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Center for Computational Systems Medicine level1
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Fusion Gene Summary

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Fusion Gene Sample Information

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Fusion ORF Analysis

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Fusion Amino Acid Sequences

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Fusion Protein Functional Features

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Fusion Protein-Protein Interaction

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Related drugs with this fusion protein

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Related disease with this fusion protein

Fusion Protein:NXF1-KLK10

Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: NXF1-KLK10
FusionPDB ID: 61203
FusionGDB2.0 ID: 61203
HgeneTgene
Gene symbol

NXF1

KLK10

Gene ID

10482

5655

Gene namenuclear RNA export factor 1kallikrein related peptidase 10
SynonymsMEX67|TAPNES1|PRSSL1
Cytomap

11q12.3

19q13.41

Type of geneprotein-codingprotein-coding
Descriptionnuclear RNA export factor 1mRNA export factor TAPtip associating proteintip-associated proteinkallikrein-10breast normal epithelial cell associated serine proteasekallikrein 10 protein 1kallikrein 10 protein 12kallikrein 10 protein 13kallikrein 10 protein 2kallikrein 10 protein 3kallikrein 10 protein 4kallikrein 10 protein 5kallikrein 10
Modification date2020031320200313
UniProtAcc.

O43240

Ensembl transtripts involved in fusion geneENST idsENST00000294172, ENST00000532297, 
ENST00000439713, ENST00000531131, 
ENST00000531709, ENST00000533048, 
ENST00000309958, ENST00000358789, 
ENST00000391805, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score10 X 13 X 7=9107 X 6 X 3=126
# samples 128
** MAII scorelog2(12/910*10)=-2.92283213947754
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(8/126*10)=-0.655351828612554
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)

PubMed: NXF1 [Title/Abstract] AND KLK10 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)NXF1(62567848)-KLK10(51520546), # samples:1
Anticipated loss of major functional domain due to fusion event.NXF1-KLK10 seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF.
NXF1-KLK10 seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF.
NXF1-KLK10 seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame ORF.
NXF1-KLK10 seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame ORF.
NXF1-KLK10 seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
NXF1-KLK10 seems lost the major protein functional domain in Tgene partner, which is a tumor suppressor due to the frame-shifted ORF.
* 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
HgeneNXF1

GO:0006406

mRNA export from nucleus

19165146|28984244


check buttonFusion gene breakpoints across NXF1 (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 KLK10 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure


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Fusion Gene Sample Information

check buttonFusion gene information from FusionGDB2.0.
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
ChimerDB4OVTCGA-24-1546NXF1chr11

62567848

-KLK10chr19

51520546

-


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Fusion ORF Analysis


check buttonFusion information from ORFfinder translation from full-length transcript sequence from FusionPDB.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandSeq length
(transcript)		BP loci
(transcript)		Predicted start
(transcript)		Predicted stop
(transcript)		Seq length
(amino acids)
ENST00000532297NXF1chr1162567848-ENST00000309958KLK10chr1951520546-445016466301853407
ENST00000532297NXF1chr1162567848-ENST00000391805KLK10chr1951520546-444416466301853407
ENST00000532297NXF1chr1162567848-ENST00000358789KLK10chr1951520546-291916466301853407

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
ENST00000532297ENST00000309958NXF1chr1162567848-KLK10chr1951520546-0.0046906880.9953093
ENST00000532297ENST00000391805NXF1chr1162567848-KLK10chr1951520546-0.0046719450.99532807
ENST00000532297ENST00000358789NXF1chr1162567848-KLK10chr1951520546-0.0081638050.99183613

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Fusion Amino Acid Sequences


check button For individual full-length fusion transcript sequence from FusionPDB, we ran ORFfinder and chose the longest ORF among the all predicted ones.
>FusionGDB ID_FusionGDB isoform ID_FGname_Hgene_Hchr_Hbp_Henst_Tgene_Tchr_Tbp_Tenst_length(fusion AA) seq_BP

