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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:KIF2A-NDUFAF2 (FusionGDB2 ID:HG3796TG91942)

Fusion Gene Summary for KIF2A-NDUFAF2

check button Fusion gene summary
Fusion gene informationFusion gene name: KIF2A-NDUFAF2
Fusion gene ID: hg3796tg91942
HgeneTgene
Gene symbol

KIF2A

NDUFAF2

Gene ID

3796

91942

Gene namekinesin family member 2ANADH:ubiquinone oxidoreductase complex assembly factor 2
SynonymsCDCBM3|HK2|KIF2B17.2L|MC1DN10|MMTN|NDUFA12L|mimitin
Cytomap('KIF2A')('NDUFAF2')

5q12.1

5q12.1

Type of geneprotein-codingprotein-coding
Descriptionkinesin-like protein KIF2AKinesin, heavy chain, 2kinesin heavy chain member 2Akinesin-2NADH dehydrogenase [ubiquinone] 1 alpha subcomplex assembly factor 2Myc-induced mitochondrial proteinNADH dehydrogenase (ubiquinone) 1 alpha subcomplex, assembly factor 2NADH dehydrogenase (ubiquinone) complex I, assembly factor 2NADH dehydrogenase 1
Modification date2020031820200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000509663, ENST00000401507, 
ENST00000407818, ENST00000381103, 
ENST00000506857, 
Fusion gene scores* DoF score4 X 2 X 5=4013 X 7 X 9=819
# samples 615
** MAII scorelog2(6/40*10)=0.584962500721156
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
log2(15/819*10)=-2.44890095114513
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: KIF2A [Title/Abstract] AND NDUFAF2 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointKIF2A(61602363)-NDUFAF2(60368951), # samples:1
Anticipated loss of major functional domain due to fusion event.KIF2A-NDUFAF2 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.
KIF2A-NDUFAF2 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.
* 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
HgeneKIF2A

GO:0007052

mitotic spindle organization

18411309


check buttonFusion gene breakpoints across KIF2A (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 NDUFAF2 (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
* 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
ChimerDB4STADTCGA-VQ-A92DKIF2Achr5

61602363

+NDUFAF2chr5

60368951

+


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Fusion Gene ORF analysis for KIF2A-NDUFAF2

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-3CDSENST00000509663ENST00000296597KIF2Achr5

61602363

+NDUFAF2chr5

60368951

+
3UTR-3UTRENST00000509663ENST00000512623KIF2Achr5

61602363

+NDUFAF2chr5

60368951

+
3UTR-intronENST00000509663ENST00000511107KIF2Achr5

61602363

+NDUFAF2chr5

60368951

+
5CDS-3UTRENST00000401507ENST00000512623KIF2Achr5

61602363

+NDUFAF2chr5

60368951

+
5CDS-3UTRENST00000407818ENST00000512623KIF2Achr5

61602363

+NDUFAF2chr5

60368951

+
5CDS-intronENST00000401507ENST00000511107KIF2Achr5

61602363

+NDUFAF2chr5

60368951

+
5CDS-intronENST00000407818ENST00000511107KIF2Achr5

61602363

+NDUFAF2chr5

60368951

+
5UTR-3CDSENST00000381103ENST00000296597KIF2Achr5

61602363

+NDUFAF2chr5

60368951

+
5UTR-3UTRENST00000381103ENST00000512623KIF2Achr5

61602363

+NDUFAF2chr5

60368951

+
5UTR-intronENST00000381103ENST00000511107KIF2Achr5

61602363

+NDUFAF2chr5

60368951

+
In-frameENST00000401507ENST00000296597KIF2Achr5

61602363

+NDUFAF2chr5

60368951

+
In-frameENST00000407818ENST00000296597KIF2Achr5

61602363

+NDUFAF2chr5

60368951

+
intron-3CDSENST00000506857ENST00000296597KIF2Achr5

61602363

+NDUFAF2chr5

60368951

+
intron-3UTRENST00000506857ENST00000512623KIF2Achr5

61602363

+NDUFAF2chr5

60368951

+
intron-intronENST00000506857ENST00000511107KIF2Achr5

61602363

+NDUFAF2chr5

60368951

+

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)
ENST00000401507KIF2Achr561602363+ENST00000296597NDUFAF2chr560368951+829375155757200
ENST00000407818KIF2Achr561602363+ENST00000296597NDUFAF2chr560368951+5398521467148

