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Center for Computational Systems Medicine
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FusionGeneSummary

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FusionProtFeature

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FusionGeneSequence

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FusionGenePPI

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RelatedDrugs

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RelatedDiseases

Fusion gene ID: 24470

FusionGeneSummary for NLK_VBP1

check button Fusion gene summary
Fusion gene informationFusion gene name: NLK_VBP1
Fusion gene ID: 24470
HgeneTgene
Gene symbol

NLK

VBP1

Gene ID

51701

7411

Gene namenemo like kinaseVHL binding protein 1
Synonyms-HIBBJ46|PFD3|PFDN3|VBP-1
Cytomap

17q11.2

Xq28

Type of geneprotein-codingprotein-coding
Descriptionserine/threonine-protein kinase NLKprefoldin subunit 3von Hippel-Lindau binding protein 1
Modification date2018052320180523
UniProtAcc

Q9UBE8

P61758

Ensembl transtripts involved in fusion geneENST00000407008, ENST00000583517, 
ENST00000582037, 
ENST00000535916, 
ENST00000286428, ENST00000459836, 
Fusion gene scores* DoF score13 X 7 X 8=7284 X 4 X 4=64
# samples 154
** MAII scorelog2(15/728*10)=-2.27897594970282
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(4/64*10)=-0.678071905112638
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: NLK [Title/Abstract] AND VBP1 [Title/Abstract] AND fusion [Title/Abstract]

Functional or gene categories assigned by FusionGDB annotation
* 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
HgeneNLK

GO:0050821

protein stabilization

25512613


check button Fusion gene information from three resources
(ChiTars (NAR, 2018), tumorfusions (NAR, 2018), Gao et al. (Cell, 2018))
* 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.
Data typeSourceCancer typeSampleHgeneHchrHbpHstrandTgeneTchrTbpTstrand
TCGALDBRCATCGA-EW-A1OZ-01ANLKchr17

26370357

+VBP1chrX

154464510

+
* LD: Li Ding group's fusion gene list
  RV: Roel Verhaak group's fusion gene list
  ChiTaRs fusion database

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
Frame-shiftENST00000407008ENST00000535916NLKchr17

26370357

+VBP1chrX

154464510

+
Frame-shiftENST00000407008ENST00000286428NLKchr17

26370357

+VBP1chrX

154464510

+
5CDS-3UTRENST00000407008ENST00000459836NLKchr17

26370357

+VBP1chrX

154464510

+
3UTR-3CDSENST00000583517ENST00000535916NLKchr17

26370357

+VBP1chrX

154464510

+
3UTR-3CDSENST00000583517ENST00000286428NLKchr17

26370357

+VBP1chrX

154464510

+
3UTR-3UTRENST00000583517ENST00000459836NLKchr17

26370357

+VBP1chrX

154464510

+
Frame-shiftENST00000582037ENST00000535916NLKchr17

26370357

+VBP1chrX

154464510

+
Frame-shiftENST00000582037ENST00000286428NLKchr17

26370357

+VBP1chrX

154464510

+
5CDS-3UTRENST00000582037ENST00000459836NLKchr17

26370357

+VBP1chrX

154464510

+

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FusionProtFeatures for NLK_VBP1


