{"gene":"IFT46","run_date":"2026-04-28T18:06:53","timeline":{"discoveries":[{"year":2007,"finding":"IFT46 is a core IFT complex B protein required for complex B stability; null mutation in Chlamydomonas causes short paralyzed flagella lacking dynein arms, reduced levels of most complex B proteins, and central pair defects. A spontaneous suppressor mutation restores complex B levels and flagellar length but not outer dynein arms, demonstrating that IFT46 is specifically required for transporting outer dynein arms into flagella.","method":"Insertional mutagenesis, suppressor genetics, Western blot, electron microscopy, flagellar reconstitution in Chlamydomonas","journal":"The Journal of cell biology","confidence":"High","confidence_rationale":"Tier 2 — genetic epistasis (suppressor screen) with multiple orthogonal readouts, replicated across organisms","pmids":["17312020"],"is_preprint":false},{"year":2010,"finding":"IFT46 directly interacts with both IFT88 and IFT52, and together these three core IFT-B subunits form a ternary complex within the IFT-B core. Recombinant IFT46 introduced by electroporation rescues flagellar assembly in an ift46 mutant and localizes to moving IFT particles in vivo.","method":"Yeast two-hybrid, bacterial co-expression, chemical cross-linking, electroporation rescue assay, in vivo live imaging","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1–2 — direct interaction confirmed by multiple orthogonal methods (Y2H + co-expression + cross-linking + rescue)","pmids":["20435895"],"is_preprint":false},{"year":2015,"finding":"IFT46 localizes to the basal body in zebrafish ciliated tissues; morpholino knockdown of ift46 causes kidney cysts, pericardial edema, shortened cilia in kidney and spinal canal, and ciliary defects in otic vesicles and lateral line hair cells. Ift46 knockout mice display randomization of heart looping, indicating a role in left-right axis patterning, and show defects in brain, neural tube, and heart development.","method":"Morpholino knockdown in zebrafish, Ift46 knockout mouse generation, immunofluorescence, electron microscopy","journal":"Developmental biology","confidence":"High","confidence_rationale":"Tier 2 — loss-of-function in two vertebrate models with defined ciliary and developmental phenotypic readouts","pmids":["25722189"],"is_preprint":false},{"year":2017,"finding":"The crystal structure of Chlamydomonas ODA16 reveals an 80-residue N-terminal domain and a C-terminal 8-bladed β-propeller domain, both required for association with the N-terminal 147 residues of IFT46 (Kd ≈ 200 nM). The C-terminal β-propeller of ODA16 (but not the N-terminal domain) is required for interaction with outer dynein arms extracted from axonemes, defining an architectural model for ODA16-mediated IFT of outer dynein arms via IFT46.","method":"X-ray crystallography, ITC/binding measurements, pulldown with axonemal ODAs, deletion mutagenesis","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1 — crystal structure combined with quantitative binding and mutagenesis","pmids":["28298440"],"is_preprint":false},{"year":2017,"finding":"The IFT46 N-terminus (residues 1–147) is required for import of outer dynein arms and their cargo adaptor ODA16 into flagella; the C-terminal 240 amino acids of IFT46 are sufficient to assemble into and stabilize IFT-B but cannot support outer arm dynein transport. The suppression of ift46-1 was shown to result from transposon MRC1 insertion producing a C-terminal IFT46 fusion protein.","method":"Molecular characterization of suppressor allele, flagellar protein analysis by Western blot and immunofluorescence, genetic complementation with IFT46 truncations in Chlamydomonas","journal":"Molecular biology of the cell","confidence":"High","confidence_rationale":"Tier 2 — domain-specific functional dissection with multiple genetic and biochemical readouts","pmids":["28701346"],"is_preprint":false},{"year":2017,"finding":"KIF17 interacts with the IFT46–IFT56 dimer within the IFT-B complex through its C-terminal sequence immediately upstream of its nuclear localization signal (NLS). KIF17 requires both IFT-B binding (via IFT46–IFT56) and its NLS (which binds importin α) for ciliary entry, but is dispensable for ciliogenesis and intraciliary IFT-B trafficking in mammalian cells.","method":"Visible immunoprecipitation assay, deletion mutagenesis, live-cell imaging, ciliary entry assays in mammalian cells","journal":"Molecular biology of the cell","confidence":"High","confidence_rationale":"Tier 2 — reciprocal interaction mapping plus functional dissection with multiple truncation constructs","pmids":["28077622"],"is_preprint":false},{"year":2017,"finding":"IFT52 recruits IFT46 to basal bodies through direct interaction with residues L285 and L286 within the C-terminal basal body targeting sequence (BBTS3, residues 246–321) of IFT46. This BBTS3 sequence is also sufficient for ciliary targeting and bidirectional IFT movement. IFT52, but not IFT81, IFT88, IFT122, FLA10, or DHC1b, is required for IFT46 basal body localization, indicating IFT52 and IFT46 preassemble in the cytoplasm before targeting to basal bodies.","method":"Truncation mapping in ift46-1 Chlamydomonas, site-directed mutagenesis, ectopic nuclear expression, IFT/motor mutant analysis, fluorescence microscopy","journal":"Journal of cell science","confidence":"High","confidence_rationale":"Tier 2 — specific residue-level mutagenesis combined with multiple genetic backgrounds and localization assays","pmids":["28302912"],"is_preprint":false},{"year":2018,"finding":"In Paramecium, GFP-IFT46 localizes to basal bodies and to cilia undergoing biogenesis. RNAi depletion of IFT46 reduces cilia number and length, and causes abnormal accumulation of IFT57-GFP in the cortex and cytoplasm rather than in cilia, demonstrating IFT46 is essential for trafficking IFT proteins between cytoplasm and cilia.","method":"GFP fusion live imaging, RNAi knockdown, immunofluorescence microscopy in Paramecium","journal":"Scientific reports","confidence":"Medium","confidence_rationale":"Tier 2 — loss-of-function with defined cargo mislocalization readout, single organism/lab","pmids":["29915351"],"is_preprint":false},{"year":2007,"finding":"Mouse IFT46 (mIFT46) protein localizes to the primary cilium of chondrocytes, is preferentially expressed in early hypertrophic chondrocytes of the growth plate, and is regulated by BMP-2. siRNA knockdown of mIFT46 in cultured chondrocytes specifically upregulates expression of several skeletogenesis-related genes. Morpholino knockdown in zebrafish causes dorsalization and tail duplication, demonstrating a developmental role beyond cartilage.","method":"Polyclonal antibody generation, immunofluorescence localization