{"gene":"IFT46","run_date":"2026-06-10T01:55:22","timeline":{"discoveries":[{"year":2007,"finding":"IFT46 is a component of IFT complex B in Chlamydomonas reinhardtii; null mutants have greatly reduced levels of most complex B proteins, indicating IFT46 is required for complex B stability. A partial suppressor that restores complex B levels (without restoring IFT46) still fails to transport outer dynein arms into flagella, demonstrating that IFT46 is specifically required for transport of outer dynein arms into flagella.","method":"Insertional mutant analysis, suppressor genetics, axonemal ultrastructure (electron microscopy), Western blot for IFT complex B proteins","journal":"The Journal of cell biology","confidence":"High","confidence_rationale":"Tier 2 / Strong — genetic epistasis with suppressor screen, multiple orthogonal methods (EM ultrastructure, biochemistry), replicated in follow-up studies","pmids":["17312020"],"is_preprint":false},{"year":2010,"finding":"IFT46 directly interacts with IFT88 and IFT52 within IFT complex B core, and together these three proteins form a ternary complex. The IFT46 C-terminus (residues within the C-terminal 240 aa) is sufficient to assemble into and stabilize IFT-B, but the N-terminus is required for outer dynein arm transport.","method":"Yeast two-hybrid, bacterial co-expression, chemical cross-linking, electroporation rescue of ift46 mutant with recombinant IFT46","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1 / Moderate — direct protein interaction established by yeast two-hybrid plus bacterial co-expression reconstitution and chemical cross-linking, single lab but multiple orthogonal methods","pmids":["20435895"],"is_preprint":false},{"year":2017,"finding":"The N-terminus of IFT46 (first 147 residues) is required for interaction with the cargo adaptor ODA16 and for intraflagellar transport of outer dynein arms. The IFT46 C-terminus alone can stabilize IFT-B but cannot support ODA16 import or outer arm dynein transport into flagella.","method":"Chlamydomonas suppressor mutant analysis (transposon insertion creating truncated fusion protein), flagellar protein analysis by Western blot, immunofluorescence","journal":"Molecular biology of the cell","confidence":"High","confidence_rationale":"Tier 2 / Strong — domain-dissection genetic approach with matched biochemical readouts, consistent with structural data from independent lab (PMID:28298440)","pmids":["28701346"],"is_preprint":false},{"year":2017,"finding":"Crystal structure of Chlamydomonas ODA16 revealed an 80-residue N-terminal domain and a C-terminal 8-bladed β-propeller domain; both are required for binding the N-terminal 147 residues of IFT46 with a Kd ~200 nM. The C-terminal β-propeller (but not the N-terminal domain) of ODA16 is required for interaction with outer dynein arms, providing an architectural model for ODA16-mediated IFT of ODAs via IFT46.","method":"X-ray crystallography (high-resolution crystal structure of CrODA16), binding mapping by truncation/mutagenesis, ITC or equivalent affinity measurement (Kd ~200 nM), co-immunoprecipitation with axonemal ODAs","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1 / Moderate — crystal structure plus domain mutagenesis plus affinity measurement, single lab but multiple orthogonal methods","pmids":["28298440"],"is_preprint":false},{"year":2017,"finding":"IFT52 recruits IFT46 to the basal body via direct interaction with residues L285 and L286 in the C-terminal sequence (residues 246–321, BBTS3) of IFT46; this sequence is both necessary and sufficient for basal body and ciliary targeting. Ectopic nuclear expression of the IFT52 C-terminal domain re-routes IFT46 to nuclei, confirming the IFT52–IFT46 interaction drives localization.","method":"Expression of IFT46 truncation constructs in ift46-1 mutant, site-directed mutagenesis (L285/L286), co-immunoprecipitation, IFT/motor mutant epistasis, ectopic nuclear targeting