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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:NUPL1-KL (FusionGDB2 ID:HG9818TG9365)

Fusion Gene Summary for NUPL1-KL

check button Fusion gene summary
Fusion gene informationFusion gene name: NUPL1-KL
Fusion gene ID: hg9818tg9365
HgeneTgene
Gene symbol

NUPL1

KL

Gene ID

9818

9365

Gene namenucleoporin 58klotho
SynonymsNUP45|NUPL1|PRO2463HFTC3
Cytomap('NUP58','NUPL1')('KL','KL')

13q12.13

13q13.1

Type of geneprotein-codingprotein-coding
Descriptionnucleoporin p58/p4558 kDa nucleoporinnucleoporin 58kDanucleoporin like 1nucleoporin-like protein 1klotho
Modification date2020031320200329
UniProtAcc.

Q9UEF7

Ensembl transtripts involved in fusion geneENST00000466694, ENST00000381718, 
ENST00000381736, ENST00000463407, 
Fusion gene scores* DoF score4 X 3 X 4=484 X 4 X 2=32
# samples 44
** MAII scorelog2(4/48*10)=-0.263034405833794
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(4/32*10)=0.321928094887362
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context

PubMed: NUPL1 [Title/Abstract] AND KL [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointNUPL1(25876018)-KL(33627904), # samples:2
NUP58(25876018)-KL(33627904), # 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


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
ChimerDB4SKCMTCGA-EE-A29C-06ANUP58chr13

25876018

+KLchr13

33627904

+
ChimerDB4SKCMTCGA-EE-A29C-06ANUPL1chr13

25876018

-KLchr13

33627904

+
ChimerDB4SKCMTCGA-EE-A29C-06ANUPL1chr13

25876018

+KLchr13

33627904

+


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Fusion Gene ORF analysis for NUPL1-KL

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-3UTRENST00000466694ENST00000380099NUPL1chr13

25876018

+KLchr13

33627904

+
3UTR-3UTRENST00000466694ENST00000487852NUPL1chr13

25876018

+KLchr13

33627904

+
3UTR-5UTRENST00000466694ENST00000426690NUPL1chr13

25876018

+KLchr13

33627904

+
5CDS-3UTRENST00000381718ENST00000380099NUPL1chr13

25876018

+KLchr13

33627904

+
5CDS-3UTRENST00000381718ENST00000487852NUPL1chr13

25876018

+KLchr13

33627904

+
5CDS-3UTRENST00000381736ENST00000380099NUPL1chr13

25876018

+KLchr13

33627904

+
5CDS-3UTRENST00000381736ENST00000487852NUPL1chr13

25876018

+KLchr13

33627904

+
5CDS-3UTRENST00000463407ENST00000380099NUPL1chr13

25876018

+KLchr13

33627904

+
5CDS-3UTRENST00000463407ENST00000487852NUPL1chr13

25876018

+KLchr13

33627904

+
5CDS-5UTRENST00000381718ENST00000426690NUPL1chr13

25876018

+KLchr13

33627904

+
5CDS-5UTRENST00000381736ENST00000426690NUPL1chr13

25876018

+KLchr13

33627904

+
5CDS-5UTRENST00000463407ENST00000426690NUPL1chr13

25876018

+KLchr13

33627904

+

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 NUPL1-KL


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)
NUPL1chr1325876018+KLchr1333627903+2.82E-050.99997175
NUPL1chr1325876018+KLchr1333627903+2.82E-050.99997175


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 NUPL1-KL


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/:25876018/:33627904)
- 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
.KL

Q9UEF7

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: May have weak glycosidase activity towards glucuronylated steroids. However, it lacks essential active site Glu residues at positions 239 and 872, suggesting it may be inactive as a glycosidase in vivo. May be involved in the regulation of calcium and phosphorus homeostasis by inhibiting the synthesis of active vitamin D (By similarity). Essential factor for the specific interaction between FGF23 and FGFR1 (By similarity). {ECO:0000250}.; FUNCTION: The Klotho peptide generated by cleavage of the membrane-bound isoform may be an anti-aging circulating hormone which would extend life span by inhibiting insulin/IGF1 signaling. {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 NUPL1-KL


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 NUPL1-KL


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 NUPL1-KL


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 NUPL1-KL


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneC0025261Memory Disorders2CTD_human
TgeneC0231341Premature aging syndrome2CTD_human
TgeneC0233794Memory impairment2CTD_human
TgeneC0751292Age-Related Memory Disorders2CTD_human
TgeneC0751293Memory Disorder, Semantic2CTD_human
TgeneC0751294Memory Disorder, Spatial2CTD_human
TgeneC0751295Memory Loss2CTD_human
TgeneC1876187TUMORAL CALCINOSIS, HYPERPHOSPHATEMIC, FAMILIAL2ORPHANET
TgeneC4692564TUMORAL CALCINOSIS, HYPERPHOSPHATEMIC, FAMILIAL, 12ORPHANET
TgeneC0001787Osteoporosis, Age-Related1CTD_human
TgeneC0003850Arteriosclerosis1CTD_human
TgeneC0006663Calcinosis1CTD_human
TgeneC0010054Coronary Arteriosclerosis1CTD_human
TgeneC0011860Diabetes Mellitus, Non-Insulin-Dependent1CTD_human
TgeneC0013990Pathological accumulation of air in tissues1CTD_human
TgeneC0020437Hypercalcemia1CTD_human
TgeneC0021359Infertility1CTD_human
TgeneC0022658Kidney Diseases1CTD_human
TgeneC0023186Learning Disorders1CTD_human
TgeneC0026141Milk-Alkali Syndrome1CTD_human
TgeneC0029456Osteoporosis1CTD_human
TgeneC0029459Osteoporosis, Senile1CTD_human
TgeneC0037274Dermatologic disorders1CTD_human
TgeneC0085681Hyperphosphatemia (disorder)1CTD_human
TgeneC0263628Tumoral calcinosis1CTD_human
TgeneC0268080Hypercalcemia, Idiopathic, of Infancy1CTD_human
TgeneC0521174Microcalcification1CTD_human
TgeneC0729353Subfertility1CTD_human
TgeneC0751262Adult Learning Disorders1CTD_human
TgeneC0751263Learning Disturbance1CTD_human
TgeneC0751265Learning Disabilities1CTD_human
TgeneC0751406Post-Traumatic Osteoporosis1CTD_human
TgeneC1330966Developmental Academic Disorder1CTD_human
TgeneC1956346Coronary Artery Disease1CTD_human
TgeneC2931105Hypercalciuria, childhood idiopathic1CTD_human
TgeneC4074771Sterility, Reproductive1CTD_human
TgeneC4693864TUMORAL CALCINOSIS, HYPERPHOSPHATEMIC, FAMILIAL, 31GENOMICS_ENGLAND;UNIPROT