{"gene":"NEK11","run_date":"2026-06-10T05:19:52","timeline":{"discoveries":[{"year":2009,"finding":"NEK11 directly phosphorylates CDC25A on specific residues required for beta-TrCP-mediated polyubiquitylation and proteasome-dependent degradation of CDC25A, thereby enforcing the DNA damage-induced G2/M checkpoint. CHK1 directly activates NEK11 by phosphorylating it on Ser273, placing CHK1 and NEK11 in a single linear pathway controlling CDC25A proteolysis.","method":"shRNA library screen, RNAi depletion, in vitro kinase assay, co-immunoprecipitation, proteasome inhibitor experiments, site-directed mutagenesis of phosphorylation sites","journal":"Nature cell biology","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — direct in vitro kinase assay demonstrating NEK11 phosphorylates CDC25A, CHK1-NEK11 phosphorylation confirmed, multiple orthogonal methods (shRNA screen, kinase assay, mutagenesis, ubiquitylation assay), replicated in follow-up publication (PMID:20090422)","pmids":["19734889","20090422"],"is_preprint":false},{"year":2002,"finding":"NEK11 (Nek11L and Nek11S isoforms) is a serine/threonine kinase whose activity is activated in response to DNA-damaging agents and replication inhibitors in a caffeine-sensitive manner, implicating it downstream of ATM/ATR. Expression of kinase-dead Nek11L (K61R) reduced aphidicolin-induced S-phase arrest and increased cell lethality, establishing a role in the S-phase checkpoint. Subcellular localization of Nek11 protein changes between interphase and prometaphase.","method":"Molecular cloning, biochemical kinase assays, expression of wild-type and kinase-negative (K61R) mutants, caffeine inhibition, cell-cycle analysis by flow cytometry, subcellular fractionation/immunostaining","journal":"The Journal of biological chemistry","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — kinase assay with dominant-negative mutant and defined cellular phenotype, single lab with multiple orthogonal methods","pmids":["12154088"],"is_preprint":false},{"year":2004,"finding":"NEK11 physically interacts with NEK2A (but not NEK2B) at the nucleolus; this interaction requires the non-catalytic C-terminal regions of both kinases and is dependent on NEK2A autophosphorylation. NEK2A directly phosphorylates NEK11 in its C-terminal non-catalytic region, relieving autoinhibition caused by an intramolecular interaction between the C-terminal domain and the N-terminal catalytic domain, thereby elevating NEK11 kinase activity. This interaction is enhanced in G1/S-arrested cells.","method":"Co-immunoprecipitation of endogenous proteins, in vitro kinase assay, domain mapping with deletion mutants, autoinhibition assay using truncated NEK11 constructs","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — reciprocal co-IP of endogenous proteins, in vitro kinase assay showing direct NEK2A phosphorylation of NEK11, domain mapping, mechanistic autoinhibition model validated by multiple methods in one study","pmids":["15161910"],"is_preprint":false},{"year":2015,"finding":"NEK11 depletion in HCT116 colorectal cancer cells prevents G2/M arrest induced by ionizing radiation or irinotecan and promotes p53-dependent apoptosis. The four splice variants of Nek11 (L/S/C/D) are predominantly cytoplasmic but undergo nucleocytoplasmic shuttling via adjacent nuclear import and export signals in the C-terminal non-catalytic domain. Nek11S in particular has an important role in the DNA damage response.","method":"RNAi-mediated depletion, flow cytometry (cell-cycle analysis), apoptosis assays, live-cell imaging/nuclear localization studies, isoform-specific analysis","journal":"PloS one","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — clean RNAi knockdown with defined cell-cycle phenotype and localization data, single lab with multiple orthogonal readouts","pmids":["26501353"],"is_preprint":false},{"year":2016,"finding":"NEK11 localizes to meiotic spindles at MI and MII stages in mouse oocytes. Knockdown of Nek11 by siRNA did not affect germinal vesicle breakdown or first polar body extrusion, but caused formation of 2-cell-like eggs, demonstrating a role for NEK11 in regulating asymmetric cell division during oocyte meiotic maturation.","method":"Western blotting, MYC-tagged mRNA microinjection, immunofluorescent staining, siRNA knockdown, oocyte maturation assays","journal":"Biochemical and biophysical research communications","confidence":"Medium","confidence_rationale":"Tier 2–3 / Moderate — direct localization by immunofluorescence linked