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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:KPNB1-MDH1 (FusionGDB2 ID:43421)

Fusion Gene Summary for KPNB1-MDH1

check button Fusion gene summary
Fusion gene informationFusion gene name: KPNB1-MDH1
Fusion gene ID: 43421
HgeneTgene
Gene symbol

KPNB1

MDH1

Gene ID

3837

4190

Gene namekaryopherin subunit beta 1malate dehydrogenase 1
SynonymsIMB1|IPO1|IPOB|Impnb|NTF97HEL-S-32|MDH-s|MDHA|MGC:1375|MOR2
Cytomap

17q21.32

2p15

Type of geneprotein-codingprotein-coding
Descriptionimportin subunit beta-1PTAC97importin 1importin 90importin beta-1 subunitkaryopherin (importin) beta 1nuclear factor p97pore targeting complex 97 kDa subunitmalate dehydrogenase, cytoplasmicmalate dehydrogenase, peroxisomalcytosolic malate dehydrogenasediiodophenylpyruvate reductaseepididymis secretory protein Li 32malate dehydrogenase 1, NAD (soluble)soluble malate dehydrogenase
Modification date2020031320200313
UniProtAcc

Q14974

P40925

Ensembl transtripts involved in fusion geneENST00000290158, ENST00000535458, 
ENST00000537679, ENST00000540627, 
ENST00000577918, 		ENST00000233114, 
ENST00000409476, ENST00000409908, 
ENST00000394423, ENST00000462944, 
ENST00000539945, ENST00000544381, 
Fusion gene scores* DoF score10 X 11 X 5=5506 X 8 X 4=192
# samples 129
** MAII scorelog2(12/550*10)=-2.1963972128035
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(9/192*10)=-1.09310940439148
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: KPNB1 [Title/Abstract] AND MDH1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointKPNB1(45757968)-MDH1(63816113), # samples:7
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
HgeneKPNB1

GO:0006606

protein import into nucleus

7615630|15964792

HgeneKPNB1

GO:0006610

ribosomal protein import into nucleus

9687515


check buttonFusion gene breakpoints across KPNB1 (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 MDH1 (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
ChiTaRS5.0N/ABM741416KPNB1chr17

45757968

+MDH1chr2

63816113

+
ChiTaRS5.0N/ABM741420KPNB1chr17

45757968

+MDH1chr2

63816113

+
ChiTaRS5.0N/ABM745157KPNB1chr17

45757968

+MDH1chr2

63816113

+
ChiTaRS5.0N/ABM751800KPNB1chr17

45757968

+MDH1chr2

63816113

+
ChiTaRS5.0N/ABM767348KPNB1chr17

45757968

+MDH1chr2

63816113

+
ChiTaRS5.0N/ABM768064KPNB1chr17

45757968

+MDH1chr2

63816113

+
ChiTaRS5.0N/ABM768103KPNB1chr17

45757968

+MDH1chr2

63816113

+


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Fusion Gene ORF analysis for KPNB1-MDH1

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
5CDS-5UTRENST00000290158ENST00000233114KPNB1chr17