>61203_61203_1_NXF1-KLK10_NXF1_chr11_62567848_ENST00000532297_KLK10_chr19_51520546_ENST00000309958_length(amino acids)=407AA_BP=338
MADEGKSYSEHDDERVNFPQRKKKGRGPFRWKYGEGNRRSGRGGSGIRSSRLEEDDGDVAMSDAQDGPRVRYNPYTTRPNRRGDTWHDRD
RIHVTVRRDRAPPERGGAGTSQDGTSKNWFKITIPYGRKYDKAWLLSMIQSKCSVPFTPIEFHYENTRAQFFVEDASTASALKAVNYKIL
DRENRRISIIINSSAPPHTILNELKPEQVEQLKLIMSKRYDGSQQALDLKGLRSDPDLVAQNIDVVLNRRSCMAATLRIIEENIPELLSL
NLSNNRLYRLDDMSSIVQKAPNLKILNLSGNELKSERELDKIKGLKLEELWLDGNSLCDTFRDQSTYISRRGGAAPPKRHALGPRSLWLP

--------------------------------------------------------------

>61203_61203_2_NXF1-KLK10_NXF1_chr11_62567848_ENST00000532297_KLK10_chr19_51520546_ENST00000358789_length(amino acids)=407AA_BP=338
MADEGKSYSEHDDERVNFPQRKKKGRGPFRWKYGEGNRRSGRGGSGIRSSRLEEDDGDVAMSDAQDGPRVRYNPYTTRPNRRGDTWHDRD
RIHVTVRRDRAPPERGGAGTSQDGTSKNWFKITIPYGRKYDKAWLLSMIQSKCSVPFTPIEFHYENTRAQFFVEDASTASALKAVNYKIL
DRENRRISIIINSSAPPHTILNELKPEQVEQLKLIMSKRYDGSQQALDLKGLRSDPDLVAQNIDVVLNRRSCMAATLRIIEENIPELLSL
NLSNNRLYRLDDMSSIVQKAPNLKILNLSGNELKSERELDKIKGLKLEELWLDGNSLCDTFRDQSTYISRRGGAAPPKRHALGPRSLWLP

--------------------------------------------------------------

>61203_61203_3_NXF1-KLK10_NXF1_chr11_62567848_ENST00000532297_KLK10_chr19_51520546_ENST00000391805_length(amino acids)=407AA_BP=338
MADEGKSYSEHDDERVNFPQRKKKGRGPFRWKYGEGNRRSGRGGSGIRSSRLEEDDGDVAMSDAQDGPRVRYNPYTTRPNRRGDTWHDRD
RIHVTVRRDRAPPERGGAGTSQDGTSKNWFKITIPYGRKYDKAWLLSMIQSKCSVPFTPIEFHYENTRAQFFVEDASTASALKAVNYKIL
DRENRRISIIINSSAPPHTILNELKPEQVEQLKLIMSKRYDGSQQALDLKGLRSDPDLVAQNIDVVLNRRSCMAATLRIIEENIPELLSL
NLSNNRLYRLDDMSSIVQKAPNLKILNLSGNELKSERELDKIKGLKLEELWLDGNSLCDTFRDQSTYISRRGGAAPPKRHALGPRSLWLP

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Fusion Protein Functional Features


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/chr11:62567848/chr19:51520546)
- 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
.KLK10

O43240

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.FUNCTION: Has a tumor-suppressor role for NES1 in breast and prostate cancer.

