CILK1 Gene

Name ciliogenesis associated kinase 1
Description Eukaryotic protein kinases are enzymes that belong to a very extensive family of proteins which share a conserved catalytic core common with both serine/threonine and tyrosine protein kinases. This gene encodes an intestinal serine/threonine kinase harboring a dual phosphorylation site found in mitogen-activating protein (MAP) kinases. The protein localizes to the intestinal crypt region and is thought to be important in intestinal epithelial cell proliferation and differentiation. Alternative splicing has been observed at this locus and two variants, encoding the same isoform, have been identified. [provided by RefSeq, Jul 2008]
Summary
{"type": "root", "children": [{"type": "p", "children": [{"type": "t", "text": "\n Ciliogenesis‐associated kinase 1 (CILK1), also known as intestinal cell kinase (ICK), is a highly conserved serine/threonine kinase that plays a critical role in modulating the structure and function of primary cilia. Localized predominantly at the proximal region of cilia near the basal bodies, CILK1 regulates ciliary length and intraflagellar transport by phosphorylating key substrates, thereby ensuring proper assembly and disassembly of the ciliary compartment."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "1"}]}, {"type": "t", "text": " Disruption of CILK1 function, as observed in knockout models, leads to elongated cilia and aberrant Sonic Hedgehog signaling, which underlies several congenital disorders such as endocrine-cerebro-osteodysplasia (ECO) syndrome."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "2"}]}, {"type": "t", "text": " Precise activation of CILK1 requires its nuclear localization and dual phosphorylation of its conserved TDY motif—a process that is critically dependent on upstream kinases like CAK1."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "3"}]}, {"type": "t", "text": " Mutations such as the R272Q variant impair nuclear translocation and kinase activity of CILK1, thereby disrupting ciliary homeostasis and downstream developmental signaling cascades."}, {"type": "fg", "children": [{"type": "fg_f", "ref": "5"}]}, {"type": "t", "text": " Collectively, these findings underscore the pivotal role of CILK1 in maintaining ciliary integrity and highlight how its dysregulation contributes to developmental pathology and may influence disease processes where altered ciliary dynamics are implicated."}, {"type": "fg", "children": [{"type": "fg_fs", "start_ref": "1", "end_ref": "3"}, {"type": "fg_f", "ref": "5"}, {"type": "fg_f", "ref": "4"}]}, {"type": "t", "text": "\n "}]}, {"type": "rg", "children": [{"type": "r", "ref": 1, "children": [{"type": "t", "text": "Ying Yang, Niina Roine, Tomi P Mäkelä "}, {"type": "b", "children": [{"type": "t", "text": "CCRK depletion inhibits glioblastoma cell proliferation in a cilium-dependent manner."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "EMBO Rep (2013)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1038/embor.2013.80"}], "href": "https://doi.org/10.1038/embor.2013.80"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "23743448"}], "href": "https://pubmed.ncbi.nlm.nih.gov/23743448"}]}, {"type": "r", "ref": 2, "children": [{"type": "t", "text": "Heejung Moon, Jieun Song, Jeong-Oh Shin, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Intestinal cell kinase, a protein associated with endocrine-cerebro-osteodysplasia syndrome, is a key regulator of cilia length and Hedgehog signaling."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Proc Natl Acad Sci U S A (2014)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1073/pnas.1323161111"}], "href": "https://doi.org/10.1073/pnas.1323161111"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "24853502"}], "href": "https://pubmed.ncbi.nlm.nih.gov/24853502"}]}, {"type": "r", "ref": 3, "children": [{"type": "t", "text": "Zheng Fu, Melanie J Schroeder, Jeffrey Shabanowitz, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Activation of a nuclear Cdc2-related kinase within a mitogen-activated protein kinase-like TDY motif by autophosphorylation and cyclin-dependent protein kinase-activating kinase."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Mol Cell Biol (2005)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1128/MCB.25.14.6047-6064.2005"}], "href": "https://doi.org/10.1128/MCB.25.14.6047-6064.2005"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "15988018"}], "href": "https://pubmed.ncbi.nlm.nih.gov/15988018"}]}, {"type": "r", "ref": 4, "children": [{"type": "t", "text": "Zheng Fu, Katherine A Larson, Raghu K Chitta, et al. "}, {"type": "b", "children": [{"type": "t", "text": "Identification of yin-yang regulators and a phosphorylation consensus for male germ cell-associated kinase (MAK)-related kinase."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Mol Cell Biol (2006)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1128/MCB.00816-06"}], "href": "https://doi.org/10.1128/MCB.00816-06"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "16954377"}], "href": "https://pubmed.ncbi.nlm.nih.gov/16954377"}]}, {"type": "r", "ref": 5, "children": [{"type": "t", "text": "Piya Lahiry, Jian Wang, John F Robinson, et al. "}, {"type": "b", "children": [{"type": "t", "text": "A multiplex human syndrome implicates a key role for intestinal cell kinase in development of central nervous, skeletal, and endocrine systems."}]}, {"type": "t", "text": " "}, {"type": "i", "children": [{"type": "t", "text": "Am J Hum Genet (2009)"}]}, {"type": "t", "text": " DOI: "}, {"type": "a", "children": [{"type": "t", "text": "10.1016/j.ajhg.2008.12.017"}], "href": "https://doi.org/10.1016/j.ajhg.2008.12.017"}, {"type": "t", "text": " PMID: "}, {"type": "a", "children": [{"type": "t", "text": "19185282"}], "href": "https://pubmed.ncbi.nlm.nih.gov/19185282"}]}]}]}
NCBI Gene ID 22858
API
Download Associations
Predicted Functions View CILK1's ARCHS4 Predicted Functions.
Co-expressed Genes View CILK1's ARCHS4 Predicted Functions.
Expression in Tissues and Cell Lines View CILK1's ARCHS4 Predicted Functions.

