{"gene":"ANKS6","run_date":"2026-06-09T22:02:43","timeline":{"discoveries":[{"year":2013,"finding":"ANKS6 localizes to the proximal cilium (inversin compartment) and forms a molecular module with NEK8 (NPHP9), INVS (NPHP2), and NPHP3. Knockdown in zebrafish and Xenopus causes renal/laterality defects consistent with loss of other NPHP proteins, placing ANKS6 at the center of this nephronophthisis module.","method":"Co-immunoprecipitation, subcellular localization by immunofluorescence, knockdown in zebrafish and Xenopus laevis with phenotypic readout, network analysis","journal":"Nature genetics","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal Co-IP, in vivo knockdown in two model organisms, replicated by multiple subsequent studies","pmids":["23793029"],"is_preprint":false},{"year":2013,"finding":"The oxygen sensor HIF1AN hydroxylates ANKS6 and INVS, and this hydroxylation alters the composition of the ANKS6-INVS-NPHP3 module. Knockdown of Hif1an in Xenopus phenocopies loss of other NPHP proteins.","method":"Biochemical hydroxylation assay, co-immunoprecipitation, Xenopus knockdown with phenotypic readout","journal":"Nature genetics","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct biochemical assay with in vivo validation, single lab","pmids":["23793029"],"is_preprint":false},{"year":2015,"finding":"ANKS6 is a substrate and activator of the ciliary kinase NEK8: ANKS6 binds to the NEK8 kinase domain to activate it, and ANKS6 requires NEK8 for its localization to the ciliary inversin compartment (IC). The Anks6(Streaker) mouse mutation decreases ANKS6-NEK8 interaction and prevents NEK8 activation; the Nek8(Roc) mutation inactivates NEK8 kinase while preserving ANKS6 localization.","method":"Co-immunoprecipitation, in vivo mouse genetic analysis (Anks6 Streaker and Nek8 Roc mutants), kinase activity assays, immunofluorescence localization","journal":"Nature communications","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal Co-IP, multiple mouse mutant alleles, kinase activity assay, functionally validated with specific phenotypic readouts","pmids":["25599650"],"is_preprint":false},{"year":2014,"finding":"The SAM domain of ANKS6 directly binds to the SAM domain of ANKS3. Crystal structures of ANKS3-SAM polymer and the ANKS3-SAM/ANKS6-SAM complex reveal that ANKS3-SAM polymerizes and ANKS6-SAM binds to one end of the polymer. The disease-causing R823W mutation dramatically destabilizes the ANKS6 SAM domain, abolishing interaction with ANKS3-SAM.","method":"X-ray crystallography (crystal structures of ANKS3-SAM polymer and ANKS3-SAM/ANKS6-SAM complex), biochemical binding assays, site-directed mutagenesis","journal":"BMC structural biology","confidence":"High","confidence_rationale":"Tier 1 / Strong — crystal structures with mutagenesis and biochemical validation; independently supported by subsequent studies","pmids":["24998259"],"is_preprint":false},{"year":2017,"finding":"ANKS3 recruits ANKS6 to BICC1, and together the three proteins cooperatively generate giant macromolecular complexes. Neither ANKS3 nor ANKS6 alone formed macroscopic homopolymers in vivo. A crystal structure of Bicc1-SAM polymer reveals a canonical head-to-tail polymer with flexible subunit interface orientations; SAM domains and flanking sequences as well as SAM-independent interactions shape these assemblies.","method":"Crystal structure of Bicc1-SAM polymer, co-immunoprecipitation, mapping of domain interactions with full-length and truncated proteins, in vivo complex formation assays","journal":"Structure","confidence":"High","confidence_rationale":"Tier 1 / Moderate — crystal structure combined with biochemical domain mapping and in vivo complex analysis, single lab","pmids":["29290488"],"is_preprint":false},{"year":2015,"finding":"The I747N missense mutation in the ANKS6 SAM domain (identified by ENU mutagenesis in mice) disrupts the interaction between ANKS6 and BICC1 (but not ANKS3-ANKS6 interaction, which is disrupted by R823W in rats), demonstrating that the ANKS6 SAM domain mediates distinct interactions with ANKS3 and BICC1, and that either disruption can cause cystic kidney disease.","method":"ENU mutagenesis screen, co-immunoprecipitation, comparative phenotype analysis in rat and mouse models","journal":"Kidney international","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP with two distinct disease mutants in two independent animal models, single lab","pmids":["26039630"],"is_preprint":false},{"year":2015,"finding":"ANKS3 and ANKS6 directly interact through their SAM domains; the rat R823W mutation at position 823 of ANKS6 is key for ANKS3 binding. ANKS3 co-localizes with ANKS6 in mouse renal cilia in vivo.","method":"Yeast two-hybrid, co-immunoprecipitation, immunofluorescence localization in mouse renal cilia, LNA antisense knockdown","journal":"PloS one","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — yeast two-hybrid plus Co-IP and in vivo localization, single lab","pmids":["26327442"],"is_preprint":false},{"year":2018,"finding":"INV and NPHP3 cooperate in the inversin compartment of renal cilia to promote ANKS6 phosphorylation by NEK8. Loss of ciliary NPHP3 (via disruption of UNC119-dependent myristoylation signal) impairs ANKS6 phosphorylation without altering ANKS6 ciliary localization, and non-phosphorylated ANKS6 