in primary cilia, siRNA knockdown with gene expression analysis, zebrafish morpholino injection","journal":"The Journal of biological chemistry","confidence":"Medium","confidence_rationale":"Tier 2–3 — localization confirmed by antibody staining; functional role by KD phenotype in two systems","pmids":["17720815"],"is_preprint":false},{"year":2022,"finding":"SARS-CoV-2 ORF10 interacts with ZYG11B to enhance CUL2ZYG11B E3 ligase activity, leading to increased ubiquitination and proteasomal degradation of IFT46. Loss of IFT46 impairs both cilia biogenesis and maintenance. Exposure of hACE2 mice to SARS-CoV-2 or ORF10 alone, and ORF10 expression in primary human nasal epithelial cells, recapitulates cilia dysfunction phenotypes.","method":"Co-immunoprecipitation, ubiquitination assays, proteasome inhibitor rescue, mouse in vivo model, primary human nasal epithelial cell culture, ciliary imaging","journal":"The Journal of cell biology","confidence":"High","confidence_rationale":"Tier 2 — biochemical mechanism (CUL2ZYG11B-mediated ubiquitination of IFT46) validated in vitro and in multiple in vivo models","pmids":["35674692"],"is_preprint":false},{"year":2026,"finding":"IFT46 regulates autophagy flux in mouse collecting duct cells; Ift46 deficiency increases Limk2 protein levels through impaired autophagy-mediated degradation. Limk2 directly interacts with p62/sequestosome-1 (confirmed by co-IP), and autophagy induction suppresses Limk2 stability. In Ift46-deficient mice and human ADPKD, upregulated Limk2 promotes partial epithelial-to-mesenchymal transition (EMT) and contributes to renal cyst formation through the 'Ift46-autophagy-Limk2' axis.","method":"RNA sequencing, co-immunoprecipitation, 3D culture cyst model, conditional knockout mice, autophagy modulating drugs, human ADPKD tissue analysis","journal":"Cell communication and signaling","confidence":"Medium","confidence_rationale":"Tier 2 — multiple orthogonal methods (co-IP, KO mouse, human tissue) in single lab identifying novel non-ciliary IFT46 pathway","pmids":["41680856"],"is_preprint":false}],"current_model":"IFT46 is a core IFT-B complex protein whose N-terminus directly binds the cargo adaptor ODA16 (Kd ~200 nM) to mediate intraflagellar transport of outer dynein arms into cilia, while its C-terminus (residues 246–321) mediates IFT-B complex assembly/stability and basal body targeting via direct interaction with IFT52 (residues L285/L286); within IFT-B, IFT46 also forms a direct ternary complex with IFT88 and IFT52, presents an IFT46–IFT56 dimer interface for KIF17 ciliary entry, is targeted for ubiquitin-proteasomal degradation by the SARS-CoV-2 ORF10-hijacked CUL2ZYG11B ligase, and additionally regulates autophagy flux to control Limk2 stability and partial EMT in kidney collecting duct cells."},"narrative":{"teleology":[{"year":2007,"claim":"Establishing that IFT46 is a core IFT-B subunit required both for complex B stability/flagellar assembly and specifically for outer dynein arm transport resolved whether individual IFT-B proteins have cargo-selective roles beyond structural scaffolding.","evidence":"Insertional mutagenesis and suppressor genetics in Chlamydomonas with Western blot and EM readouts","pmids":["17312020"],"confidence":"High","gaps":["Direct binding partners within IFT-B were not identified","Mechanism by which IFT46 recognizes outer dynein arms was unknown","Vertebrate developmental roles had not been tested"]},{"year":2007,"claim":"Demonstrating IFT46 localization to primary cilia of mammalian chondrocytes and its regulation by BMP-2 extended IFT46 function from Chlamydomonas to vertebrate developmental signaling contexts.","evidence":"Immunofluorescence localization in mouse chondrocytes, siRNA knockdown gene expression analysis, zebrafish morpholino injection","pmids":["17720815"],"confidence":"Medium","gaps":["Single lab with antibody-based localization; independent confirmation lacking at that time","Mechanism linking IFT46 to skeletogenesis gene regulation was not elucidated"]},{"year":2010,"claim":"Identifying IFT46 as forming a direct ternary complex with IFT52 and IFT88 defined the core IFT-B architecture and showed these three subunits constitute a minimal IFT-B assembly unit.","evidence":"Yeast two-hybrid, bacterial co-expression, chemical cross-linking, electroporation rescue and live imaging in Chlamydomonas","pmids":["20435895"],"confidence":"High","gaps":["Atomic-resolution structure of the ternary complex was not available","Relative contributions of IFT52 versus IFT88 binding to IFT46 stability were unclear"]},{"year":2015,"claim":"Knockout and knockdown studies in zebrafish and mouse proved IFT46 is essential for vertebrate ciliogenesis and left-right axis patterning, establishing it as a ciliopathy-relevant gene.","evidence":"Morpholino knockdown in zebrafish and Ift46 knockout mouse generation with EM, immunofluorescence, and developmental phenotyping","pmids":["25722189"],"confidence":"High","gaps":["No human ciliopathy mutations in IFT46 had been identified","Whether specific cilia subtypes have differential IFT46 dependence was untested"]},{"year":2017,"claim":"Structural and biochemical dissection of the IFT46–ODA16 interaction revealed that the IFT46 N-terminus (residues 1–147) binds ODA16's β-propeller domain with ~200 nM affinity, while ODA16 separately contacts outer dynein arms, establishing the architectural basis for cargo-selective IFT.","evidence":"X-ray crystallography of ODA16, ITC binding measurements, pulldown with axonemal ODAs, deletion mutagenesis in Chlamydomonas","pmids":["28298440","28701346"],"confidence":"High","gaps":["Atomic structure of the IFT46–ODA16 binary complex was not resolved","Whether other cargo adaptors bind a similar IFT46 surface was unknown"]},{"year":2017,"claim":"Mapping the IFT46 C-terminal BBTS3 domain (residues 246–321) and the critical L285/L286 residues for IFT52 binding revealed that IFT52–IFT46 preassembly in the cytoplasm is required for basal body targeting, separating complex assembly from cargo-loading functions.","evidence":"Truncation mapping, site-directed mutagenesis, motor/IFT mutant analysis, and fluorescence microscopy in Chlamydomonas","pmids":["28302912"],"confidence":"High","gaps":["Structural basis for IFT52–IFT46 BBTS3 interaction was not determined at atomic resolution","Cytoplasmic versus basal body assembly sequence for the full IFT-B complex remained incomplete"]},{"year":2017,"claim":"Discovery that the IFT46–IFT56 dimer provides the binding interface for KIF17 ciliary entry revealed a second cargo/motor-adaptor role for IFT46 distinct from its ODA16-binding function.","evidence":"Visible immunoprecipitation assay, deletion mutagenesis, live-cell imaging, and ciliary