{"gene":"ANKS6","run_date":"2026-04-28T17:12:37","timeline":{"discoveries":[{"year":2013,"finding":"ANKS6 localizes to the proximal cilium (inversin compartment) and functions as a central component of a nephronophthisis module, directly connecting NEK8 (NPHP9) to INVS (NPHP2) and NPHP3. The oxygen sensor HIF1AN hydroxylates ANKS6 and INVS, altering the composition of the ANKS6-INVS-NPHP3 module.","method":"Co-immunoprecipitation, knockdown in zebrafish and Xenopus laevis, network analysis, identification of HIF1AN as hydroxylase","journal":"Nature genetics","confidence":"High","confidence_rationale":"Tier 2 — reciprocal Co-IP, in vivo knockdown with defined phenotypes, PTM identification, replicated across labs","pmids":["23793029"],"is_preprint":false},{"year":2015,"finding":"ANKS6 is both a substrate and activator of the ciliary kinase NEK8: ANKS6 binds to the NEK8 kinase domain to activate it, while ANKS6 itself requires NEK8 for proper localization to the ciliary inversin compartment. The Anks6(Streaker) mouse mutation reduces ANKS6 interaction with NEK8, precluding NEK8 activation, whereas the Nek8(Roc) mutation inactivates NEK8 kinase function while preserving ANKS6 localization.","method":"Co-immunoprecipitation, mouse genetic models (Anks6(Streaker) and Nek8(Roc) point mutations), kinase activity assays, immunofluorescence localization","journal":"Nature communications","confidence":"High","confidence_rationale":"Tier 2 — reciprocal Co-IP, two independent mouse mutants with distinct mechanistic phenotypes, kinase activation assay","pmids":["25599650"],"is_preprint":false},{"year":2014,"finding":"The SAM domain of ANKS6 directly binds one end of ANKS3-SAM polymers, forming a heterodimeric complex. The disease-causing R823W point mutation dramatically destabilizes the ANKS6 SAM domain, abolishing its interaction with ANKS3-SAM. Crystal structures of the ANKS3-SAM polymer and the ANKS3-SAM/ANKS6-SAM complex were determined.","method":"X-ray crystallography, in vitro binding assays, mutagenesis (R823W), biochemical characterization of SAM domain interactions","journal":"BMC structural biology","confidence":"High","confidence_rationale":"Tier 1 — crystal structure with mutagenesis and biochemical validation in a single study","pmids":["24998259"],"is_preprint":false},{"year":2018,"finding":"INV (NPHP2/INVS) and NPHP3 cooperate in the ciliary inversin compartment to promote phosphorylation of ANKS6 by NEK8. Loss of ciliary NPHP3 (via mutation of its UNC119-binding myristoylation signal) impairs ANKS6 phosphorylation and causes accumulation of non-phosphorylated ANKS6 in cystic kidneys, identifying ANKS6 as a signal mediator linking cilia to the cytoplasm.","method":"Knock-in mouse model (Nphp3 G2A) with defective ciliary localization signal, phosphorylation analysis, immunofluorescence, co-immunoprecipitation","journal":"Kidney international","confidence":"High","confidence_rationale":"Tier 2 — in vivo mouse model with biochemical phosphorylation readout and localization studies","pmids":["29395339"],"is_preprint":false},{"year":2017,"finding":"ANKS3 recruits ANKS6 to BICC1, and together the three proteins cooperatively form giant macromolecular complexes through combined SAM domain interactions, flanking sequences, and SAM-independent protein-protein and protein-mRNA interactions. Neither ANKS3 nor ANKS6 alone formed macroscopic homopolymers in vivo.","method":"Crystal structure of Bicc1-SAM polymer, co-immunoprecipitation, in vivo interaction mapping of full-length and domain constructs","journal":"Structure","confidence":"High","confidence_rationale":"Tier 1-2 — crystal structure plus biochemical validation of cooperative complex formation","pmids":["29290488"],"is_preprint":false},{"year":2015,"finding":"ANKS6 SAM domain interacts with BICC1 in addition to ANKS3; the I747N mutation in mouse ANKS6 SAM domain disrupts the ANKS6-BICC1 interaction (distinct from R823W which disrupts ANKS6-ANKS3), and causes renal cysts, demonstrating the SAM domain mediates different protein complexes critical for kidney structure.","method":"ENU mutagenesis screen, co-immunoprecipitation, comparative phenotypic analysis of rat (R823W) and mouse (I747N) models","journal":"Kidney international","confidence":"Medium","confidence_rationale":"Tier 2 — Co-IP with in vivo genetic models, single lab","pmids":["26039630"],"is_preprint":false},{"year":2015,"finding":"ANKS3 and ANKS6 interact directly through their SAM domains, and ANKS3 co-localizes with ANKS6 in mouse renal cilia. Yeast two-hybrid and co-immunoprecipitation confirmed the interaction, with amino acid 823 in ANKS6 being critical for binding.","method":"Yeast two-hybrid, co-immunoprecipitation, in vivo ciliary co-localization by immunofluorescence","journal":"PloS one","confidence":"Medium","confidence_rationale":"Tier 2-3 — two orthogonal methods (Y2H + Co-IP) with in vivo localization, single lab","pmids":["26327442"],"is_preprint":false},{"year":2020,"finding":"ANKS6 binds to Hippo pathway effector proteins YAP1, TAZ, and TEAD4 and promotes their transcriptional activity. Loss of Anks6 in knockout mice causes dysregulation of YAP transcriptional activity in biliary epithelial cells, leading to bile duct morphogenesis defects and ductal plate malformations, establishing ANKS6 as an antagonist of Hippo signaling during liver development.","method":"Anks6 knockout mouse model, co-immunoprecipitation (ANKS6 with YAP1/TAZ/TEAD4), biochemical analyses, histology, expression studies","journal":"Human molecular genetics","confidence":"High","confidence_rationale":"Tier 2 — KO mouse with defined phenotype plus direct protein interaction demonstrated by Co-IP, multiple pathway components tested","pmids":["32886109"],"is_preprint":false},{"year":2010,"finding":"Transgenic overexpression of the mutant Anks6(p.R823W) in renal tubular epithelium causes polycystic kidney disease in a dominant-negative fashion, establishing a causal link between the R823W mutation and cystogenesis, with cyst development accompanied by enhanced c-myc expression, proliferation, apoptosis, and lack of p21 up-regulation.","method":"Transgenic