experiment","journal":"Journal of cell science","confidence":"High","confidence_rationale":"Tier 2 / Moderate — mutagenesis of specific residues combined with localization rescue and epistasis in multiple IFT/motor mutants, single lab but multiple orthogonal approaches","pmids":["28302912"],"is_preprint":false},{"year":2017,"finding":"KIF17 (homodimeric kinesin-2) interacts with the IFT46–IFT56 dimer within the IFT-B complex through KIF17's C-terminal sequence immediately upstream of its nuclear localization signal (NLS). This IFT-B binding (via IFT46–IFT56) is required for KIF17 entry into cilia across the permeability barrier, whereas KIF17 is dispensable for ciliogenesis and IFT-B trafficking itself.","method":"Visible immunoprecipitation (VIP) assay, deletion mapping of KIF17 C-terminus, RNAi/rescue in mammalian cells","journal":"Molecular biology of the cell","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — reciprocal interaction shown by VIP assay with domain mapping, single lab, single primary method for the interaction","pmids":["28077622"],"is_preprint":false},{"year":2015,"finding":"IFT46 localizes to the basal body in zebrafish ciliated cells; morpholino knockdown of ift46 causes shortened/absent cilia in kidney and spinal canal, and Ift46 knockout mice show randomized heart looping (defective left-right axis patterning), establishing an essential role for IFT46 in vertebrate ciliogenesis.","method":"Morpholino knockdown in zebrafish, Ift46 knockout mice, immunofluorescence localization, electron microscopy of cilia","journal":"Developmental biology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — loss-of-function in two vertebrate models with specific ciliary phenotype readout, but no molecular mechanism beyond IFT-B role established","pmids":["25722189"],"is_preprint":false},{"year":2018,"finding":"In Paramecium, IFT46 depletion (RNAi) causes IFT57-GFP to abnormally accumulate in the cortex and cytoplasm rather than enter cilia, demonstrating that IFT46 is essential for trafficking IFT-B proteins between the cytoplasm and cilia.","method":"RNAi knockdown in Paramecium, GFP-tagged IFT57 localization by fluorescence microscopy","journal":"Scientific reports","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — clean RNAi KD with specific fluorescent cargo-trafficking readout, single lab, single organism model","pmids":["29915351"],"is_preprint":false},{"year":2026,"finding":"In mouse collecting duct cells, Ift46 deficiency impairs autophagy flux, which leads to increased Limk2 protein translation. Limk2 directly interacts with the autophagy receptor p62/SQSTM1 (verified by co-immunoprecipitation). The resulting elevated Limk2 promotes partial epithelial-to-mesenchymal transition and contributes to renal cyst formation. This 'Ift46-autophagy-Limk2' axis was validated in collecting duct-specific Ift46-knockout mice and in human ADPKD samples.","method":"RNA-seq of Ift46 knockdown cells, co-immunoprecipitation (Limk2–p62 interaction), 3D culture cyst model, collecting duct-specific Ift46 knockout mice, autophagy flux assays with pharmacological modulators","journal":"Cell communication and signaling : CCS","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — Co-IP for Limk2-p62 interaction, KO mouse model with phenotype, multiple methods but single lab and novel pathway not yet independently replicated","pmids":["41680856"],"is_preprint":false}],"current_model":"IFT46 is a core IFT complex B protein whose N-terminus directly binds the cargo adaptor ODA16 (Kd ~200 nM, structurally defined) to mediate intraflagellar transport of outer dynein arms into cilia, while its C-terminus (residues 246–321) interacts with IFT52 (at L285/L286) to stabilize the complex B core and mediate basal body/ciliary targeting; IFT46 also forms part of an IFT46–IFT56 dimer that recruits KIF17 into cilia, and beyond ciliogenesis, IFT46 regulates autophagy flux to control Limk2 stability and partial EMT in renal epithelial cells."