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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:DNMT3A-KIF3C

Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: DNMT3A-KIF3C
FusionPDB ID: 23711
FusionGDB2.0 ID: 23711
HgeneTgene
Gene symbol

DNMT3A

KIF3C

Gene ID

1788

3797

Gene nameDNA methyltransferase 3 alphakinesin family member 3C
SynonymsDNMT3A2|HESJAS|M.HsaIIIA|TBRS-
Cytomap

2p23.3

2p23.3

Type of geneprotein-codingprotein-coding
DescriptionDNA (cytosine-5)-methyltransferase 3ADNA (cytosine-5-)-methyltransferase 3 alphaDNA MTase HsaIIIADNA cytosine methyltransferase 3A2kinesin-like protein KIF3CKIF3C variant protein
Modification date2020032220200313
UniProtAcc

Q9Y6K1

O14782

Ensembl transtripts involved in fusion geneENST idsENST00000264709, ENST00000321117, 
ENST00000406659, ENST00000380746, 
ENST00000402667, ENST00000474887, 
ENST00000496378, ENST00000264712, 
ENST00000405914, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score8 X 10 X 7=5605 X 5 X 3=75
# samples 95
** MAII scorelog2(9/560*10)=-2.63742992061529
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(5/75*10)=-0.584962500721156
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)

PubMed: DNMT3A [Title/Abstract] AND KIF3C [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)DNMT3A(25536781)-KIF3C(26152932), # samples:1
Anticipated loss of major functional domain due to fusion event.DNMT3A-KIF3C 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.
DNMT3A-KIF3C 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.
DNMT3A-KIF3C seems lost the major protein functional domain in Hgene partner, which is a cell metabolism gene due to the frame-shifted ORF.
DNMT3A-KIF3C seems lost the major protein functional domain in Hgene partner, which is a CGC due to the frame-shifted ORF.
DNMT3A-KIF3C seems lost the major protein functional domain in Hgene partner, which is a epigenetic factor due to the frame-shifted ORF.
DNMT3A-KIF3C seems lost the major protein functional domain in Hgene partner, which is a IUPHAR drug target due to the frame-shifted ORF.
DNMT3A-KIF3C seems lost the major protein functional domain in Hgene partner, which is a tumor suppressor due to the frame-shifted ORF.
DNMT3A-KIF3C seems lost the major protein functional domain in Tgene partner, which is a essential gene 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
HgeneDNMT3A

GO:0006306

DNA methylation

12138111|19786833|23042785


check buttonFusion gene breakpoints across DNMT3A (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 KIF3C (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
ChimerDB4STADTCGA-VQ-A925DNMT3Achr2

25536781

-KIF3Cchr2

26152932

-


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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)
ENST00000321117DNMT3Achr225536781-ENST00000264712KIF3Cchr226152932-3061309280684134
ENST00000321117DNMT3Achr225536781-ENST00000405914KIF3Cchr226152932-910309280684134

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
ENST00000321117ENST00000264712DNMT3Achr225536781-KIF3Cchr226152932-0.695334550.30466548
ENST00000321117ENST00000405914DNMT3Achr225536781-KIF3Cchr226152932-0.223291250.7767087

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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

>23711_23711_1_DNMT3A-KIF3C_DNMT3A_chr2_25536781_ENST00000321117_KIF3C_chr2_26152932_ENST00000264712_length(amino acids)=134AA_BP=9
MLRSGRRTESSSSQMKKRPTSAVGYKRPISQYARVAMAMGSHPRYRAENIMFLELDVSPPAVFEMEFSHDQEQDPRALHMERLMRLDSFL

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

>23711_23711_2_DNMT3A-KIF3C_DNMT3A_chr2_25536781_ENST00000321117_KIF3C_chr2_26152932_ENST00000405914_length(amino acids)=134AA_BP=9
MLRSGRRTESSSSQMKKRPTSAVGYKRPISQYARVAMAMGSHPRYRAENIMFLELDVSPPAVFEMEFSHDQEQDPRALHMERLMRLDSFL

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

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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/chr2:25536781/chr2:26152932)
- 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
DNMT3A

Q9Y6K1

KIF3C

O14782

FUNCTION: Required for genome-wide de novo methylation and is essential for the establishment of DNA methylation patterns during development. DNA methylation is coordinated with methylation of histones. It modifies DNA in a non-processive manner and also methylates non-CpG sites. May preferentially methylate DNA linker between 2 nucleosomal cores and is inhibited by histone H1. Plays a role in paternal and maternal imprinting. Required for methylation of most imprinted loci in germ cells. Acts as a transcriptional corepressor for ZBTB18. Recruited to trimethylated 'Lys-36' of histone H3 (H3K36me3) sites. Can actively repress transcription through the recruitment of HDAC activity. {ECO:0000269|PubMed:16357870, ECO:0000269|PubMed:30478443}.FUNCTION: Microtubule-based anterograde translocator for membranous organelles. {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.
- Retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note