rat model overexpressing mutant Anks6(R823W), Northern blot, in situ hybridization, histology","journal":"The American journal of pathology","confidence":"Medium","confidence_rationale":"Tier 2 — in vivo transgenic model establishing causal role with multiple cellular readouts, single lab","pmids":["21119215"],"is_preprint":false},{"year":2014,"finding":"Loss-of-function mutations in ANKS6 are associated with increased levels of total and active β-catenin in precystic tubuli in Han:SPRD Cy/+ rats, suggesting that ANKS6 mutations may contribute to nephronophthisis through dysregulation of Wnt/β-catenin signaling.","method":"Immunohistochemistry in human embryonic kidney tissue and rat model, β-catenin activity assays","journal":"Journal of the American Society of Nephrology : JASN","confidence":"Low","confidence_rationale":"Tier 3 — single method in rat model, no direct mechanistic link established","pmids":["24610927"],"is_preprint":false},{"year":2022,"finding":"ANKS6 deficiency in patient-derived fibroblasts leads to impaired integrity of the ciliary inversin compartment, reduced cilia length, dysregulation of YAP nuclear localization, disrupted ciliary YAP localization, altered Wnt target gene transcription, and deranged subcellular localization of endocytic recycling compartment components.","method":"Patient-derived fibroblasts, immunofluorescence, YAP localization analysis, β-catenin/GSK3β phosphorylation analysis","journal":"Human molecular genetics","confidence":"Medium","confidence_rationale":"Tier 2 — patient-derived cell model with multiple orthogonal pathway readouts, single lab","pmids":["34740236"],"is_preprint":false},{"year":2023,"finding":"ANKS6 regulates Bicc1 ribonucleoprotein complex assembly: ANKS6 induces structural remodeling of associated ANKS3, modulating ANKS3's C-terminal coiled-coil domain interaction with Bicc1 that otherwise inhibits mRNA binding. In vitro reconstitution and AlphaFold structure predictions revealed a novel ANKS3-Bicc1 interaction mode regulated by ANKS6.","method":"In vitro reconstitution, AlphaFold structure prediction with biochemical validation, CRISPR-engineered truncations in mouse, mRNA decay assays","journal":"PLoS biology","confidence":"High","confidence_rationale":"Tier 1-2 — in vitro reconstitution plus in vivo genetic validation and structural prediction with biochemical confirmation","pmids":["37733651"],"is_preprint":false},{"year":2023,"finding":"ANKS6, when co-recruited by ANKS3, reinstates Bicc1 condensation and ribonucleoparticle assembly after ANKS3-mediated dispersal of Bicc1 granules. ANKS3 disperses Bicc1 granules and releases bound mRNAs, while ANKS6 co-recruitment by ANKS3 restores Bicc1 polymerization and mRNA sequestration, representing a dual regulatory mechanism for Bicc1 phase transitioning.","method":"Live cell imaging of condensate/granule dynamics, RNA binding assays, co-immunoprecipitation, overexpression/knockdown in cell lines","journal":"iScience","confidence":"Medium","confidence_rationale":"Tier 2 — cell-based and biochemical assays with multiple readouts, single lab","pmids":["37275520"],"is_preprint":false},{"year":2024,"finding":"In C. elegans, the Inversin complex (containing INVS/MLT-4, NEK8/NEKL-2, and the ANKS6 ortholog) is activated by dimerization. Stimulated dimerization of MLT-4 (INVS) or NEKL-2 (NEK8) using optogenetics is sufficient to activate the complex, and dimerization of NEKL-2 bypasses a lethal MLT-4 mutant, demonstrating that dynamic switching between an active dimer and an inactive monomer gates Inversin complex output.","method":"C. elegans genetics, genome engineering (RFP tags, monomerization), optogenetic stimulation of dimerization, gain-of-function allele characterization","journal":"bioRxiv","confidence":"Medium","confidence_rationale":"Tier 2 — orthogonal genetic and optogenetic approaches in C. elegans ortholog, preprint not yet peer-reviewed","pmids":["bio_10.1101_2024.05.17.594761"],"is_preprint":true},{"year":2022,"finding":"In Anks6 liver-specific knockout mice, portal fibrosis development coincides with accumulation of inflammatory M1-like macrophages in the periportal tissue; depletion of macrophages with clodronate liposomes reduced inflammatory gene expression, fibrosis, and biliary dysfunction, establishing a causal role for macrophage-driven inflammation downstream of ANKS6 deficiency in hepatic fibrosis.","method":"Liver-specific Anks6 knockout mouse, clodronate liposome macrophage depletion, flow cytometry, gene expression analysis, histology","journal":"FASEB journal","confidence":"Medium","confidence_rationale":"Tier 2 — KO model with depletion rescue experiment establishing macrophage causality, single lab","pmids":["35032404"],"is_preprint":false}],"current_model":"ANKS6 is a ciliary inversin compartment protein that acts as a central scaffold and signal mediator: it activates NEK8 kinase by binding its kinase domain, is itself phosphorylated by NEK8 (promoted by INV/NPHP3), interacts with INVS/NPHP2 and NPHP3 to form a nephronophthisis module, engages ANKS3 and BICC1 through SAM domain interactions to regulate Bicc1 ribonucleoprotein assembly and mRNA phase transitioning, and promotes YAP1/TAZ/TEAD4 transcriptional activity to antagonize Hippo signaling during bile duct development, with disease-causing mutations (R823W, I747N) disrupting these specific protein-protein interactions."