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
ENST00000401507ENST00000296597KIF2Achr561602363+NDUFAF2chr560368951+0.0086384210.99136156
ENST00000407818ENST00000296597KIF2Achr561602363+NDUFAF2chr560368951+0.0075282140.9924718

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Fusion Genomic Features for KIF2A-NDUFAF2


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)
KIF2Achr561602363+NDUFAF2chr560368951+4.68E-111
KIF2Achr561602363+NDUFAF2chr560368951+4.68E-111

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.
genomic feature of top 1%

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Fusion Protein Features for KIF2A-NDUFAF2


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/chr5:61602363/chr5:60368951)
- 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
..
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: 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}.

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
HgeneKIF2Achr5:61602363chr5:60368951ENST00000381103+121660_6990687.0Coiled coilOntology_term=ECO:0000255
HgeneKIF2Achr5:61602363chr5:60368951ENST00000401507+120660_69921707.0Coiled coilOntology_term=ECO:0000255
HgeneKIF2Achr5:61602363chr5:60368951ENST00000407818+121660_69921745.0Coiled coilOntology_term=ECO:0000255
HgeneKIF2Achr5:61602363chr5:60368951ENST00000506857+120660_6990661.0Coiled coilOntology_term=ECO:0000255
HgeneKIF2Achr5:61602363chr5:60368951ENST00000381103+121223_5530687.0DomainKinesin motor
HgeneKIF2Achr5:61602363chr5:60368951ENST00000401507+120223_55321707.0DomainKinesin motor
HgeneKIF2Achr5:61602363chr5:60368951ENST00000407818+121223_55321745.0DomainKinesin motor
HgeneKIF2Achr5:61602363chr5:60368951ENST00000506857+120223_5530661.0DomainKinesin motor
HgeneKIF2Achr5:61602363chr5:60368951ENST00000381103+121313_3200687.0Nucleotide bindingNote=ATP
HgeneKIF2Achr5:61602363chr5:60368951ENST00000401507+120313_32021707.0Nucleotide bindingNote=ATP
HgeneKIF2Achr5:61602363chr5:60368951ENST00000407818+121313_32021745.0Nucleotide bindingNote=ATP
HgeneKIF2Achr5:61602363chr5:60368951ENST00000506857+120313_3200661.0Nucleotide bindingNote=ATP
HgeneKIF2Achr5:61602363chr5:60368951ENST00000381103+1211_2170687.0RegionGlobular
HgeneKIF2Achr5:61602363chr5:60368951ENST00000401507+1201_21721707.0RegionGlobular
HgeneKIF2Achr5:61602363chr5:60368951ENST00000407818+1211_21721745.0RegionGlobular
HgeneKIF2Achr5:61602363chr5:60368951ENST00000506857+1201_2170661.0RegionGlobular


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Fusion Gene Sequence for KIF2A-NDUFAF2


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.
>42680_42680_1_KIF2A-NDUFAF2_KIF2A_chr5_61602363_ENST00000401507_NDUFAF2_chr5_60368951_ENST00000296597_length(transcript)=829nt_BP=375nt
GCCTCCCCAGCGTCGGCTCCCCGGCGGGCGGTGCGGGCCCTCCCACTCTACCCCGCGCCGTCTCACGGCCCCGGCCCTAGCTTCACCCCG
ACTACCCGGCGTGCGCGTCCTCCTGCCGGCCTGCAGGCCCGGGGCCTCCGCCTGCTTCCCCACAGCTGCTCCTTGCGGCCCCGCTTGCGT
TCACGCTGTCGCCCGGGCCGGCGCGGCCGCGGGCAACCGCTCCCCCTCCCACACCTACCCCGCCCCCTCCCCGCCTTTTCCGCCCTCCGG
TCCCCCTCCCTCGGCCCGCTGCTGCTGCTCCAGATGAGGTGATGGCAACGGCCAACTTCGGCAAGATCCAGATCGGGATTTACGTGGAGA
TCAAGCGCAGCGATGGACAAACTATTCGAGAGAAAAGAATTGTAGAAGCAGCAAATAAAAAAGAAGTAGACTATGAAGCAGGGGATATTC
CAACAGAATGGGAAGCTTGGATTAGAAGAACAAGAAAGACTCCACCTACTATGGAGGAAATACTAAAGAATGAAAAACACAGAGAAGAAA
TCAAAATAAAAAGCCAAGATTTTTATGAAAAAGAAAAACTCCTTAGTAAAGAGACCAGTGAGGAACTCCTGCCTCCACCAGTTCAAACTC
AAATTAAAGGCCATGCCTCTGCTCCATACTTTGGAAAGGAAGAACCCTCAGTGGCTCCCAGCAGCACTGGTAAAACCTTTCAGCCAGGAT
CCTGGATGCCACGAGATGGCAAGAGCCACAATCAATGAATGCATTATGGTCAAATCTTTTCATGTATATGGATGTGACTATTTTAACAAA

