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KNL1 (cancer susceptibility candidate 5)

Written2016-10Masato Takimoto, Jean-Loup Huret
Institute for Genetic Medicine, Hokkaido University, Sapporo, Hokkaido, Japan. (MT); Genetics, Dept Medical Information, University of Poitiers, CHU Poitiers Hospital, F-86021 Poitiers, France. (JLH)
This article is an update of :
2012-06Masato Takimoto
Institute for Genetic Medicine, Hokkaido University, Sapporo, Hokkaido, Japan
2006-09Masato Takimoto
Institute for Genetic Medicine, Hokkaido University, Sapporo, Hokkaido, Japan
2000-03Jean-Loup Huret, Christiane Charrin
Genetics, Dept Medical Information, University of Poitiers, CHU Poitiers Hospital, F-86021 Poitiers, France (JLH); Service d'Hematologie, Hopital Edouard Herriot, Lyon, France (CC).

Abstract Review on KNL1, with data on DNA, on the protein encoded, and where the gene is implicated.

Keywords KNL1

(Note : for Links provided by Atlas : click)


Alias (NCBI)CT29
HGNC (Hugo) KNL1
HGNC Alias symbD40
HGNC Alias namecancer/testis antigen 29
 kinetochore null 1 homolog (C. elegans)
 blinkin, bub-linking kinetochore protein
 protein phosphatase 1, regulatory subunit 55
HGNC Previous nameMCPH4
HGNC Previous namemicrocephaly, primary autosomal recessive 4
 cancer susceptibility candidate 5
LocusID (NCBI) 57082
Atlas_Id 318
Location 15q15.1  [Link to chromosome band 15q15]
Location_base_pair Starts at 40594249 and ends at 40664341 bp from pter ( according to GRCh38/hg38-Dec_2013)  [Mapping KNL1.png]
Fusion genes
(updated 2017)
Data from Atlas, Mitelman, Cosmic Fusion, Fusion Cancer, TCGA fusion databases with official HUGO symbols (see references in chromosomal bands)
KMT2A (11q23.3)::KNL1 (15q15.1)KNL1 (15q15.1)::ADAMTS9-AS2 (3p14.1)KNL1 (15q15.1)::KMT2A (11q23.3)


Note Whole genomic size is about 70 kbp, but consists of 27 exons.
Transcription KNL1 mRNA expression is dominant in normal human testis and slight expression are observed in other organs, such as placenta. Analysis on cancer cell lines, such as HeLa, gave single band with 8.5 kb. There is another alternative splicing site at the 5' side of this gene that generates a short exon with 78 bp in cDNA. There are potential other alternative splicing at cancer cell lines.
Analysis on testis mRNA shows two bands with size of approximately 6 and 8,5 kb which are probably derived from the two isoforms.