},"narrative":{"teleology":[{"year":2010,"claim":"Establishing that the R823W mutation is sufficient to cause polycystic kidney disease resolved whether ANKS6 dysfunction is directly causative of cystogenesis rather than merely associated.","evidence":"Transgenic rat overexpressing mutant Anks6(R823W) in renal epithelium developed dominant-negative cystic disease with enhanced proliferation and c-myc expression","pmids":["21119215"],"confidence":"Medium","gaps":["Mechanism by which R823W acts as dominant-negative was unknown","Direct molecular targets of ANKS6 unidentified at this stage","Relationship to ciliary function not established"]},{"year":2013,"claim":"Identifying ANKS6 as a central hub connecting NEK8, INVS, and NPHP3 at the ciliary inversin compartment established the molecular logic of the nephronophthisis signaling module and explained how distinct NPHP gene products converge.","evidence":"Reciprocal Co-IP, zebrafish/Xenopus knockdown, and identification of HIF1AN-mediated hydroxylation of ANKS6 and INVS","pmids":["23793029"],"confidence":"High","gaps":["Functional consequence of HIF1AN hydroxylation on module activity unknown","Directionality of signal flow through the module unresolved"]},{"year":2014,"claim":"Solving the crystal structure of the ANKS3-SAM/ANKS6-SAM complex revealed the atomic basis of ANKS6 SAM domain interactions and demonstrated that R823W destabilizes the SAM fold, explaining loss of ANKS3 binding.","evidence":"X-ray crystallography of ANKS3-SAM polymer and ANKS3-SAM/ANKS6-SAM heterodimer, mutagenesis, in vitro binding assays","pmids":["24998259"],"confidence":"High","gaps":["Downstream signaling consequences of ANKS3-ANKS6 disruption unclear","Whether additional SAM-domain partners exist was not tested"]},{"year":2015,"claim":"Demonstrating that ANKS6 both activates NEK8 kinase and requires NEK8 for its own ciliary localization established a mutual-dependence relationship, while the I747N mutation defined a second SAM-domain interaction surface specific for BICC1.","evidence":"Kinase activity assays, Co-IP, and comparative analysis of Anks6(Streaker) and Nek8(Roc) mouse mutants; ENU mutagenesis screen identifying I747N in mouse","pmids":["25599650","26039630"],"confidence":"High","gaps":["NEK8 substrates downstream of ANKS6-mediated activation not identified","How I747N and R823W mutations produce overlapping yet distinct phenotypes at the cellular level"]},{"year":2017,"claim":"Showing that ANKS3 recruits ANKS6 to BICC1 and that the three proteins cooperatively form giant macromolecular complexes revealed a hierarchical assembly mechanism dependent on combined SAM and non-SAM interactions.","evidence":"Crystal structure of Bicc1-SAM polymer, Co-IP, domain-mapping of full-length constructs","pmids":["29290488"],"confidence":"High","gaps":["Functional RNA targets of the ANKS3-ANKS6-BICC1 complex unknown","Stoichiometry and dynamics of the complex in vivo unresolved"]},{"year":2018,"claim":"Establishing that NPHP3 ciliary localization is required for NEK8-mediated phosphorylation of ANKS6 defined ANKS6 as a signal mediator that relays ciliary events to the cytoplasm.","evidence":"Nphp3 G2A knock-in mouse with defective myristoylation/ciliary targeting; phosphorylation analysis of ANKS6","pmids":["29395339"],"confidence":"High","gaps":["Identity of ANKS6 phosphorylation sites not mapped","Cytoplasmic effectors of phosphorylated ANKS6 unknown"]},{"year":2020,"claim":"Discovery that ANKS6 binds YAP1/TAZ/TEAD4 and promotes their transcriptional activity identified a non-ciliary effector output, explaining bile duct morphogenesis defects in Anks6 knockouts as Hippo pathway dysregulation.","evidence":"Anks6 KO mouse with ductal plate malformations, Co-IP of ANKS6 with YAP1/TAZ/TEAD4","pmids":["32886109"],"confidence":"High","gaps":["Whether ANKS6 regulation of Hippo signaling is cilium-dependent or independent unclear","Direct versus indirect mechanism of ANKS6 promotion of YAP/TAZ activity not distinguished"]},{"year":2022,"claim":"Patient-derived fibroblasts confirmed that ANKS6 deficiency impairs inversin compartment integrity, cilia length, and YAP nuclear localization in human cells, while liver-specific knockout revealed macrophage-driven inflammation as a downstream driver of portal fibrosis.","evidence":"Patient fibroblasts with immunofluorescence/pathway analysis; liver-specific Anks6 KO with clodronate liposome macrophage depletion rescuing fibrosis","pmids":["34740236","35032404"],"confidence":"Medium","gaps":["Whether ciliary and Hippo/Wnt phenotypes represent a single linear pathway or parallel outputs unresolved","Cell-autonomous versus non-cell-autonomous contributions to kidney pathology not distinguished"]},{"year":2023,"claim":"Reconstitution and live-imaging studies revealed a dual regulatory cycle in which ANKS3 disperses Bicc1 condensates and releases mRNAs, while ANKS6 co-recruitment by ANKS3 restores Bicc1 polymerization and mRNA sequestration, establishing ANKS6 as a positive regulator of ribonucleoprotein phase transitioning.","evidence":"In vitro reconstitution with AlphaFold-guided mutagenesis, CRISPR truncations in mouse, live-cell imaging of condensate dynamics, RNA binding assays","pmids":["37733651","37275520"],"confidence":"High","gaps":["Specific mRNA targets regulated by this ANKS3-ANKS6-BICC1 cycle in vivo not identified","Whether phase-transition regulation connects to NEK8 kinase activity unknown"]},{"year":null,"claim":"Key unresolved questions include the identity of NEK8 substrates downstream of ANKS6-mediated activation, the specific ANKS6 phosphorylation sites and their functional consequences, the in vivo RNA targets of the ANKS6-ANKS3-BICC1 condensate cycle, and whether ANKS6 regulation of Hippo signaling is cilium-dependent.","evidence":"","pmids":[],"confidence":"Low","gaps":["NEK8 downstream substrates unidentified","ANKS6 phosphosite mapping lacking","In vivo mRNA targets of BICC1 condensates regulated by ANKS6 unknown"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[0,1,4]},{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[1,11,12]},{"term_id":"GO:0140110","term_label":"transcription regulator activity","supporting_discovery_ids":[7]}],"localization":[{"term_id":"GO:0005929","term_label":"cilium","supporting_discovery_ids":[0,1,3,6]},{"term_id":"GO:0005829","term_label":"cytosol","supporting_discovery_ids":[3,12]}],"pathway":[{"term_id":"R-HSA-162582","term_label":"Signal Transduction","supporting_discovery_ids":[7,10]},{"term_id":"R-HSA-1852241","term_label":"Organelle biogenesis and maintenance","supporting_discovery_ids":[0,1,3]},{"term_id":"R-HSA-1266738","term_label":"Developmental Biology","supporting_discovery_ids":[7,14]},{"term_id":"R-HSA-1643685","term_label":"Disease","supporting_discovery_ids":[8,9]}],"complexes":["Inversin compartment complex (ANKS6-NEK8-INVS-NPHP3)","ANKS3-ANKS6-BICC1 