accumulates at high levels in cystic kidneys. ANKS6 functions as a signal mediator linking cilia to the cytoplasm to regulate kidney morphogenesis.","method":"Generation of Nphp3 G2A knock-in mice, immunofluorescence, phosphorylation assays/western blot, comparison with Inv mutant mice","journal":"Kidney international","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genetic mouse model with phosphorylation readout and localization experiments, single lab","pmids":["29395339"],"is_preprint":false},{"year":2010,"finding":"Transgenic overexpression of the R823W Anks6 mutant in rat renal tubular epithelium causes polycystic kidney disease in a dominant-negative manner, demonstrating a causal link between the Anks6(R823W) mutation and cystogenesis. Cyst development is accompanied by enhanced c-myc expression, continuous proliferation, apoptosis, de-differentiation, and absence of p21 translational up-regulation.","method":"Transgenic rat model with renal tubular-specific overexpression of Anks6(p.R823W), Northern blot, in situ hybridization, histology","journal":"The American journal of pathology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — in vivo transgenic model with defined molecular and cellular phenotypes, single lab","pmids":["21119215"],"is_preprint":false},{"year":2020,"finding":"ANKS6 is required for bile duct morphogenesis and cholangiocyte differentiation in the liver. Loss of Anks6 causes ciliary abnormalities, ductal plate remodeling defects, and periportal fibrosis. Mechanistically, ANKS6 antagonizes Hippo signaling by binding to YAP1, TAZ, and TEAD4 and promoting their transcriptional activity; loss of ANKS6 leads to YAP transcriptional dysregulation in bile duct epithelial cells.","method":"Anks6 knockout mouse model, co-immunoprecipitation (ANKS6 with YAP1/TAZ/TEAD4), gene expression analyses, histology, biochemical assays","journal":"Human molecular genetics","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — KO mouse with defined cellular phenotype plus Co-IP identifying binding partners, single lab","pmids":["32886109"],"is_preprint":false},{"year":2022,"finding":"ANKS6 deficiency in patient-derived fibroblasts impairs the integrity of the ciliary inversin compartment (reduced cilia length), causes dysregulation of Hippo signaling through nuclear YAP imbalance and disrupted ciliary YAP localization, and alters Wnt target gene transcription and active β-catenin/GSK3β expression. ANKS6 deficiency also deranges subcellular localization of endocytic recycling compartment components upon ciliation.","method":"Patient-derived fibroblast in vitro model, immunofluorescence, western blot, transcriptional activity assays, immunohistochemistry on renal biopsies","journal":"Human molecular genetics","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — patient-derived cell model with multiple orthogonal readouts, single lab","pmids":["34740236"],"is_preprint":false},{"year":2023,"finding":"ANKS6 regulates BICC1 ribonucleoprotein (RNP) complex assembly and organ laterality determination. ANKS6 induces structural remodeling of ANKS3, relieving an inhibitory interaction between ANKS3's C-terminal coiled-coil domain and BICC1 that otherwise blocks target mRNA (Dand5 3' UTR) binding. This dual regulation is validated by in vitro reconstitution and AlphaFold structure predictions.","method":"AlphaFold structure predictions, in vitro reconstitution of protein complexes, CRISPR-engineered ANKS3 truncation in zebrafish, mRNA decay assays, biochemical binding assays","journal":"PLoS biology","confidence":"Medium","confidence_rationale":"Tier 1 / Moderate — in vitro reconstitution and structural prediction with biochemical validation, single lab","pmids":["37733651"],"is_preprint":false},{"year":2023,"finding":"ANKS6, recruited by ANKS3, reinstates BICC1 condensation and ribonucleoparticle assembly after ANKS3-mediated dispersal of Bicc1 granules, demonstrating that ANKS6 and ANKS3 exert opposing regulatory effects on Bicc1 phase transitioning and client mRNA immobilization.","method":"Cell-based condensate/granule assays, co-immunoprecipitation, RNA binding assays, live-cell imaging of phase transitioning","journal":"iScience","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple functional assays examining phase transitioning and mRNA regulation, single lab","pmids":["37275520"],"is_preprint":false},{"year":2022,"finding":"ANKS6-deficient livers exhibit accumulation of inflammatory M1-like macrophages in periportal fibrotic tissue, and macrophage depletion by clodronate liposomes reduces inflammatory gene expression, fibrosis, and biliary dysfunction in liver-specific Anks6 KO mice, establishing a causal role for macrophage-mediated inflammation in ANKS6-deficiency-associated congenital hepatic fibrosis.","method":"Liver-specific Anks6 KO mouse model, clodronate liposome macrophage depletion, flow cytometry, gene expression analysis, histology","journal":"FASEB journal","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genetic KO model with pharmacological intervention and multiple cellular readouts, single lab","pmids":["35032404"],"is_preprint":false},{"year":2014,"finding":"In the Han:SPRD Cy/+ rat model, increased levels of both total and active β-catenin were detected in precystic tubuli, suggesting ANKS6 mutations