Affinage

CEP164

Centrosomal protein of 164 kDa · UniProt Q9UPV0

Length
1460 aa
Mass
164.3 kDa
Annotated
2026-04-28
22 papers in source corpus 20 papers cited in narrative 20 extracted findings

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

CEP164 is a distal appendage protein of the mother centriole that serves as a master scaffold for ciliogenesis initiation, vesicle docking, and intraflagellar transport, while also participating in DNA damage signaling and Hedgehog pathway regulation. CEP164 homodimerizes via its central coiled-coil domain to anchor at the mother centriole and directly recruits the kinase TTBK2 through multivalent electrostatic interactions involving its intrinsically disordered region, forming phase-separated condensates that drive CP110 removal and IFT machinery assembly (PMID:24982133, PMID:40305080, PMID:40483689). In multiciliated cells, CEP164 controls vesicle recruitment, ciliary vesicle formation, basal body docking, and recruitment of Chibby1, while in photoreceptors it is continuously required for IFT complex maintenance after initial cilium assembly (PMID:29244804, PMID:36074756). CEP164 is phosphorylated at Ser186 by ATR/ATM and facilitates CHK1 activation in the DNA damage response, and independently scaffolds GLI2 at the centriole to regulate Hedgehog target gene expression (PMID:18283122, PMID:37199136).

Mechanistic history

Synthesis pass · year-by-year structured walk · 13 steps
  1. 2007 High

    Establishing where CEP164 resides on the centriole and that it is required for ciliogenesis answered the fundamental question of which appendage structure initiates primary cilium formation.

    Evidence Immunogold EM and siRNA knockdown in mammalian cells

    PMID:17954613

    Open questions at the time
    • Mechanism by which CEP164 promotes ciliogenesis unknown
    • Binding partners at distal appendages unidentified
    • Whether CEP164 has functions beyond ciliogenesis not addressed
  2. 2008 High

    Discovering that CEP164 is an ATR/ATM substrate and mediator of CHK1 activation revealed an unexpected role for a centrosomal protein in the DNA damage checkpoint, raising the question of whether its ciliary and DDR roles are separable.

    Evidence In vitro kinase assay, siRNA knockdown with phospho-specific readouts, Ser186 mutagenesis

    PMID:18283122

    Open questions at the time
    • Nuclear localization of CEP164 not confirmed by independent approach
    • Relative importance of DDR versus ciliary function unclear
    • Structural basis of ATR/ATM interaction unknown
  3. 2009 Medium

    The finding that CEP164 binds the NER factor XPA and is recruited to UV-damage sites extended the DDR role to nucleotide excision repair, but relied on a single laboratory.

    Evidence Co-immunoprecipitation with XPA domain mapping, siRNA knockdown, XPA-mutant fibroblast complementation

    PMID:19197159

    Open questions at the time
    • Not independently replicated
    • Whether XPA interaction occurs at centriole or in nucleus not resolved
    • Direct biochemical reconstitution of CEP164 in NER not performed
  4. 2012 High

    Linking CEP164 to the ZNF423/NPHP10/TIP60 DNA damage network and demonstrating a nephronophthisis-like ciliopathy upon cep164 loss in zebrafish established CEP164 as a ciliopathy gene with potential dual ciliary-DDR etiology.

    Evidence Immunofluorescence co-localization at DNA damage foci, zebrafish morpholino knockdown, siRNA sensitivity assays

    PMID:22863007

    Open questions at the time
    • Whether kidney phenotype is due to DDR defect or cilia loss not distinguished
    • Human disease-causing mutations not yet identified at this point
  5. 2014 High

    Demonstrating that CEP164 directly recruits TTBK2 to the basal body and that a CEP164-TTBK2 chimera bypasses the need for full-length CEP164 established TTBK2 recruitment as the primary mechanistic function of CEP164 in ciliogenesis.

    Evidence Co-immunoprecipitation, domain mapping, chimeric rescue in CEP164-depleted cells, TTBK2 motif mutagenesis, in vitro kinase assays

    PMID:24982133 PMID:25297623

    Open questions at the time
    • Structural basis of CEP164-TTBK2 interface not yet resolved at atomic level
    • Whether TTBK2 phosphorylation of CEP164 is regulatory not established
    • How TTBK2 triggers CP110 removal mechanistically unknown
  6. 2016 Medium

    Genome-edited CEP164-null RPE cells showing no DDR defect and no nuclear CEP164 challenged the proposed DNA damage response role, sharpening the debate about whether the DDR phenotype reflects an indirect consequence of cilia loss or off-target siRNA effects.

