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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:NKD1-BRD7

Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: NKD1-BRD7
FusionPDB ID: 59266
FusionGDB2.0 ID: 59266
HgeneTgene
Gene symbol

NKD1

BRD7

Gene ID

85407

29117

Gene nameNKD inhibitor of WNT signaling pathway 1bromodomain containing 7
SynonymsNaked1BP75|CELTIX1|NAG4
Cytomap

16q12.1

16q12.1

Type of geneprotein-codingprotein-coding
Descriptionprotein naked cuticle homolog 1Dvl-binding proteinNKD1, WNT signaling pathway inhibitornaked cuticle homolog 1naked cuticle-1naked-1bromodomain-containing protein 775 kDa bromodomain proteinprotein CELTIX-1
Modification date2020031320200313
UniProtAcc

Q969G9

Q9NPI1

Ensembl transtripts involved in fusion geneENST idsENST00000564336, ENST00000268459, 
ENST00000394688, ENST00000394689, 
ENST00000401491, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score7 X 4 X 6=1685 X 5 X 3=75
# samples 85
** MAII scorelog2(8/168*10)=-1.0703893278914
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: NKD1 [Title/Abstract] AND BRD7 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)NKD1(50583466)-BRD7(50388833), # samples:1
Anticipated loss of major functional domain due to fusion event.NKD1-BRD7 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.
NKD1-BRD7 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.
NKD1-BRD7 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.
NKD1-BRD7 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
TgeneBRD7

GO:0006357

regulation of transcription by RNA polymerase II

12489984

TgeneBRD7

GO:0008285

negative regulation of cell proliferation

20228809

TgeneBRD7

GO:0035066

positive regulation of histone acetylation

20228809

TgeneBRD7

GO:0045892

negative regulation of transcription, DNA-templated

16265664

TgeneBRD7

GO:0045893

positive regulation of transcription, DNA-templated

20228809

TgeneBRD7

GO:2000134

negative regulation of G1/S transition of mitotic cell cycle

16265664


check buttonFusion gene breakpoints across NKD1 (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 BRD7 (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
ChimerDB4BRCATCGA-AO-A0JE-01ANKD1chr16

50583466

+BRD7chr16

50388833

-


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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)
ENST00000268459NKD1chr1650583466+ENST00000394688BRD7chr1650388833-53684161342113659
ENST00000268459NKD1chr1650583466+ENST00000394689BRD7chr1650388833-22984161342116660

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
ENST00000268459ENST00000394688NKD1chr1650583466+BRD7chr1650388833-0.000400030.9996
ENST00000268459ENST00000394689NKD1chr1650583466+BRD7chr1650388833-0.0020337190.9979663

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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

>59266_59266_1_NKD1-BRD7_NKD1_chr16_50583466_ENST00000268459_BRD7_chr16_50388833_ENST00000394688_length(amino acids)=659AA_BP=10
MLREEESQGRRQARGPGAWLRDAPGRRSPSMGKLHSKPAAVCKRRESPEGDSFAVSAAWARKGIEEWIGRQRCPGGVSGPRQLRLAGTIG
RSTREDKKKRDRDRVENEAEKDLQCHAPVRLDLPPEKPLTSSLAKQEEVEQTPLQEALNQLMRQLQRKDPSAFFSFPVTDFIAPGYSMII
KHPMDFSTMKEKIKNNDYQSIEELKDNFKLMCTNAMIYNKPETIYYKAAKKLLHSGMKILSQERIQSLKQSIDFMADLQKTRKQKDGTDT
SQSGEDGGCWQREREDSGDAEAHAFKSPSKENKKKDKDMLEDKFKSNNLEREQEQLDRIVKESGGKLTRRLVNSQCEFERRKPDGTTTLG
LLHPVDPIVGEPGYCPVRLGMTTGRLQSGVNTLQGFKEDKRNKVTPVLYLNYGPYSSYAPHYDSTFANISKDDSDLIYSTYGEDSDLPSD
FSIHEFLATCQDYPYVMADSLLDVLTKGGHSRTLQEMEMSLPEDEGHTRTLDTAKEMEITEVEPPGRLDSSTQDRLIALKAVTNFGVPVE
VFDSEEAEIFQKKLDETTRLLRELQEAQNERLSTRPPPNMICLLGPSYREMHLAEQVTNNLKELAQQVTPGDIVSTYGVRKAMGISIPSP