entry assays in mammalian cells","pmids":["28077622"],"confidence":"High","gaps":["Whether IFT46–IFT56 binding to KIF17 is regulated remains unknown","Functional consequence of disrupting KIF17–IFT46 interaction on specific ciliary signaling pathways was not determined"]},{"year":2022,"claim":"Demonstrating that SARS-CoV-2 ORF10 hijacks CUL2^ZYG11B to ubiquitinate and degrade IFT46, impairing cilia biogenesis and maintenance, identified a viral mechanism for disrupting mucociliary clearance.","evidence":"Co-immunoprecipitation, ubiquitination assays, proteasome inhibitor rescue, hACE2 mouse model, primary human nasal epithelial cell culture","pmids":["35674692"],"confidence":"High","gaps":["The specific ubiquitination sites on IFT46 were not mapped","Whether other IFT-B subunits are co-degraded or destabilized secondarily was not fully addressed","Clinical relevance for COVID-19 airway pathology requires further patient-level evidence"]},{"year":2026,"claim":"Identifying that IFT46 regulates autophagy flux to control Limk2 stability and partial EMT in kidney collecting duct cells uncovered a non-canonical, cilia-independent function linked to cystic kidney disease.","evidence":"RNA-seq, co-immunoprecipitation, conditional knockout mice, 3D cyst culture model, autophagy-modulating drugs, human ADPKD tissue analysis","pmids":["41680856"],"confidence":"Medium","gaps":["Single-lab finding; independent replication of the IFT46–autophagy–Limk2 axis is needed","Mechanism by which IFT46 controls autophagy flux is not defined","Whether the autophagy role is fully independent of cilia or partially coupled remains unclear"]},{"year":null,"claim":"Key unresolved questions include the atomic structure of the IFT46–ODA16 binary complex, whether IFT46 has additional non-ciliary functions in other tissues, and whether human IFT46 mutations cause a defined ciliopathy.","evidence":"","pmids":[],"confidence":"High","gaps":["No human disease-causing mutations in IFT46 have been reported","Full reconstitution of IFT46-dependent cargo loading onto IFT trains has not been achieved","The autophagy-regulatory mechanism of IFT46 at the molecular level is undefined"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0005198","term_label":"structural molecule activity","supporting_discovery_ids":[0,1,6]},{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[3,4,5]}],"localization":[{"term_id":"GO:0005929","term_label":"cilium","supporting_discovery_ids":[0,2,7,8]},{"term_id":"GO:0005815","term_label":"microtubule organizing center","supporting_discovery_ids":[2,6,7]},{"term_id":"GO:0005829","term_label":"cytosol","supporting_discovery_ids":[6]}],"pathway":[{"term_id":"R-HSA-1852241","term_label":"Organelle biogenesis and maintenance","supporting_discovery_ids":[0,1,2,6,7,9]},{"term_id":"R-HSA-9612973","term_label":"Autophagy","supporting_discovery_ids":[10]},{"term_id":"R-HSA-1266738","term_label":"Developmental Biology","supporting_discovery_ids":[2,8]}],"complexes":["IFT-B complex"],"partners":["IFT52","IFT88","IFT56","ODA16","KIF17","ZYG11B","LIMK2"],"other_free_text":[]},"mechanistic_narrative":"IFT46 is a core subunit of the intraflagellar transport complex B (IFT-B) that is essential for ciliogenesis, ciliary cargo delivery, and cilium-dependent developmental signaling. Its C-terminal domain (residues 246–321, including L285/L286) mediates direct binding to IFT52 for basal body targeting and IFT-B complex assembly/stability, while its N-terminal domain (residues 1–147) binds the cargo adaptor ODA16 (Kd ~200 nM) to specifically transport outer dynein arms into cilia; IFT46 also forms a ternary complex with IFT52 and IFT88, and its dimer interface with IFT56 is required for KIF17 ciliary entry [PMID:17312020, PMID:20435895, PMID:28298440, PMID:28077622, PMID:28302912]. Loss of IFT46 in vertebrates causes kidney cysts, left-right patterning defects, and shortened cilia, and SARS-CoV-2 ORF10 hijacks the CUL2^ZYG11B E3 ligase to ubiquitinate and degrade IFT46, impairing ciliary biogenesis and maintenance [PMID:25722189, PMID:35674692]. IFT46 also regulates autophagy flux in kidney collecting duct cells, where its deficiency stabilizes Limk2 to promote partial epithelial-to-mesenchymal transition and renal cyst formation [PMID:41680856]."},"prefetch_data":{"uniprot":{"accession":"Q9NQC8","full_name":"Intraflagellar transport protein 46 homolog","aliases":[],"length_aa":304,"mass_kda":34.3,"function":"Forms part of a complex involved in intraflagellar transport (IFT), the bi-directional movement of particles required for the assembly, maintenance and functioning of primary cilia. May play a role in chondrocyte maturation and skeletogenesis (By similarity)","subcellular_location":"Cytoplasm, cytoskeleton, cilium basal body; Cell projection, cilium","url":"https://www.uniprot.org/uniprotkb/Q9NQC8/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/IFT46","classification":"Not Classified","n_dependent_lines":1,"n_total_lines":1208,"dependency_fraction":0.0008278145695364238},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[{"gene":"HSPB11","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/search/IFT46","total_profiled":1310},"omim":[{"mim_id":"620742","title":"INTRAFLAGELLAR TRANSPORT 70B; IFT70B","url":"https://www.omim.org/entry/620742"},{"mim_id":"620741","title":"INTRAFLAGELLAR TRANSPORT 70A; IFT70A","url":"https://www.omim.org/entry/620741"},{"mim_id":"620506","title":"INTRAFLAGELLAR TRANSPORT 46; IFT46","url":"https://www.omim.org/entry/620506"},{"mim_id":"620279","title":"DYNEIN ASSEMBLY FACTOR WITH WD REPEATS 1; DAW1","url":"https://www.omim.org/entry/620279"},{"mim_id":"618763","title":"JOUBERT SYNDROME 36; JBTS36","url":"https://www.omim.org/entry/618763"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Approved","locations":[{"location":"Actin filaments","reliability":"Approved"},{"location":"Primary cilium","reliability":"Approved"},{"location":"Principal piece","reliability":"Approved"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/IFT46"},"hgnc":{"alias_symbol":["C11orf2","FLJ21827","FAP32","CFAP32"],"prev_symbol":["C11orf60"]},"alphafold":{"accession":"Q9NQC8","domains":[{"cath_id":"-","chopping":"115-194","consensus_level":"medium","plddt":78.06,"start":115,"end":194},{"cath_id":"-","chopping":"208-279","consensus_level":"high","plddt":83.9653,"start":208,"end":279}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9NQC8","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q9NQC8-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q9NQC8-F1-predicted_aligned_error_v6.png","plddt_mean":69.75},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=IFT46","jax_strain_url":"https://www.jax.org/strain/search?query=IFT46"},"sequence":{"accession":"Q9NQC8","fasta_url":"https://rest.uniprot.org/uniprotkb/Q9NQC8.