    Evidence CRISPR and auxin-inducible degron in RPE cells, clonogenic survival assay, cell fractionation

    PMID:26966185

    Open questions at the time
    • Discrepancy with prior DDR studies not fully resolved—cell type or context dependence possible
    • Only one cell type tested in null setting
    • Conditional in vivo DDR analysis not performed
  7. 2017 High

    Conditional knockout in multiciliated cells revealed that CEP164 controls vesicle docking, Cby1 recruitment, and selective membrane protein targeting at basal bodies, establishing its role in multiciliogenesis as distinct from its primary ciliogenesis mechanism.

    Evidence FoxJ1-Cre conditional KO mice, primary tracheal cultures, EM ultrastructure

    PMID:29244804

    Open questions at the time
    • Whether CEP164 has different binding partners in multiciliated vs. monociliated cells not addressed
    • Mechanism of vesicle recruitment by CEP164 not molecularly defined
  8. 2019 Medium

    Collecting duct-specific deletion causing cystic kidney disease driven by hyperproliferation demonstrated that CEP164 loss phenocopies classic ciliopathic renal cystogenesis in vivo.

    Evidence Conditional KO mice, cell cycle analysis, roscovitine rescue

    PMID:31248650

    Open questions at the time
    • Whether cyst formation involves DDR defects or is purely cilia-dependent not distinguished
    • Contribution of Hedgehog signaling to cystogenesis not evaluated
  9. 2021 High

    Structural resolution of the CEP164-TTBK2 binding interface and demonstration that ciliopathic mutations disrupt this interaction provided the first atomic-level explanation for disease-causing CEP164 variants.

    Evidence NMR, biochemical interaction assays, mutagenesis of ciliopathy alleles

    PMID:34499853

    Open questions at the time
    • Full-length CEP164 structure not determined
    • Structure of CEP164 at the distal appendage in situ unknown
  10. 2022 High

    Post-ciliogenesis deletion in photoreceptors showing IFT depletion and outer segment instability established that CEP164 is not only required for cilium initiation but also for continuous maintenance of IFT trafficking.

    Evidence Conditional and tamoxifen-inducible rod-specific KO mice, IFT component immunofluorescence, pulse-chase disc labeling

    PMID:36074756

    Open questions at the time
    • Whether maintenance role depends on TTBK2 not tested
    • Whether other distal appendage proteins compensate partially is unknown
  11. 2023 Medium

    Mapping the CEP164-GLI2 physical interaction and showing that a dominant-negative fragment upregulates Hh-target genes established that CEP164 restrains Hedgehog signaling at the centriole independently of primary cilia.

    Evidence Co-immunoprecipitation, domain mapping, dominant-negative expression, gene expression analysis in PDAC cells

    PMID:37199136

    Open questions at the time
    • Whether GLI2 scaffolding is relevant in non-cancer cell contexts unknown
    • Structural basis of CEP164-GLI2 interaction unresolved
    • Single-lab finding not independently replicated
  12. 2024 Medium

    Osteoblast-specific CEP164 deletion causing both cilia loss and increased γH2AX foci reignited support for a non-ciliary DDR function in specific cell types, partially reconciling conflicting earlier reports.

    Evidence Cell-type-specific conditional KO mice, γH2AX immunofluorescence, skeletal analysis

    PMID:39612644

    Open questions at the time
    • Whether γH2AX increase is a direct or indirect consequence of CEP164 loss not resolved
    • Mechanism of nuclear CEP164 function in osteoblasts not defined
  13. 2025 Medium

    Demonstrating that CEP164 homodimerizes for centriolar anchoring and undergoes phase separation with TTBK2 via its disordered region provided a biophysical mechanism for how CEP164 concentrates TTBK2 at distal appendages to trigger ciliogenesis.

    Evidence Phase separation assays, charge-mutation analysis, live-cell condensate imaging, KO cell reconstitution with chimeric/truncation constructs

    PMID:40305080 PMID:40483689

    Open questions at the time
    • Physiological relevance of phase separation in vivo not established with condensate-disrupting mutations in animal models
    • Whether other distal appendage components participate in condensate formation unknown

Open questions

Synthesis pass · forward-looking unresolved questions
  • Key unresolved questions include whether CEP164 has a bona fide direct nuclear DDR function or whether DDR phenotypes are secondary to centrosomal/ciliary disruption, the full-length structure of CEP164 and its in situ architecture at distal appendages, and the mechanism by which CEP164-mediated vesicle enlargement triggers axoneme extension.
  • DDR role remains contested across cell types and experimental approaches
  • No full-length CEP164 structure available
  • Vesicle enlargement mechanism molecularly undefined