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.
- Retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneNXF1chr11:62567848chr19:51520546ENST00000294172-1021119_198338.6666666666667620.0DomainNote=RRM
HgeneNXF1chr11:62567848chr19:51520546ENST00000532297-1122119_198338.6666666666667620.0DomainNote=RRM
HgeneNXF1chr11:62567848chr19:51520546ENST00000294172-102167_100338.6666666666667620.0MotifNote=Nuclear localization signal
HgeneNXF1chr11:62567848chr19:51520546ENST00000294172-102183_110338.6666666666667620.0MotifNote=Nuclear export signal
HgeneNXF1chr11:62567848chr19:51520546ENST00000532297-112267_100338.6666666666667620.0MotifNote=Nuclear localization signal
HgeneNXF1chr11:62567848chr19:51520546ENST00000532297-112283_110338.6666666666667620.0MotifNote=Nuclear export signal
HgeneNXF1chr11:62567848chr19:51520546ENST00000294172-10212_118338.6666666666667620.0RegionNote=RNA-binding (RBD)
HgeneNXF1chr11:62567848chr19:51520546ENST00000294172-10212_60338.6666666666667620.0RegionNote=Minor non-specific RNA-binding
HgeneNXF1chr11:62567848chr19:51520546ENST00000294172-102161_118338.6666666666667620.0RegionNote=Major non-specific RNA-binding
HgeneNXF1chr11:62567848chr19:51520546ENST00000532297-11222_118338.6666666666667620.0RegionNote=RNA-binding (RBD)
HgeneNXF1chr11:62567848chr19:51520546ENST00000532297-11222_60338.6666666666667620.0RegionNote=Minor non-specific RNA-binding
HgeneNXF1chr11:62567848chr19:51520546ENST00000532297-112261_118338.6666666666667620.0RegionNote=Major non-specific RNA-binding
HgeneNXF1chr11:62567848chr19:51520546ENST00000294172-1021266_291338.6666666666667620.0RepeatNote=LRR 1
HgeneNXF1chr11:62567848chr19:51520546ENST00000294172-1021292_315338.6666666666667620.0RepeatNote=LRR 2
HgeneNXF1chr11:62567848chr19:51520546ENST00000532297-1122266_291338.6666666666667620.0RepeatNote=LRR 1
HgeneNXF1chr11:62567848chr19:51520546ENST00000532297-1122292_315338.6666666666667620.0RepeatNote=LRR 2
TgeneKLK10chr11:62567848chr19:51520546ENST000003099581647_27429.333333333333332277.0DomainPeptidase S1
TgeneKLK10chr11:62567848chr19:51520546ENST000003587891647_27429.333333333333332277.0DomainPeptidase S1
TgeneKLK10chr11:62567848chr19:51520546ENST000003918051647_27429.333333333333332277.0DomainPeptidase S1