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q9NQC8/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9NQC8"}},"corpus_meta":[{"pmid":"17312020","id":"PMC_17312020","title":"Functional 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Genetic suppressor analysis showed that restoring IFT-B stability without IFT46 still fails to transport outer dynein arms into flagella, demonstrating that IFT46 is specifically and uniquely required for outer dynein arm transport into flagella.\",\n      \"method\": \"Insertional null mutant in Chlamydomonas, partial suppressor genetic epistasis, western blotting of IFT proteins, electron microscopy of axonemal ultrastructure\",\n      \"journal\": \"The Journal of cell biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1/2 — clean null mutant + suppressor epistasis + ultrastructural readout, foundational paper with 186 citations, replicated by later work\",\n      \"pmids\": [\"17312020\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"IFT46 directly interacts with IFT88 and IFT52, and the three proteins together form a ternary complex within the IFT complex B core; IFT46 is positioned within a ~500 kDa core IFT-B sub-complex.\",\n      \"method\": \"Yeast two-hybrid, bacterial co-expression, chemical cross-linking, electroporation of recombinant IFT46 to rescue flagellar assembly\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — direct binary and ternary interaction confirmed by orthogonal methods (Y2H + bacterial co-expression + cross-linking), functional rescue by electroporation\",\n      \"pmids\": [\"20435895\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"The N-terminal 147 residues of IFT46 bind directly to the ODA16 cargo adaptor (Kd ~200 nM); ODA16 contains an N-terminal domain and a C-terminal 8-bladed β-propeller, both required for IFT46 binding, while only the β-propeller is required for binding outer dynein arms. Crystal structure of ODA16 revealed the structural basis of this adaptor function.\",\n      \"method\": \"X-ray crystallography of CrODA16, isothermal titration calorimetry, deletion mapping of binding interfaces, pulldown with axonemal ODAs\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — crystal structure combined with quantitative binding assays and domain-mapping mutagenesis\",\n      \"pmids\": [\"28298440\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"The IFT46 N-terminus (absent in the spontaneous suppressor of ift46-1, which expresses only the C-terminal 240 aa) is specifically required for import of ODA16 and outer dynein arms into flagella, while the C-terminus alone is sufficient to stabilize IFT-B and support flagellar elongation.\",\n      \"method\": \"Molecular characterization of a spontaneous suppressor allele (MRC1 transposon insertion creating C-terminal IFT46 fusion protein), flagellar western blot, immunofluorescence of ODA16\",\n      \"journal\": \"Molecular biology of the cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — defined molecular lesion (transposon insertion) mapped to specific domain with clear functional consequence, replicated across labs\",\n      \"pmids\": [\"28701346\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"IFT52 recruits IFT46 to basal bodies via direct interaction with residues L285 and L286 in the C-terminal domain of IFT46 (BBTS3, residues 246–321); this C-terminal sequence is also sufficient for ciliary targeting and bidirectional IFT movement. IFT46 basal body localization depends on IFT52 but not on IFT81, IFT88, IFT122, FLA10, or DHC1b.\",\n      \"method\": \"Truncation constructs expressed in ift46-1 mutant, YFP localization, co-immunoprecipitation, ectopic nuclear expression of IFT52 C-terminal domain causing nuclear re-routing of IFT46, IFT/motor mutant epistasis\",\n      \"journal\": \"Journal of cell science\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — multiple orthogonal methods including domain mapping, genetic epistasis, and ectopic misdirection experiment\",\n      \"pmids\": [\"28302912\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"KIF17 (homodimeric kinesin-2) interacts with the IFT46–IFT56 dimer within IFT-B through its C-terminal sequence upstream of its NLS; this interaction is required for KIF17 entry into cilia but not for intraciliary trafficking. Both IFT-B binding and the NLS (bound by importin-α) are necessary for ciliary entry of KIF17.\",\n      \"method\": \"Visible immunoprecipitation (VIP) assay, deletion mapping, siRNA knockdown of IFT46/IFT56, live-cell imaging of KIF17-GFP\",\n      \"journal\": \"Molecular biology of the cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — VIP assay for direct interaction plus loss-of-function (siRNA) with specific ciliary entry phenotype and domain-level mapping\",\n      \"pmids\": [\"28077622\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"IFT46 localizes to the basal body in zebrafish ciliated cells; morpholino knockdown results in shortened/absent cilia in kidney and spinal canal, and IFT46 knockout mice display randomized heart looping (defective L/R patterning), demonstrating an essential in vivo role in vertebrate ciliogenesis.\",\n      \"method\": \"Morpholino knockdown in zebrafish, IFT46 knockout mice (homozygous lethal), immunofluorescence localization, electron microscopy of cilia\",\n      \"journal\": \"Developmental biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — clean KO/KD with specific ciliary phenotypic readout in two vertebrate models\",\n      \"pmids\": [\"25722189\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"In Paramecium, IFT46 depletion causes abnormal accumulation of IFT57-GFP in the cortex and cytoplasm rather than normal cycling into cilia, indicating that IFT46 is essential for trafficking IFT-B cargo proteins between cytoplasm and cilia.\",\n      \"method\": \"RNAi knockdown in Paramecium, GFP-tagged IFT57 localization, cilia length/number measurement, transcriptomics\",\n      \"journal\": \"Scientific reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 — single-organism RNAi + GFP localization; mechanistic inference supported by direct imaging\",\n      \"pmids\": [\"29915351\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"IFT46 regulates autophagy flux in mouse collecting duct cells; IFT46 deficiency leads to increased LIMK2 translation (stabilized by impaired autophagy-mediated degradation of p62/sequestosome-1 which directly interacts with LIMK2), promoting partial EMT and renal cystogenesis. Autophagy induction suppresses LIMK2 and cystogenesis.