNPM1chr5:170832389chr5:170819948ENST00000351986010120_1320266.0Compositional biasNote=Asp/Glu-rich (acidic)
TgeneNPM1chr5:170832389chr5:170819948ENST00000351986010161_1880266.0Compositional biasNote=Asp/Glu-rich (highly acidic)
TgeneNPM1chr5:170832389chr5:170819948ENST000003519860101_90266.0Compositional biasNote=Met-rich
TgeneNPM1chr5:170832389chr5:170819948ENST00000393820010120_1320260.0Compositional biasNote=Asp/Glu-rich (acidic)
TgeneNPM1chr5:170832389chr5:170819948ENST00000393820010161_1880260.0Compositional biasNote=Asp/Glu-rich (highly acidic)
TgeneNPM1chr5:170832389chr5:170819948ENST000003938200101_90260.0Compositional biasNote=Met-rich
TgeneNPM1chr5:170832389chr5:170819948ENST00000517671012120_1320295.0Compositional biasNote=Asp/Glu-rich (acidic)
TgeneNPM1chr5:170832389chr5:170819948ENST00000517671012161_1880295.0Compositional biasNote=Asp/Glu-rich (highly acidic)
TgeneNPM1chr5:170832389chr5:170819948ENST000005176710121_90295.0Compositional biasNote=Met-rich
TgeneNPM1chr5:170832389chr5:170819948ENST00000296930011152_1570295.0MotifNuclear localization signal
TgeneNPM1chr5:170832389chr5:170819948ENST00000296930011191_1970295.0MotifNuclear localization signal
TgeneNPM1chr5:170832389chr5:170819948ENST00000351986010152_1570266.0MotifNuclear localization signal
TgeneNPM1chr5:170832389chr5:170819948ENST00000351986010191_1970266.0MotifNuclear localization signal
TgeneNPM1chr5:170832389chr5:170819948ENST00000393820010152_1570260.0MotifNuclear localization signal
TgeneNPM1chr5:170832389chr5:170819948ENST00000393820010191_1970260.0MotifNuclear localization signal
TgeneNPM1chr5:170832389chr5:170819948ENST00000517671012152_1570295.0MotifNuclear localization signal
TgeneNPM1chr5:170832389chr5:170819948ENST00000517671012191_1970295.0MotifNuclear localization signal
TgeneNPM1chr5:170832389chr5:170819948ENST00000296930011243_2940295.0RegionNote=Required for nucleolar localization
TgeneNPM1chr5:170832389chr5:170819948ENST00000351986010243_2940266.0RegionNote=Required for nucleolar localization
TgeneNPM1chr5:170832389chr5:170819948ENST00000393820010243_2940260.0RegionNote=Required for nucleolar localization
TgeneNPM1chr5:170832389chr5:170819948ENST00000517671012243_2940295.0RegionNote=Required for nucleolar localization

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneNPM1chr5:170832389chr5:170819948ENST00000296930+111120_1320295.0Compositional biasNote=Asp/Glu-rich (acidic)
HgeneNPM1chr5:170832389chr5:170819948ENST00000296930+111161_1880295.0Compositional biasNote=Asp/Glu-rich (highly acidic)
HgeneNPM1chr5:170832389chr5:170819948ENST00000296930+1111_90295.0Compositional biasNote=Met-rich
HgeneNPM1chr5:170832389chr5:170819948ENST00000351986+110120_1320266.0Compositional biasNote=Asp/Glu-rich (acidic)
HgeneNPM1chr5:170832389chr5:170819948ENST00000351986+110161_1880266.0Compositional biasNote=Asp/Glu-rich (highly acidic)
HgeneNPM1chr5:170832389chr5:170819948ENST00000351986+1101_90266.0Compositional biasNote=Met-rich
HgeneNPM1chr5:170832389chr5:170819948ENST00000393820+110120_1320260.0Compositional biasNote=Asp/Glu-rich (acidic)
HgeneNPM1chr5:170832389chr5:170819948ENST00000393820+110161_1880260.0Compositional biasNote=Asp/Glu-rich (highly acidic)
HgeneNPM1chr5:170832389chr5:170819948ENST00000393820+1101_90260.0Compositional biasNote=Met-rich
HgeneNPM1chr5:170832389chr5:170819948ENST00000517671+112120_1320295.0Compositional biasNote=Asp/Glu-rich (acidic)
HgeneNPM1chr5:170832389chr5:170819948ENST00000517671+112161_1880295.0Compositional biasNote=Asp/Glu-rich (highly acidic)
HgeneNPM1chr5:170832389chr5:170819948ENST00000517671+1121_90295.0Compositional biasNote=Met-rich
HgeneNPM1chr5:170832389chr5:170819948ENST00000296930+111152_1570295.0MotifNuclear localization signal
HgeneNPM1chr5:170832389chr5:170819948ENST00000296930+111191_1970295.0MotifNuclear localization signal
HgeneNPM1chr5:170832389chr5:170819948ENST00000351986+110152_1570266.0MotifNuclear localization signal
HgeneNPM1chr5:170832389chr5:170819948ENST00000351986+110191_1970266.0MotifNuclear localization signal
HgeneNPM1chr5:170832389chr5:170819948ENST00000393820+110152_1570260.0MotifNuclear localization signal
HgeneNPM1chr5:170832389chr5:170819948ENST00000393820+110191_1970260.0MotifNuclear localization signal
HgeneNPM1chr5:170832389chr5:170819948ENST00000517671+112152_1570295.0MotifNuclear localization signal
HgeneNPM1chr5:170832389chr5:170819948ENST00000517671+112191_1970295.0MotifNuclear localization signal
HgeneNPM1chr5:170832389chr5:170819948ENST00000296930+111243_2940295.0RegionNote=Required for nucleolar localization
HgeneNPM1chr5:170832389chr5:170819948ENST00000351986+110243_2940266.0RegionNote=Required for nucleolar localization
HgeneNPM1chr5:170832389chr5:170819948ENST00000393820+110243_2940260.0RegionNote=Required for nucleolar localization
HgeneNPM1chr5:170832389chr5:170819948ENST00000517671+112243_2940295.0RegionNote=Required for nucleolar localization


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Fusion Gene Sequence for NPM1-NPM1


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 NPM1-NPM1


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 NPM1-NPM1


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 NPM1-NPM1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource