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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:DNMT3A-NCKAP1 (FusionGDB2 ID:23692)

Fusion Gene Summary for DNMT3A-NCKAP1

check button Fusion gene summary
Fusion gene informationFusion gene name: DNMT3A-NCKAP1
Fusion gene ID: 23692
HgeneTgene
Gene symbol

DNMT3A

NCKAP1

Gene ID

1788

10787

Gene nameDNA methyltransferase 3 alphaNCK associated protein 1
SynonymsDNMT3A2|HESJAS|M.HsaIIIA|TBRSHEM2|NAP1|NAP125|p125Nap1
Cytomap

2p23.3

2q32.1

Type of geneprotein-codingprotein-coding
DescriptionDNA (cytosine-5)-methyltransferase 3ADNA (cytosine-5-)-methyltransferase 3 alphaDNA MTase HsaIIIADNA cytosine methyltransferase 3A2nck-associated protein 1membrane-associated protein HEM-2
Modification date2020032220200327
UniProtAcc.

P55160

Ensembl transtripts involved in fusion geneENST00000321117, ENST00000264709, 
ENST00000406659, ENST00000380746, 
ENST00000402667, ENST00000474887, 
ENST00000361354, ENST00000360982, 
ENST00000478449, 
Fusion gene scores* DoF score8 X 10 X 7=56014 X 14 X 8=1568
# samples 917
** MAII scorelog2(9/560*10)=-2.63742992061529
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(17/1568*10)=-3.20531890797751
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: DNMT3A [Title/Abstract] AND NCKAP1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointDNMT3A(25564694)-NCKAP1(183853914), # samples:1
DNMT3A(25565298)-NCKAP1(183853914), # samples:1
DNMT3A(25564695)-NCKAP1(183853914), # 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
HgeneDNMT3A

GO:0006306

DNA methylation

12138111|19786833|23042785

TgeneNCKAP1

GO:0016601

Rac protein signal transduction

21107423

TgeneNCKAP1

GO:2000601

positive regulation of Arp2/3 complex-mediated actin nucleation

21107423


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.

check buttonFusion gene breakpoints across NCKAP1 (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
ChimerDB4OVTCGA-13-0908DNMT3Achr2

25564694

-NCKAP1chr2

183853914

-
ChimerDB4OVTCGA-13-0908DNMT3Achr2

25565298

-NCKAP1chr2

183853914

-
ChimerDB4OVTCGA-13-0908-01BDNMT3Achr2

25564695

-NCKAP1chr2

183853914

-


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Fusion Gene ORF analysis for DNMT3A-NCKAP1

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
5UTR-3CDSENST00000321117ENST00000361354DNMT3Achr2

25564694

-NCKAP1chr2

183853914

-
5UTR-3CDSENST00000321117ENST00000360982DNMT3Achr2

25564694

-NCKAP1chr2

183853914

-
5UTR-intronENST00000321117ENST00000478449DNMT3Achr2

25564694

-NCKAP1chr2

183853914

-
intron-3CDSENST00000264709ENST00000361354DNMT3Achr2

25564694

-NCKAP1chr2

183853914

-
intron-3CDSENST00000264709ENST00000360982DNMT3Achr2

25564694

-NCKAP1chr2

183853914

-
intron-intronENST00000264709ENST00000478449DNMT3Achr2

25564694

-NCKAP1chr2

183853914

-
intron-3CDSENST00000406659ENST00000361354DNMT3Achr2

25564694

-NCKAP1chr2

183853914

-
intron-3CDSENST00000406659ENST00000360982DNMT3Achr2

25564694

-NCKAP1chr2

183853914

-
intron-intronENST00000406659ENST00000478449DNMT3Achr2

25564694

-NCKAP1chr2

183853914

-
intron-3CDSENST00000380746ENST00000361354DNMT3Achr2

25564694

-NCKAP1chr2

183853914

-
intron-3CDSENST00000380746ENST00000360982DNMT3Achr2

25564694

-NCKAP1chr2

183853914

-
intron-intronENST00000380746ENST00000478449DNMT3Achr2

25564694

-NCKAP1chr2

183853914

-
intron-3CDSENST00000402667ENST00000361354DNMT3Achr2

25564694

-NCKAP1chr2

183853914

-
intron-3CDSENST00000402667ENST00000360982DNMT3Achr2

25564694

-NCKAP1chr2

183853914

-
intron-intronENST00000402667ENST00000478449DNMT3Achr2

25564694

-NCKAP1chr2

183853914

-
intron-3CDSENST00000474887ENST00000361354DNMT3Achr2

25564694

-NCKAP1chr2

183853914

-
intron-3CDSENST00000474887ENST00000360982DNMT3Achr2

25564694

-NCKAP1chr2

183853914

-
intron-intronENST00000474887ENST00000478449DNMT3Achr2

25564694

-NCKAP1chr2

183853914

-
intron-3CDSENST00000321117ENST00000361354DNMT3Achr2

25565298

-NCKAP1chr2

183853914

-
intron-3CDSENST00000321117ENST00000360982DNMT3Achr2

25565298

-NCKAP1chr2

183853914

-
intron-intronENST00000321117ENST00000478449DNMT3Achr2

25565298

-NCKAP1chr2

183853914

-
5UTR-3CDSENST00000264709ENST00000361354DNMT3Achr2

25565298

-NCKAP1chr2

183853914

-
5UTR-3CDSENST00000264709ENST00000360982DNMT3Achr2

25565298

-NCKAP1chr2

183853914

-
5UTR-intronENST00000264709ENST00000478449DNMT3Achr2

25565298

-NCKAP1chr2

183853914

-
5UTR-3CDSENST00000406659ENST00000361354DNMT3Achr2

25565298

-NCKAP1chr2

183853914

-
5UTR-3CDSENST00000406659ENST00000360982DNMT3Achr2

25565298

-NCKAP1chr2

183853914

-
5UTR-intronENST00000406659ENST00000478449DNMT3Achr2

25565298

-NCKAP1chr2

183853914

-
intron-3CDSENST00000380746ENST00000361354DNMT3Achr2

25565298

-NCKAP1chr2

183853914

-
intron-3CDSENST00000380746ENST00000360982DNMT3Achr2

25565298

-NCKAP1chr2

183853914

-
intron-intronENST00000380746ENST00000478449DNMT3Achr2

25565298

-NCKAP1chr2

183853914

-
intron-3CDSENST00000402667ENST00000361354DNMT3Achr2

25565298

-NCKAP1chr2

183853914

-
intron-3CDSENST00000402667ENST00000360982DNMT3Achr2

25565298

-NCKAP1chr2

183853914

-
intron-intronENST00000402667ENST00000478449DNMT3Achr2

25565298

-NCKAP1chr2

183853914

-
intron-3CDSENST00000474887ENST00000361354DNMT3Achr2

25565298

-NCKAP1chr2

183853914

-
intron-3CDSENST00000474887ENST00000360982DNMT3Achr2

25565298

-NCKAP1chr2

183853914

-
intron-intronENST00000474887ENST00000478449DNMT3Achr2

25565298

-NCKAP1chr2

183853914

-
5UTR-3CDSENST00000321117ENST00000361354DNMT3Achr2

25564695

-NCKAP1chr2

183853914

-
5UTR-3CDSENST00000321117ENST00000360982DNMT3Achr2

25564695

-NCKAP1chr2

183853914

-
5UTR-intronENST00000321117ENST00000478449DNMT3Achr2

25564695

-NCKAP1chr2

183853914

-
intron-3CDSENST00000264709ENST00000361354DNMT3Achr2

25564695

-NCKAP1chr2

183853914

-
intron-3CDSENST00000264709ENST00000360982DNMT3Achr2

25564695

-NCKAP1chr2

183853914

-
intron-intronENST00000264709ENST00000478449DNMT3Achr2

25564695

-NCKAP1chr2

183853914

-
intron-3CDSENST00000406659ENST00000361354DNMT3Achr2

25564695

-NCKAP1chr2

183853914

-
intron-3CDSENST00000406659ENST00000360982DNMT3Achr2

25564695

-NCKAP1chr2

183853914

-
intron-intronENST00000406659ENST00000478449DNMT3Achr2

25564695

-NCKAP1chr2

183853914

-
intron-3CDSENST00000380746ENST00000361354DNMT3Achr2

25564695

-NCKAP1chr2

183853914

-
intron-3CDSENST00000380746ENST00000360982DNMT3Achr2

25564695

-NCKAP1chr2

183853914

-
intron-intronENST00000380746ENST00000478449DNMT3Achr2

25564695

-NCKAP1chr2

183853914

-
intron-3CDSENST00000402667ENST00000361354DNMT3Achr2

25564695

-NCKAP1chr2

183853914

-
intron-3CDSENST00000402667ENST00000360982DNMT3Achr2

25564695

-NCKAP1chr2

183853914

-
intron-intronENST00000402667ENST00000478449DNMT3Achr2

25564695

-NCKAP1chr2

183853914

-
intron-3CDSENST00000474887ENST00000361354DNMT3Achr2

25564695

-NCKAP1chr2

183853914

-
intron-3CDSENST00000474887ENST00000360982DNMT3Achr2

25564695

-NCKAP1chr2

183853914

-
intron-intronENST00000474887ENST00000478449DNMT3Achr2

25564695

-NCKAP1chr2

183853914

-

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 DNMT3A-NCKAP1


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 DNMT3A-NCKAP1


check button Go to

FGviewer for the breakpoints of :-:

.
- FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels.
FGviewer

check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
.NCKAP1

P55160

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: Essential hematopoietic-specific regulator of the actin cytoskeleton (Probable). Controls lymphocyte development, activation, proliferation and homeostasis, erythrocyte membrane stability, as well as phagocytosis and migration by neutrophils and macrophages (PubMed:16417406, PubMed:17696648). Component of the WAVE2 complex which signals downstream of RAC to stimulate F-actin polymerization. Required for stabilization and/or translation of the WAVE2 complex proteins in hematopoietic cells (By similarity). Exhibits complex cycles of activation and inhibition to generate waves of propagating the assembly with actin (PubMed:16417406). Also involved in mechanisms WAVE-independent to regulate myosin and actin polymerization during neutrophil chemotaxis (PubMed:17696648). {ECO:0000250|UniProtKB:Q8K1X4, ECO:0000269|PubMed:16417406, ECO:0000269|PubMed:17696648, ECO:0000303|PubMed:20969869}.

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 DNMT3A-NCKAP1


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 DNMT3A-NCKAP1


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 DNMT3A-NCKAP1


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 DNMT3A-NCKAP1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneDNMT3AC4014545Tatton Brown Rahman syndrome4CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
HgeneDNMT3AC0018273Growth Disorders2CTD_human
HgeneDNMT3AC0079774Peripheral T-Cell Lymphoma2CTD_human
HgeneDNMT3AC0006142Malignant neoplasm of breast1CTD_human
HgeneDNMT3AC0010346Crohn Disease1CTD_human
HgeneDNMT3AC0013336Dwarfism1CTD_human
HgeneDNMT3AC0020796Profound Mental Retardation1CTD_human
HgeneDNMT3AC0020981Angioimmunoblastic Lymphadenopathy1CTD_human
HgeneDNMT3AC0023465Acute monocytic leukemia1CTD_human
HgeneDNMT3AC0023487Acute Promyelocytic Leukemia1CTD_human
HgeneDNMT3AC0024121Lung Neoplasms1CTD_human
HgeneDNMT3AC0025363Mental Retardation, Psychosocial1CTD_human
HgeneDNMT3AC0025958Microcephaly1CTD_human
HgeneDNMT3AC0027643Neoplasm Recurrence, Local1CTD_human
HgeneDNMT3AC0036920Sezary Syndrome1CTD_human
HgeneDNMT3AC0079773Lymphoma, T-Cell, Cutaneous1CTD_human
HgeneDNMT3AC0156147Crohn's disease of large bowel1CTD_human
HgeneDNMT3AC0242379Malignant neoplasm of lung1CTD_human
HgeneDNMT3AC0265202Seckel syndrome1GENOMICS_ENGLAND
HgeneDNMT3AC0267380Crohn's disease of the ileum1CTD_human
HgeneDNMT3AC0282631Facies1CTD_human
HgeneDNMT3AC0349639Juvenile Myelomonocytic Leukemia1CTD_human
HgeneDNMT3AC0376407Granulomatous Slack Skin1CTD_human
HgeneDNMT3AC0376634Craniofacial Abnormalities1CTD_human
HgeneDNMT3AC0678202Regional enteritis1CTD_human
HgeneDNMT3AC0678222Breast Carcinoma1CTD_human
HgeneDNMT3AC0917816Mental deficiency1CTD_human
HgeneDNMT3AC0949272IIeocolitis1CTD_human
HgeneDNMT3AC1257931Mammary Neoplasms, Human1CTD_human
HgeneDNMT3AC1458155Mammary Neoplasms1CTD_human
HgeneDNMT3AC1510586Autism Spectrum Disorders1CTD_human
HgeneDNMT3AC1956147Microlissencephaly1CTD_human
HgeneDNMT3AC2931852Clear-cell metastatic renal cell carcinoma1CTD_human
HgeneDNMT3AC3496069cocaine use1PSYGENET
HgeneDNMT3AC3714756Intellectual Disability1CTD_human
HgeneDNMT3AC3853041Severe Congenital Microcephaly1CTD_human
HgeneDNMT3AC4704874Mammary Carcinoma, Human1CTD_human
TgeneNCKAP1C1535926Neurodevelopmental Disorders1CTD_human