ribonucleoprotein complex"],"partners":["NEK8","INVS","NPHP3","ANKS3","BICC1","YAP1","TAZ","TEAD4"],"other_free_text":[]},"mechanistic_narrative":"ANKS6 is a ciliary inversin compartment scaffold that integrates kinase signaling, ribonucleoprotein regulation, and transcriptional control in epithelial morphogenesis. It directly binds and activates the NEK8 kinase through its kinase domain while simultaneously connecting NEK8 to INVS/NPHP2 and NPHP3, forming a nephronophthisis signaling module in which ANKS6 is itself phosphorylated by NEK8 in a manner dependent on ciliary NPHP3 localization [PMID:23793029, PMID:25599650, PMID:29395339]. Through its SAM domain, ANKS6 caps ANKS3 polymers and cooperatively assembles with ANKS3 and BICC1 into macromolecular condensates that regulate Bicc1 mRNA phase transitioning and ribonucleoprotein granule dynamics, with disease-causing mutations R823W and I747N selectively disrupting the ANKS3 and BICC1 interactions respectively [PMID:24998259, PMID:29290488, PMID:37733651, PMID:37275520]. ANKS6 also binds YAP1, TAZ, and TEAD4 to promote their transcriptional activity, and loss of Anks6 causes bile duct malformations and nephronophthisis-associated cystic kidney disease [PMID:32886109, PMID:21119215]."},"prefetch_data":{"uniprot":{"accession":"Q68DC2","full_name":"Ankyrin repeat and SAM domain-containing protein 6","aliases":["Ankyrin repeat domain-containing protein 14","SamCystin","Sterile alpha motif domain-containing protein 6","SAM domain-containing protein 6"],"length_aa":871,"mass_kda":92.2,"function":"Required for renal function","subcellular_location":"Cell projection, cilium; Cytoplasm","url":"https://www.uniprot.org/uniprotkb/Q68DC2/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/ANKS6","classification":"Not Classified","n_dependent_lines":203,"n_total_lines":1208,"dependency_fraction":0.16804635761589404},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[{"gene":"CALM1","stoichiometry":0.2},{"gene":"CALM2","stoichiometry":0.2},{"gene":"CALM3","stoichiometry":0.2},{"gene":"CETN3","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/search/ANKS6","total_profiled":1310},"omim":[{"mim_id":"617310","title":"ANKYRIN REPEAT AND STERILE ALPHA MOTIF DOMAINS-CONTAINING PROTEIN 3; ANKS3","url":"https://www.omim.org/entry/617310"},{"mim_id":"615382","title":"NEPHRONOPHTHISIS 16; NPHP16","url":"https://www.omim.org/entry/615382"},{"mim_id":"615370","title":"ANKYRIN REPEAT AND STERILE ALPHA MOTIF DOMAINS-CONTAINING PROTEIN 6; ANKS6","url":"https://www.omim.org/entry/615370"},{"mim_id":"609799","title":"NIMA-RELATED KINASE 8; NEK8","url":"https://www.omim.org/entry/609799"},{"mim_id":"608002","title":"NEPHROCYSTIN 3; NPHP3","url":"https://www.omim.org/entry/608002"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Approved","locations":[{"location":"Nucleoli fibrillar center","reliability":"Approved"},{"location":"Primary cilium","reliability":"Approved"},{"location":"Cytosol","reliability":"Additional"}],"tissue_specificity":"Tissue enhanced","tissue_distribution":"Detected in many","driving_tissues":[{"tissue":"brain","ntpm":26.4}],"url":"https://www.proteinatlas.org/search/ANKS6"},"hgnc":{"alias_symbol":["FLJ36928","NPHP16"],"prev_symbol":["SAMD6","ANKRD14"]},"alphafold":{"accession":"Q68DC2","domains":[{"cath_id":"1.25.40.20","chopping":"218-286","consensus_level":"medium","plddt":87.2596,"start":218,"end":286},{"cath_id":"1.25.40.20","chopping":"294-419","consensus_level":"medium","plddt":84.0954,"start":294,"end":419},{"cath_id":"1.10.287","chopping":"800-844","consensus_level":"medium","plddt":72.1573,"start":800,"end":844}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q68DC2","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q68DC2-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q68DC2-F1-predicted_aligned_error_v6.png","plddt_mean":59.88},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=ANKS6","jax_strain_url":"https://www.jax.org/strain/search?query=ANKS6"},"sequence":{"accession":"Q68DC2","fasta_url":"https://rest.uniprot.org/uniprotkb/Q68DC2.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q68DC2/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q68DC2"}},"corpus_meta":[{"pmid":"23793029","id":"PMC_23793029","title":"ANKS6 is a central component of a nephronophthisis module linking NEK8 to INVS and NPHP3.","date":"2013","source":"Nature genetics","url":"https://pubmed.ncbi.nlm.nih.gov/23793029","citation_count":170,"is_preprint":false},{"pmid":"25599650","id":"PMC_25599650","title":"ANKS6 is the critical activator of NEK8 kinase in embryonic situs determination and organ patterning.","date":"2015","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/25599650","citation_count":47,"is_preprint":false},{"pmid":"24998259","id":"PMC_24998259","title":"Characterization of the SAM domain of the PKD-related protein ANKS6 and its interaction with ANKS3.","date":"2014","source":"BMC structural biology","url":"https://pubmed.ncbi.nlm.nih.gov/24998259","citation_count":41,"is_preprint":false},{"pmid":"24610927","id":"PMC_24610927","title":"Mutations in ANKS6 cause a nephronophthisis-like phenotype with ESRD.","date":"2014","source":"Journal of the American Society of Nephrology : JASN","url":"https://pubmed.ncbi.nlm.nih.gov/24610927","citation_count":33,"is_preprint":false},{"pmid":"29290488","id":"PMC_29290488","title":"Crystal Structure of Bicc1 SAM Polymer and Mapping of Interactions between the Ciliopathy-Associated Proteins Bicc1, ANKS3, and ANKS6.","date":"2017","source":"Structure (London, England : 1993)","url":"https://pubmed.ncbi.nlm.nih.gov/29290488","citation_count":22,"is_preprint":false},{"pmid":"21119215","id":"PMC_21119215","title":"Transgenic overexpression of Anks6(p.R823W) causes polycystic kidney disease in rats.","date":"2010","source":"The American journal of pathology","url":"https://pubmed.ncbi.nlm.nih.gov/21119215","citation_count":22,"is_preprint":false},{"pmid":"26039630","id":"PMC_26039630","title":"The SAM domain of ANKS6 has different interacting partners and mutations can induce different cystic phenotypes.","date":"2015","source":"Kidney 