  Figure 1. Domain structure of KNL1 protein. Brown arrows indicate protein interactions, and blue arrows and line with T-shape indicate phosphorylation and dephosphorylation, respectively. MT :microtubules. KT : kinetochore.
Description Encodes 1833 amino acids and 2342 amino acids.
The KLN1 protein contains: conserved motifs, which are the following: a (S/G)ILK motif (aa 25-28), a RRVSF motif (aa 57-61), and, for BUB3 recognition, MELT repeats (aa 140-161, 308-329, 474-494, 562-582, 750-769, 859-882, 902-924, 940-962, 1025-1044, 1073-1096, 1114-1136, 1152-1174). The Bubs recognition KI motifs KI(D/N)XXXF(L/I)XXLK, are KIDTTSFLANLK (aa 202-213) for BUB1, and KIDFNDFIKRLK (aa 238-249) for BUB1B: (BUBR1); a nuclear localization signal (aa 1789-1803); a coiled coil region (aa 1942-2133) and the ZWINT (Zwint-1) binding region (aa 1834 or 19811 for a smaller region -2108); and RWD repeats (aa 2109- 2353) With the NSL1 (hMis14)-binding region (aa 2109-2316), according to Kiyomitsu et al., 2011, VEGA checking, and SwissProt.
Expression KNL1 protein expressions with molecular weight of approximately 250 kDa and 300 kDa are observed in human testicular germ cells and cancer cell lines.
Localisation In germ cell of testis, significant high expressions of KNL1 protein are observed in nucleus of spermatocytes and slightly in spermatogonia. It is noteworthy that round spermatids express significantly high KNL1 protein in their pre-acrosome. As KNL1 protein has no hydrophobic signal peptide in its amino terminus, it probably localizes outer surface of pre-acrosome membrane of spermatids inside of the cells..
In mitosis KNL1 protein is localized in kinetochore in a human cancer cell line.
Function KNL1 is a large of kinetochore protein, constituting KMN (KNL1/ MIS12 complex/ NDC80 complex) network. KMN network is the central hub of outer kinetochore, not only connecting mitotic chromosomes and spindles but also coordinating microtubule-binding, chromosome congression and spindle assembly checkpoint (SAC) signaling. There are two microtubule binding activity in KMN network, one in NDC80 and the other in KNL1. KNL1 protein binds directly microtubule through its far N-terminal region, consisting of 68 amino acids, in vitro, and indirectly through the interactions with MIS12 and NDC80 complexes at its C-terminus. KNL1 depletion affects metaphase chromosome congression. In C. elegans,
The depletion preclude metaphase chromosomal congression, while in yeast, Drosophila and human cells, the depletions show partial alignment phenotypes, in which some chromosomes congress to the equator but many chromosomes remain stranded near the spindle poles. In the N-terminus of KNL1 protein, AURKB (Aurora kinase B) phosphorylates SILK and RVSF motifs, and then disrupts the interaction between KNL1 and protein phosphatase I (PP1), which also binds the motifs. KNL1 augments Aurora B kinase activity that phosphorylates outer kinetochore protein, such as NDC80, resulting in reduction its microtubule-binding activity. Protein phosphatase 2A ( PP2A) is recruited by BUB1B (BubR1), one of SAC protein. Both PP1 and PPA2 are suggested to counteract Aurora B kinase activity. Especially, PP1 was shown to stabilize microtubule attachments to kinetochores probably through KNL1, while Aurora B kinase destabilizes microtubule-binding by NDC80 phosphorylation as described. The destabilized binding of KNL1 to microtubules is presumably important for correcting and eliminating erroneous kinetochore-microtubule attachment during SAC.
It is suggested that the bindings with microtubule and with PP1 also play roles in SAC silencing. Although their binding sites are in close proximity, one of their bindings do not affect the other, and they contribute independently to the silencing of SAC. Two KI motifs, KI1 and KI2, localized in the N-terminus, bind SAC protein, BUB1 and BUB1B, respectively, through tetratricopeptide repeats (TPRs) of the proteins, resulting into folding the motifs into short alpha-helices. Although BUB1 fragment with mutation in KI-binding domain was not able to bind to KNL1 in vitro, BUB1 and BUB1B mutants with KI-binding sites were able to attach to kinetochore. Mutations in the BUB3-binding domain (BUB3-BD) in BUB1 and BUB1B prevent kinetochore localization of the SAC protein. BUB1 fragment consisting only of N-terminus with TPRs does not localize to kinetochore and longer fragments that accommodate BUB3-BD did. Those results suggest that BUB3-BD of BUB1 and BUB1B, rather than TPRs, is critical for their recruitment to kinetochore and that the interaction between TPRs of Bub proteins and KI-motif of KNL1 might play a subsidiary role in the localization of BUB1 and BUB1B to kinetochore. In response to SAC signal, the first step of this response is phosphorylation of MELT motifs of KNL1, located in the N-terminal and central region, by Mps1 kinase, and then the phosphorylated MELT motifs bind BUB3/BUB1complex, mediating SAC signaling. KNL1- BUB3-BUB1(KBB) complex binds MXD1 (MAD1)/ MAD2L1 (MAD2) complex, and then, together with MAD1 phosphorylation by Msp1, the binding leads to CDC20/MAD2 formation, an essential part of Mitotic Checkpoint Complex (MCC) that inhibits Anaphase Promoting Complex/Cyclosome (APC/C).
Recently, it suggested that there are two pathways for recruiting MAD1-MAD2 that results in SAC activation. One is the pathway through KBB, as described above, the other is KNTC1 (ROD)-RW10- ZWILCH, (RZZ) complex, which interacts with KNL1 through ZWINT (Zwint-1 protein). The former is required for SAC activation when kinetochores are misaligned but is not essential when kinetochores are unattached from microtubules. The latter binds SPDL1 (Spindly protein) and MAD1-MAD2, and causes the anaphase-onset delay in response to unattached kinetochore independently of the former.
It was suggested that the binding of KNL1 with microtubules and with PP1 contribute to silencing of SAC, in which motor protein dynein, moving along on microtubules, is suggested to work to strip MAD1-MAD2. The C-terminal region of KNL1 interacts with MIS12 and Zwint-1 protein, through RWD motif and coiled-coiled region, respectively. The binding with the former plays role in connecting inner kinetochore with KNL1 and the latter mediates the interaction of KNL1 with RZZ complex which works in SAC regulation as described above.

