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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: 18526

FusionGeneSummary for KHDC1_NLK

check button Fusion gene summary
Fusion gene informationFusion gene name: KHDC1_NLK
Fusion gene ID: 18526
HgeneTgene
Gene symbol

KHDC1

NLK

Gene ID

80759

51701

Gene nameKH domain containing 1nemo like kinase
SynonymsC6orf147|C6orf148|Em:AC019205.8|NDG1|bA257K9.4-
Cytomap

6q13

17q11.2

Type of geneprotein-codingprotein-coding
DescriptionKH homology domain-containing protein 1KH homology domain containing 1serine/threonine-protein kinase NLK
Modification date2018032920180523
UniProtAcc

Q4VXA5

Q9UBE8

Ensembl transtripts involved in fusion geneENST00000257765, ENST00000370384, 
ENST00000484801, 
ENST00000407008, 
ENST00000583517, ENST00000582037, 
Fusion gene scores* DoF score3 X 2 X 2=128 X 7 X 4=224
# samples 311
** MAII scorelog2(3/12*10)=1.32192809488736
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
log2(11/224*10)=-1.02599520853294
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: KHDC1 [Title/Abstract] AND NLK [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
TgeneNLK

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-A1-A0SO-01AKHDC1chr6

74001721

-NLKchr17

26449629

+
* 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
intron-3CDSENST00000257765ENST00000407008KHDC1chr6

74001721

-NLKchr17

26449629

+
intron-intronENST00000257765ENST00000583517KHDC1chr6

74001721

-NLKchr17

26449629

+
intron-intronENST00000257765ENST00000582037KHDC1chr6

74001721

-NLKchr17

26449629

+
In-frameENST00000370384ENST00000407008KHDC1chr6

74001721

-NLKchr17

26449629

+
5CDS-intronENST00000370384ENST00000583517KHDC1chr6

74001721

-NLKchr17

26449629

+
5CDS-intronENST00000370384ENST00000582037KHDC1chr6

74001721

-NLKchr17

26449629

+
5UTR-3CDSENST00000484801ENST00000407008KHDC1chr6

74001721

-NLKchr17

26449629

+
5UTR-intronENST00000484801ENST00000583517KHDC1chr6

74001721

-NLKchr17

26449629

+
5UTR-intronENST00000484801ENST00000582037KHDC1chr6

74001721

-NLKchr17

26449629

+

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FusionProtFeatures for KHDC1_NLK


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
KHDC1

Q4VXA5

NLK

Q9UBE8

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}.

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 KHDC1_NLK


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.
>In-frame_KHDC1_ENST00000370384_chr6_74001721_-_NLK_ENST00000407008_chr17_26449629_+_444aa
MLSAFQRLFRVLFVIETVSEYGVLIFITGWPFLQTLAMLLIGTVSFHLWIRRNRERNSRSGKTRCRSKRSVTDPRDGKRVALKKMPNVFQ
NLVSCKRVFRELKMLCFFKHDNVLSALDILQPPHIDTFEEITVVTELMQSDLHKIIVSPQPLSSDHVKVFLTQILRGLKTLHSAGILHRD
IKPGNLLVNSNCVLKICDFGLARVEELDESRHMTQEVVTQTTRAPEILMGSRHYSNAIDIWSVGCIFAELLGRRILFQAQSPIQQLDLIT
DLLGTPSLEAMRTACEGAKAHILRGPHKQPSLPVLTTLSSQATHEAVHLLCRMLVFDPSKRISAKDALAHPYLDEGRLRTHTCMCKCCFS