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0060090 molecular adaptor activity 5 GO:0098772 molecular function regulator activity 3
Localization
GO:0005815 microtubule organizing center 5 GO:0005929 cilium 3 GO:0005634 nucleus 2
Pathway
R-HSA-1852241 Organelle biogenesis and maintenance 5 R-HSA-162582 Signal Transduction 2 R-HSA-1640170 Cell Cycle 2 R-HSA-73894 DNA Repair 2
Partners
ATMATRCBY1GLI2INPP5ETTBK2XPA

Evidence

Reading pass · 20 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
2007 CEP164 localizes specifically to the distal appendages of mature centrioles (mother centrioles), as demonstrated by immunogold electron microscopy, and is indispensable for primary cilium formation. Its localization is independent of subdistal appendage components ninein and Cep170. siRNA knockdown screen, immunogold electron microscopy, immunofluorescence The Journal of cell biology High 17954613
2008 CEP164 interacts with both ATR and ATM kinases and is phosphorylated at Ser186 by ATR/ATM in vitro and in vivo upon replication stress, UV, and ionizing radiation. CEP164 knockdown reduces DNA damage-induced phosphorylation of RPA, H2AX, MDC1, CHK2, and CHK1 (but not NBS1), and impairs G2/M checkpoint and nuclear division, placing CEP164 as a mediator in the ATR/ATM-dependent DNA damage response pathway downstream of MDC1. In vitro kinase assay, siRNA knockdown, immunoprecipitation, phospho-specific antibodies Genes & development High 18283122
2009 Upon UV irradiation, CEP164 physically interacts with the NER factor XPA (binding to XPA amino acids 4–97), and this interaction is required for CEP164 recruitment to cyclobutane pyrimidine dimer (CPD) sites. CEP164 knockdown impairs UV-induced CHK1 phosphorylation, linking CEP164 to both NER and checkpoint signaling. Co-immunoprecipitation, chromatin immunoprecipitation, immunofluorescence, siRNA knockdown, XPA-mutant fibroblast complementation Cell cycle (Georgetown, Tex.) Medium 19197159
2012 Upon induced DNA damage, CEP164 colocalizes with ZNF423 and NPHP10 at nuclear foci positive for TIP60 (known to activate ATM at DNA damage sites). CEP164 knockdown causes cellular sensitivity to DNA damaging agents, and cep164 knockdown in zebrafish results in dysregulated DDR and a nephronophthisis-related ciliopathy phenotype. Immunofluorescence co-localization at DNA damage foci, siRNA knockdown sensitivity assay, zebrafish morpholino knockdown Cell High 22863007
2012 CEP164 physically interacts with the ciliary/centrosomal protein INPP5E, and is part of a functional protein network with ARL13B, INPP5E, and PDE6D that is involved in INPP5E ciliary targeting and Joubert syndrome/nephronophthisis pathogenesis. Co-immunoprecipitation, protein-protein interaction network analysis Proceedings of the National Academy of Sciences of the United States of America Medium 23150559
2014 CEP164 recruits TTBK2 to the basal body by direct complex formation; the interaction domains were mapped and shown to be essential. Ciliogenesis can be restored in CEP164-depleted cells by chimeric proteins fusing TTBK2 to the C-terminal centriole-targeting domain of CEP164, demonstrating that a primary function of CEP164 is positioning TTBK2 at the centriole to trigger CP110 removal and IFT protein recruitment. Co-immunoprecipitation, domain mapping, siRNA knockdown, chimeric protein rescue, immunofluorescence Proceedings of the National Academy of Sciences of the United States of America High 24982133
2014 TTBK2 binds CEP164 through a proline-rich motif on TTBK2 (distinct from the SxIP motifs used to bind EB1), and this interaction—not EB1 binding—is essential for centriolar localization of TTBK2, CP110 removal, and ciliogenesis. TTBK2 can phosphorylate CEP164 and Cep97, and TTBK2 kinase activity inhibits the CEP164–Dishevelled-3 interaction. Mutagenesis of TTBK2 binding motifs, co-immunoprecipitation, rescue experiments in TTBK2-depleted cells, in vitro kinase assay Genes to cells : devoted to molecular & cellular mechanisms High 25297623
2014 CEP164 knockdown in RPE-FUCCI cells causes accelerated cell cycle entry but prolonged S-phase, increased apoptosis, and induction of epithelial-to-mesenchymal transition. These phenotypes are rescued by wild-type CEP164 but not disease-associated mutants, linking CEP164 to cell cycle regulation and fibrosis relevant to nephronophthisis. Live cell imaging with FUCCI reporter, FACS, CyQuant proliferation assay, siRNA knockdown, mutant complementation, zebrafish morpholino PLoS genetics Medium 25340510
2016 Genome-edited CEP164-null human RPE cells show complete loss of primary cilia but no defect in DNA damage responses to ionizing or UV irradiation, and no nuclear localization of CEP164 was detected, challenging the proposed DNA damage response role of CEP164. Genome editing (auxin-inducible degron and CRISPR), immunofluorescence for localization, clonogenic survival assay, cell fractionation Journal of cell science Medium 26966185