Implicated in

Note KNL1 expression was observed in many human cancer cell lines and primary cancers derived from different organs and tissues. In one study, KNL1 mRNA expression was detected in all the cancer cell lines examined and positive in 31 out of 103 primary human cancers (30%). As KNL1 is overexpressed in normal testis, KNL1 is a member of Cancer/Testis gene family. Among the primary cancers examined lung cancer showed the highest positive rate, more than 40%, and its clincopathological characteristics are significantly correlated with KNL1 mRNA expression as described below.
Entity Leukemia
Note A small subset of leukemia with a t(11;15)(q23;q14) has been described for long and has often be referred as: t(11;15)(q23;q15) MLL/AF15q14. KMT2A, (previous symbol: mixed leukemia gene (MLL)) is translocated with KNL1 (previous symbol CASC5, originally described as AF15q14), which makes research of published cases often arduous.
  • t(11;15)(q23;q15) and/or KMT2A/KNL1
    Data on 16 cases with a t(11;15)(q23;q14-15), according to (Yang et al., 2014) are the following: there was 2 of myelodysplastic syndrome (MDS) cases, 10 acute myeloid leukemia (AML) cases (2 M1, 4 M2, 3 M4, and 1 NOS), and 4 acute lymphoblastic leukemia (ALL) cases. Mean age of the patients was 20.6 years (range 1-54); there were 11 males and 5 females. Abnormalities of chromosome 3 were seen in 10 out of 16 cases. Out of 8 patients for whom clinical data were available, only 3 are in complete remission, whereas 5 patients died with a mean survival period of 10.4 months.

    Of 7 cases with a t(11;15)(q23;q15) and KMT2A/KNL1 hybrid gene and fusion protein ((Chinwalla et al., 2003; Kuefer et al., 2003; Meyer et al., 2006; Yang et al., 2014). Diagnosis was: therapy related MDS (t-MDS) in 2 cases, AML in 4 cases (1 M2, 2 AML-M4, 1 AML-NOS), and 1 de novo T-ALL. Sex ratio was 5M:1F; There was 3 children and 4 adult patients. Of three cases with data on survival, patients died at: 8 mths, 8 mths, and 22 mths. Of four cases with documented karyotypes: the karyotype was a complex karyotype with markers in two cases, abnormalities of chromosome 3 were seen in three cases, +21 in two cases. KMT2A (MLL) exon 8, 9, or 10 were fused to exon 10, 11 or 12 of KNL1, the fusion protein contains the 1362 or 1418 first aa from MLL with aa 1796, 1818 or 1819 from KNL1 (according to authors and/or VEGA).
  • A t(3;15;p14;q15) KNL1/ ADAMTS9-AS2 is mentioned, without further data in the ChiTARS database (Gorohovski et al., 2016) as a chimeric EST (dbEST Id:12413828; accession BQ375909).
    Entity Lung cancer
    Note In one study on primary lung cancer, KNL1 mRNA expression was observed in more than 40% of the cases, which is the highest among all the different types of cancers examined. The study also revealed that clinicopathological findings correlates with KNL1 expression. KNL1 mRNA expression is more frequent in the tumors with low differentiation than the ones with moderate and high differentiation. Further, the tumors derived from smoker express higher incidence of KNL1 mRNA than the ones from non-smoker.
    Entity Spermatogenesis
    Note KNL1 mRNA was highly expressed in normal testis. As KNL1 protein expressions were observed in spermatogonia and spermatocytes in seminiferous tube of human testes, this protein may also play a role in cell division as a kinetochore protein in meiotic cells. It is noteworthy that KNL1 protein is also significantly expressed in pre-acrosome of spermatids, especially from its early stage, suggesting that KNL1 might be playing important role in the formation of acrosome, an essential organelle for fertilization. KNL1 expressions in testes of the patients with infertility were significantly lower than normal ones.
    Entity Microcephaly
    Disease Autosomal recessive primary microcephaly (MCPH) is a very rare neuro-developmental disorder with brain size reduction, no structural malformation of the brain at birth, mild-to moderate mental retardation and absence of other neurological or somatic disease. There are 12 genetic loci responsible for MCPH, and it was suggested that one of the responsible genetic locus, MCPH4, resides on chromosome 15. Subsequently, the study on the patients with MCPH4 of consanguineous families in Morocco revealed that a homozygous missense mutation was observed in exon 18 of KNL1 gene. This point mutation caused skipping this exon in splicing reaction in the mRNA maturation of KNL1, suggesting that the affected nucleotide is a part of Exonic splicing enhancers. The mutation resulted in frame-shift and truncation of KNL1 protein. As RWD repeats at near its carboxy terminus were deleted by this mutation, the truncated protein is no longer able to bind to Mis12, leading to the defected recruitment of KNL1 protein to kinetochore. One of the patients in the Morroco families has cryptorchidism in addition to microcephaly. The results of studies on MCH4 is a direct demonstration that KNL1 is essential to cell division in vivo.