to functional phenotype via siRNA knockdown, single lab with multiple orthogonal methods","pmids":["27150633"],"is_preprint":false},{"year":2011,"finding":"NEK11 acts as a relay kinase in a hierarchical phosphorylation cascade on CDC25A: CHK1 phosphorylates CDC25A on Ser76, and NEK11 (or CK1α) then relays phosphorylation to Ser82 in the DSG motif, promoting beta-TrCP recognition and CDC25A ubiquitination/degradation.","method":"In vitro kinase assay, hierarchical phosphorylation assay, CDC25A stabilization upon kinase depletion","journal":"Cell cycle (Georgetown, Tex.)","confidence":"Medium","confidence_rationale":"Tier 1–2 / Moderate — in vitro kinase relay assay with defined substrates, single lab but mechanistically supported by independent work (PMID:19734889)","pmids":["21252624"],"is_preprint":false},{"year":2019,"finding":"A nonsense variant in NEK11 (c.1120C>T, p.Arg374Ter) co-segregates with melanoma in a familial melanoma pedigree. The truncated protein undergoes proteasomal degradation, resulting in strongly reduced NEK11 expression (loss-of-function). Somatic loss of the wild-type allele was demonstrated in a tumor from a variant carrier, consistent with a tumor suppressor role.","method":"Whole-exome sequencing, co-segregation analysis (five affected family members), digital droplet PCR, functional in vitro assays (proteasome inhibition, protein expression analysis)","journal":"Journal of medical genetics","confidence":"Medium","confidence_rationale":"Tier 2–3 / Moderate — functional demonstration of proteasomal degradation of truncated protein, loss of heterozygosity in tumor, single family/lab","pmids":["31704778"],"is_preprint":false}],"current_model":"NEK11 is a serine/threonine kinase that functions as a key effector in the DNA damage checkpoint: it is activated by CHK1-mediated phosphorylation on Ser273, and in turn directly phosphorylates CDC25A on residues required for beta-TrCP-mediated ubiquitylation and proteasomal degradation, thereby enforcing G2/M arrest; NEK11 is also activated by NEK2A at the nucleolus via direct phosphorylation that relieves NEK11 autoinhibition, participates in the S-phase checkpoint, localizes to meiotic spindles where it regulates asymmetric oocyte division, and undergoes nucleocytoplasmic shuttling through NLS/NES signals in its C-terminal non-catalytic domain."},"narrative":{"mechanistic_narrative":"NEK11 is a serine/threonine kinase that operates as an effector of the DNA damage and replication checkpoints, coupling upstream checkpoint signaling to the destruction of CDC25A and enforcement of cell-cycle arrest [PMID:19734889, PMID:20090422, PMID:12154088]. Its kinase activity is induced by DNA-damaging agents and replication inhibitors in a caffeine-sensitive manner, and loss of catalytic function compromises aphidicolin-induced S-phase arrest, placing NEK11 downstream of ATM/ATR signaling [PMID:12154088]. In the G2/M checkpoint, CHK1 directly activates NEK11 by phosphorylating Ser273, and NEK11 in turn directly phosphorylates CDC25A on residues required for beta-TrCP-mediated polyubiquitylation and proteasomal degradation; mechanistically, NEK11 functions as a relay kinase that adds the Ser82 phosphate in the CDC25A DSG motif following CHK1 phosphorylation of Ser76, completing the phosphodegron recognized by beta-TrCP [PMID:19734889, PMID:20090422, PMID:21252624]. NEK11 activity is additionally controlled by NEK2A, which interacts with NEK11 at the nucleolus and directly phosphorylates its C-terminal non-catalytic region to relieve an autoinhibitory intramolecular contact between that domain and the N-terminal catalytic domain [PMID:15161910]. Consistent with a checkpoint-enforcing role, NEK11 depletion abrogates G2/M arrest after ionizing radiation or irinotecan and shifts cells toward p53-dependent apoptosis, and its splice isoforms shuttle between cytoplasm and nucleus via nuclear import and export signals in the C-terminal non-catalytic domain [PMID:26501353]. NEK11 also localizes to meiotic spindles and regulates asymmetric oocyte division [PMID:27150633]. A loss-of-function nonsense variant co-segregating with familial melanoma, together with somatic loss of the wild-type allele in a carrier's tumor, links NEK11 to melanoma as a candidate tumor suppressor [PMID:31704778].","teleology":[{"year":2002,"claim":"Established NEK11 as a DNA-damage- and replication-responsive kinase, answering whether this NEK family member participates in checkpoint signaling rather than only mitosis.","evidence":"Molecular