>42680_42680_1_KIF2A-NDUFAF2_KIF2A_chr5_61602363_ENST00000401507_NDUFAF2_chr5_60368951_ENST00000296597_length(amino acids)=200AA_BP=73
MLLAAPLAFTLSPGPARPRATAPPPTPTPPPPRLFRPPVPLPRPAAAAPDEVMATANFGKIQIGIYVEIKRSDGQTIREKRIVEAANKKE
VDYEAGDIPTEWEAWIRRTRKTPPTMEEILKNEKHREEIKIKSQDFYEKEKLLSKETSEELLPPPVQTQIKGHASAPYFGKEEPSVAPSS

--------------------------------------------------------------
>42680_42680_2_KIF2A-NDUFAF2_KIF2A_chr5_61602363_ENST00000407818_NDUFAF2_chr5_60368951_ENST00000296597_length(transcript)=539nt_BP=85nt
GCTGCTGCTCCAGATGAGGTGATGGCAACGGCCAACTTCGGCAAGATCCAGATCGGGATTTACGTGGAGATCAAGCGCAGCGATGGACAA
ACTATTCGAGAGAAAAGAATTGTAGAAGCAGCAAATAAAAAAGAAGTAGACTATGAAGCAGGGGATATTCCAACAGAATGGGAAGCTTGG
ATTAGAAGAACAAGAAAGACTCCACCTACTATGGAGGAAATACTAAAGAATGAAAAACACAGAGAAGAAATCAAAATAAAAAGCCAAGAT
TTTTATGAAAAAGAAAAACTCCTTAGTAAAGAGACCAGTGAGGAACTCCTGCCTCCACCAGTTCAAACTCAAATTAAAGGCCATGCCTCT
GCTCCATACTTTGGAAAGGAAGAACCCTCAGTGGCTCCCAGCAGCACTGGTAAAACCTTTCAGCCAGGATCCTGGATGCCACGAGATGGC

>42680_42680_2_KIF2A-NDUFAF2_KIF2A_chr5_61602363_ENST00000407818_NDUFAF2_chr5_60368951_ENST00000296597_length(amino acids)=148AA_BP=21
MATANFGKIQIGIYVEIKRSDGQTIREKRIVEAANKKEVDYEAGDIPTEWEAWIRRTRKTPPTMEEILKNEKHREEIKIKSQDFYEKEKL

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

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Fusion Gene PPI Analysis for KIF2A-NDUFAF2


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 KIF2A-NDUFAF2


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 KIF2A-NDUFAF2


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneKIF2AC3809414CORTICAL DYSPLASIA, COMPLEX, WITH OTHER BRAIN MALFORMATIONS 32CTD_human;GENOMICS_ENGLAND;UNIPROT
HgeneKIF2AC0025958Microcephaly1CTD_human
HgeneKIF2AC0036341Schizophrenia1PSYGENET
HgeneKIF2AC0431380Cortical Dysplasia1CTD_human
HgeneKIF2AC1955869Malformations of Cortical Development1CTD_human
HgeneKIF2AC1956147Microlissencephaly1CTD_human
HgeneKIF2AC3853041Severe Congenital Microcephaly1CTD_human
TgeneC1838979MITOCHONDRIAL COMPLEX I DEFICIENCY4GENOMICS_ENGLAND;ORPHANET
TgeneC0023264Leigh Disease2GENOMICS_ENGLAND
TgeneC4748768MITOCHONDRIAL COMPLEX I DEFICIENCY, NUCLEAR TYPE 102GENOMICS_ENGLAND
TgeneC0752107Brain Diseases, Metabolic, Inherited1CTD_human
TgeneC0752109Brain Diseases, Metabolic, Inborn1CTD_human
TgeneC0752110Central Nervous System Inborn Metabolic Diseases1CTD_human