may contribute to cystogenesis via dysregulation of Wnt/β-catenin signaling.","method":"Immunohistochemistry in Han:SPRD Cy/+ rat kidney tissue","journal":"Journal of the American Society of Nephrology","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single IHC-based observation without mechanistic follow-up, single lab","pmids":["24610927"],"is_preprint":false}],"current_model":"ANKS6 is a ciliary inversin-compartment protein that sits at the center of a nephronophthisis module: it binds and activates the kinase NEK8 (via its kinase domain), undergoes NEK8-mediated phosphorylation promoted cooperatively by INV and NPHP3, and interacts through its SAM domain with ANKS3 (forming a heterodimer at the end of ANKS3-SAM polymers) and with BICC1 to regulate ribonucleoprotein complex assembly and Dand5 mRNA decay for organ laterality; disease-causing SAM-domain mutations (R823W, I747N) selectively disrupt either the ANKS3 or BICC1 interaction; in the liver, ANKS6 promotes YAP1/TAZ/TEAD4 transcriptional activity by binding these Hippo pathway effectors, and its loss leads to YAP dysregulation, bile duct malformation, and macrophage-driven periportal fibrosis."},"narrative":{"mechanistic_narrative":"ANKS6 is a ciliary inversin-compartment protein that functions as the central organizer of a nephronophthisis signaling module governing kidney morphogenesis, organ laterality, and bile duct development [PMID:23793029]. Within the proximal cilium, ANKS6 binds the kinase domain of NEK8 to activate the kinase and in turn requires NEK8 for its own localization to the inversin compartment; this reciprocal dependence is dissected by the Anks6(Streaker) and Nek8(Roc) mouse alleles [PMID:25599650]. ANKS6 itself is a NEK8 substrate whose phosphorylation is cooperatively promoted by INV and NPHP3, positioning ANKS6 as a signal mediator that relays information from the cilium to the cytoplasm to control kidney morphogenesis [PMID:29395339]. Through its SAM domain, ANKS6 binds the end of an ANKS3-SAM polymer, and ANKS3 in turn recruits ANKS6 to BICC1 to build giant macromolecular ribonucleoprotein assemblies [PMID:24998259, PMID:29290488]; ANKS6 remodels ANKS3 to relieve an autoinhibitory interaction that otherwise blocks BICC1 binding to the Dand5 3' UTR, thereby regulating mRNA decay and left-right laterality [PMID:37733651]. The disease-causing SAM-domain mutations partition these activities — R823W destabilizes the ANKS6 SAM domain and abolishes the ANKS3 interaction, whereas I747N selectively disrupts the BICC1 interaction, and either lesion causes cystic kidney disease [PMID:24998259, PMID:26039630]. Beyond the cilium, ANKS6 antagonizes Hippo signaling by binding YAP1, TAZ, and TEAD4 to promote their transcriptional activity, and its loss in liver drives YAP dysregulation, bile duct malformation, and macrophage-driven periportal fibrosis [PMID:32886109, PMID:35032404].","teleology":[{"year":2013,"claim":"Established that ANKS6 is not an isolated factor but the centerpiece of a defined ciliary nephronophthisis module, answering where ANKS6 acts and with which NPHP proteins.","evidence":"Co-IP, immunofluorescence localization, and knockdown in zebrafish and Xenopus with renal/laterality phenotypes","pmids":["23793029"],"confidence":"High","gaps":["Did not define the biochemical activity of ANKS6 within the module","Mechanism by which the module controls morphogenesis unresolved"]},{"year":2013,"claim":"Tested how the module is regulated, showing the oxygen sensor HIF1AN hydroxylates ANKS6 and INVS to alter module composition.","evidence":"Biochemical hydroxylation assay, Co-IP, and Xenopus knockdown","pmids":["23793029"],"confidence":"Medium","gaps":["Hydroxylation sites and stoichiometry not fully mapped","Physiological oxygen-dependence in mammalian kidney not established"]},{"year":2015,"claim":"Defined the enzymatic relationship at the module's core: ANKS6 binds and activates NEK8 and depends on NEK8 for ciliary localization, separating activation from localization with distinct mutant alleles.","evidence":"Reciprocal Co-IP, Anks6(Streaker) and Nek8(Roc) mouse mutants, and kinase activity assays","pmids":["25599650"],"confidence":"High","gaps":["Downstream NEK8 substrates beyond ANKS6 not identified","Structural basis of ANKS6-NEK8 kinase-domain binding unresolved"]},{"year":2014,"claim":"Resolved the structural basis of ANKS6 self-assembly, showing its SAM domain caps an ANKS3-SAM polymer and that R823W destabilizes the domain to abolish binding.","evidence":"X-ray crystallography of ANKS3-SAM polymer and ANKS3/ANKS6-SAM complex with mutagenesis","pmids":["24998259"],"confidence":"High","gaps":["Functional consequence of polymer capping in cilia not directly tested","Does not address the separate BICC1 interaction"]},{"year":2015,"claim":"Showed the ANKS6 SAM domain mediates two genetically separable interactions, with I747N disrupting BICC1 binding and R823W disrupting ANKS3 binding, each independently causing cystic kidney disease.","evidence":"ENU mutagenesis screen, Co-IP, and comparative phenotyping in rat and mouse","pmids":["26039630","26327442"],"confidence":"Medium","gaps":["Structural mechanism distinguishing the two SAM interactions not resolved","Relative contribution of each interaction to disease severity unclear"]},{"year":2010,"claim":"Demonstrated