cloning, kinase assays with wild-type and kinase-dead (K61R) mutants, caffeine inhibition, and cell-cycle analysis in mammalian cells","pmids":["12154088"],"confidence":"Medium","gaps":["Direct substrates not identified at this stage","Precise upstream activator (ATM vs ATR) not resolved beyond caffeine sensitivity","Mechanism connecting NEK11 activity to S-phase arrest unknown"]},{"year":2004,"claim":"Defined how NEK11 catalytic output is switched on, showing NEK2A phosphorylation relieves an intramolecular autoinhibitory contact in NEK11.","evidence":"Reciprocal co-IP of endogenous proteins, in vitro kinase assays, and domain mapping with deletion/truncation constructs at the nucleolus","pmids":["15161910"],"confidence":"High","gaps":["Phosphorylation sites on NEK11 targeted by NEK2A not precisely mapped","Physiological trigger coupling NEK2A-NEK11 activation to checkpoint contexts unclear","Relationship between nucleolar activation and downstream CDC25A control not connected"]},{"year":2009,"claim":"Placed NEK11 in a linear CHK1→NEK11→CDC25A pathway, answering how the G2/M checkpoint triggers CDC25A destruction.","evidence":"shRNA screen, RNAi depletion, in vitro kinase assays, co-IP, proteasome inhibitor experiments, and phosphosite mutagenesis (CHK1 phosphorylates NEK11 Ser273; NEK11 phosphorylates CDC25A)","pmids":["19734889","20090422"],"confidence":"High","gaps":["Structural basis of NEK11 substrate recognition on CDC25A not resolved","Whether NEK2A activation feeds into this CHK1-driven arm not tested"]},{"year":2011,"claim":"Refined the mechanism to a hierarchical phosphorylation relay, clarifying the exact CDC25A residues and division of labor between CHK1 and NEK11/CK1α.","evidence":"In vitro hierarchical phosphorylation assays and CDC25A stabilization upon kinase depletion (CHK1 on Ser76, NEK11/CK1α on Ser82 of the DSG motif)","pmids":["21252624"],"confidence":"Medium","gaps":["Relative in vivo contributions of NEK11 versus CK1α not quantified","Context-dependence of which relay kinase acts not established"]},{"year":2015,"claim":"Connected NEK11 checkpoint function to cell fate and clarified isoform localization control, showing depletion abrogates arrest and promotes p53-dependent apoptosis.","evidence":"Isoform-specific RNAi, flow cytometry, apoptosis assays, and nucleocytoplasmic shuttling analysis in HCT116 cells","pmids":["26501353"],"confidence":"Medium","gaps":["Signals/regulators governing NLS/NES-driven shuttling not identified","Distinct functions of the four splice variants only partly resolved"]},{"year":2016,"claim":"Extended NEK11 function beyond the somatic checkpoint to meiosis, showing a role in asymmetric oocyte division.","evidence":"Immunofluorescence localization to meiotic spindles plus siRNA knockdown producing 2-cell-like eggs in mouse oocytes","pmids":["27150633"],"confidence":"Medium","gaps":["Molecular substrates of NEK11 at the meiotic spindle not identified","Whether checkpoint partners (CHK1/CDC25A) mediate this role unknown"]},{"year":2019,"claim":"Implicated NEK11 as a candidate tumor suppressor, linking loss-of-function to familial melanoma.","evidence":"Whole-exome sequencing and co-segregation in a melanoma pedigree, with functional demonstration of proteasomal degradation of the truncated protein and tumor loss of the wild-type allele","pmids":["31704778"],"confidence":"Medium","gaps":["Single family; broader genetic replication absent in the corpus","Mechanistic link between checkpoint loss and melanoma not directly demonstrated"]},{"year":null,"claim":"How NEK11's nucleolar NEK2A-driven activation, its CHK1-dependent checkpoint role, and its meiotic spindle function are integrated remains unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No structural model of NEK11 substrate or activator engagement","Substrates beyond CDC25A not defined","Tumor-suppressor mechanism in melanoma not mechanistically tied to checkpoint substrates"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0140096","term_label":"catalytic activity, acting on a protein","supporting_discovery_ids":[0,2,5]},{"term_id":"GO:0016740","term_label":"transferase activity","supporting_discovery_ids":[0,1,2,5]}],"localization":[{"term_id":"GO:0005730","term_label":"nucleolus","supporting_discovery_ids":[2]},{"term_id":"GO:0005829","term_label":"cytosol","supporting_discovery_ids":[3]},{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[3]}],"pathway":[{"term_id":"R-HSA-1640170","term_label":"Cell