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Societies for Experimental Biology","url":"https://pubmed.ncbi.nlm.nih.gov/35032404","citation_count":6,"is_preprint":false},{"pmid":"31635528","id":"PMC_31635528","title":"Clinical and Pathological Features of a Newborn With Compound Heterozygous ANKS6 Variants.","date":"2019","source":"Pediatric and developmental pathology : the official journal of the Society for Pediatric Pathology and the Paediatric Pathology Society","url":"https://pubmed.ncbi.nlm.nih.gov/31635528","citation_count":6,"is_preprint":false},{"pmid":"37733651","id":"PMC_37733651","title":"Bicc1 ribonucleoprotein complexes specifying organ laterality are licensed by ANKS6-induced structural remodeling of associated ANKS3.","date":"2023","source":"PLoS biology","url":"https://pubmed.ncbi.nlm.nih.gov/37733651","citation_count":5,"is_preprint":false},{"pmid":"37275520","id":"PMC_37275520","title":"Antagonistic interactions among structured domains in the multivalent Bicc1-ANKS3-ANKS6 protein network govern phase transitioning of target mRNAs.","date":"2023","source":"iScience","url":"https://pubmed.ncbi.nlm.nih.gov/37275520","citation_count":4,"is_preprint":false},{"pmid":"31678577","id":"PMC_31678577","title":"Whole-exome sequencing identifies a novel compound heterozygous mutation of ANKS6 gene in a Chinese nephronophthisis patient.","date":"2019","source":"Clinica chimica acta; international journal of clinical chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/31678577","citation_count":4,"is_preprint":false},{"pmid":"31041607","id":"PMC_31041607","title":"Metabolic perturbations caused by depletion of nephronophthisis factor Anks6 in mIMCD3 cells.","date":"2019","source":"Metabolomics : Official journal of the Metabolomic Society","url":"https://pubmed.ncbi.nlm.nih.gov/31041607","citation_count":4,"is_preprint":false},{"pmid":"39596574","id":"PMC_39596574","title":"ANKS6 Variants Underlie Polycystic Kidneys in Prenatal and Neonatal Cases.","date":"2024","source":"Genes","url":"https://pubmed.ncbi.nlm.nih.gov/39596574","citation_count":1,"is_preprint":false},{"pmid":"37525964","id":"PMC_37525964","title":"Biallelic ANKS6 null variants cause notable extrarenal phenotypes in a nephronophthisis patient and lead to hepatobiliary abnormalities by YAP1 deficiency.","date":"2023","source":"Clinical genetics","url":"https://pubmed.ncbi.nlm.nih.gov/37525964","citation_count":1,"is_preprint":false},{"pmid":"41811399","id":"PMC_41811399","title":"A Novel Anks6 Nonsense Variant Promotes Polycystic Kidney Disease in Han:SPRD-Cy Rats and its Homozygosity is Prenatally Lethal.","date":"2026","source":"Kidney360","url":"https://pubmed.ncbi.nlm.nih.gov/41811399","citation_count":0,"is_preprint":false},{"pmid":null,"id":"bio_10.1101_2024.05.17.594761","title":"Dimerization activates the Inversin complex in<i>C. elegans</i>","date":"2024-05-18","source":"bioRxiv","url":"https://doi.org/10.1101/2024.05.17.594761","citation_count":0,"is_preprint":true}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":11912,"output_tokens":3832,"usd":0.046608},"stage2":{"model":"claude-opus-4-6","input_tokens":7250,"output_tokens":2829,"usd":0.160463},"total_usd":0.207071,"stage1_batch_id":"msgbatch_01TqNM6p6FsoMBT2jzQTwKBr","stage2_batch_id":"msgbatch_01Ya473eco8sTHbvRymQaU8o","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2013,\n      \"finding\": \"ANKS6 localizes to the proximal cilium (inversin compartment) and functions as a central component of a nephronophthisis module, directly connecting NEK8 (NPHP9) to INVS (NPHP2) and NPHP3. The oxygen sensor HIF1AN hydroxylates ANKS6 and INVS, altering the composition of the ANKS6-INVS-NPHP3 module.\",\n      \"method\": \"Co-immunoprecipitation, knockdown in zebrafish and Xenopus laevis, network analysis, identification of HIF1AN as hydroxylase\",\n      \"journal\": \"Nature genetics\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — reciprocal Co-IP, in vivo knockdown with defined phenotypes, PTM identification, replicated across labs\",\n      \"pmids\": [\"23793029\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"ANKS6 is both a substrate and activator of the ciliary kinase NEK8: ANKS6 binds to the NEK8 kinase domain to activate it, while ANKS6 itself requires NEK8 for proper localization to the ciliary inversin compartment. The Anks6(Streaker) mouse mutation reduces ANKS6 interaction with NEK8, precluding NEK8 activation, whereas the Nek8(Roc) mutation inactivates NEK8 kinase function while preserving ANKS6 localization.\",\n      \"method\": \"Co-immunoprecipitation, mouse genetic models (Anks6(Streaker) and Nek8(Roc) point mutations), kinase activity assays, immunofluorescence localization\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — reciprocal Co-IP, two independent mouse mutants with distinct mechanistic phenotypes, kinase activation assay\",\n      \"pmids\": [\"25599650\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"The SAM domain of ANKS6 directly binds one end of ANKS3-SAM polymers, forming a heterodimeric complex. The disease-causing R823W point mutation dramatically destabilizes the ANKS6 SAM domain, abolishing its interaction with ANKS3-SAM. Crystal structures of the ANKS3-SAM polymer and the ANKS3-SAM/ANKS6-SAM complex were determined.\",\n      \"method\": \"X-ray crystallography, in vitro binding assays, mutagenesis (R823W), biochemical characterization of SAM domain interactions\",\n      \"journal\": \"BMC structural biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — crystal structure with mutagenesis and biochemical validation in a single study\",\n      \"pmids\": [\"24998259\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"INV (NPHP2/INVS) and NPHP3 cooperate in the ciliary inversin compartment to promote phosphorylation of ANKS6 by NEK8. Loss of ciliary NPHP3 (via mutation of its UNC119-binding myristoylation signal) impairs ANKS6 phosphorylation and causes accumulation of non-phosphorylated ANKS6 in cystic kidneys, identifying ANKS6 as a signal mediator linking cilia to the cytoplasm.