\",\n      \"method\": \"RNA-seq of Ift46-knockdown cells, co-immunoprecipitation of LIMK2 and p62, 3D culture cyst assay, collecting duct-specific Ift46-KO mice, pharmacological autophagy manipulation\",\n      \"journal\": \"Cell communication and signaling : CCS\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — Co-IP for direct LIMK2-p62 interaction, in vivo KO model, multiple orthogonal methods; single lab, novel axis requiring independent replication\",\n      \"pmids\": [\"41680856\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"IFT46 is a core IFT complex B protein that (1) stabilizes the entire IFT-B complex through its C-terminal domain, (2) uses its N-terminal domain to bind the ODA16 cargo adaptor (crystal-structure-resolved interaction, Kd ~200 nM) and thereby mediates intraflagellar transport of outer dynein arms into cilia, (3) is recruited to basal bodies by a direct interaction with IFT52 via residues L285/L286, (4) binds the IFT56 subunit to capture KIF17 for ciliary entry, and (5) outside its canonical IFT role, regulates autophagy flux to control LIMK2 protein levels and suppress renal cystogenesis.\"\n}\n```\n\n--- ROUND 2 (R2/R3, augmented corpus) ---\n\n```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2007,\n      \"finding\": \"IFT46 is a core IFT complex B protein required for complex B stability; null mutation in Chlamydomonas causes short paralyzed flagella lacking dynein arms, reduced levels of most complex B proteins, and central pair defects. A spontaneous suppressor mutation restores complex B levels and flagellar length but not outer dynein arms, demonstrating that IFT46 is specifically required for transporting outer dynein arms into flagella.\",\n      \"method\": \"Insertional mutagenesis, suppressor genetics, Western blot, electron microscopy, flagellar reconstitution in Chlamydomonas\",\n      \"journal\": \"The Journal of cell biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — genetic epistasis (suppressor screen) with multiple orthogonal readouts, replicated across organisms\",\n      \"pmids\": [\"17312020\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"IFT46 directly interacts with both IFT88 and IFT52, and together these three core IFT-B subunits form a ternary complex within the IFT-B core. Recombinant IFT46 introduced by electroporation rescues flagellar assembly in an ift46 mutant and localizes to moving IFT particles in vivo.\",\n      \"method\": \"Yeast two-hybrid, bacterial co-expression, chemical cross-linking, electroporation rescue assay, in vivo live imaging\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 — direct interaction confirmed by multiple orthogonal methods (Y2H + co-expression + cross-linking + rescue)\",\n      \"pmids\": [\"20435895\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"IFT46 localizes to the basal body in zebrafish ciliated tissues; morpholino knockdown of ift46 causes kidney cysts, pericardial edema, shortened cilia in kidney and spinal canal, and ciliary defects in otic vesicles and lateral line hair cells. Ift46 knockout mice display randomization of heart looping, indicating a role in left-right axis patterning, and show defects in brain, neural tube, and heart development.\",\n      \"method\": \"Morpholino knockdown in zebrafish, Ift46 knockout mouse generation, immunofluorescence, electron microscopy\",\n      \"journal\": \"Developmental biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — loss-of-function in two vertebrate models with defined ciliary and developmental phenotypic readouts\",\n      \"pmids\": [\"25722189\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"The crystal structure of Chlamydomonas ODA16 reveals an 80-residue N-terminal domain and a C-terminal 8-bladed β-propeller domain, both required for association with the N-terminal 147 residues of IFT46 (Kd ≈ 200 nM). The C-terminal β-propeller of ODA16 (but not the N-terminal domain) is required for interaction with outer dynein arms extracted from axonemes, defining an architectural model for ODA16-mediated IFT of outer dynein arms via IFT46.\",\n      \"method\": \"X-ray crystallography, ITC/binding measurements, pulldown with axonemal ODAs, deletion mutagenesis\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — crystal structure combined with quantitative binding and mutagenesis\",\n      \"pmids\": [\"28298440\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"The IFT46 N-terminus (residues 1–147) is required for import of outer dynein arms and their cargo adaptor ODA16 into flagella; the C-terminal 240 amino acids of IFT46 are sufficient to assemble into and stabilize IFT-B but cannot support outer arm dynein transport. The suppression of ift46-1 was shown to result from transposon MRC1 insertion producing a C-terminal IFT46 fusion protein.\",\n      \"method\": \"Molecular characterization of suppressor allele, flagellar protein analysis by Western blot and immunofluorescence, genetic complementation with IFT46 truncations in Chlamydomonas\",\n      \"journal\": \"Molecular biology of the cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — domain-specific functional dissection with multiple genetic and biochemical readouts\",\n      \"pmids\": [\"28701346\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"KIF17 interacts with the IFT46–IFT56 dimer within the IFT-B complex through its C-terminal sequence immediately upstream of its nuclear localization signal (NLS). KIF17 requires both IFT-B binding (via IFT46–IFT56) and its NLS (which binds importin α) for ciliary entry, but is dispensable for ciliogenesis and intraciliary IFT-B trafficking in mammalian cells.\",\n      \"method\": \"Visible immunoprecipitation assay, deletion mutagenesis, live-cell imaging, ciliary entry assays in mammalian cells\",\n      \"journal\": \"Molecular biology of the cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — reciprocal interaction mapping plus functional dissection with multiple truncation constructs\",\n      \"pmids\": [\"28077622\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"IFT52 recruits IFT46 to basal bodies through direct interaction with residues L285 and L286 within the C-terminal basal body targeting sequence (BBTS3, residues 246–321) of IFT46. This BBTS3 sequence is also sufficient for ciliary targeting and bidirectional IFT movement. IFT52, but not IFT81, IFT88, IFT122, FLA10, or DHC1b, is required for IFT46 basal body localization, indicating IFT52 and IFT46 preassemble in the cytoplasm before targeting to basal bodies.