Cycle","supporting_discovery_ids":[0,1,3]},{"term_id":"R-HSA-8953897","term_label":"Cellular responses to stimuli","supporting_discovery_ids":[0,1]},{"term_id":"R-HSA-5357801","term_label":"Programmed Cell Death","supporting_discovery_ids":[3]}],"complexes":[],"partners":["CHK1","CDC25A","NEK2A","BTRC"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q8NG66","full_name":"Serine/threonine-protein kinase Nek11","aliases":["Never in mitosis A-related kinase 11","NimA-related protein kinase 11"],"length_aa":645,"mass_kda":74.2,"function":"Protein kinase which plays an important role in the G2/M checkpoint response to DNA damage. Controls degradation of CDC25A by directly phosphorylating it on residues whose phosphorylation is required for BTRC-mediated polyubiquitination and degradation","subcellular_location":"Nucleus; Nucleus, nucleolus","url":"https://www.uniprot.org/uniprotkb/Q8NG66/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/NEK11","classification":"Not Classified","n_dependent_lines":0,"n_total_lines":1208,"dependency_fraction":0.0},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/NEK11","total_profiled":1310},"omim":[{"mim_id":"609779","title":"NIMA-RELATED KINASE 11; NEK11","url":"https://www.omim.org/entry/609779"},{"mim_id":"604043","title":"NIMA-RELATED KINASE 2; NEK2","url":"https://www.omim.org/entry/604043"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Nucleoplasm","reliability":"Supported"}],"tissue_specificity":"Tissue enhanced","tissue_distribution":"Detected in many","driving_tissues":[{"tissue":"choroid plexus","ntpm":41.9}],"url":"https://www.proteinatlas.org/search/NEK11"},"hgnc":{"alias_symbol":["FLJ23495"],"prev_symbol":[]},"alphafold":{"accession":"Q8NG66","domains":[{"cath_id":"1.10.510.10","chopping":"27-295","consensus_level":"medium","plddt":85.2254,"start":27,"end":295}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q8NG66","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q8NG66-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q8NG66-F1-predicted_aligned_error_v6.png","plddt_mean":68.31},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=NEK11","jax_strain_url":"https://www.jax.org/strain/search?query=NEK11"},"sequence":{"accession":"Q8NG66","fasta_url":"https://rest.uniprot.org/uniprotkb/Q8NG66.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q8NG66/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q8NG66"}},"corpus_meta":[{"pmid":"23132929","id":"PMC_23132929","title":"Cell cycle regulation by the NEK 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Nek11 is a novel target of Nek2A in G1/S-arrested cells.","date":"2004","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/15161910","citation_count":32,"is_preprint":false},{"pmid":"20090422","id":"PMC_20090422","title":"NEK11: linking CHK1 and CDC25A in DNA damage checkpoint signaling.","date":"2010","source":"Cell cycle (Georgetown, Tex.)","url":"https://pubmed.ncbi.nlm.nih.gov/20090422","citation_count":26,"is_preprint":false},{"pmid":"29216821","id":"PMC_29216821","title":"Molecular targets and signaling pathways regulated by nuclear translocation of syndecan-1.","date":"2017","source":"BMC cell biology","url":"https://pubmed.ncbi.nlm.nih.gov/29216821","citation_count":25,"is_preprint":false},{"pmid":"34419048","id":"PMC_34419048","title":"NEK7 promotes gastric cancer progression as a cell proliferation regulator.","date":"2021","source":"Cancer cell 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and proteasome-dependent degradation of CDC25A, thereby enforcing the DNA damage-induced G2/M checkpoint. CHK1 directly activates NEK11 by phosphorylating it on Ser273, placing CHK1 and NEK11 in a single linear pathway controlling CDC25A proteolysis.\",\n      \"method\": \"shRNA library screen, RNAi depletion, in vitro kinase assay, co-immunoprecipitation, proteasome inhibitor experiments, site-directed mutagenesis of phosphorylation sites\",\n      \"journal\": \"Nature cell biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — direct in vitro kinase assay demonstrating NEK11 phosphorylates CDC25A, CHK1-NEK11 phosphorylation confirmed, multiple orthogonal methods (shRNA screen, kinase assay, mutagenesis, ubiquitylation assay), replicated in follow-up publication (PMID:20090422)\",\n      \"pmids\": [\"19734889\", \"20090422\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2002,\n      \"finding\": \"NEK11 (Nek11L and Nek11S isoforms) is a serine/threonine kinase whose activity is activated in response to DNA-damaging agents and replication inhibitors in a caffeine-sensitive manner, implicating it downstream of ATM/ATR. Expression of kinase-dead Nek11L (K61R) reduced aphidicolin-induced S-phase arrest and increased cell lethality, establishing a role in the S-phase checkpoint. Subcellular localization of Nek11 protein changes between interphase and prometaphase.