45757968

+MDH1chr2

63816113

+
5CDS-5UTRENST00000290158ENST00000409476KPNB1chr17

45757968

+MDH1chr2

63816113

+
5CDS-5UTRENST00000290158ENST00000409908KPNB1chr17

45757968

+MDH1chr2

63816113

+
5CDS-5UTRENST00000535458ENST00000233114KPNB1chr17

45757968

+MDH1chr2

63816113

+
5CDS-5UTRENST00000535458ENST00000409476KPNB1chr17

45757968

+MDH1chr2

63816113

+
5CDS-5UTRENST00000535458ENST00000409908KPNB1chr17

45757968

+MDH1chr2

63816113

+
5CDS-5UTRENST00000537679ENST00000233114KPNB1chr17

45757968

+MDH1chr2

63816113

+
5CDS-5UTRENST00000537679ENST00000409476KPNB1chr17

45757968

+MDH1chr2

63816113

+
5CDS-5UTRENST00000537679ENST00000409908KPNB1chr17

45757968

+MDH1chr2

63816113

+
5CDS-5UTRENST00000540627ENST00000233114KPNB1chr17

45757968

+MDH1chr2

63816113

+
5CDS-5UTRENST00000540627ENST00000409476KPNB1chr17

45757968

+MDH1chr2

63816113

+
5CDS-5UTRENST00000540627ENST00000409908KPNB1chr17

45757968

+MDH1chr2

63816113

+
5CDS-intronENST00000290158ENST00000394423KPNB1chr17

45757968

+MDH1chr2

63816113

+
5CDS-intronENST00000290158ENST00000462944KPNB1chr17

45757968

+MDH1chr2

63816113

+
5CDS-intronENST00000290158ENST00000539945KPNB1chr17

45757968

+MDH1chr2

63816113

+
5CDS-intronENST00000290158ENST00000544381KPNB1chr17

45757968

+MDH1chr2

63816113

+
5CDS-intronENST00000535458ENST00000394423KPNB1chr17

45757968

+MDH1chr2

63816113

+
5CDS-intronENST00000535458ENST00000462944KPNB1chr17

45757968

+MDH1chr2

63816113

+
5CDS-intronENST00000535458ENST00000539945KPNB1chr17

45757968

+MDH1chr2

63816113

+
5CDS-intronENST00000535458ENST00000544381KPNB1chr17

45757968

+MDH1chr2

63816113

+
5CDS-intronENST00000537679ENST00000394423KPNB1chr17

45757968

+MDH1chr2

63816113

+
5CDS-intronENST00000537679ENST00000462944KPNB1chr17

45757968

+MDH1chr2

63816113

+
5CDS-intronENST00000537679ENST00000539945KPNB1chr17

45757968

+MDH1chr2

63816113

+
5CDS-intronENST00000537679ENST00000544381KPNB1chr17

45757968

+MDH1chr2

63816113

+
5CDS-intronENST00000540627ENST00000394423KPNB1chr17

45757968

+MDH1chr2

63816113

+
5CDS-intronENST00000540627ENST00000462944KPNB1chr17

45757968

+MDH1chr2

63816113

+
5CDS-intronENST00000540627ENST00000539945KPNB1chr17

45757968

+MDH1chr2

63816113

+
5CDS-intronENST00000540627ENST00000544381KPNB1chr17

45757968

+MDH1chr2

63816113

+
intron-5UTRENST00000577918ENST00000233114KPNB1chr17

45757968

+MDH1chr2

63816113

+
intron-5UTRENST00000577918ENST00000409476KPNB1chr17

45757968

+MDH1chr2

63816113

+
intron-5UTRENST00000577918ENST00000409908KPNB1chr17

45757968

+MDH1chr2

63816113

+
intron-intronENST00000577918ENST00000394423KPNB1chr17

45757968

+MDH1chr2

63816113

+
intron-intronENST00000577918ENST00000462944KPNB1chr17

45757968

+MDH1chr2

63816113

+
intron-intronENST00000577918ENST00000539945KPNB1chr17

45757968

+MDH1chr2

63816113

+
intron-intronENST00000577918ENST00000544381KPNB1chr17

45757968

+MDH1chr2

63816113

+

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 KPNB1-MDH1


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.

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 KPNB1-MDH1


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/:45757968/:63816113)
- 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
KPNB1

Q14974

MDH1

P40925

FUNCTION: Functions in nuclear protein import, either in association with an adapter protein, like an importin-alpha subunit, which binds to nuclear localization signals (NLS) in cargo substrates, or by acting as autonomous nuclear transport receptor. Acting autonomously, serves itself as NLS receptor. Docking of the importin/substrate complex to the nuclear pore complex (NPC) is mediated by KPNB1 through binding to nucleoporin FxFG repeats and the complex is subsequently translocated through the pore by an energy requiring, Ran-dependent mechanism. At the nucleoplasmic side of the NPC, Ran binds to importin-beta and the three components separate and importin-alpha and -beta are re-exported from the nucleus to the cytoplasm where GTP hydrolysis releases Ran from importin. The directionality of nuclear import is thought to be conferred by an asymmetric distribution of the GTP- and GDP-bound forms of Ran between the cytoplasm and nucleus. Mediates autonomously the nuclear import of ribosomal proteins RPL23A, RPS7 and RPL5. Binds to a beta-like import receptor binding (BIB) domain of RPL23A. In association with IPO7 mediates the nuclear import of H1 histone. In vitro, mediates nuclear import of H2A, H2B, H3 and H4 histones. In case of HIV-1 infection, binds and mediates the nuclear import of HIV-1 Rev. Imports SNAI1 and PRKCI into the nucleus. {ECO:0000269|PubMed:10228156, ECO:0000269|PubMed:11891849, ECO:0000269|PubMed:19386897, ECO:0000269|PubMed:24699649, ECO:0000269|PubMed:9687515}.FUNCTION: Catalyzes the reduction of aromatic alpha-keto acids in the presence of NADH (PubMed:3052244). Plays essential roles in the malate-aspartate shuttle and the tricarboxylic acid cycle, important in mitochondrial NADH supply for oxidative phosphorylation (PubMed:31538237). {ECO:0000269|PubMed:3052244, ECO:0000269|PubMed:31538237}.

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 KPNB1-MDH1


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 KPNB1-MDH1


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 KPNB1-MDH1


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 KPNB1-MDH1


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