\",\n      \"method\": \"Truncation mapping in ift46-1 Chlamydomonas, site-directed mutagenesis, ectopic nuclear expression, IFT/motor mutant analysis, fluorescence microscopy\",\n      \"journal\": \"Journal of cell science\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — specific residue-level mutagenesis combined with multiple genetic backgrounds and localization assays\",\n      \"pmids\": [\"28302912\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"In Paramecium, GFP-IFT46 localizes to basal bodies and to cilia undergoing biogenesis. RNAi depletion of IFT46 reduces cilia number and length, and causes abnormal accumulation of IFT57-GFP in the cortex and cytoplasm rather than in cilia, demonstrating IFT46 is essential for trafficking IFT proteins between cytoplasm and cilia.\",\n      \"method\": \"GFP fusion live imaging, RNAi knockdown, immunofluorescence microscopy in Paramecium\",\n      \"journal\": \"Scientific reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — loss-of-function with defined cargo mislocalization readout, single organism/lab\",\n      \"pmids\": [\"29915351\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2007,\n      \"finding\": \"Mouse IFT46 (mIFT46) protein localizes to the primary cilium of chondrocytes, is preferentially expressed in early hypertrophic chondrocytes of the growth plate, and is regulated by BMP-2. siRNA knockdown of mIFT46 in cultured chondrocytes specifically upregulates expression of several skeletogenesis-related genes. Morpholino knockdown in zebrafish causes dorsalization and tail duplication, demonstrating a developmental role beyond cartilage.\",\n      \"method\": \"Polyclonal antibody generation, immunofluorescence localization in primary cilia, siRNA knockdown with gene expression analysis, zebrafish morpholino injection\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2–3 — localization confirmed by antibody staining; functional role by KD phenotype in two systems\",\n      \"pmids\": [\"17720815\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"SARS-CoV-2 ORF10 interacts with ZYG11B to enhance CUL2ZYG11B E3 ligase activity, leading to increased ubiquitination and proteasomal degradation of IFT46. Loss of IFT46 impairs both cilia biogenesis and maintenance. Exposure of hACE2 mice to SARS-CoV-2 or ORF10 alone, and ORF10 expression in primary human nasal epithelial cells, recapitulates cilia dysfunction phenotypes.\",\n      \"method\": \"Co-immunoprecipitation, ubiquitination assays, proteasome inhibitor rescue, mouse in vivo model, primary human nasal epithelial cell culture, ciliary imaging\",\n      \"journal\": \"The Journal of cell biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — biochemical mechanism (CUL2ZYG11B-mediated ubiquitination of IFT46) validated in vitro and in multiple in vivo models\",\n      \"pmids\": [\"35674692\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"IFT46 regulates autophagy flux in mouse collecting duct cells; Ift46 deficiency increases Limk2 protein levels through impaired autophagy-mediated degradation. Limk2 directly interacts with p62/sequestosome-1 (confirmed by co-IP), and autophagy induction suppresses Limk2 stability. In Ift46-deficient mice and human ADPKD, upregulated Limk2 promotes partial epithelial-to-mesenchymal transition (EMT) and contributes to renal cyst formation through the 'Ift46-autophagy-Limk2' axis.\",\n      \"method\": \"RNA sequencing, co-immunoprecipitation, 3D culture cyst model, conditional knockout mice, autophagy modulating drugs, human ADPKD tissue analysis\",\n      \"journal\": \"Cell communication and signaling\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — multiple orthogonal methods (co-IP, KO mouse, human tissue) in single lab identifying novel non-ciliary IFT46 pathway\",\n      \"pmids\": [\"41680856\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"IFT46 is a core IFT-B complex protein whose N-terminus directly binds the cargo adaptor ODA16 (Kd ~200 nM) to mediate intraflagellar transport of outer dynein arms into cilia, while its C-terminus (residues 246–321) mediates IFT-B complex assembly/stability and basal body targeting via direct interaction with IFT52 (residues L285/L286); within IFT-B, IFT46 also forms a direct ternary complex with IFT88 and IFT52, presents an IFT46–IFT56 dimer interface for KIF17 ciliary entry, is targeted for ubiquitin-proteasomal degradation by the SARS-CoV-2 ORF10-hijacked CUL2ZYG11B ligase, and additionally regulates autophagy flux to control Limk2 stability and partial EMT in kidney collecting duct cells.\"\n}\n```","stage2_raw":"```json\n{\n  \"mechanistic_narrative\": \"IFT46 is a core subunit of the intraflagellar transport complex B (IFT-B) that serves dual roles in maintaining IFT-B stability and selectively loading ciliary cargo for transport. Its C-terminal domain stabilizes IFT-B and mediates recruitment to basal bodies through a direct interaction with IFT52 at residues L285/L286, while the N-terminal domain binds the ODA16 cargo adaptor (Kd ~200 nM) to specifically mediate outer dynein arm import into cilia [PMID:17312020, PMID:28298440, PMID:28701346, PMID:28302912]. IFT46 also forms a dimer with IFT56 that captures KIF17 for ciliary entry, and its loss in vertebrates causes defective ciliogenesis with randomized left–right patterning [PMID:28077622, PMID:25722189]. Outside canonical IFT function, IFT46 deficiency in renal collecting duct cells impairs autophagy flux, stabilizing LIMK2 via p62 and promoting cystogenesis [PMID:41680856].\",\n  \"teleology\": [\n    {\n      \"year\": 2007,\n      \"claim\": \"The first loss-of-function analysis established that IFT46 is required both for global IFT-B stability and, independently, for selective transport of outer dynein arms into flagella — separating a structural role from a cargo-specific role within a single IFT subunit.\",\n      \"evidence\": \"Insertional null mutant and spontaneous suppressor in Chlamydomonas with western blot and EM ultrastructure\",\n      \"pmids\": [\"17312020\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Identity of the IFT46 domain responsible for ODA specificity unknown\",\n        \"Direct binding partners within IFT-B not mapped\",\n        \"Vertebrate relevance not tested\"\n      ]\n    },\n    {\n      \"year\": 2010,\n      \"claim\": \"Biochemical reconstitution showed that IFT46 directly contacts IFT52 and IFT88 to form a ternary core sub-complex within IFT-B, establishing its position in the complex architecture.\",\n      \"evidence\": \"Yeast two-hybrid, bacterial co-expression, cross-linking, and electroporation rescue in Chlamydomonas\",\n      \"pmids\": [\"20435895\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Structural basis of the IFT46–IFT52–IFT88 ternary complex not resolved\",\n        \"No information on how IFT46 contacts cargo adaptors\"\n      ]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Vertebrate models demonstrated that IFT46 is essential for ciliogenesis in vivo: zebrafish knockdown shortened cilia, and mouse knockout randomized heart looping, linking IFT46 to left–right axis determination.