\",\n      \"method\": \"Molecular cloning, biochemical kinase assays, expression of wild-type and kinase-negative (K61R) mutants, caffeine inhibition, cell-cycle analysis by flow cytometry, subcellular fractionation/immunostaining\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — kinase assay with dominant-negative mutant and defined cellular phenotype, single lab with multiple orthogonal methods\",\n      \"pmids\": [\"12154088\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2004,\n      \"finding\": \"NEK11 physically interacts with NEK2A (but not NEK2B) at the nucleolus; this interaction requires the non-catalytic C-terminal regions of both kinases and is dependent on NEK2A autophosphorylation. NEK2A directly phosphorylates NEK11 in its C-terminal non-catalytic region, relieving autoinhibition caused by an intramolecular interaction between the C-terminal domain and the N-terminal catalytic domain, thereby elevating NEK11 kinase activity. This interaction is enhanced in G1/S-arrested cells.\",\n      \"method\": \"Co-immunoprecipitation of endogenous proteins, in vitro kinase assay, domain mapping with deletion mutants, autoinhibition assay using truncated NEK11 constructs\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — reciprocal co-IP of endogenous proteins, in vitro kinase assay showing direct NEK2A phosphorylation of NEK11, domain mapping, mechanistic autoinhibition model validated by multiple methods in one study\",\n      \"pmids\": [\"15161910\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"NEK11 depletion in HCT116 colorectal cancer cells prevents G2/M arrest induced by ionizing radiation or irinotecan and promotes p53-dependent apoptosis. The four splice variants of Nek11 (L/S/C/D) are predominantly cytoplasmic but undergo nucleocytoplasmic shuttling via adjacent nuclear import and export signals in the C-terminal non-catalytic domain. Nek11S in particular has an important role in the DNA damage response.\",\n      \"method\": \"RNAi-mediated depletion, flow cytometry (cell-cycle analysis), apoptosis assays, live-cell imaging/nuclear localization studies, isoform-specific analysis\",\n      \"journal\": \"PloS one\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — clean RNAi knockdown with defined cell-cycle phenotype and localization data, single lab with multiple orthogonal readouts\",\n      \"pmids\": [\"26501353\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"NEK11 localizes to meiotic spindles at MI and MII stages in mouse oocytes. Knockdown of Nek11 by siRNA did not affect germinal vesicle breakdown or first polar body extrusion, but caused formation of 2-cell-like eggs, demonstrating a role for NEK11 in regulating asymmetric cell division during oocyte meiotic maturation.\",\n      \"method\": \"Western blotting, MYC-tagged mRNA microinjection, immunofluorescent staining, siRNA knockdown, oocyte maturation assays\",\n      \"journal\": \"Biochemical and biophysical research communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2–3 / Moderate — direct localization by immunofluorescence linked to functional phenotype via siRNA knockdown, single lab with multiple orthogonal methods\",\n      \"pmids\": [\"27150633\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"NEK11 acts as a relay kinase in a hierarchical phosphorylation cascade on CDC25A: CHK1 phosphorylates CDC25A on Ser76, and NEK11 (or CK1α) then relays phosphorylation to Ser82 in the DSG motif, promoting beta-TrCP recognition and CDC25A ubiquitination/degradation.\",\n      \"method\": \"In vitro kinase assay, hierarchical phosphorylation assay, CDC25A stabilization upon kinase depletion\",\n      \"journal\": \"Cell cycle (Georgetown, Tex.)\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1–2 / Moderate — in vitro kinase relay assay with defined substrates, single lab but mechanistically supported by independent work (PMID:19734889)\",\n      \"pmids\": [\"21252624\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"A nonsense variant in NEK11 (c.1120C>T, p.Arg374Ter) co-segregates with melanoma in a familial melanoma pedigree. The truncated protein undergoes proteasomal degradation, resulting in strongly reduced NEK11 expression (loss-of-function). Somatic loss of the wild-type allele was demonstrated in a tumor from a variant carrier, consistent with a tumor suppressor role.