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

Q9UBE8

VBP1

P61758

Serine/threonine-protein kinase that regulates a numberof transcription factors with key roles in cell fatedetermination. Positive effector of the non-canonical Wntsignaling pathway, acting downstream of WNT5A, MAP3K7/TAK1 andHIPK2. Activation of this pathway causes binding to andphosphorylation of the histone methyltransferase SETDB1. The NLK-SETDB1 complex subsequently interacts with PPARG, leading tomethylation of PPARG target promoters at histone H3K9 andtranscriptional silencing. The resulting loss of PPARG target genetranscription inhibits adipogenesis and promotesosteoblastogenesis in mesenchymal stem cells (MSCs). Negativeregulator of the canonical Wnt/beta-catenin signaling pathway.Binds to and phosphorylates TCF7L2/TCF4 and LEF1, promoting thedissociation of the TCF7L2/LEF1/beta-catenin complex from DNA, aswell as the ubiquitination and subsequent proteolysis of LEF1.Together these effects inhibit the transcriptional activation ofcanonical Wnt/beta-catenin target genes. Negative regulator of theNotch signaling pathway. Binds to and phosphorylates NOTCH1,thereby preventing the formation of a transcriptionally activeternary complex of NOTCH1, RBPJ/RBPSUH and MAML1. Negativeregulator of the MYB family of transcription factors.Phosphorylation of MYB leads to its subsequent proteolysis whilephosphorylation of MYBL1 and MYBL2 inhibits their interaction withthe coactivator CREBBP. Other transcription factors may also beinhibited by direct phosphorylation of CREBBP itself. Actsdownstream of IL6 and MAP3K7/TAK1 to phosphorylate STAT3, which isin turn required for activation of NLK by MAP3K7/TAK1. Upon IL1Bstimulus, cooperates with ATF5 to activate the transactivationactivity of C/EBP subfamily members. Phosphorylates ATF5 but alsostabilizes ATF5 protein levels in a kinase-independent manner(PubMed:25512613). {ECO:0000250|UniProtKB:O54949,ECO:0000269|PubMed:12482967, ECO:0000269|PubMed:14960582,ECO:0000269|PubMed:15004007, ECO:0000269|PubMed:15764709,ECO:0000269|PubMed:17952062, ECO:0000269|PubMed:20061393,ECO:0000269|PubMed:20118921, ECO:0000269|PubMed:20874444,ECO:0000269|PubMed:21454679, ECO:0000269|PubMed:25512613}. Binds specifically to cytosolic chaperonin (c-CPN) andtransfers target proteins to it. Binds to nascent polypeptidechain and promotes folding in an environment in which there aremany competing pathways for nonnative proteins.{ECO:0000269|PubMed:9630229}.

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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FusionGeneSequence for NLK_VBP1


check button For in-frame fusion transcripts, we provide the fusion transcript sequences and fusion amino acid sequences.
(nt: nucleotides, aa: amino acids)

* Fusion amino acid sequences.

* Fusion transcript sequences (only coding sequence (CDS) region).

* Fusion transcript sequences (Full-length transcript).

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FusionGenePPI for NLK_VBP1


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
NLKLEF1, CTNNB1, TCF7L2, FBXW4, FBXW5, SKP2, CUL1, MYB, HIPK2, MYBL1, MYBL2, CREBBP, FOXO4, FOXO1, FOXO3, ASGR1, ELAVL1, USP4, ATXN1, TAB2, MAP3K7, NLK, SMAD4, RCHY1, SDR16C5, KPNB1, RANBP2, C2orf44, FAM222B, FAM222A, RNF219, TNKS1BP1, SKI, RANGAP1, TLE3, CEP97, PASK, CNOT2, CCP110, UBAP2L, TRPS1, CNOT11, BACH1, CNOT3, SHANK2, PKM, TP53, MDM2, GRN, KRTAP5-9, ZHX3, QRICH1, KRTAP4-2, KRTAP10-3, KRTAP5-6, STAT5AVBP1VHL, PFDN2, MSH4, PAN2, PRPF4, PPP2CB, TUBA3E, XRCC6, PIK3R3, FBXW8, MKNK2, PFDN4, PFDN5, PFDN6, KARS, EPRS, GARS, NUBP2, NAB2, IARS, DARS, CLNS1A, QARS, TRMT1, PSMC2, METTL21B, HDAC1, VCP, MAPK7, SSB, TNPO1, UBQLN2, ANP32A, ARPC1B, ARPC4, PPP3CA, RABGGTA, TTLL12, FKBP6, PNMA1, UBL7, DCAF5, PEX7, CBS, FLNA, TXNDC12, DCUN1D1, FLNB, GOLPH3, PFDN1, RNASEH2B, SEC24B, XPNPEP1, BTRC, EWSR1, POC1A, POC1B, ANAPC15, PTPN21, DUSP16, DUSP8, DUSP9, MTM1, PHKB, COPRS, CCDC101, SUPT6H, PDRG1, STK26, GSPT1, GNB2


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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RelatedDrugs for NLK_VBP1


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.0 2018-04-02)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

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RelatedDiseases for NLK_VBP1


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