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

>59266_59266_2_NKD1-BRD7_NKD1_chr16_50583466_ENST00000268459_BRD7_chr16_50388833_ENST00000394689_length(amino acids)=660AA_BP=10
MLREEESQGRRQARGPGAWLRDAPGRRSPSMGKLHSKPAAVCKRRESPEGDSFAVSAAWARKGIEEWIGRQRCPGGVSGPRQLRLAGTIG
RSTREDKKKRDRDRVENEAEKDLQCHAPVRLDLPPEKPLTSSLAKQEEVEQTPLQEALNQLMRQLQRKDPSAFFSFPVTDFIAPGYSMII
KHPMDFSTMKEKIKNNDYQSIEELKDNFKLMCTNAMIYNKPETIYYKAAKKLLHSGMKILSQERIQSLKQSIDFMADLQKTRKQKDGTDT
SQSGEDGGCWQREREDSGDAEAHAFKSPSKENKKKDKDMLEDKFKSNNLEREQEQLDRIVKESGGKLTRRLVNSQCEFERRKPDGTTTLG
LLHPVDPIVGEPGYCPVRLGMTTGRLQSGVNTLQGFKEDKRNKVTPVLYLNYGPYSSYAPHYDSTFANISKDDSDLIYSTYGEDSDLPSD
FSIHEFLATCQDYPYVMADSLLDVLTKGGHSRTLQEMEMSLPEDEGHTRTLDTAKEMEQITEVEPPGRLDSSTQDRLIALKAVTNFGVPV
EVFDSEEAEIFQKKLDETTRLLRELQEAQNERLSTRPPPNMICLLGPSYREMHLAEQVTNNLKELAQQVTPGDIVSTYGVRKAMGISIPS

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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/chr16:50583466/chr16:50388833)
- 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
NKD1

Q969G9

BRD7

Q9NPI1

FUNCTION: Cell autonomous antagonist of the canonical Wnt signaling pathway. May activate a second Wnt signaling pathway that controls planar cell polarity. {ECO:0000269|PubMed:11752446, ECO:0000269|PubMed:15687260, ECO:0000269|PubMed:16567647}.FUNCTION: Acts both as coactivator and as corepressor. May play a role in chromatin remodeling. Activator of the Wnt signaling pathway in a DVL1-dependent manner by negatively regulating the GSK3B phosphotransferase activity. Induces dephosphorylation of GSK3B at 'Tyr-216'. Down-regulates TRIM24-mediated activation of transcriptional activation by AR (By similarity). Transcriptional corepressor that down-regulates the expression of target genes. Binds to target promoters, leading to increased histone H3 acetylation at 'Lys-9' (H3K9ac). Binds to the ESR1 promoter. Recruits BRCA1 and POU2F1 to the ESR1 promoter. Coactivator for TP53-mediated activation of transcription of a set of target genes. Required for TP53-mediated cell-cycle arrest in response to oncogene activation. Promotes acetylation of TP53 at 'Lys-382', and thereby promotes efficient recruitment of TP53 to target promoters. Inhibits cell cycle progression from G1 to S phase. {ECO:0000250, ECO:0000269|PubMed:16265664, ECO:0000269|PubMed:16475162, ECO:0000269|PubMed:20215511, ECO:0000269|PubMed:20228809, ECO:0000269|PubMed:20660729}.

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
TgeneBRD7chr16:50583466chr16:50388833ENST00000394688117536_56786.0652.0Coiled coilOntology_term=ECO:0000255
TgeneBRD7chr16:50583466chr16:50388833ENST00000394689117536_56786.0653.0Coiled coilOntology_term=ECO:0000255
TgeneBRD7chr16:50583466chr16:50388833ENST00000394688117148_21886.0652.0DomainBromo
TgeneBRD7chr16:50583466chr16:50388833ENST00000394689117148_21886.0653.0DomainBromo

- Not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneNKD1chr16:50583466chr16:50388833ENST00000268459+310144_15564.0471.0Calcium bindingOntology_term=ECO:0000255
HgeneNKD1chr16:50583466chr16:50388833ENST00000268459+310452_46664.0471.0Compositional biasNote=His-rich
HgeneNKD1chr16:50583466chr16:50388833ENST00000268459+310131_16664.0471.0DomainEF-hand
TgeneBRD7chr16:50583466chr16:50388833ENST000003946881173_9186.0652.0Compositional biasNote=Lys-rich
TgeneBRD7chr16:50583466chr16:50388833ENST000003946891173_9186.0653.0Compositional biasNote=Lys-rich
TgeneBRD7chr16:50583466chr16:50388833ENST0000039468811765_9686.0652.0MotifNuclear localization signal
TgeneBRD7chr16:50583466chr16:50388833ENST0000039468911765_9686.0653.0MotifNuclear localization signal


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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
NKD1
BRD7


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
HgeneNKD1chr16:50583466chr16:50388833ENST00000268459+310125_19064.0471.0DVL1%2C DVL2 and DVL3


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Related Drugs to NKD1-BRD7


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 NKD1-BRD7


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