\",\n      \"method\": \"Whole-exome sequencing, co-segregation analysis (five affected family members), digital droplet PCR, functional in vitro assays (proteasome inhibition, protein expression analysis)\",\n      \"journal\": \"Journal of medical genetics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2–3 / Moderate — functional demonstration of proteasomal degradation of truncated protein, loss of heterozygosity in tumor, single family/lab\",\n      \"pmids\": [\"31704778\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"NEK11 is a serine/threonine kinase that functions as a key effector in the DNA damage checkpoint: it is activated by CHK1-mediated phosphorylation on Ser273, and in turn directly phosphorylates CDC25A on residues required for beta-TrCP-mediated ubiquitylation and proteasomal degradation, thereby enforcing G2/M arrest; NEK11 is also activated by NEK2A at the nucleolus via direct phosphorylation that relieves NEK11 autoinhibition, participates in the S-phase checkpoint, localizes to meiotic spindles where it regulates asymmetric oocyte division, and undergoes nucleocytoplasmic shuttling through NLS/NES signals in its C-terminal non-catalytic domain.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"NEK11 is a serine/threonine kinase that operates as an effector of the DNA damage and replication checkpoints, coupling upstream checkpoint signaling to the destruction of CDC25A and enforcement of cell-cycle arrest [#0, #1]. Its kinase activity is induced by DNA-damaging agents and replication inhibitors in a caffeine-sensitive manner, and loss of catalytic function compromises aphidicolin-induced S-phase arrest, placing NEK11 downstream of ATM/ATR signaling [#1]. In the G2/M checkpoint, CHK1 directly activates NEK11 by phosphorylating Ser273, and NEK11 in turn directly phosphorylates CDC25A on residues required for beta-TrCP-mediated polyubiquitylation and proteasomal degradation; mechanistically, NEK11 functions as a relay kinase that adds the Ser82 phosphate in the CDC25A DSG motif following CHK1 phosphorylation of Ser76, completing the phosphodegron recognized by beta-TrCP [#0, #5]. NEK11 activity is additionally controlled by NEK2A, which interacts with NEK11 at the nucleolus and directly phosphorylates its C-terminal non-catalytic region to relieve an autoinhibitory intramolecular contact between that domain and the N-terminal catalytic domain [#2]. Consistent with a checkpoint-enforcing role, NEK11 depletion abrogates G2/M arrest after ionizing radiation or irinotecan and shifts cells toward p53-dependent apoptosis, and its splice isoforms shuttle between cytoplasm and nucleus via nuclear import and export signals in the C-terminal non-catalytic domain [#3]. NEK11 also localizes to meiotic spindles and regulates asymmetric oocyte division [#4]. A loss-of-function nonsense variant co-segregating with familial melanoma, together with somatic loss of the wild-type allele in a carrier's tumor, links NEK11 to melanoma as a candidate tumor suppressor [#6].\",\n  \"teleology\": [\n    {\n      \"year\": 2002,\n      \"claim\": \"Established NEK11 as a DNA-damage- and replication-responsive kinase, answering whether this NEK family member participates in checkpoint signaling rather than only mitosis.\",\n      \"evidence\": \"Molecular cloning, kinase assays with wild-type and kinase-dead (K61R) mutants, caffeine inhibition, and cell-cycle analysis in mammalian cells\",\n      \"pmids\": [\"12154088\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Direct substrates not identified at this stage\",\n        \"Precise upstream activator (ATM vs ATR) not resolved beyond caffeine sensitivity\",\n        \"Mechanism connecting NEK11 activity to S-phase arrest unknown\"\n      ]\n    },\n    {\n      \"year\": 2004,\n      \"claim\": \"Defined how NEK11 catalytic output is switched on, showing NEK2A phosphorylation relieves an intramolecular autoinhibitory contact in NEK11.\",\n      \"evidence\": \"Reciprocal co-IP of endogenous proteins, in vitro kinase assays, and domain mapping with deletion/truncation constructs at the nucleolus\",\n      \"pmids\": [\"15161910\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Phosphorylation sites on NEK11 targeted by NEK2A not precisely mapped\",\n        \"Physiological trigger coupling NEK2A-NEK11 activation to checkpoint contexts unclear\",\n        \"Relationship between nucleolar activation and downstream CDC25A control not connected\"\n      ]\n    },\n    {\n      \"year\": 2009,\n      \"claim\": \"Placed NEK11 in a linear CHK1\\u2192NEK11\\u2192CDC25A pathway, answering how the G2/M checkpoint triggers CDC25A destruction.