* Fusion transcript sequences (only coding sequence (CDS) region).
>In-frame_KHDC1_ENST00000370384_chr6_74001721_-_NLK_ENST00000407008_chr17_26449629_+_1332nt
ATGCTGTCGGCCTTCCAGAGGCTGTTCCGAGTCTTATTTGTGATTGAAACAGTCTCAGAATACGGAGTCCTGATCTTCATTTATGGATGG
CCCTTTCTCCAGACCCTTGCGATGCTCCTGATCGGGACAGTGTCTTTCCACCTTTGGATCCGCAGAAATCGAGAGAGAAACTCAAGGAGC
GGAAAGACTAGATGCCGATCCAAAAGGTCAGTAACAGATCCAAGAGATGGAAAGAGAGTAGCGCTCAAAAAGATGCCCAACGTCTTCCAG
AATCTGGTCTCTTGCAAAAGGGTCTTCCGGGAATTGAAGATGTTGTGTTTTTTTAAGCATGATAATGTACTCTCTGCCCTTGACATACTC
CAACCTCCACACATTGACTATTTTGAAGAAATATATGTTGTCACAGAATTGATGCAGAGTGACCTACATAAAATTATCGTCTCTCCTCAA
CCACTCAGCTCAGATCATGTCAAAGTTTTTCTTTATCAGATTTTGCGAGGTTTGAAATATCTCCATTCAGCTGGCATTTTACATCGAGAC
ATTAAGCCAGGGAATCTCCTTGTGAACAGCAACTGTGTTCTAAAGATTTGTGATTTTGGATTGGCCAGAGTGGAAGAATTAGATGAATCC
CGTCATATGACTCAGGAAGTTGTTACTCAGTATTATCGGGCTCCAGAAATCCTGATGGGCAGCCGTCATTACAGCAATGCTATTGACATC
TGGTCTGTGGGATGTATCTTTGCAGAACTACTAGGACGAAGAATATTGTTTCAGGCACAGAGTCCCATTCAGCAGTTGGATTTGATCACG
GATCTGTTGGGCACACCATCACTGGAAGCAATGAGGACAGCTTGTGAAGGCGCTAAGGCACATATACTCAGGGGTCCTCATAAACAGCCA
TCTCTTCCTGTACTCTATACCCTGTCTAGCCAGGCTACACATGAAGCTGTTCATCTCCTTTGCAGGATGTTGGTCTTTGATCCATCCAAA
AGAATATCCGCTAAGGATGCCTTAGCCCACCCCTACCTAGATGAAGGGCGACTACGATATCACACATGTATGTGTAAATGTTGCTTTTCC
ACCTCCACTGGAAGAGTTTATACCAGTGACTTTGAGCCTGTCACCAATCCCAAATTTGATGACACTTTCGAGAAGAACCTCAGTTCTGTC
CGACAGGTTAAAGAAATTATTCATCAGTTCATTTTGGAACAGCAGAAAGGAAACAGAGTGCCTCTCTGCATCAACCCTCAGTCTGCTGCT