2017 CEP164 is required for multiciliogenesis in airway/ependymal/oviduct multiciliated cells via regulation of small vesicle recruitment, ciliary vesicle formation, and basal body docking. CEP164 is also necessary for recruitment of Chibby1 (Cby1) and its binding partners FAM92A and FAM92B to the ciliary base, and for selective ciliary targeting of membrane-associated proteins Rab8, Rab11, and Arl13b, but is dispensable for IFT component recruitment in multiciliated cells. Conditional knockout mouse model (FoxJ1-Cre), primary tracheal cell cultures, immunofluorescence, electron microscopy PLoS genetics High 29244804
2019 Collecting duct-specific deletion of Cep164 abolishes primary cilia from collecting duct epithelium and leads to postnatal cystic kidney disease driven by tubular hyperproliferation, as demonstrated by cell cycle and biochemical studies. Conditional knockout mouse, histology, cell cycle analysis, roscovitine pharmacological rescue Kidney international Medium 31248650
2020 CEP164 co-localizes with the GLI2 transcription factor at the mother centriole and controls GLI2 activation, thereby regulating Cyclin D-CDK6 expression. Loss of CEP164 enhances clonogenicity and alters cell cycle progression in pancreatic cancer cells independently of primary cilia loss. CEP164 CRISPR knockout, immunofluorescence co-localization, cell cycle analysis, clonogenic assay Frontiers in cell and developmental biology Medium 33251215
2021 Structural and biochemical analysis of the CEP164–TTBK2 complex revealed how two ciliopathic CEP164 mutations disrupt the interaction with TTBK2, and showed that binding to CEP164 influences TTBK2 activities. Biochemical interaction assays, NMR, structural analysis, mutagenesis of ciliopathy alleles Structure (London, England : 1993) High 34499853
2021 CEP164 recruits Chibby1 (Cby1) to basal bodies to facilitate basal body docking and ciliogenesis in efferent duct multiciliated cells; loss of CEP164 causes basal body accumulation in the cytoplasm and loss of multicilia, leading to sperm agglutination and male infertility. FoxJ1-Cre conditional KO mice, immunofluorescence, TEM ultrastructure Reproduction (Cambridge, England) Medium 34085951
2022 Post-ciliogenesis deletion of CEP164 in rod photoreceptors impairs intraflagellar transport (IFT-B and IFT-A components become depleted at basal body and cilium tips) and causes outer segment instability, demonstrating that CEP164 is required for ongoing IFT recruitment and stabilization after initial cilium assembly. Conditional rod-specific and tamoxifen-inducible KO mice, immunofluorescence, pulse-chase disc labeling PLoS genetics High 36074756
2023 CEP164 physically interacts with GLI2 at the mother centriole; ectopic expression of the GLI2-binding region of CEP164 disrupts centriolar GLI2 localization and upregulates Hh-target gene expression in PDAC cells, demonstrating that the CEP164–GLI2 association controls Hh signaling independently of primary cilia. Co-immunoprecipitation, domain mapping, ectopic expression of binding-domain fragment, immunofluorescence, gene expression analysis Biochemical and biophysical research communications Medium 37199136
2024 Osteoblast-specific deletion of CEP164 causes bone development defects and increases γH2AX-positive cells, indicating CEP164 has both ciliary (cilia loss) and non-ciliary (DNA damage response) functions in osteoblasts, while chondrocyte-specific deletion has no overt phenotype. Cell type-specific conditional KO mice, immunofluorescence for γH2AX, skeletal analysis Biochemical and biophysical research communications Medium 39612644
2025 CEP164 contains a long intrinsically disordered region and undergoes phase separation with TTBK2 through multivalent electrostatic interactions, forming dynamic condensates at distal appendages that facilitate efficient TTBK2 recruitment and initiation of ciliogenesis. Phase separation assays, truncation/charge-mutation analysis, live-cell imaging of condensates, immunofluorescence Cell reports Medium 40483689
2025 CEP164 homodimerizes via its central coiled-coil region, and this homodimerization is necessary for mother centriole localization of CEP164 and subsequent TTBK2 recruitment. TTBK2 kinase activity and its interaction with CEP164 are both required for IFT-A, IFT-B, and dynein-2 recruitment to the mother centriole and CP110 removal. CEP164-KO and TTBK2-KO cell lines, expression of chimeric/truncation constructs, immunofluorescence Molecular biology of the cell Medium 40305080
2025 CEP164 at the mother centriole distal appendages is required for enlargement of small docked vesicles, an early triggering step for ciliogenesis progression upstream of axoneme growth, as revealed by 3D quantitative isotropic ultrastructure imaging. Isotropic 3D ultrastructure imaging (cryo-ET/FIB-SEM), CEP164 depletion, quantitative vesicle analysis bioRxivpreprint Medium bio_10.1101_2025.08.20.670930