\",\n      \"evidence\": \"shRNA screen, RNAi depletion, in vitro kinase assays, co-IP, proteasome inhibitor experiments, and phosphosite mutagenesis (CHK1 phosphorylates NEK11 Ser273; NEK11 phosphorylates CDC25A)\",\n      \"pmids\": [\"19734889\", \"20090422\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Structural basis of NEK11 substrate recognition on CDC25A not resolved\",\n        \"Whether NEK2A activation feeds into this CHK1-driven arm not tested\"\n      ]\n    },\n    {\n      \"year\": 2011,\n      \"claim\": \"Refined the mechanism to a hierarchical phosphorylation relay, clarifying the exact CDC25A residues and division of labor between CHK1 and NEK11/CK1\\u03b1.\",\n      \"evidence\": \"In vitro hierarchical phosphorylation assays and CDC25A stabilization upon kinase depletion (CHK1 on Ser76, NEK11/CK1\\u03b1 on Ser82 of the DSG motif)\",\n      \"pmids\": [\"21252624\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Relative in vivo contributions of NEK11 versus CK1\\u03b1 not quantified\",\n        \"Context-dependence of which relay kinase acts not established\"\n      ]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Connected NEK11 checkpoint function to cell fate and clarified isoform localization control, showing depletion abrogates arrest and promotes p53-dependent apoptosis.\",\n      \"evidence\": \"Isoform-specific RNAi, flow cytometry, apoptosis assays, and nucleocytoplasmic shuttling analysis in HCT116 cells\",\n      \"pmids\": [\"26501353\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Signals/regulators governing NLS/NES-driven shuttling not identified\",\n        \"Distinct functions of the four splice variants only partly resolved\"\n      ]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"Extended NEK11 function beyond the somatic checkpoint to meiosis, showing a role in asymmetric oocyte division.\",\n      \"evidence\": \"Immunofluorescence localization to meiotic spindles plus siRNA knockdown producing 2-cell-like eggs in mouse oocytes\",\n      \"pmids\": [\"27150633\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Molecular substrates of NEK11 at the meiotic spindle not identified\",\n        \"Whether checkpoint partners (CHK1/CDC25A) mediate this role unknown\"\n      ]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Implicated NEK11 as a candidate tumor suppressor, linking loss-of-function to familial melanoma.\",\n      \"evidence\": \"Whole-exome sequencing and co-segregation in a melanoma pedigree, with functional demonstration of proteasomal degradation of the truncated protein and tumor loss of the wild-type allele\",\n      \"pmids\": [\"31704778\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Single family; broader genetic replication absent in the corpus\",\n        \"Mechanistic link between checkpoint loss and melanoma not directly demonstrated\"\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How NEK11's nucleolar NEK2A-driven activation, its CHK1-dependent checkpoint role, and its meiotic spindle function are integrated remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"No structural model of NEK11 substrate or activator engagement\",\n        \"Substrates beyond CDC25A not defined\",\n        \"Tumor-suppressor mechanism in melanoma not mechanistically tied to checkpoint substrates\"\n      ]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0140096\", \"supporting_discovery_ids\": [0, 2, 5]},\n      {\"term_id\": \"GO:0016740\", \"supporting_discovery_ids\": [0, 1, 2, 5]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005730\", \"supporting_discovery_ids\": [2]},\n      {\"term_id\": \"GO:0005829\", \"supporting_discovery_ids\": [3]},\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [3]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-1640170\", \"supporting_discovery_ids\": [0, 1, 3]},\n      {\"term_id\": \"R-HSA-8953897\", \"supporting_discovery_ids\": [0, 1]},\n      {\"term_id\": \"R-HSA-5357801\", \"supporting_discovery_ids\": [3]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\"CHK1\", \"CDC25A\", \"NEK2A\", \"BTRC\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":7,"faith_total":7,"faith_pct":100.0}}