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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:GPNMB-NUPL2 (FusionGDB2 ID:34219)

Fusion Gene Summary for GPNMB-NUPL2

check button Fusion gene summary
Fusion gene informationFusion gene name: GPNMB-NUPL2
Fusion gene ID: 34219
HgeneTgene
Gene symbol

GPNMB

NUPL2

Gene ID

10457

11097

Gene nameglycoprotein nmbnucleoporin 42
SynonymsHGFIN|NMB|PLCA3CG1|NLP-1|NLP_1|NUPL2|hCG1
Cytomap

7p15.3

7p15.3

Type of geneprotein-codingprotein-coding
Descriptiontransmembrane glycoprotein NMBglycoprotein (transmembrane) nmbglycoprotein nmb-like proteinglycoprotein nonmetastatic melanoma protein Bhematopoietic growth factor inducible neurokinin-1hematopoietic growth factor inducible neurokinin-1 typeosteoactnucleoporin NUP42H_RG271G13.9NUP42 homolognucleoporin hCG1nucleoporin like 2nucleoporin-like protein 1nucleoporin-like protein 2
Modification date2020031520200313
UniProtAcc

Q14956

.
Ensembl transtripts involved in fusion geneENST00000258733, ENST00000381990, 
ENST00000409458, ENST00000539136, 
ENST00000453162, ENST00000478451, 
ENST00000258742, ENST00000410002, 
ENST00000487595, 
Fusion gene scores* DoF score4 X 4 X 4=643 X 2 X 2=12
# samples 53
** MAII scorelog2(5/64*10)=-0.356143810225275
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(3/12*10)=1.32192809488736
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context

PubMed: GPNMB [Title/Abstract] AND NUPL2 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointGPNMB(23293931)-NUPL2(23224689), # 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
HgeneGPNMB

GO:0001818

negative regulation of cytokine production

19350579

HgeneGPNMB

GO:0001934

positive regulation of protein phosphorylation

22891158

HgeneGPNMB

GO:0030335

positive regulation of cell migration

20711474

HgeneGPNMB

GO:0031954

positive regulation of protein autophosphorylation

19350579

HgeneGPNMB

GO:0034103

regulation of tissue remodeling

25010402

HgeneGPNMB

GO:0042130

negative regulation of T cell proliferation

19350579

HgeneGPNMB

GO:2000134

negative regulation of G1/S transition of mitotic cell cycle

19350579


check buttonFusion gene breakpoints across GPNMB (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 NUPL2 (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
ChimerDB4BRCATCGA-E9-A1NA-01AGPNMBchr7

23293931

+NUPL2chr7

23224689

+
ChimerDB4BRCATCGA-E9-A1NA-01AGPNMBchr7

23293931

+NUPL2chr7

23224689

+
ChimerDB4BRCATCGA-E9-A1NA-01AGPNMBchr7

23293931

-NUPL2chr7

23224689

+


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Fusion Gene ORF analysis for GPNMB-NUPL2

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
In-frameENST00000258733ENST00000258742GPNMBchr7

23293931

+NUPL2chr7

23224689

+
In-frameENST00000258733ENST00000410002GPNMBchr7

23293931

+NUPL2chr7

23224689

+
5CDS-3UTRENST00000258733ENST00000487595GPNMBchr7

23293931

+NUPL2chr7

23224689

+
In-frameENST00000381990ENST00000258742GPNMBchr7

23293931

+NUPL2chr7

23224689

+
In-frameENST00000381990ENST00000410002GPNMBchr7

23293931

+NUPL2chr7

23224689

+
5CDS-3UTRENST00000381990ENST00000487595GPNMBchr7

23293931

+NUPL2chr7

23224689

+
In-frameENST00000409458ENST00000258742GPNMBchr7

23293931

+NUPL2chr7

23224689

+
In-frameENST00000409458ENST00000410002GPNMBchr7

23293931

+NUPL2chr7

23224689

+
5CDS-3UTRENST00000409458ENST00000487595GPNMBchr7

23293931

+NUPL2chr7

23224689

+
intron-3CDSENST00000539136ENST00000258742GPNMBchr7

23293931

+NUPL2chr7

23224689

+
intron-3CDSENST00000539136ENST00000410002GPNMBchr7

23293931

+NUPL2chr7

23224689

+
intron-3UTRENST00000539136ENST00000487595GPNMBchr7

23293931

+NUPL2chr7

23224689

+
In-frameENST00000453162ENST00000258742GPNMBchr7

23293931

+NUPL2chr7

23224689

+
In-frameENST00000453162ENST00000410002GPNMBchr7

23293931

+NUPL2chr7

23224689

+
5CDS-3UTRENST00000453162ENST00000487595GPNMBchr7

23293931

+NUPL2chr7

23224689

+
intron-3CDSENST00000478451ENST00000258742GPNMBchr7

23293931

+NUPL2chr7

23224689

+
intron-3CDSENST00000478451ENST00000410002GPNMBchr7

23293931

+NUPL2chr7

23224689

+
intron-3UTRENST00000478451ENST00000487595GPNMBchr7

23293931

+NUPL2chr7

23224689

+

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 GPNMB-NUPL2


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)
GPNMBchr723293931+NUPL2chr723224688+0.000208130.9997919
GPNMBchr723293931+NUPL2chr723224688+0.000208130.9997919

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 GPNMB-NUPL2


check button Go to

FGviewer for the breakpoints of chr7:23293931-chr7:23224689

.
- 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
GPNMB

Q14956

.
FUNCTION: Could be a melanogenic enzyme. {ECO:0000250}.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.