causality between the Anks6(R823W) mutation and cystogenesis in a dominant-negative manner, linking the lesion to proliferation, apoptosis, and c-myc dysregulation.","evidence":"Transgenic rat with tubule-specific Anks6(R823W) overexpression, Northern blot, in situ hybridization, histology","pmids":["21119215"],"confidence":"Medium","gaps":["Molecular pathway connecting R823W to c-myc/proliferation not defined","Dominant-negative target not identified"]},{"year":2018,"claim":"Established that INV and NPHP3 cooperatively promote NEK8-mediated ANKS6 phosphorylation, defining ANKS6 as a cilium-to-cytoplasm signal mediator whose phosphorylation is lost in cystic kidneys.","evidence":"Nphp3 G2A knock-in mice, phosphorylation/western readouts, comparison with Inv mutants","pmids":["29395339"],"confidence":"Medium","gaps":["Phosphosites on ANKS6 not mapped","Downstream effectors of phospho-ANKS6 not identified"]},{"year":2017,"claim":"Showed ANKS3 recruits ANKS6 to BICC1 so the three cooperatively form giant macromolecular complexes, with neither ANKS protein homopolymerizing alone in vivo.","evidence":"Crystal structure of Bicc1-SAM polymer, Co-IP, and domain-mapping complex assays","pmids":["29290488"],"confidence":"High","gaps":["Functional output of the giant complexes not directly assayed here","SAM-independent contributions not fully delineated"]},{"year":2023,"claim":"Defined the RNA-regulatory mechanism: ANKS6 remodels ANKS3 to relieve autoinhibition and license BICC1 binding to Dand5 mRNA, and oppositely tunes BICC1 condensation, linking the module to laterality and mRNA decay.","evidence":"AlphaFold predictions, in vitro reconstitution, CRISPR ANKS3 truncation in zebrafish, mRNA decay and condensate/phase-transition assays","pmids":["37733651","37275520"],"confidence":"Medium","gaps":["In vivo confirmation of Dand5 mRNA control by ANKS6 in mammals limited","How ciliary signaling couples to RNP regulation unresolved"]},{"year":2020,"claim":"Extended ANKS6 function to liver, showing it antagonizes Hippo signaling by binding YAP1/TAZ/TEAD4 to promote their transcription, with loss causing bile duct malformation and fibrosis.","evidence":"Anks6 knockout mouse, Co-IP with YAP1/TAZ/TEAD4, gene expression and histology","pmids":["32886109"],"confidence":"Medium","gaps":["Direct vs indirect nature of YAP/TAZ/TEAD4 binding not structurally resolved","Link between ciliary ANKS6 and Hippo regulation unclear"]},{"year":2022,"claim":"Connected ANKS6 deficiency to disease cell biology, showing impaired inversin-compartment integrity, YAP/Wnt dysregulation, and macrophage-driven periportal fibrosis as a causal inflammatory mechanism.","evidence":"Patient-derived fibroblasts with orthogonal readouts; liver-specific Anks6 KO with clodronate macrophage depletion","pmids":["34740236","35032404"],"confidence":"Medium","gaps":["Signal linking ANKS6 loss to M1 macrophage recruitment not identified","Direct mechanism coupling cilia defects to YAP/Wnt imbalance unresolved"]},{"year":null,"claim":"How ciliary signaling, NEK8-dependent phosphorylation, SAM-domain assembly, and downstream YAP/Wnt and BICC1-RNP outputs are integrated into a single coherent control of kidney and liver morphogenesis remains unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No unified model linking phospho-state of ANKS6 to its scaffolding and transcriptional roles","ANKS6 phosphosites and their functional consequences uncharacterized","Direct structural basis for YAP1/TAZ/TEAD4 binding unknown"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[3,4,11]},{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[2]},{"term_id":"GO:0140110","term_label":"transcription regulator activity","supporting_discovery_ids":[9]}],"localization":[{"term_id":"GO:0005929","term_label":"cilium","supporting_discovery_ids":[0,2,6]},{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[9,10]}],"pathway":[{"term_id":"R-HSA-162582","term_label":"Signal Transduction","supporting_discovery_ids":[9,10]},{"term_id":"R-HSA-8953854","term_label":"Metabolism of RNA","supporting_discovery_ids":[11,12]},{"term_id":"R-HSA-1266738","term_label":"Developmental Biology","supporting_discovery_ids":[0,9]}],"complexes":["ANKS6-NEK8-INVS-NPHP3 inversin-compartment module","ANKS3-ANKS6-BICC1 ribonucleoprotein complex"],"partners":["NEK8","INVS","NPHP3","ANKS3","BICC1","YAP1","TAZ","TEAD4"],"other_free_text":[]}},"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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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}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":12282,"output_tokens":3958,"usd":0.048108,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":11700,"output_tokens":4012,"usd":0.0794,"stage2_stop_reason":"end_turn"},"total_usd":0.127508,"stage1_batch_id":"msgbatch_0179Z2pxRYBsXi2xADneafRw","stage2_batch_id":"msgbatch_01LaY9ZaVdgjWArcZo9eqQE5","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 forms a molecular module with NEK8 (NPHP9), INVS (NPHP2), and NPHP3. Knockdown in zebrafish and Xenopus causes renal/laterality defects consistent with loss of other NPHP proteins, placing ANKS6 at the center of this nephronophthisis module.