- Not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneDNMT3Achr2:25536781chr2:26152932ENST00000264709-223292_35024.0913.0DomainPWWP
HgeneDNMT3Achr2:25536781chr2:26152932ENST00000264709-223482_61424.0913.0DomainADD
HgeneDNMT3Achr2:25536781chr2:26152932ENST00000264709-223634_91224.0913.0DomainSAM-dependent MTase C5-type
HgeneDNMT3Achr2:25536781chr2:26152932ENST00000321117-223292_35024.0913.0DomainPWWP
HgeneDNMT3Achr2:25536781chr2:26152932ENST00000321117-223482_61424.0913.0DomainADD
HgeneDNMT3Achr2:25536781chr2:26152932ENST00000321117-223634_91224.0913.0DomainSAM-dependent MTase C5-type
HgeneDNMT3Achr2:25536781chr2:26152932ENST00000380746-119292_3500724.0DomainPWWP
HgeneDNMT3Achr2:25536781chr2:26152932ENST00000380746-119482_6140724.0DomainADD
HgeneDNMT3Achr2:25536781chr2:26152932ENST00000380746-119634_9120724.0DomainSAM-dependent MTase C5-type
HgeneDNMT3Achr2:25536781chr2:26152932ENST00000402667-118292_3500690.0DomainPWWP
HgeneDNMT3Achr2:25536781chr2:26152932ENST00000402667-118482_6140690.0DomainADD
HgeneDNMT3Achr2:25536781chr2:26152932ENST00000402667-118634_9120690.0DomainSAM-dependent MTase C5-type
HgeneDNMT3Achr2:25536781chr2:26152932ENST00000406659-24292_35024.0167.0DomainPWWP
HgeneDNMT3Achr2:25536781chr2:26152932ENST00000406659-24482_61424.0167.0DomainADD
HgeneDNMT3Achr2:25536781chr2:26152932ENST00000406659-24634_91224.0167.0DomainSAM-dependent MTase C5-type
HgeneDNMT3Achr2:25536781chr2:26152932ENST00000264709-223641_64524.0913.0RegionS-adenosyl-L-methionine binding
HgeneDNMT3Achr2:25536781chr2:26152932ENST00000264709-223686_68824.0913.0RegionS-adenosyl-L-methionine binding
HgeneDNMT3Achr2:25536781chr2:26152932ENST00000264709-223891_89324.0913.0RegionS-adenosyl-L-methionine binding
HgeneDNMT3Achr2:25536781chr2:26152932ENST00000321117-223641_64524.0913.0RegionS-adenosyl-L-methionine binding
HgeneDNMT3Achr2:25536781chr2:26152932ENST00000321117-223686_68824.0913.0RegionS-adenosyl-L-methionine binding
HgeneDNMT3Achr2:25536781chr2:26152932ENST00000321117-223891_89324.0913.0RegionS-adenosyl-L-methionine binding
HgeneDNMT3Achr2:25536781chr2:26152932ENST00000380746-119641_6450724.0RegionS-adenosyl-L-methionine binding
HgeneDNMT3Achr2:25536781chr2:26152932ENST00000380746-119686_6880724.0RegionS-adenosyl-L-methionine binding
HgeneDNMT3Achr2:25536781chr2:26152932ENST00000380746-119891_8930724.0RegionS-adenosyl-L-methionine binding
HgeneDNMT3Achr2:25536781chr2:26152932ENST00000402667-118641_6450690.0RegionS-adenosyl-L-methionine binding
HgeneDNMT3Achr2:25536781chr2:26152932ENST00000402667-118686_6880690.0RegionS-adenosyl-L-methionine binding
HgeneDNMT3Achr2:25536781chr2:26152932ENST00000402667-118891_8930690.0RegionS-adenosyl-L-methionine binding
HgeneDNMT3Achr2:25536781chr2:26152932ENST00000406659-24641_64524.0167.0RegionS-adenosyl-L-methionine binding
HgeneDNMT3Achr2:25536781chr2:26152932ENST00000406659-24686_68824.0167.0RegionS-adenosyl-L-methionine binding
HgeneDNMT3Achr2:25536781chr2:26152932ENST00000406659-24891_89324.0167.0RegionS-adenosyl-L-methionine binding
HgeneDNMT3Achr2:25536781chr2:26152932ENST00000264709-223493_52324.0913.0Zinc fingerGATA-type%3B atypical
HgeneDNMT3Achr2:25536781chr2:26152932ENST00000264709-223534_59024.0913.0Zinc fingerPHD-type%3B atypical
HgeneDNMT3Achr2:25536781chr2:26152932ENST00000321117-223493_52324.0913.0Zinc fingerGATA-type%3B atypical
HgeneDNMT3Achr2:25536781chr2:26152932ENST00000321117-223534_59024.0913.0Zinc fingerPHD-type%3B atypical
HgeneDNMT3Achr2:25536781chr2:26152932ENST00000380746-119493_5230724.0Zinc fingerGATA-type%3B atypical
HgeneDNMT3Achr2:25536781chr2:26152932ENST00000380746-119534_5900724.0Zinc fingerPHD-type%3B atypical
HgeneDNMT3Achr2:25536781chr2:26152932ENST00000402667-118493_5230690.0Zinc fingerGATA-type%3B atypical
HgeneDNMT3Achr2:25536781chr2:26152932ENST00000402667-118534_5900690.0Zinc fingerPHD-type%3B atypical
HgeneDNMT3Achr2:25536781chr2:26152932ENST00000406659-24493_52324.0167.0Zinc fingerGATA-type%3B atypical
HgeneDNMT3Achr2:25536781chr2:26152932ENST00000406659-24534_59024.0167.0Zinc fingerPHD-type%3B atypical
TgeneKIF3Cchr2:25536781chr2:26152932ENST0000026471248376_629668.6666666666666794.0Coiled coilOntology_term=ECO:0000255
TgeneKIF3Cchr2:25536781chr2:26152932ENST0000040591459376_629668.6666666666666794.0Coiled coilOntology_term=ECO:0000255
TgeneKIF3Cchr2:25536781chr2:26152932ENST0000026471248270_284668.6666666666666794.0Compositional biasNote=Poly-Gly
TgeneKIF3Cchr2:25536781chr2:26152932ENST0000026471248438_441668.6666666666666794.0Compositional biasNote=Poly-Asn
TgeneKIF3Cchr2:25536781chr2:26152932ENST0000040591459270_284668.6666666666666794.0Compositional biasNote=Poly-Gly
TgeneKIF3Cchr2:25536781chr2:26152932ENST0000040591459438_441668.6666666666666794.0Compositional biasNote=Poly-Asn
TgeneKIF3Cchr2:25536781chr2:26152932ENST000002647124810_365668.6666666666666794.0DomainKinesin motor
TgeneKIF3Cchr2:25536781chr2:26152932ENST000004059145910_365668.6666666666666794.0DomainKinesin motor
TgeneKIF3Cchr2:25536781chr2:26152932ENST000002647124897_104668.6666666666666794.0Nucleotide bindingNote=ATP
TgeneKIF3Cchr2:25536781chr2:26152932ENST000004059145997_104668.6666666666666794.0Nucleotide bindingNote=ATP
TgeneKIF3Cchr2:25536781chr2:26152932ENST0000026471248630_793668.6666666666666794.0RegionGlobular
TgeneKIF3Cchr2:25536781chr2:26152932ENST0000040591459630_793668.6666666666666794.0RegionGlobular