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    This paper should be referenced as such :
    Masato Takimoto, Jean-Loup Huret
    KNL1 (cancer susceptibility candidate 5)
    Atlas Genet Cytogenet Oncol Haematol. 2017;21(6):200-204.
    Free journal version : [ pdf ]   [ DOI ]
    History of this paper:
    Huret, JL ; Charrin, C. AF15q14 (ALL1 fused gene from 15q14). Atlas Genet Cytogenet Oncol Haematol. 2000;4(2):50-50.
    Takimoto, M. CASC5 (cancer sensitibity candidate 5). Atlas Genet Cytogenet Oncol Haematol. 2007;11(1):8-9.
    Takimoto, M. CASC5 (cancer susceptibility candidate 5). Atlas Genet Cytogenet Oncol Haematol. 2013;17(1):1-2.

    Other Leukemias implicated (Data extracted from papers in the Atlas) [ 3 ]
      11q23 rearrangements (KMT2A) in leukaemia
    t(11;15)(q23;q14) KMT2A::CASC5
    t(11;15)(q23;q14):t(11;15)(q23;q15) KMT2A::KNL1

    External links


    HGNC (Hugo)KNL1   24054
    Entrez_Gene (NCBI)KNL1    kinetochore scaffold 1
    AliasesAF15Q14; CASC5; CT29; D40; 
    MCPH4; PPP1R55; Spc7; hKNL-1; hSpc105
    GeneCards (Weizmann)KNL1
    Ensembl hg19 (Hinxton)ENSG00000137812 [Gene_View]
    Ensembl hg38 (Hinxton)ENSG00000137812 [Gene_View]  ENSG00000137812 [Sequence]  chr15:40594249-40664341 [Contig_View]  KNL1 [Vega]
    ICGC DataPortalENSG00000137812
    TCGA cBioPortalKNL1
    AceView (NCBI)KNL1
    Genatlas (Paris)KNL1
    SOURCE (Princeton)KNL1
    Genetics Home Reference (NIH)KNL1
    Genomic and cartography
    GoldenPath hg38 (UCSC)KNL1  -     chr15:40594249-40664341 +  15q15.1   [Description]    (hg38-Dec_2013)
    GoldenPath hg19 (UCSC)KNL1  -     15q15.1   [Description]    (hg19-Feb_2009)
    GoldenPathKNL1 - 15q15.1 [CytoView hg19]  KNL1 - 15q15.1 [CytoView hg38]
    Genome Data Viewer NCBIKNL1 [Mapview hg19]  
    OMIM604321   609173   
    Gene and transcription
    Genbank (Entrez)AB022190 AB046790 AF173994 AF248041 AF461041
    RefSeq transcript (Entrez)NM_144508 NM_170589
    Consensus coding sequences : CCDS (NCBI)KNL1
    Gene ExpressionKNL1 [ NCBI-GEO ]   KNL1 [ EBI - ARRAY_EXPRESS ]   KNL1 [ SEEK ]   KNL1 [ MEM ]
    Gene Expression Viewer (FireBrowse)KNL1 [ Firebrowse - Broad ]
    GenevisibleExpression of KNL1 in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
    BioGPS (Tissue expression)57082
    GTEX Portal (Tissue expression)KNL1
    Human Protein AtlasENSG00000137812-KNL1 [pathology]   [cell]   [tissue]
    Protein : pattern, domain, 3D structure
    UniProt/SwissProtQ8NG31   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
    NextProtQ8NG31  [Sequence]  [Exons]  [Medical]  [Publications]
    With graphics : InterProQ8NG31
    Domains : Interpro (EBI)Blinkin    KNL1_MELT_rep    Knl1_RWD_C   
    Domain families : Pfam (Sanger)Knl1_RWD_C (PF18210)    MELT (PF19221)   
    Domain families : Pfam (NCBI)pfam18210    pfam19221   
    Conserved Domain (NCBI)KNL1
    PDB (RSDB)3SI5    4A1G    4NF9    4NFA   
    PDB Europe3SI5    4A1G    4NF9    4NFA   
    PDB (PDBSum)3SI5    4A1G    4NF9    4NFA   
    PDB (IMB)3SI5    4A1G    4NF9    4NFA   
    Structural Biology KnowledgeBase3SI5    4A1G    4NF9    4NFA   
    SCOP (Structural Classification of Proteins)3SI5    4A1G    4NF9    4NFA   
    CATH (Classification of proteins structures)3SI5    4A1G    4NF9    4NFA   
    AlphaFold pdb e-kbQ8NG31   
    Human Protein Atlas [tissue]ENSG00000137812-KNL1 [tissue]