Source papers

Stage 0 corpus · 22 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
2007 Cep164, a novel centriole appendage protein required for primary cilium formation. The Journal of cell biology 425 17954613
2012 Exome capture reveals ZNF423 and CEP164 mutations, linking renal ciliopathies to DNA damage response signaling. Cell 316 22863007
2012 ARL13B, PDE6D, and CEP164 form a functional network for INPP5E ciliary targeting. Proceedings of the National Academy of Sciences of the United States of America 196 23150559
2014 Cep164 triggers ciliogenesis by recruiting Tau tubulin kinase 2 to the mother centriole. Proceedings of the National Academy of Sciences of the United States of America 155 24982133
2008 Cep164 is a mediator protein required for the maintenance of genomic stability through modulation of MDC1, RPA, and CHK1. Genes & development 79 18283122
2014 Nephronophthisis-associated CEP164 regulates cell cycle progression, apoptosis and epithelial-to-mesenchymal transition. PLoS genetics 63 25340510
2014 Binding to Cep164, but not EB1, is essential for centriolar localization of TTBK2 and its function in ciliogenesis. Genes to cells : devoted to molecular & cellular mechanisms 55 25297623
2017 Conditional knockout mice for the distal appendage protein CEP164 reveal its essential roles in airway multiciliated cell differentiation. PLoS genetics 52 29244804
2009 UV-dependent interaction between Cep164 and XPA mediates localization of Cep164 at sites of DNA damage and UV sensitivity. Cell cycle (Georgetown, Tex.) 34 19197159
2016 CEP164-null cells generated by genome editing show a ciliation defect with intact DNA repair capacity. Journal of cell science 33 26966185
2021 CEP164 is essential for efferent duct multiciliogenesis and male fertility. Reproduction (Cambridge, England) 25 34085951
2021 Molecular mechanisms underlying the role of the centriolar CEP164-TTBK2 complex in ciliopathies. Structure (London, England : 1993) 20 34499853
2022 Deletion of CEP164 in mouse photoreceptors post-ciliogenesis interrupts ciliary intraflagellar transport (IFT). PLoS genetics 19 36074756
2019 Roscovitine blocks collecting duct cyst growth in Cep164-deficient kidneys. Kidney international 15 31248650
2020 CEP164 Deficiency Causes Hyperproliferation of Pancreatic Cancer Cells. Frontiers in cell and developmental biology 12 33251215
2020 Embryonic and foetal expression patterns of the ciliopathy gene CEP164. PloS one 8 31990917
2022 Biallelic variants in CEP164 cause a motile ciliopathy-like syndrome. Clinical genetics 6 36273371
2023 CEP164-GLI2 association ensures the hedgehog signaling in pancreatic cancer cells. Biochemical and biophysical research communications 3 37199136
2025 Phase separation of TTBK2 and CEP164 is necessary for ciliogenesis. Cell reports 2 40483689
2025 Coordinated roles of the CEP164 homodimer and TTBK2 are required for recruitment of the IFT machinery to the mother centriole for ciliogenesis. Molecular biology of the cell 1 40305080
2024 Disruption of distal appendage protein CEP164 causes skeletal malformation in mice. Biochemical and biophysical research communications 1 39612644
2026 Ameloblastoma Displays Primary Cilia Maintenance and CEP164 Overexpression. Journal of dental research 0 41733187