\",\n      \"method\": \"Co-immunoprecipitation, subcellular localization by immunofluorescence, knockdown in zebrafish and Xenopus laevis with phenotypic readout, network analysis\",\n      \"journal\": \"Nature genetics\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal Co-IP, in vivo knockdown in two model organisms, replicated by multiple subsequent studies\",\n      \"pmids\": [\"23793029\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"The oxygen sensor HIF1AN hydroxylates ANKS6 and INVS, and this hydroxylation alters the composition of the ANKS6-INVS-NPHP3 module. Knockdown of Hif1an in Xenopus phenocopies loss of other NPHP proteins.\",\n      \"method\": \"Biochemical hydroxylation assay, co-immunoprecipitation, Xenopus knockdown with phenotypic readout\",\n      \"journal\": \"Nature genetics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct biochemical assay with in vivo validation, single lab\",\n      \"pmids\": [\"23793029\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"ANKS6 is a substrate and activator of the ciliary kinase NEK8: ANKS6 binds to the NEK8 kinase domain to activate it, and ANKS6 requires NEK8 for its localization to the ciliary inversin compartment (IC). The Anks6(Streaker) mouse mutation decreases ANKS6-NEK8 interaction and prevents NEK8 activation; the Nek8(Roc) mutation inactivates NEK8 kinase while preserving ANKS6 localization.\",\n      \"method\": \"Co-immunoprecipitation, in vivo mouse genetic analysis (Anks6 Streaker and Nek8 Roc mutants), kinase activity assays, immunofluorescence localization\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal Co-IP, multiple mouse mutant alleles, kinase activity assay, functionally validated with specific phenotypic readouts\",\n      \"pmids\": [\"25599650\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"The SAM domain of ANKS6 directly binds to the SAM domain of ANKS3. Crystal structures of ANKS3-SAM polymer and the ANKS3-SAM/ANKS6-SAM complex reveal that ANKS3-SAM polymerizes and ANKS6-SAM binds to one end of the polymer. The disease-causing R823W mutation dramatically destabilizes the ANKS6 SAM domain, abolishing interaction with ANKS3-SAM.\",\n      \"method\": \"X-ray crystallography (crystal structures of ANKS3-SAM polymer and ANKS3-SAM/ANKS6-SAM complex), biochemical binding assays, site-directed mutagenesis\",\n      \"journal\": \"BMC structural biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — crystal structures with mutagenesis and biochemical validation; independently supported by subsequent studies\",\n      \"pmids\": [\"24998259\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"ANKS3 recruits ANKS6 to BICC1, and together the three proteins cooperatively generate giant macromolecular complexes. Neither ANKS3 nor ANKS6 alone formed macroscopic homopolymers in vivo. A crystal structure of Bicc1-SAM polymer reveals a canonical head-to-tail polymer with flexible subunit interface orientations; SAM domains and flanking sequences as well as SAM-independent interactions shape these assemblies.\",\n      \"method\": \"Crystal structure of Bicc1-SAM polymer, co-immunoprecipitation, mapping of domain interactions with full-length and truncated proteins, in vivo complex formation assays\",\n      \"journal\": \"Structure\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — crystal structure combined with biochemical domain mapping and in vivo complex analysis, single lab\",\n      \"pmids\": [\"29290488\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"The I747N missense mutation in the ANKS6 SAM domain (identified by ENU mutagenesis in mice) disrupts the interaction between ANKS6 and BICC1 (but not ANKS3-ANKS6 interaction, which is disrupted by R823W in rats), demonstrating that the ANKS6 SAM domain mediates distinct interactions with ANKS3 and BICC1, and that either disruption can cause cystic kidney disease.\",\n      \"method\": \"ENU mutagenesis screen, co-immunoprecipitation, comparative phenotype analysis in rat and mouse models\",\n      \"journal\": \"Kidney international\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP with two distinct disease mutants in two independent animal models, single lab\",\n      \"pmids\": [\"26039630\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"ANKS3 and ANKS6 directly interact through their SAM domains; the rat R823W mutation at position 823 of ANKS6 is key for ANKS3 binding. ANKS3 co-localizes with ANKS6 in mouse renal cilia in vivo.\",\n      \"method\": \"Yeast two-hybrid, co-immunoprecipitation, immunofluorescence localization in mouse renal cilia, LNA antisense knockdown\",\n      \"journal\": \"PloS one\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — yeast two-hybrid plus Co-IP and in vivo localization, single lab\",\n      \"pmids\": [\"26327442\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"INV and NPHP3 cooperate in the inversin compartment of renal cilia to promote ANKS6 phosphorylation by NEK8. Loss of ciliary NPHP3 (via disruption of UNC119-dependent myristoylation signal) impairs ANKS6 phosphorylation without altering ANKS6 ciliary localization, and non-phosphorylated ANKS6 accumulates at high levels in cystic kidneys. ANKS6 functions as a signal mediator linking cilia to the cytoplasm to regulate kidney morphogenesis.