\",\n      \"method\": \"Knock-in mouse model (Nphp3 G2A) with defective ciliary localization signal, phosphorylation analysis, immunofluorescence, co-immunoprecipitation\",\n      \"journal\": \"Kidney international\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — in vivo mouse model with biochemical phosphorylation readout and localization studies\",\n      \"pmids\": [\"29395339\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"ANKS3 recruits ANKS6 to BICC1, and together the three proteins cooperatively form giant macromolecular complexes through combined SAM domain interactions, flanking sequences, and SAM-independent protein-protein and protein-mRNA interactions. Neither ANKS3 nor ANKS6 alone formed macroscopic homopolymers in vivo.\",\n      \"method\": \"Crystal structure of Bicc1-SAM polymer, co-immunoprecipitation, in vivo interaction mapping of full-length and domain constructs\",\n      \"journal\": \"Structure\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 — crystal structure plus biochemical validation of cooperative complex formation\",\n      \"pmids\": [\"29290488\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"ANKS6 SAM domain interacts with BICC1 in addition to ANKS3; the I747N mutation in mouse ANKS6 SAM domain disrupts the ANKS6-BICC1 interaction (distinct from R823W which disrupts ANKS6-ANKS3), and causes renal cysts, demonstrating the SAM domain mediates different protein complexes critical for kidney structure.\",\n      \"method\": \"ENU mutagenesis screen, co-immunoprecipitation, comparative phenotypic analysis of rat (R823W) and mouse (I747N) models\",\n      \"journal\": \"Kidney international\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — Co-IP with in vivo genetic models, single lab\",\n      \"pmids\": [\"26039630\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"ANKS3 and ANKS6 interact directly through their SAM domains, and ANKS3 co-localizes with ANKS6 in mouse renal cilia. Yeast two-hybrid and co-immunoprecipitation confirmed the interaction, with amino acid 823 in ANKS6 being critical for binding.\",\n      \"method\": \"Yeast two-hybrid, co-immunoprecipitation, in vivo ciliary co-localization by immunofluorescence\",\n      \"journal\": \"PloS one\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 — two orthogonal methods (Y2H + Co-IP) with in vivo localization, single lab\",\n      \"pmids\": [\"26327442\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"ANKS6 binds to Hippo pathway effector proteins YAP1, TAZ, and TEAD4 and promotes their transcriptional activity. Loss of Anks6 in knockout mice causes dysregulation of YAP transcriptional activity in biliary epithelial cells, leading to bile duct morphogenesis defects and ductal plate malformations, establishing ANKS6 as an antagonist of Hippo signaling during liver development.\",\n      \"method\": \"Anks6 knockout mouse model, co-immunoprecipitation (ANKS6 with YAP1/TAZ/TEAD4), biochemical analyses, histology, expression studies\",\n      \"journal\": \"Human molecular genetics\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — KO mouse with defined phenotype plus direct protein interaction demonstrated by Co-IP, multiple pathway components tested\",\n      \"pmids\": [\"32886109\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"Transgenic overexpression of the mutant Anks6(p.R823W) in renal tubular epithelium causes polycystic kidney disease in a dominant-negative fashion, establishing a causal link between the R823W mutation and cystogenesis, with cyst development accompanied by enhanced c-myc expression, proliferation, apoptosis, and lack of p21 up-regulation.\",\n      \"method\": \"Transgenic rat model overexpressing mutant Anks6(R823W), Northern blot, in situ hybridization, histology\",\n      \"journal\": \"The American journal of pathology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — in vivo transgenic model establishing causal role with multiple cellular readouts, single lab\",\n      \"pmids\": [\"21119215\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"Loss-of-function mutations in ANKS6 are associated with increased levels of total and active β-catenin in precystic tubuli in Han:SPRD Cy/+ rats, suggesting that ANKS6 mutations may contribute to nephronophthisis through dysregulation of Wnt/β-catenin signaling.\",\n      \"method\": \"Immunohistochemistry in human embryonic kidney tissue and rat model, β-catenin activity assays\",\n      \"journal\": \"Journal of the American Society of Nephrology : JASN\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 — single method in rat model, no direct mechanistic link established\",\n      \"pmids\": [\"24610927\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"ANKS6 deficiency in patient-derived fibroblasts leads to impaired integrity of the ciliary inversin compartment, reduced cilia length, dysregulation of YAP nuclear localization, disrupted ciliary YAP localization, altered Wnt target gene transcription, and deranged subcellular localization of endocytic recycling compartment components.\",\n      \"method\": \"Patient-derived fibroblasts, immunofluorescence, YAP localization analysis, β-catenin/GSK3β phosphorylation analysis\",\n      \"journal\": \"Human molecular genetics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — patient-derived cell model with multiple orthogonal pathway readouts, single lab\",\n      \"pmids\": [\"34740236\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"ANKS6 regulates Bicc1 ribonucleoprotein complex assembly: ANKS6 induces structural remodeling of associated ANKS3, modulating ANKS3's C-terminal coiled-coil domain interaction with Bicc1 that otherwise inhibits mRNA binding. In vitro reconstitution and AlphaFold structure predictions revealed a novel ANKS3-Bicc1 interaction mode regulated by ANKS6.