* Fusion transcript sequences (Full-length transcript).
>In-frame_KHDC1_ENST00000370384_chr6_74001721_-_NLK_ENST00000407008_chr17_26449629_+_3578nt
GGCGGAAGAGGCGGGTCCAGGGCGGTGTAATTAAGGCGCGGAGCCCAGACCCTCCTGCTACAGTGCCTCGGGCTTTCCTGGAGGCGGGCG
GCGGGATGCTGCTCCGTTCTCCGGGTCCTCTCCTCCGGTTCTTGTCGTTTGGTCACGCCCTCAGTTCAGTCGGTTATTGGAAAACGATCA
AGGCCCAAAGATGGTTTACGTGGCGTTGTGGATGTTATCACCGTTGTTTGGTGACCGAGCCTGGAGCTTGAGCCCTGGGACGTCTTGCCA
GCCGCATGTGGTCCCGTGCCCACTTCTCGCGGTGGCGCGTTAATCCACCTAGACTGTGCATTGGTCCAGTCTGGGTTGACCCCGACCCGA
AGTGGCCCTTTCCTTCGCGTCCTGAACTTCGCTTCTCCGTCGGTGTCTGGTCTCTTCCCGCCGGCGGGCTCTGCGGTGGCGGGAGGAGCT
GTACTACTCGTGCCTTAGCGCACCCTTACTTTCCCAGGCCAGAAACGCGAAATGCTGTCGGCCTTCCAGAGGCTGTTCCGAGTCTTATTT
GTGATTGAAACAGTCTCAGAATACGGAGTCCTGATCTTCATTTATGGATGGCCCTTTCTCCAGACCCTTGCGATGCTCCTGATCGGGACA
GTGTCTTTCCACCTTTGGATCCGCAGAAATCGAGAGAGAAACTCAAGGAGCGGAAAGACTAGATGCCGATCCAAAAGGTCAGTAACAGAT
CCAAGAGATGGAAAGAGAGTAGCGCTCAAAAAGATGCCCAACGTCTTCCAGAATCTGGTCTCTTGCAAAAGGGTCTTCCGGGAATTGAAG
ATGTTGTGTTTTTTTAAGCATGATAATGTACTCTCTGCCCTTGACATACTCCAACCTCCACACATTGACTATTTTGAAGAAATATATGTT
GTCACAGAATTGATGCAGAGTGACCTACATAAAATTATCGTCTCTCCTCAACCACTCAGCTCAGATCATGTCAAAGTTTTTCTTTATCAG
ATTTTGCGAGGTTTGAAATATCTCCATTCAGCTGGCATTTTACATCGAGACATTAAGCCAGGGAATCTCCTTGTGAACAGCAACTGTGTT
CTAAAGATTTGTGATTTTGGATTGGCCAGAGTGGAAGAATTAGATGAATCCCGTCATATGACTCAGGAAGTTGTTACTCAGTATTATCGG
GCTCCAGAAATCCTGATGGGCAGCCGTCATTACAGCAATGCTATTGACATCTGGTCTGTGGGATGTATCTTTGCAGAACTACTAGGACGA
AGAATATTGTTTCAGGCACAGAGTCCCATTCAGCAGTTGGATTTGATCACGGATCTGTTGGGCACACCATCACTGGAAGCAATGAGGACA
GCTTGTGAAGGCGCTAAGGCACATATACTCAGGGGTCCTCATAAACAGCCATCTCTTCCTGTACTCTATACCCTGTCTAGCCAGGCTACA
CATGAAGCTGTTCATCTCCTTTGCAGGATGTTGGTCTTTGATCCATCCAAAAGAATATCCGCTAAGGATGCCTTAGCCCACCCCTACCTA
GATGAAGGGCGACTACGATATCACACATGTATGTGTAAATGTTGCTTTTCCACCTCCACTGGAAGAGTTTATACCAGTGACTTTGAGCCT
GTCACCAATCCCAAATTTGATGACACTTTCGAGAAGAACCTCAGTTCTGTCCGACAGGTTAAAGAAATTATTCATCAGTTCATTTTGGAA
CAGCAGAAAGGAAACAGAGTGCCTCTCTGCATCAACCCTCAGTCTGCTGCTTTTAAGAGCTTTATTAGTTCCACTGTTGCTCAGCCATCT
GAGATGCCCCCATCTCCTCTGGTGTGGGAGTGATGGTGGAAGATAATGTACTACTGAAGATGTAATGTAGCTTTCCACTGGAGTCTGGGA
TTTGCAATTCTGGAGGTTAATCATGCTTGTACTGTAATTTTACTAATGAAGTTTTAAATTAACAACCACTACTTGTATGATATGAATAAT
ATTTAGAAATGTTACTAGACTTTTAATCTTGTAAAGTGGTTGTGCTTTTAGAAGAAAAATATTTTACCCAGAGTTGCACATGTTTTATGA
ATTTAGTGCAGCTGTTATGGCTCACCTCAGAACAAAAGAGAATTGAACCAAATTTGGGAGTTTGGGGTTTTATGTTTTGTTTTTCTTTTC
TAAAATGAAGTGAGATTGTTCACACACACACACACACACACACACACACACAAACACAAAGGACAGTCATACATTTTGATATTTGAGCCA
TTCCTAAAGATTTGGGGTTTTCTAAAACTAAAGAATCTAGGAACCTTGCCTGCGACCAATCATGGAGCCACGTGAGCTGATCGTGGCTGC
ACCTGGGGGGAGGGTAGGGAGGAGGGGCATGCCACCTAATGATCAAGCCCTATAATTAGCTTCTCATTAGAGCCGTGATGGTGATGTGTG
CTGTCTAAAATCCAATGTTGTGGGTAGAGAGAATGAGTTTGTGACTAGGAGAGACTAAACTTTTGTTTTCCTTACCCAGTATAAATATAT
ATATATATATTTAATCTATTTTTATTAGAAGTTTTTCTGCTCTTTCTTACATAAAAGAACCCCAAGCATGCATCTTTCATGTGTGTAAAT
AATTCATTTCTGGGCTAATTTCAAAAGAATCCCAATATTGCTGTATAGAAAGAGAACTAGCTTGCACATTTTAGGTCTGTGAAATTTTGT
GAGACTTTTCCTGCACTGGACAGTAAAAAAATAATAAAAGACAAAAACAAATTTAAAAAAAAATTTAAGCCACAAAAAAAGGCACATAGG
GAATTATGTCAAATGTGTTTGTGTCCTTAGGCAAAGCTGTGGGAGTCTTGAAATGTCACAGTAGTAAATAACTTATTACTTTTTGACAAG
TTCTTTTTTTCTGTTGGAACACTGAATTCTTCTGTGCATATGTACATATGAATACAAATCGAAGGCCTCTACCTCCTGGAGTTATACAAC
TTGGCTTGTTTACCTCCACATGCTGATGATGACTATTTTTTTTTTTTGAGTTCAGTGTGGAGACTTGAAACTTGAATGTCCCTTCCAACT
TTTATATTAAAAATAAAAAGACAAGAAAATTGAAGATCATTTTTCACCTGTACAAGGAATACTAATGGATCGTCTTAAAATTGGTCTAGG
AAAAAACCTTGGTGTGTGTTATGGACAATTAACTGTTAAAGTTATTGTAAGTTATCTGTATTTAGCAGAGTATTTTCAACTTGAGTGATC
TGAGCTGAATTTGAAGACTATTAATAAGTTATGTTTGGAAGTTTTAACTTCAATGAAGTAATTATTTGCTGTGAAAGAAACAAACATTGA
ATTACTAAACAAAGATGGTGCAATATCTTTGTTTTTTTTTTATGAGGCTCCTGAGAATCAACCCAACTGAAGCATTTCAATTCACTTGAA
TGAGAAACGTGTTTAGTATCAAAAGAGCCCAAGAAGACACTGGTGTGAAAGGTACAATCTCAGAGGTTGGTCAATTACCGTGGCACACTT


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FusionGenePPI for KHDC1_NLK


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
KHDC1NLKLEF1, 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, STAT5A


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 KHDC1_NLK


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 KHDC1_NLK


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