\",\n      \"evidence\": \"Morpholino knockdown in zebrafish and homozygous knockout mice with EM and immunofluorescence\",\n      \"pmids\": [\"25722189\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Specific IFT-B subunit dependencies not examined in vertebrates\",\n        \"Whether ODA transport function is conserved in mammalian cilia not tested\"\n      ]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Three concurrent studies resolved the domain-level logic of IFT46: the N-terminus binds ODA16 with nanomolar affinity (crystal-structure-guided), the C-terminus (BBTS3) suffices for IFT-B stability and basal body recruitment via IFT52 (L285/L286), and the IFT46–IFT56 dimer captures KIF17 for ciliary import.\",\n      \"evidence\": \"X-ray crystallography and ITC of ODA16 (PMID:28298440); suppressor allele domain mapping (PMID:28701346); truncation/misdirection experiments in Chlamydomonas (PMID:28302912); VIP assay and siRNA of IFT46/IFT56 for KIF17 entry (PMID:28077622)\",\n      \"pmids\": [\"28298440\", \"28701346\", \"28302912\", \"28077622\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Full atomic structure of IFT46 in complex with IFT52 not available\",\n        \"Whether additional cargoes bind the IFT46 N-terminal domain beyond ODA16 is unknown\",\n        \"Relative contributions of IFT46–IFT56 vs. importin-α to KIF17 ciliary entry not quantified\"\n      ]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"IFT46 depletion in Paramecium caused cytoplasmic accumulation of IFT57, showing that IFT46 is required for normal IFT-B cycling between cytoplasm and cilia across diverse ciliated organisms.\",\n      \"evidence\": \"RNAi knockdown in Paramecium with GFP-IFT57 localization\",\n      \"pmids\": [\"29915351\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Whether the trafficking defect reflects IFT-B assembly failure or transport initiation failure not distinguished\",\n        \"Single-organism study without biochemical reconstitution\"\n      ]\n    },\n    {\n      \"year\": 2026,\n      \"claim\": \"A non-canonical function was uncovered: IFT46 regulates autophagy flux in renal collecting duct cells, and its loss stabilizes LIMK2 through impaired p62-mediated autophagic degradation, driving partial EMT and cystogenesis.\",\n      \"evidence\": \"Collecting duct-specific Ift46-KO mice, co-IP of LIMK2–p62, 3D cyst assays, pharmacological autophagy modulation\",\n      \"pmids\": [\"41680856\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Mechanism by which IFT46 controls autophagy flux is not defined\",\n        \"Single-lab finding requiring independent replication\",\n        \"Whether this autophagy role is cilia-dependent or cilia-independent is unresolved\"\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"Key open questions include whether IFT46 transports additional ciliary cargoes beyond ODA16 and KIF17, how IFT46 mechanistically regulates autophagy, and the full atomic structure of IFT46 within the intact IFT-B complex.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"No complete atomic structure of IFT46 within the native IFT-B complex\",\n        \"Full cargo repertoire of IFT46 N-terminal domain unknown\",\n        \"Molecular mechanism linking IFT46 to autophagy not characterized\"\n      ]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [0, 2, 3, 5]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005929\", \"supporting_discovery_ids\": [0, 4, 6]},\n      {\"term_id\": \"GO:0005815\", \"supporting_discovery_ids\": [4, 6]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-1852241\", \"supporting_discovery_ids\": [0, 4, 6]},\n      {\"term_id\": \"R-HSA-9612973\", \"supporting_discovery_ids\": [8]},\n      {\"term_id\": \"R-HSA-9609507\", \"supporting_discovery_ids\": [0, 2, 5]}\n    ],\n    \"complexes\": [\n      \"IFT-B complex\"\n    ],\n    \"partners\": [\n      \"IFT52\",\n      \"IFT88\",\n      \"ODA16\",\n      \"IFT56\",\n      \"KIF17\",\n      \"LIMK2\",\n      \"SQSTM1\"\n    ],\n    \"other_free_text\": []\n  }\n}\n```\n\n--- ROUND 2 (R2/R3, augmented corpus) ---\n\n```json\n{\n  \"mechanistic_narrative\": \"IFT46 is a core subunit of the intraflagellar transport complex B (IFT-B) that is essential for ciliogenesis, ciliary cargo delivery, and cilium-dependent developmental signaling. Its C-terminal domain (residues 246–321, including L285/L286) mediates direct binding to IFT52 for basal body targeting and IFT-B complex assembly/stability, while its N-terminal domain (residues 1–147) binds the cargo adaptor ODA16 (Kd ~200 nM) to specifically transport outer dynein arms into cilia; IFT46 also forms a ternary complex with IFT52 and IFT88, and its dimer interface with IFT56 is required for KIF17 ciliary entry [PMID:17312020, PMID:20435895, PMID:28298440, PMID:28077622, PMID:28302912]. Loss of IFT46 in vertebrates causes kidney cysts, left-right patterning defects, and shortened cilia, and SARS-CoV-2 ORF10 hijacks the CUL2^ZYG11B E3 ligase to ubiquitinate and degrade IFT46, impairing ciliary biogenesis and maintenance [PMID:25722189, PMID:35674692]. IFT46 also regulates autophagy flux in kidney collecting duct cells, where its deficiency stabilizes Limk2 to promote partial epithelial-to-mesenchymal transition and renal cyst formation [PMID:41680856].\",\n  \"teleology\": [\n    {\n      \"year\": 2007,\n      \"claim\": \"Establishing that IFT46 is a core IFT-B subunit required both for complex B stability/flagellar assembly and specifically for outer dynein arm transport resolved whether individual IFT-B proteins have cargo-selective roles beyond structural scaffolding.\",\n      \"evidence\": \"Insertional mutagenesis and suppressor genetics in Chlamydomonas with Western blot and EM readouts\",\n      \"pmids\": [\"17312020\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Direct binding partners within IFT-B were not identified\",\n        \"Mechanism by which IFT46 recognizes outer dynein arms was unknown\",\n        \"Vertebrate developmental roles had not been tested\"\n      ]\n    },\n    {\n      \"year\": 2007,\n      \"claim\": \"Demonstrating IFT46 localization to primary cilia of mammalian chondrocytes and its regulation by BMP-2 extended IFT46 function from Chlamydomonas to vertebrate developmental signaling contexts.