\",\n      \"method\": \"In vitro reconstitution, AlphaFold structure prediction with biochemical validation, CRISPR-engineered truncations in mouse, mRNA decay assays\",\n      \"journal\": \"PLoS biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 — in vitro reconstitution plus in vivo genetic validation and structural prediction with biochemical confirmation\",\n      \"pmids\": [\"37733651\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"ANKS6, when co-recruited by ANKS3, reinstates Bicc1 condensation and ribonucleoparticle assembly after ANKS3-mediated dispersal of Bicc1 granules. ANKS3 disperses Bicc1 granules and releases bound mRNAs, while ANKS6 co-recruitment by ANKS3 restores Bicc1 polymerization and mRNA sequestration, representing a dual regulatory mechanism for Bicc1 phase transitioning.\",\n      \"method\": \"Live cell imaging of condensate/granule dynamics, RNA binding assays, co-immunoprecipitation, overexpression/knockdown in cell lines\",\n      \"journal\": \"iScience\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — cell-based and biochemical assays with multiple readouts, single lab\",\n      \"pmids\": [\"37275520\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"In C. elegans, the Inversin complex (containing INVS/MLT-4, NEK8/NEKL-2, and the ANKS6 ortholog) is activated by dimerization. Stimulated dimerization of MLT-4 (INVS) or NEKL-2 (NEK8) using optogenetics is sufficient to activate the complex, and dimerization of NEKL-2 bypasses a lethal MLT-4 mutant, demonstrating that dynamic switching between an active dimer and an inactive monomer gates Inversin complex output.\",\n      \"method\": \"C. elegans genetics, genome engineering (RFP tags, monomerization), optogenetic stimulation of dimerization, gain-of-function allele characterization\",\n      \"journal\": \"bioRxiv\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — orthogonal genetic and optogenetic approaches in C. elegans ortholog, preprint not yet peer-reviewed\",\n      \"pmids\": [\"bio_10.1101_2024.05.17.594761\"],\n      \"is_preprint\": true\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"In Anks6 liver-specific knockout mice, portal fibrosis development coincides with accumulation of inflammatory M1-like macrophages in the periportal tissue; depletion of macrophages with clodronate liposomes reduced inflammatory gene expression, fibrosis, and biliary dysfunction, establishing a causal role for macrophage-driven inflammation downstream of ANKS6 deficiency in hepatic fibrosis.\",\n      \"method\": \"Liver-specific Anks6 knockout mouse, clodronate liposome macrophage depletion, flow cytometry, gene expression analysis, histology\",\n      \"journal\": \"FASEB journal\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — KO model with depletion rescue experiment establishing macrophage causality, single lab\",\n      \"pmids\": [\"35032404\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"ANKS6 is a ciliary inversin compartment protein that acts as a central scaffold and signal mediator: it activates NEK8 kinase by binding its kinase domain, is itself phosphorylated by NEK8 (promoted by INV/NPHP3), interacts with INVS/NPHP2 and NPHP3 to form a nephronophthisis module, engages ANKS3 and BICC1 through SAM domain interactions to regulate Bicc1 ribonucleoprotein assembly and mRNA phase transitioning, and promotes YAP1/TAZ/TEAD4 transcriptional activity to antagonize Hippo signaling during bile duct development, with disease-causing mutations (R823W, I747N) disrupting these specific protein-protein interactions.\"\n}\n```","stage2_raw":"```json\n{\n  \"mechanistic_narrative\": \"ANKS6 is a ciliary inversin compartment scaffold that integrates kinase signaling, ribonucleoprotein regulation, and transcriptional control in epithelial morphogenesis. It directly binds and activates the NEK8 kinase through its kinase domain while simultaneously connecting NEK8 to INVS/NPHP2 and NPHP3, forming a nephronophthisis signaling module in which ANKS6 is itself phosphorylated by NEK8 in a manner dependent on ciliary NPHP3 localization [PMID:23793029, PMID:25599650, PMID:29395339]. Through its SAM domain, ANKS6 caps ANKS3 polymers and cooperatively assembles with ANKS3 and BICC1 into macromolecular condensates that regulate Bicc1 mRNA phase transitioning and ribonucleoprotein granule dynamics, with disease-causing mutations R823W and I747N selectively disrupting the ANKS3 and BICC1 interactions respectively [PMID:24998259, PMID:29290488, PMID:37733651, PMID:37275520]. ANKS6 also binds YAP1, TAZ, and TEAD4 to promote their transcriptional activity, and loss of Anks6 causes bile duct malformations and nephronophthisis-associated cystic kidney disease [PMID:32886109, PMID:21119215].\",\n  \"teleology\": [\n    {\n      \"year\": 2010,\n      \"claim\": \"Establishing that the R823W mutation is sufficient to cause polycystic kidney disease resolved whether ANKS6 dysfunction is directly causative of cystogenesis rather than merely associated.\",\n      \"evidence\": \"Transgenic rat overexpressing mutant Anks6(R823W) in renal epithelium developed dominant-negative cystic disease with enhanced proliferation and c-myc expression\",\n      \"pmids\": [\"21119215\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanism by which R823W acts as dominant-negative was unknown\", \"Direct molecular targets of ANKS6 unidentified at this stage\", \"Relationship to ciliary function not established\"]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"Identifying ANKS6 as a central hub connecting NEK8, INVS, and NPHP3 at the ciliary inversin compartment established the molecular logic of the nephronophthisis signaling module and explained how distinct NPHP gene products converge.\",\n      \"evidence\": \"Reciprocal Co-IP, zebrafish/Xenopus knockdown, and identification of HIF1AN-mediated hydroxylation of ANKS6 and INVS\",\n      \"pmids\": [\"23793029\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Functional consequence of HIF1AN hydroxylation on module activity unknown\", \"Directionality of signal flow through the module unresolved\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Solving the crystal structure of the ANKS3-SAM/ANKS6-SAM complex revealed the atomic basis of ANKS6 SAM domain interactions and demonstrated that R823W destabilizes the SAM fold, explaining loss of ANKS3 binding.