- Not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneNXF1chr11:62567848chr19:51520546ENST00000294172-1021551_561338.6666666666667620.0Compositional biasNote=Pro-rich
HgeneNXF1chr11:62567848chr19:51520546ENST00000439713-110551_5610357.0Compositional biasNote=Pro-rich
HgeneNXF1chr11:62567848chr19:51520546ENST00000531709-120551_5610380.6666666666667Compositional biasNote=Pro-rich
HgeneNXF1chr11:62567848chr19:51520546ENST00000532297-1122551_561338.6666666666667620.0Compositional biasNote=Pro-rich
HgeneNXF1chr11:62567848chr19:51520546ENST00000294172-1021386_536338.6666666666667620.0DomainNTF2
HgeneNXF1chr11:62567848chr19:51520546ENST00000294172-1021565_619338.6666666666667620.0DomainTAP-C
HgeneNXF1chr11:62567848chr19:51520546ENST00000439713-110119_1980357.0DomainNote=RRM
HgeneNXF1chr11:62567848chr19:51520546ENST00000439713-110386_5360357.0DomainNTF2
HgeneNXF1chr11:62567848chr19:51520546ENST00000439713-110565_6190357.0DomainTAP-C
HgeneNXF1chr11:62567848chr19:51520546ENST00000531709-120119_1980380.6666666666667DomainNote=RRM
HgeneNXF1chr11:62567848chr19:51520546ENST00000531709-120386_5360380.6666666666667DomainNTF2
HgeneNXF1chr11:62567848chr19:51520546ENST00000531709-120565_6190380.6666666666667DomainTAP-C
HgeneNXF1chr11:62567848chr19:51520546ENST00000532297-1122386_536338.6666666666667620.0DomainNTF2
HgeneNXF1chr11:62567848chr19:51520546ENST00000532297-1122565_619338.6666666666667620.0DomainTAP-C
HgeneNXF1chr11:62567848chr19:51520546ENST00000439713-11067_1000357.0MotifNote=Nuclear localization signal
HgeneNXF1chr11:62567848chr19:51520546ENST00000439713-11083_1100357.0MotifNote=Nuclear export signal
HgeneNXF1chr11:62567848chr19:51520546ENST00000531709-12067_1000380.6666666666667MotifNote=Nuclear localization signal
HgeneNXF1chr11:62567848chr19:51520546ENST00000531709-12083_1100380.6666666666667MotifNote=Nuclear export signal
HgeneNXF1chr11:62567848chr19:51520546ENST00000439713-1102_1180357.0RegionNote=RNA-binding (RBD)
HgeneNXF1chr11:62567848chr19:51520546ENST00000439713-1102_600357.0RegionNote=Minor non-specific RNA-binding
HgeneNXF1chr11:62567848chr19:51520546ENST00000439713-11061_1180357.0RegionNote=Major non-specific RNA-binding
HgeneNXF1chr11:62567848chr19:51520546ENST00000531709-1202_1180380.6666666666667RegionNote=RNA-binding (RBD)
HgeneNXF1chr11:62567848chr19:51520546ENST00000531709-1202_600380.6666666666667RegionNote=Minor non-specific RNA-binding
HgeneNXF1chr11:62567848chr19:51520546ENST00000531709-12061_1180380.6666666666667RegionNote=Major non-specific RNA-binding
HgeneNXF1chr11:62567848chr19:51520546ENST00000294172-1021316_343338.6666666666667620.0RepeatNote=LRR 3
HgeneNXF1chr11:62567848chr19:51520546ENST00000294172-1021344_371338.6666666666667620.0RepeatNote=LRR 4
HgeneNXF1chr11:62567848chr19:51520546ENST00000439713-110266_2910357.0RepeatNote=LRR 1
HgeneNXF1chr11:62567848chr19:51520546ENST00000439713-110292_3150357.0RepeatNote=LRR 2
HgeneNXF1chr11:62567848chr19:51520546ENST00000439713-110316_3430357.0RepeatNote=LRR 3
HgeneNXF1chr11:62567848chr19:51520546ENST00000439713-110344_3710357.0RepeatNote=LRR 4
HgeneNXF1chr11:62567848chr19:51520546ENST00000531709-120266_2910380.6666666666667RepeatNote=LRR 1
HgeneNXF1chr11:62567848chr19:51520546ENST00000531709-120292_3150380.6666666666667RepeatNote=LRR 2
HgeneNXF1chr11:62567848chr19:51520546ENST00000531709-120316_3430380.6666666666667RepeatNote=LRR 3
HgeneNXF1chr11:62567848chr19:51520546ENST00000531709-120344_3710380.6666666666667RepeatNote=LRR 4
HgeneNXF1chr11:62567848chr19:51520546ENST00000532297-1122316_343338.6666666666667620.0RepeatNote=LRR 3
HgeneNXF1chr11:62567848chr19:51520546ENST00000532297-1122344_371338.6666666666667620.0RepeatNote=LRR 4


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Fusion Protein-Protein Interaction


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 from validated records (BIOGRID-3.4.160)
GenePPI interactors


check button Protein-protein interactors based on sequence similarity (STRING)
GeneSTRING network
NXF1
KLK10


check button - Retained interactions in fusion protein (protein functional feature from UniProt).
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenStill interaction with


check button - Lost interactions due to fusion (protein functional feature from UniProt).
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with
HgeneNXF1chr11:62567848chr19:51520546ENST00000439713-1102_1980357.0ALYREF/THOC4 and LUZP4
HgeneNXF1chr11:62567848chr19:51520546ENST00000531709-1202_1980380.6666666666667ALYREF/THOC4 and LUZP4


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Related Drugs to NXF1-KLK10


check button Drugs used for this fusion-positive patient.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)
HgeneTgeneDrugSourcePMID

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Related Diseases to NXF1-KLK10


check button Diseases that have this fusion gene.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)
HgeneTgeneDiseaseSourcePMID

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