\",\n      \"method\": \"Generation of Nphp3 G2A knock-in mice, immunofluorescence, phosphorylation assays/western blot, comparison with Inv mutant mice\",\n      \"journal\": \"Kidney international\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic mouse model with phosphorylation readout and localization experiments, single lab\",\n      \"pmids\": [\"29395339\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"Transgenic overexpression of the R823W Anks6 mutant in rat renal tubular epithelium causes polycystic kidney disease in a dominant-negative manner, demonstrating a causal link between the Anks6(R823W) mutation and cystogenesis. Cyst development is accompanied by enhanced c-myc expression, continuous proliferation, apoptosis, de-differentiation, and absence of p21 translational up-regulation.\",\n      \"method\": \"Transgenic rat model with renal tubular-specific overexpression of Anks6(p.R823W), Northern blot, in situ hybridization, histology\",\n      \"journal\": \"The American journal of pathology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — in vivo transgenic model with defined molecular and cellular phenotypes, single lab\",\n      \"pmids\": [\"21119215\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"ANKS6 is required for bile duct morphogenesis and cholangiocyte differentiation in the liver. Loss of Anks6 causes ciliary abnormalities, ductal plate remodeling defects, and periportal fibrosis. Mechanistically, ANKS6 antagonizes Hippo signaling by binding to YAP1, TAZ, and TEAD4 and promoting their transcriptional activity; loss of ANKS6 leads to YAP transcriptional dysregulation in bile duct epithelial cells.\",\n      \"method\": \"Anks6 knockout mouse model, co-immunoprecipitation (ANKS6 with YAP1/TAZ/TEAD4), gene expression analyses, histology, biochemical assays\",\n      \"journal\": \"Human molecular genetics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — KO mouse with defined cellular phenotype plus Co-IP identifying binding partners, single lab\",\n      \"pmids\": [\"32886109\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"ANKS6 deficiency in patient-derived fibroblasts impairs the integrity of the ciliary inversin compartment (reduced cilia length), causes dysregulation of Hippo signaling through nuclear YAP imbalance and disrupted ciliary YAP localization, and alters Wnt target gene transcription and active β-catenin/GSK3β expression. ANKS6 deficiency also deranges subcellular localization of endocytic recycling compartment components upon ciliation.\",\n      \"method\": \"Patient-derived fibroblast in vitro model, immunofluorescence, western blot, transcriptional activity assays, immunohistochemistry on renal biopsies\",\n      \"journal\": \"Human molecular genetics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — patient-derived cell model with multiple orthogonal readouts, single lab\",\n      \"pmids\": [\"34740236\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"ANKS6 regulates BICC1 ribonucleoprotein (RNP) complex assembly and organ laterality determination. ANKS6 induces structural remodeling of ANKS3, relieving an inhibitory interaction between ANKS3's C-terminal coiled-coil domain and BICC1 that otherwise blocks target mRNA (Dand5 3' UTR) binding. This dual regulation is validated by in vitro reconstitution and AlphaFold structure predictions.\",\n      \"method\": \"AlphaFold structure predictions, in vitro reconstitution of protein complexes, CRISPR-engineered ANKS3 truncation in zebrafish, mRNA decay assays, biochemical binding assays\",\n      \"journal\": \"PLoS biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — in vitro reconstitution and structural prediction with biochemical validation, single lab\",\n      \"pmids\": [\"37733651\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"ANKS6, recruited by ANKS3, reinstates BICC1 condensation and ribonucleoparticle assembly after ANKS3-mediated dispersal of Bicc1 granules, demonstrating that ANKS6 and ANKS3 exert opposing regulatory effects on Bicc1 phase transitioning and client mRNA immobilization.\",\n      \"method\": \"Cell-based condensate/granule assays, co-immunoprecipitation, RNA binding assays, live-cell imaging of phase transitioning\",\n      \"journal\": \"iScience\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple functional assays examining phase transitioning and mRNA regulation, single lab\",\n      \"pmids\": [\"37275520\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"ANKS6-deficient livers exhibit accumulation of inflammatory M1-like macrophages in periportal fibrotic tissue, and macrophage depletion by clodronate liposomes reduces inflammatory gene expression, fibrosis, and biliary dysfunction in liver-specific Anks6 KO mice, establishing a causal role for macrophage-mediated inflammation in ANKS6-deficiency-associated congenital hepatic fibrosis.\",\n      \"method\": \"Liver-specific Anks6 KO mouse model, clodronate liposome macrophage depletion, flow cytometry, gene expression analysis, histology\",\n      \"journal\": \"FASEB journal\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic KO model with pharmacological intervention and multiple cellular readouts, single lab\",\n      \"pmids\": [\"35032404\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"In the Han:SPRD Cy/+ rat model, increased levels of both total and active β-catenin were detected in precystic tubuli, suggesting ANKS6 mutations may contribute to cystogenesis via dysregulation of Wnt/β-catenin signaling.