},"narrative":{"mechanistic_narrative":"IFT46 is a core subunit of intraflagellar transport (IFT) complex B that is essential for ciliogenesis and for the selective import of axonemal cargoes into cilia and flagella [PMID:17312020, PMID:25722189]. Its function is structurally bipartite: the C-terminal region (residues 246–321, including L285/L286) docks onto IFT52 to assemble and stabilize the IFT-B core and to drive basal-body and ciliary targeting, such that loss of IFT46 destabilizes most complex B proteins [PMID:17312020, PMID:20435895, PMID:28302912]; ectopic nuclear-tethered IFT52 re-routes IFT46 to the nucleus, confirming IFT52 directs IFT46 localization [PMID:28302912]. The N-terminal 147 residues are functionally dedicated to cargo handling, binding the cargo adaptor ODA16 with ~200 nM affinity to mediate intraflagellar transport of outer dynein arms—a role genetically separable from the protein's structural role, since an IFT46 fragment that restores complex B stability still cannot import ODA16 or outer dynein arms [PMID:17312020, PMID:28701346, PMID:28298440]. IFT46 also participates in an IFT46–IFT56 dimer that binds the homodimeric kinesin KIF17 and licenses its entry into cilia across the ciliary permeability barrier [PMID:28077622]. Across organisms IFT46 is required for trafficking of IFT-B proteins between cytoplasm and cilia, and its loss in vertebrates produces shortened or absent cilia and randomized left-right axis patterning [PMID:25722189, PMID:29915351]. Beyond ciliogenesis, IFT46 deficiency in renal collecting-duct cells impairs autophagy flux, elevating Limk2 (a p62/SQSTM1 interactor) to promote partial epithelial-to-mesenchymal transition and renal cyst formation [PMID:41680856].","teleology":[{"year":2007,"claim":"Established that IFT46 is a required structural component of IFT complex B and, separately, that it carries out a specific cargo function for outer dynein arm import—the first evidence that one IFT subunit couples assembly to selective cargo transport.","evidence":"Insertional null mutants and a suppressor that restores complex B without IFT46, with axonemal EM and Western blots in Chlamydomonas","pmids":["17312020"],"confidence":"High","gaps":["Did not map which IFT46 domains mediate structural versus cargo functions","Direct cargo adaptor for outer dynein arms not yet identified"]},{"year":2010,"claim":"Defined the molecular basis of IFT46's structural role by showing it forms a ternary core with IFT88 and IFT52, and localized the assembly determinant to the C-terminus while assigning cargo transport to the N-terminus.","evidence":"Yeast two-hybrid, bacterial co-expression, chemical cross-linking, and electroporation rescue of ift46 mutants","pmids":["20435895"],"confidence":"High","gaps":["Did not identify the N-terminal binding partner mediating dynein arm transport","Precise residues contacting IFT52 not yet defined"]},{"year":2017,"claim":"Resolved how IFT46 selects outer dynein arm cargo: its N-terminal 147 residues bind the cargo adaptor ODA16, and structural work defined the ODA16 architecture (N-terminal domain plus 8-bladed β-propeller) and the ~200 nM affinity of the interaction, linking adaptor binding to ODA recognition.","evidence":"Chlamydomonas suppressor domain dissection plus X-ray crystallography of ODA16, truncation/mutagenesis binding maps, affinity measurement, and Co-IP with axonemal ODAs","pmids":["28701346","28298440"],"confidence":"High","gaps":["Stoichiometry of the IFT46–ODA16–ODA assembly during transit not resolved","How cargo is released at the ciliary tip unknown"]},{"year":2017,"claim":"Pinpointed the targeting mechanism by showing IFT52 recruits IFT46 to the basal body through L285/L286 in a C-terminal sequence (246–321) that is necessary and sufficient for ciliary localization, with ectopic nuclear IFT52 mislocalizing IFT46.","evidence":"IFT46 truncation/site-directed