    Protein Interaction databases
    IntAct (EBI)Q8NG31
    Complex Portal (EBI)Q8NG31 CPX-5644 Kinetochore KNL1 complex
    Ontologies - Pathways
    Ontology : AmiGOkinetochore  kinetochore  acrosomal vesicle  acrosome assembly  protein binding  nucleus  nucleus  nucleoplasm  nucleoplasm  cytosol  mitotic spindle organization  attachment of spindle microtubules to kinetochore  attachment of spindle microtubules to kinetochore  nuclear body  CENP-A containing nucleosome assembly  protein localization to kinetochore  protein localization to kinetochore  cell division  
    Ontology : EGO-EBIkinetochore  kinetochore  acrosomal vesicle  acrosome assembly  protein binding  nucleus  nucleus  nucleoplasm  nucleoplasm  cytosol  mitotic spindle organization  attachment of spindle microtubules to kinetochore  attachment of spindle microtubules to kinetochore  nuclear body  CENP-A containing nucleosome assembly  protein localization to kinetochore  protein localization to kinetochore  cell division  
    REACTOMEQ8NG31 [protein]
    REACTOME PathwaysR-HSA-68877 [pathway]   
    NDEx NetworkKNL1
    Atlas of Cancer Signalling NetworkKNL1
    Wikipedia pathwaysKNL1
    Orthology - Evolution
    GeneTree (enSembl)ENSG00000137812
    Phylogenetic Trees/Animal Genes : TreeFamKNL1
    Homologs : HomoloGeneKNL1
    Homology/Alignments : Family Browser (UCSC)KNL1
    Gene fusions - Rearrangements
    Fusion : COSMICKMT2A [11q23.3]  -  KNL1 [15q15.1]  [fusion_1869]  [fusion_1870]  [fusion_1871]  [fusion_1879]  [fusion_1880]  [fusion_1881]  [fusion_1943]  
    Fusion : QuiverKNL1
    Polymorphisms : SNP and Copy number variants
    NCBI Variation ViewerKNL1 [hg38]
    dbSNP Single Nucleotide Polymorphism (NCBI)KNL1
    Exome Variant ServerKNL1
    GNOMAD BrowserENSG00000137812
    Varsome BrowserKNL1
    ACMGKNL1 variants
    Genomic Variants (DGV)KNL1 [DGVbeta]
    DECIPHERKNL1 [patients]   [syndromes]   [variants]   [genes]  
    CONAN: Copy Number AnalysisKNL1 
    ICGC Data PortalKNL1 
    TCGA Data PortalKNL1 
    Broad Tumor PortalKNL1
    OASIS PortalKNL1 [ Somatic mutations - Copy number]
    Cancer Gene: CensusKNL1 
    Somatic Mutations in Cancer : COSMICKNL1  [overview]  [genome browser]  [tissue]  [distribution]  
    Somatic Mutations in Cancer : COSMIC3DKNL1
    Mutations and Diseases : HGMDKNL1
    LOVD (Leiden Open Variation Database)[gene] [transcripts] [variants]
    DgiDB (Drug Gene Interaction Database)KNL1
    DoCM (Curated mutations)KNL1
    CIViC (Clinical Interpretations of Variants in Cancer)KNL1
    NCG (London)KNL1
    Impact of mutations[PolyPhen2] [Provean] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
    OMIM604321    609173   
    Genetic Testing Registry KNL1
    NextProtQ8NG31 [Medical]
    Target ValidationKNL1
    Huge Navigator KNL1 [HugePedia]
    Clinical trials, drugs, therapy
    Protein Interactions : CTDKNL1
    Pharm GKB GenePA142672201
    Clinical trialKNL1
    canSAR (ICR)KNL1
    DataMed IndexKNL1
    PubMed81 Pubmed reference(s) in Entrez
    GeneRIFsGene References Into Functions (Entrez)
    REVIEW articlesautomatic search in PubMed
    Last year publicationsautomatic search in PubMed

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    indexed on : Fri Oct 8 21:11:58 CEST 2021

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