\",\n      \"evidence\": \"X-ray crystallography of ANKS3-SAM polymer and ANKS3-SAM/ANKS6-SAM heterodimer, mutagenesis, in vitro binding assays\",\n      \"pmids\": [\"24998259\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Downstream signaling consequences of ANKS3-ANKS6 disruption unclear\", \"Whether additional SAM-domain partners exist was not tested\"]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Demonstrating that ANKS6 both activates NEK8 kinase and requires NEK8 for its own ciliary localization established a mutual-dependence relationship, while the I747N mutation defined a second SAM-domain interaction surface specific for BICC1.\",\n      \"evidence\": \"Kinase activity assays, Co-IP, and comparative analysis of Anks6(Streaker) and Nek8(Roc) mouse mutants; ENU mutagenesis screen identifying I747N in mouse\",\n      \"pmids\": [\"25599650\", \"26039630\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"NEK8 substrates downstream of ANKS6-mediated activation not identified\", \"How I747N and R823W mutations produce overlapping yet distinct phenotypes at the cellular level\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Showing that ANKS3 recruits ANKS6 to BICC1 and that the three proteins cooperatively form giant macromolecular complexes revealed a hierarchical assembly mechanism dependent on combined SAM and non-SAM interactions.\",\n      \"evidence\": \"Crystal structure of Bicc1-SAM polymer, Co-IP, domain-mapping of full-length constructs\",\n      \"pmids\": [\"29290488\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Functional RNA targets of the ANKS3-ANKS6-BICC1 complex unknown\", \"Stoichiometry and dynamics of the complex in vivo unresolved\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Establishing that NPHP3 ciliary localization is required for NEK8-mediated phosphorylation of ANKS6 defined ANKS6 as a signal mediator that relays ciliary events to the cytoplasm.\",\n      \"evidence\": \"Nphp3 G2A knock-in mouse with defective myristoylation/ciliary targeting; phosphorylation analysis of ANKS6\",\n      \"pmids\": [\"29395339\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Identity of ANKS6 phosphorylation sites not mapped\", \"Cytoplasmic effectors of phosphorylated ANKS6 unknown\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Discovery that ANKS6 binds YAP1/TAZ/TEAD4 and promotes their transcriptional activity identified a non-ciliary effector output, explaining bile duct morphogenesis defects in Anks6 knockouts as Hippo pathway dysregulation.\",\n      \"evidence\": \"Anks6 KO mouse with ductal plate malformations, Co-IP of ANKS6 with YAP1/TAZ/TEAD4\",\n      \"pmids\": [\"32886109\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether ANKS6 regulation of Hippo signaling is cilium-dependent or independent unclear\", \"Direct versus indirect mechanism of ANKS6 promotion of YAP/TAZ activity not distinguished\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Patient-derived fibroblasts confirmed that ANKS6 deficiency impairs inversin compartment integrity, cilia length, and YAP nuclear localization in human cells, while liver-specific knockout revealed macrophage-driven inflammation as a downstream driver of portal fibrosis.\",\n      \"evidence\": \"Patient fibroblasts with immunofluorescence/pathway analysis; liver-specific Anks6 KO with clodronate liposome macrophage depletion rescuing fibrosis\",\n      \"pmids\": [\"34740236\", \"35032404\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether ciliary and Hippo/Wnt phenotypes represent a single linear pathway or parallel outputs unresolved\", \"Cell-autonomous versus non-cell-autonomous contributions to kidney pathology not distinguished\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Reconstitution and live-imaging studies revealed a dual regulatory cycle in which ANKS3 disperses Bicc1 condensates and releases mRNAs, while ANKS6 co-recruitment by ANKS3 restores Bicc1 polymerization and mRNA sequestration, establishing ANKS6 as a positive regulator of ribonucleoprotein phase transitioning.\",\n      \"evidence\": \"In vitro reconstitution with AlphaFold-guided mutagenesis, CRISPR truncations in mouse, live-cell imaging of condensate dynamics, RNA binding assays\",\n      \"pmids\": [\"37733651\", \"37275520\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Specific mRNA targets regulated by this ANKS3-ANKS6-BICC1 cycle in vivo not identified\", \"Whether phase-transition regulation connects to NEK8 kinase activity unknown\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"Key unresolved questions include the identity of NEK8 substrates downstream of ANKS6-mediated activation, the specific ANKS6 phosphorylation sites and their functional consequences, the in vivo RNA targets of the ANKS6-ANKS3-BICC1 condensate cycle, and whether ANKS6 regulation of Hippo signaling is cilium-dependent.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"NEK8 downstream substrates unidentified\", \"ANKS6 phosphosite mapping lacking\", \"In vivo mRNA targets of BICC1 condensates regulated by ANKS6 unknown\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [0, 1, 4]},\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [1, 11, 12]},\n      {\"term_id\": \"GO:0140110\", \"supporting_discovery_ids\": [7]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005929\", \"supporting_discovery_ids\": [0, 1, 3, 6]},\n      {\"term_id\": \"GO:0005829\", \"supporting_discovery_ids\": [3, 12]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"GO:0162582\", \"supporting_discovery_ids\": [7, 10]},\n      {\"term_id\": \"R-HSA-162582\", \"supporting_discovery_ids\": [7, 10]},\n      {\"term_id\": \"R-HSA-1852241\", \"supporting_discovery_ids\": [0, 1, 3]},\n      {\"term_id\": \"R-HSA-1266738\", \"supporting_discovery_ids\": [7, 14]},\n      {\"term_id\": \"R-HSA-1643685\", \"supporting_discovery_ids\": [8, 9]}\n    ],\n    \"complexes\": [\n      \"Inversin compartment complex (ANKS6-NEK8-INVS-NPHP3)\",\n      \"ANKS3-ANKS6-BICC1 ribonucleoprotein complex\"\n    ],\n    \"partners\": [\n      \"NEK8\",\n      \"INVS\",\n      \"NPHP3\",\n      \"ANKS3\",\n      \"BICC1\",\n      \"YAP1\",\n      \"TAZ\",\n      \"TEAD4\"\n    ],\n    \"other_free_text\": []\n  }\n}\n```"}