Functional Associations

CILK1 has 1,975 functional associations with biological entities spanning 6 categories (chemical, disease, phenotype or trait, functional term, phrase or reference, cell line, cell type or tissue, gene, protein or microRNA, sequence feature) extracted from 31 datasets.

Click the + buttons to view associations for CILK1 from the datasets below.

If available, associations are ranked by standardized value

Dataset Summary
Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles tissue samples with high or low expression of CILK1 gene relative to other tissue samples from the Allen Brain Atlas Aging Dementia and Traumatic Brain Injury Tissue Sample Gene Expression Profiles dataset.
Carcinogenome Chemical Perturbation Carcinogenicity Signatures small molecule perturbations changing expression of CILK1 gene from the Carcinogenome Chemical Perturbation Carcinogenicity Signatures dataset.
CellMarker Gene-Cell Type Associations cell types associated with CILK1 gene from the CellMarker Gene-Cell Type Associations dataset.
ClinVar Gene-Phenotype Associations 2025 phenotypes associated with CILK1 gene from the curated ClinVar Gene-Phenotype Associations 2025 dataset.
CM4AI KOLF21J CRISPRi Gene Perturbation Atlas gene perturbations changing expression of CILK1 gene from the CM4AI KOLF21J CRISPRi Gene Perturbation Atlas dataset.
CM4AI U2OS Cell Map Protein Localization Assemblies assemblies containing CILK1 protein from integrated AP-MS and IF data from the CM4AI U2OS Cell Map Protein Localization Assemblies dataset.
COMPARTMENTS Curated Protein Localization Evidence Scores 2025 cellular components containing CILK1 protein from the COMPARTMENTS Curated Protein Localization Evidence Scores 2025 dataset.
COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025 cellular components co-occuring with CILK1 protein in abstracts of biomedical publications from the COMPARTMENTS Text-mining Protein Localization Evidence Scores 2025 dataset.
GO Biological Process Annotations 2025 biological processes involving CILK1 gene from the curated GO Biological Process Annotations2025 dataset.
GO Cellular Component Annotations 2025 cellular components containing CILK1 protein from the curated GO Cellular Component Annotations 2025 dataset.
GO Molecular Function Annotations 2025 molecular functions performed by CILK1 gene from the curated GO Molecular Function Annotations 2025 dataset.
GTEx eQTL 2025 SNPs regulating expression of CILK1 gene from the GTEx eQTL 2025 dataset.
GTEx Tissue Gene Expression Profiles 2023 tissues with high or low expression of CILK1 gene relative to other tissues from the GTEx Tissue Gene Expression Profiles 2023 dataset.
GWAS Catalog SNP-Phenotype Associations 2025 phenotypes associated with CILK1 gene in GWAS datasets from the GWAS Catalog SNP-Phenotype Associations 2025 dataset.
IMPC Knockout Mouse Phenotypes phenotypes of mice caused by CILK1 gene knockout from the IMPC Knockout Mouse Phenotypes dataset.