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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
DNMT3A
KIF3C


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
HgeneDNMT3Achr2:25536781chr2:26152932ENST00000264709-223199_40324.0913.0DNMT1 and DNMT3B
HgeneDNMT3Achr2:25536781chr2:26152932ENST00000321117-223199_40324.0913.0DNMT1 and DNMT3B
HgeneDNMT3Achr2:25536781chr2:26152932ENST00000380746-119199_4030724.0DNMT1 and DNMT3B
HgeneDNMT3Achr2:25536781chr2:26152932ENST00000402667-118199_4030690.0DNMT1 and DNMT3B
HgeneDNMT3Achr2:25536781chr2:26152932ENST00000406659-24199_40324.0167.0DNMT1 and DNMT3B
HgeneDNMT3Achr2:25536781chr2:26152932ENST00000264709-223494_58624.0913.0the PRC2/EED-EZH2 complex
HgeneDNMT3Achr2:25536781chr2:26152932ENST00000321117-223494_58624.0913.0the PRC2/EED-EZH2 complex
HgeneDNMT3Achr2:25536781chr2:26152932ENST00000380746-119494_5860724.0the PRC2/EED-EZH2 complex
HgeneDNMT3Achr2:25536781chr2:26152932ENST00000402667-118494_5860690.0the PRC2/EED-EZH2 complex
HgeneDNMT3Achr2:25536781chr2:26152932ENST00000406659-24494_58624.0167.0the PRC2/EED-EZH2 complex


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Related Drugs to DNMT3A-KIF3C


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 DNMT3A-KIF3C


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