\",\n      \"method\": \"Immunohistochemistry in Han:SPRD Cy/+ rat kidney tissue\",\n      \"journal\": \"Journal of the American Society of Nephrology\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single IHC-based observation without mechanistic follow-up, single lab\",\n      \"pmids\": [\"24610927\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"ANKS6 is a ciliary inversin-compartment protein that sits at the center of a nephronophthisis module: it binds and activates the kinase NEK8 (via its kinase domain), undergoes NEK8-mediated phosphorylation promoted cooperatively by INV and NPHP3, and interacts through its SAM domain with ANKS3 (forming a heterodimer at the end of ANKS3-SAM polymers) and with BICC1 to regulate ribonucleoprotein complex assembly and Dand5 mRNA decay for organ laterality; disease-causing SAM-domain mutations (R823W, I747N) selectively disrupt either the ANKS3 or BICC1 interaction; in the liver, ANKS6 promotes YAP1/TAZ/TEAD4 transcriptional activity by binding these Hippo pathway effectors, and its loss leads to YAP dysregulation, bile duct malformation, and macrophage-driven periportal fibrosis.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"ANKS6 is a ciliary inversin-compartment protein that functions as the central organizer of a nephronophthisis signaling module governing kidney morphogenesis, organ laterality, and bile duct development [#0]. Within the proximal cilium, ANKS6 binds the kinase domain of NEK8 to activate the kinase and in turn requires NEK8 for its own localization to the inversin compartment; this reciprocal dependence is dissected by the Anks6(Streaker) and Nek8(Roc) mouse alleles [#2]. ANKS6 itself is a NEK8 substrate whose phosphorylation is cooperatively promoted by INV and NPHP3, positioning ANKS6 as a signal mediator that relays information from the cilium to the cytoplasm to control kidney morphogenesis [#7]. Through its SAM domain, ANKS6 binds the end of an ANKS3-SAM polymer, and ANKS3 in turn recruits ANKS6 to BICC1 to build giant macromolecular ribonucleoprotein assemblies [#3, #4]; ANKS6 remodels ANKS3 to relieve an autoinhibitory interaction that otherwise blocks BICC1 binding to the Dand5 3' UTR, thereby regulating mRNA decay and left-right laterality [#11]. The disease-causing SAM-domain mutations partition these activities — R823W destabilizes the ANKS6 SAM domain and abolishes the ANKS3 interaction, whereas I747N selectively disrupts the BICC1 interaction, and either lesion causes cystic kidney disease [#3, #5]. Beyond the cilium, ANKS6 antagonizes Hippo signaling by binding YAP1, TAZ, and TEAD4 to promote their transcriptional activity, and its loss in liver drives YAP dysregulation, bile duct malformation, and macrophage-driven periportal fibrosis [#9, #13].\",\n  \"teleology\": [\n    {\n      \"year\": 2013,\n      \"claim\": \"Established that ANKS6 is not an isolated factor but the centerpiece of a defined ciliary nephronophthisis module, answering where ANKS6 acts and with which NPHP proteins.\",\n      \"evidence\": \"Co-IP, immunofluorescence localization, and knockdown in zebrafish and Xenopus with renal/laterality phenotypes\",\n      \"pmids\": [\"23793029\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not define the biochemical activity of ANKS6 within the module\", \"Mechanism by which the module controls morphogenesis unresolved\"]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"Tested how the module is regulated, showing the oxygen sensor HIF1AN hydroxylates ANKS6 and INVS to alter module composition.\",\n      \"evidence\": \"Biochemical hydroxylation assay, Co-IP, and Xenopus knockdown\",\n      \"pmids\": [\"23793029\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Hydroxylation sites and stoichiometry not fully mapped\", \"Physiological oxygen-dependence in mammalian kidney not established\"]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Defined the enzymatic relationship at the module's core: ANKS6 binds and activates NEK8 and depends on NEK8 for ciliary localization, separating activation from localization with distinct mutant alleles.\",\n      \"evidence\": \"Reciprocal Co-IP, Anks6(Streaker) and Nek8(Roc) mouse mutants, and kinase activity assays\",\n      \"pmids\": [\"25599650\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Downstream NEK8 substrates beyond ANKS6 not identified\", \"Structural basis of ANKS6-NEK8 kinase-domain binding unresolved\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Resolved the structural basis of ANKS6 self-assembly, showing its SAM domain caps an ANKS3-SAM polymer and that R823W destabilizes the domain to abolish binding.\",\n      \"evidence\": \"X-ray crystallography of ANKS3-SAM polymer and ANKS3/ANKS6-SAM complex with mutagenesis\",\n      \"pmids\": [\"24998259\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Functional consequence of polymer capping in cilia not directly tested\", \"Does not address the separate BICC1 interaction\"]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Showed the ANKS6 SAM domain mediates two genetically separable interactions, with I747N disrupting BICC1 binding and R823W disrupting ANKS3 binding, each independently causing cystic kidney disease.