JASPAR Predicted Human Transcription Factor Targets 2025 transcription factors regulating expression of CILK1 gene predicted using known transcription factor binding site motifs from the JASPAR Predicted Human Transcription Factor Targets dataset.
JASPAR Predicted Mouse Transcription Factor Targets 2025 transcription factors regulating expression of CILK1 gene predicted using known transcription factor binding site motifs from the JASPAR Predicted Mouse Transcription Factor Targets 2025 dataset.
LINCS L1000 CMAP Chemical Perturbation Consensus Signatures small molecule perturbations changing expression of CILK1 gene from the LINCS L1000 CMAP Chemical Perturbations Consensus Signatures dataset.
MoTrPAC Rat Endurance Exercise Training tissue samples with high or low expression of CILK1 gene relative to other tissue samples from the MoTrPAC Rat Endurance Exercise Training dataset.
PFOCR Pathway Figure Associations 2024 pathways involving CILK1 protein from the Wikipathways PFOCR 2024 dataset.
Replogle et al., Cell, 2022 K562 Essential Perturb-seq Gene Perturbation Signatures gene perturbations changing expression of CILK1 gene from the Replogle et al., Cell, 2022 K562 Essential Perturb-seq Gene Perturbation Signatures dataset.
Replogle et al., Cell, 2022 K562 Genome-wide Perturb-seq Gene Perturbation Signatures gene perturbations changing expression of CILK1 gene from the Replogle et al., Cell, 2022 K562 Genome-wide Perturb-seq Gene Perturbation Signatures dataset.
Replogle et al., Cell, 2022 RPE1 Essential Perturb-seq Gene Perturbation Signatures gene perturbations changing expression of CILK1 gene from the Replogle et al., Cell, 2022 RPE1 Essential Perturb-seq Gene Perturbation Signatures dataset.
Rummagene Transcription Factor Associations 2026 transcription factors regulating expression of CILK1 gene from the Rummagene Transcription Factor Associations 2026 dataset.
RummaGEO Drug Perturbation Signatures drug perturbations changing expression of CILK1 gene from the RummaGEO Drug Perturbation Signatures dataset.
RummaGEO Gene Perturbation Signatures gene perturbations changing expression of CILK1 gene from the RummaGEO Gene Perturbation Signatures dataset.
Sci-Plex Drug Perturbation Signatures drug perturbations changing expression of CILK1 gene from the Sci-Plex Drug Perturbation Signatures dataset.
TISSUES Curated Tissue Protein Expression Evidence Scores 2025 tissues with high expression of CILK1 protein from the TISSUES Curated Tissue Protein Expression Evidence Scores 2025 dataset.
TISSUES Experimental Tissue Protein Expression Evidence Scores 2025 tissues with high expression of CILK1 protein in proteomics datasets from the TISSUES Experimental Tissue Protein Expression Evidence Scores 2025 dataset.
TISSUES Text-mining Tissue Protein Expression Evidence Scores 2025 tissues co-occuring with CILK1 protein in abstracts of biomedical publications from the TISSUES Text-mining Tissue Protein Expression Evidence Scores 2025 dataset.
WikiPathways Pathways 2024 pathways involving CILK1 protein from the WikiPathways Pathways 2024 dataset.