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
HgeneGPNMBchr7:23293931chr7:23224689ENST00000258733+31164_66122.33333333333333561.0MotifCell attachment site
HgeneGPNMBchr7:23293931chr7:23224689ENST00000381990+31164_66122.33333333333333573.0MotifCell attachment site
TgeneNUPL2chr7:23293931chr7:23224689ENST0000025874207238_37840.333333333333336424.0Compositional biasNote=Ser-rich
TgeneNUPL2chr7:23293931chr7:23224689ENST0000025874207218_21940.333333333333336424.0RepeatNote=FG 3
TgeneNUPL2chr7:23293931chr7:23224689ENST0000025874207220_22140.333333333333336424.0RepeatNote=FG 4
TgeneNUPL2chr7:23293931chr7:23224689ENST0000025874207265_26640.333333333333336424.0RepeatNote=FG 5
TgeneNUPL2chr7:23293931chr7:23224689ENST0000025874207271_27240.333333333333336424.0RepeatNote=FG 6
TgeneNUPL2chr7:23293931chr7:23224689ENST0000025874207288_28940.333333333333336424.0RepeatNote=FG 7
TgeneNUPL2chr7:23293931chr7:23224689ENST0000025874207290_29140.333333333333336424.0RepeatNote=FG 8
TgeneNUPL2chr7:23293931chr7:23224689ENST0000025874207311_31240.333333333333336424.0RepeatNote=FG 9
TgeneNUPL2chr7:23293931chr7:23224689ENST0000025874207336_33740.333333333333336424.0RepeatNote=FG 10
TgeneNUPL2chr7:23293931chr7:23224689ENST0000025874207345_34640.333333333333336424.0RepeatNote=FG 11
TgeneNUPL2chr7:23293931chr7:23224689ENST0000025874207364_36540.333333333333336424.0RepeatNote=FG 12
TgeneNUPL2chr7:23293931chr7:23224689ENST000002587420795_9640.333333333333336424.0RepeatNote=FG 2

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneGPNMBchr7:23293931chr7:23224689ENST00000258733+311320_332122.33333333333333561.0Compositional biasNote=Poly-Pro
HgeneGPNMBchr7:23293931chr7:23224689ENST00000381990+311320_332122.33333333333333573.0Compositional biasNote=Poly-Pro
HgeneGPNMBchr7:23293931chr7:23224689ENST00000258733+311240_327122.33333333333333561.0DomainPKD
HgeneGPNMBchr7:23293931chr7:23224689ENST00000381990+311240_327122.33333333333333573.0DomainPKD
HgeneGPNMBchr7:23293931chr7:23224689ENST00000258733+31123_498122.33333333333333561.0Topological domainExtracellular
HgeneGPNMBchr7:23293931chr7:23224689ENST00000258733+311520_572122.33333333333333561.0Topological domainCytoplasmic
HgeneGPNMBchr7:23293931chr7:23224689ENST00000381990+31123_498122.33333333333333573.0Topological domainExtracellular
HgeneGPNMBchr7:23293931chr7:23224689ENST00000381990+311520_572122.33333333333333573.0Topological domainCytoplasmic
HgeneGPNMBchr7:23293931chr7:23224689ENST00000258733+311499_519122.33333333333333561.0TransmembraneHelical
HgeneGPNMBchr7:23293931chr7:23224689ENST00000381990+311499_519122.33333333333333573.0TransmembraneHelical
TgeneNUPL2chr7:23293931chr7:23224689ENST000002587420714_1540.333333333333336424.0RepeatNote=FG 1
TgeneNUPL2chr7:23293931chr7:23224689ENST00000258742071_2540.333333333333336424.0Zinc fingerC3H1-type


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Fusion Gene Sequence for GPNMB-NUPL2


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 GPNMB-NUPL2


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
TgeneNUPL2chr7:23293931chr7:23224689ENST0000025874207365_42340.333333333333336424.0GLE1
TgeneNUPL2chr7:23293931chr7:23224689ENST000002587420794_17040.333333333333336424.0HIV-1 Vpr


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 GPNMB-NUPL2


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 GPNMB-NUPL2


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneGPNMBC0009402Colorectal Carcinoma2CTD_human
HgeneGPNMBC0009404Colorectal Neoplasms2CTD_human
HgeneGPNMBC0006142Malignant neoplasm of breast1CTD_human;UNIPROT
HgeneGPNMBC0022660Kidney Failure, Acute1CTD_human
HgeneGPNMBC0023893Liver Cirrhosis, Experimental1CTD_human
HgeneGPNMBC0162557Liver Failure, Acute1CTD_human
HgeneGPNMBC0678222Breast Carcinoma1CTD_human
HgeneGPNMBC1257931Mammary Neoplasms, Human1CTD_human
HgeneGPNMBC1458155Mammary Neoplasms1CTD_human
HgeneGPNMBC1565662Acute Kidney Insufficiency1CTD_human
HgeneGPNMBC2609414Acute kidney injury1CTD_human
HgeneGPNMBC4554421AMYLOIDOSIS, PRIMARY LOCALIZED CUTANEOUS, 31GENOMICS_ENGLAND;ORPHANET
HgeneGPNMBC4554601Amyloidosis cutis dyschromia1ORPHANET
HgeneGPNMBC4704874Mammary Carcinoma, Human1CTD_human