\",\n      \"evidence\": \"ENU mutagenesis screen, Co-IP, and comparative phenotyping in rat and mouse\",\n      \"pmids\": [\"26039630\", \"26327442\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Structural mechanism distinguishing the two SAM interactions not resolved\", \"Relative contribution of each interaction to disease severity unclear\"]\n    },\n    {\n      \"year\": 2010,\n      \"claim\": \"Demonstrated causality between the Anks6(R823W) mutation and cystogenesis in a dominant-negative manner, linking the lesion to proliferation, apoptosis, and c-myc dysregulation.\",\n      \"evidence\": \"Transgenic rat with tubule-specific Anks6(R823W) overexpression, Northern blot, in situ hybridization, histology\",\n      \"pmids\": [\"21119215\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Molecular pathway connecting R823W to c-myc/proliferation not defined\", \"Dominant-negative target not identified\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Established that INV and NPHP3 cooperatively promote NEK8-mediated ANKS6 phosphorylation, defining ANKS6 as a cilium-to-cytoplasm signal mediator whose phosphorylation is lost in cystic kidneys.\",\n      \"evidence\": \"Nphp3 G2A knock-in mice, phosphorylation/western readouts, comparison with Inv mutants\",\n      \"pmids\": [\"29395339\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Phosphosites on ANKS6 not mapped\", \"Downstream effectors of phospho-ANKS6 not identified\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Showed ANKS3 recruits ANKS6 to BICC1 so the three cooperatively form giant macromolecular complexes, with neither ANKS protein homopolymerizing alone in vivo.\",\n      \"evidence\": \"Crystal structure of Bicc1-SAM polymer, Co-IP, and domain-mapping complex assays\",\n      \"pmids\": [\"29290488\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Functional output of the giant complexes not directly assayed here\", \"SAM-independent contributions not fully delineated\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Defined the RNA-regulatory mechanism: ANKS6 remodels ANKS3 to relieve autoinhibition and license BICC1 binding to Dand5 mRNA, and oppositely tunes BICC1 condensation, linking the module to laterality and mRNA decay.\",\n      \"evidence\": \"AlphaFold predictions, in vitro reconstitution, CRISPR ANKS3 truncation in zebrafish, mRNA decay and condensate/phase-transition assays\",\n      \"pmids\": [\"37733651\", \"37275520\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"In vivo confirmation of Dand5 mRNA control by ANKS6 in mammals limited\", \"How ciliary signaling couples to RNP regulation unresolved\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Extended ANKS6 function to liver, showing it antagonizes Hippo signaling by binding YAP1/TAZ/TEAD4 to promote their transcription, with loss causing bile duct malformation and fibrosis.\",\n      \"evidence\": \"Anks6 knockout mouse, Co-IP with YAP1/TAZ/TEAD4, gene expression and histology\",\n      \"pmids\": [\"32886109\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct vs indirect nature of YAP/TAZ/TEAD4 binding not structurally resolved\", \"Link between ciliary ANKS6 and Hippo regulation unclear\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Connected ANKS6 deficiency to disease cell biology, showing impaired inversin-compartment integrity, YAP/Wnt dysregulation, and macrophage-driven periportal fibrosis as a causal inflammatory mechanism.\",\n      \"evidence\": \"Patient-derived fibroblasts with orthogonal readouts; liver-specific Anks6 KO with clodronate macrophage depletion\",\n      \"pmids\": [\"34740236\", \"35032404\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Signal linking ANKS6 loss to M1 macrophage recruitment not identified\", \"Direct mechanism coupling cilia defects to YAP/Wnt imbalance unresolved\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How ciliary signaling, NEK8-dependent phosphorylation, SAM-domain assembly, and downstream YAP/Wnt and BICC1-RNP outputs are integrated into a single coherent control of kidney and liver morphogenesis remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No unified model linking phospho-state of ANKS6 to its scaffolding and transcriptional roles\", \"ANKS6 phosphosites and their functional consequences uncharacterized\", \"Direct structural basis for YAP1/TAZ/TEAD4 binding unknown\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [3, 4, 11]},\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [2]},\n      {\"term_id\": \"GO:0140110\", \"supporting_discovery_ids\": [9]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005929\", \"supporting_discovery_ids\": [0, 2, 6]},\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [9, 10]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"GO:0140097\", \"supporting_discovery_ids\": []},\n      {\"term_id\": \"R-HSA-162582\", \"supporting_discovery_ids\": [9, 10]},\n      {\"term_id\": \"R-HSA-8953854\", \"supporting_discovery_ids\": [11, 12]},\n      {\"term_id\": \"R-HSA-1266738\", \"supporting_discovery_ids\": [0, 9]}\n    ],\n    \"complexes\": [\n      \"ANKS6-NEK8-INVS-NPHP3 inversin-compartment module\",\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}","audit_flag":null,"evaluation":{"faith_supported":6,"faith_total":6,"faith_pct":100.0}}