\",\n      \"evidence\": \"Immunofluorescence localization in mouse chondrocytes, siRNA knockdown gene expression analysis, zebrafish morpholino injection\",\n      \"pmids\": [\"17720815\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Single lab with antibody-based localization; independent confirmation lacking at that time\",\n        \"Mechanism linking IFT46 to skeletogenesis gene regulation was not elucidated\"\n      ]\n    },\n    {\n      \"year\": 2010,\n      \"claim\": \"Identifying IFT46 as forming a direct ternary complex with IFT52 and IFT88 defined the core IFT-B architecture and showed these three subunits constitute a minimal IFT-B assembly unit.\",\n      \"evidence\": \"Yeast two-hybrid, bacterial co-expression, chemical cross-linking, electroporation rescue and live imaging in Chlamydomonas\",\n      \"pmids\": [\"20435895\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Atomic-resolution structure of the ternary complex was not available\",\n        \"Relative contributions of IFT52 versus IFT88 binding to IFT46 stability were unclear\"\n      ]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Knockout and knockdown studies in zebrafish and mouse proved IFT46 is essential for vertebrate ciliogenesis and left-right axis patterning, establishing it as a ciliopathy-relevant gene.\",\n      \"evidence\": \"Morpholino knockdown in zebrafish and Ift46 knockout mouse generation with EM, immunofluorescence, and developmental phenotyping\",\n      \"pmids\": [\"25722189\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"No human ciliopathy mutations in IFT46 had been identified\",\n        \"Whether specific cilia subtypes have differential IFT46 dependence was untested\"\n      ]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Structural and biochemical dissection of the IFT46–ODA16 interaction revealed that the IFT46 N-terminus (residues 1–147) binds ODA16's β-propeller domain with ~200 nM affinity, while ODA16 separately contacts outer dynein arms, establishing the architectural basis for cargo-selective IFT.\",\n      \"evidence\": \"X-ray crystallography of ODA16, ITC binding measurements, pulldown with axonemal ODAs, deletion mutagenesis in Chlamydomonas\",\n      \"pmids\": [\"28298440\", \"28701346\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Atomic structure of the IFT46–ODA16 binary complex was not resolved\",\n        \"Whether other cargo adaptors bind a similar IFT46 surface was unknown\"\n      ]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Mapping the IFT46 C-terminal BBTS3 domain (residues 246–321) and the critical L285/L286 residues for IFT52 binding revealed that IFT52–IFT46 preassembly in the cytoplasm is required for basal body targeting, separating complex assembly from cargo-loading functions.\",\n      \"evidence\": \"Truncation mapping, site-directed mutagenesis, motor/IFT mutant analysis, and fluorescence microscopy in Chlamydomonas\",\n      \"pmids\": [\"28302912\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Structural basis for IFT52–IFT46 BBTS3 interaction was not determined at atomic resolution\",\n        \"Cytoplasmic versus basal body assembly sequence for the full IFT-B complex remained incomplete\"\n      ]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Discovery that the IFT46–IFT56 dimer provides the binding interface for KIF17 ciliary entry revealed a second cargo/motor-adaptor role for IFT46 distinct from its ODA16-binding function.\",\n      \"evidence\": \"Visible immunoprecipitation assay, deletion mutagenesis, live-cell imaging, and ciliary entry assays in mammalian cells\",\n      \"pmids\": [\"28077622\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Whether IFT46–IFT56 binding to KIF17 is regulated remains unknown\",\n        \"Functional consequence of disrupting KIF17–IFT46 interaction on specific ciliary signaling pathways was not determined\"\n      ]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Demonstrating that SARS-CoV-2 ORF10 hijacks CUL2^ZYG11B to ubiquitinate and degrade IFT46, impairing cilia biogenesis and maintenance, identified a viral mechanism for disrupting mucociliary clearance.\",\n      \"evidence\": \"Co-immunoprecipitation, ubiquitination assays, proteasome inhibitor rescue, hACE2 mouse model, primary human nasal epithelial cell culture\",\n      \"pmids\": [\"35674692\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"The specific ubiquitination sites on IFT46 were not mapped\",\n        \"Whether other IFT-B subunits are co-degraded or destabilized secondarily was not fully addressed\",\n        \"Clinical relevance for COVID-19 airway pathology requires further patient-level evidence\"\n      ]\n    },\n    {\n      \"year\": 2026,\n      \"claim\": \"Identifying that IFT46 regulates autophagy flux to control Limk2 stability and partial EMT in kidney collecting duct cells uncovered a non-canonical, cilia-independent function linked to cystic kidney disease.\",\n      \"evidence\": \"RNA-seq, co-immunoprecipitation, conditional knockout mice, 3D cyst culture model, autophagy-modulating drugs, human ADPKD tissue analysis\",\n      \"pmids\": [\"41680856\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Single-lab finding; independent replication of the IFT46–autophagy–Limk2 axis is needed\",\n        \"Mechanism by which IFT46 controls autophagy flux is not defined\",\n        \"Whether the autophagy role is fully independent of cilia or partially coupled remains unclear\"\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"Key unresolved questions include the atomic structure of the IFT46–ODA16 binary complex, whether IFT46 has additional non-ciliary functions in other tissues, and whether human IFT46 mutations cause a defined ciliopathy.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"No human disease-causing mutations in IFT46 have been reported\",\n        \"Full reconstitution of IFT46-dependent cargo loading onto IFT trains has not been achieved\",\n        \"The autophagy-regulatory mechanism of IFT46 at the molecular level is undefined\"\n      ]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0005198\", \"supporting_discovery_ids\": [0, 1, 6]},\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [3, 4, 5]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005929\", \"supporting_discovery_ids\": [0, 2, 7, 8]},\n      {\"term_id\": \"GO:0005815\", \"supporting_discovery_ids\": [2, 6, 7]},\n      {\"term_id\": \"GO:0005829\", \"supporting_discovery_ids\": [6]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-1852241\", \"supporting_discovery_ids\": [0, 1, 2, 6, 7, 9]},\n      {\"term_id\": \"R-HSA-9612973\", \"supporting_discovery_ids\": [10]},\n      {\"term_id\": \"R-HSA-1266738\", \"supporting_discovery_ids\": [2, 8]}\n    ],\n    \"complexes\": [\n      \"IFT-B complex\"\n    ],\n    \"partners\": [\n      \"IFT52\",\n      \"IFT88\",\n      \"IFT56\",\n      \"ODA16\",\n      \"KIF17\",\n      \"ZYG11B\",\n      \"LIMK2\"\n    ],\n    \"other_free_text\": []\n  }\n}\n```"}