mutagenesis, Co-IP, motor-mutant epistasis, and ectopic nuclear targeting in Chlamydomonas","pmids":["28302912"],"confidence":"High","gaps":["Whether targeting precedes or follows IFT-B core assembly not resolved","Regulation of IFT52–IFT46 docking unknown"]},{"year":2017,"claim":"Extended IFT46's adaptor role beyond dynein arms by showing an IFT46–IFT56 dimer binds KIF17 and is required for KIF17 entry into cilia across the permeability barrier.","evidence":"Visible immunoprecipitation assay, KIF17 C-terminal deletion mapping, and RNAi/rescue in mammalian cells","pmids":["28077622"],"confidence":"Medium","gaps":["Interaction shown by a single primary method (VIP) from one lab","Structural basis of the IFT46–IFT56–KIF17 interaction not defined"]},{"year":2015,"claim":"Demonstrated the physiological requirement for IFT46 in vertebrate ciliogenesis and left-right patterning, generalizing the Chlamydomonas findings to development.","evidence":"Morpholino knockdown in zebrafish and Ift46 knockout mice with IF localization and ciliary EM","pmids":["25722189"],"confidence":"Medium","gaps":["No molecular mechanism beyond the IFT-B role established in vertebrates","Tissue-specific cargo dependencies not dissected"]},{"year":2018,"claim":"Confirmed IFT46's conserved role in shuttling IFT-B proteins between cytoplasm and cilia by showing IFT57 mislocalizes upon IFT46 depletion.","evidence":"RNAi knockdown in Paramecium with GFP-tagged IFT57 fluorescence localization","pmids":["29915351"],"confidence":"Medium","gaps":["Single organism, single cargo readout","Whether IFT46 acts on IFT57 directly or via complex B integrity not distinguished"]},{"year":2026,"claim":"Uncovered a non-ciliary function in which IFT46 deficiency impairs autophagy flux to stabilize Limk2 and drive partial EMT, linking IFT46 loss to renal cyst formation.","evidence":"RNA-seq, Limk2–p62 Co-IP, 3D cyst culture, collecting-duct-specific Ift46 knockout mice, and autophagy flux assays, with human ADPKD validation","pmids":["41680856"],"confidence":"Medium","gaps":["Co-IP for Limk2–p62 without reciprocal/structural validation","How IFT46 mechanistically controls autophagy flux not defined","Novel axis not yet independently replicated"]},{"year":null,"claim":"How IFT46's ciliary transport function mechanistically connects to its regulation of autophagy and Limk2 stability remains unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["Whether the autophagy phenotype is a direct IFT46 activity or a downstream consequence of cilia loss is unknown","No structural model of the IFT46 N-terminus bound to ODA16 in the full IFT-B context","Mechanism of cargo loading and release during transit not defined"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[2,3,5]},{"term_id":"GO:0005198","term_label":"structural molecule activity","supporting_discovery_ids":[0,1]}],"localization":[{"term_id":"GO:0005929","term_label":"cilium","supporting_discovery_ids":[4,6,7]},{"term_id":"GO:0005815","term_label":"microtubule organizing center","supporting_discovery_ids":[4,6]},{"term_id":"GO:0005829","term_label":"cytosol","supporting_discovery_ids":[7]}],"pathway":[{"term_id":"R-HSA-5653656","term_label":"Vesicle-mediated transport","supporting_discovery_ids":[0,2,5,7]},{"term_id":"R-HSA-1852241","term_label":"Organelle biogenesis and maintenance","supporting_discovery_ids":[6]},{"term_id":"R-HSA-9612973","term_label":"Autophagy","supporting_discovery_ids":[8]}],"complexes":["IFT complex B"],"partners":["IFT52","IFT88","ODA16","IFT56","KIF17","IFT57"],"other_free_text":[]}},"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 analysis of an individual IFT protein: IFT46 is required for transport of outer dynein arms into flagella.","date":"2007","source":"The Journal of cell biology","url":"https://pubmed.ncbi.nlm.nih.gov/17312020","citation_count":187,"is_preprint":false},{"pmid":"20435895","id":"PMC_20435895","title":"Direct interactions of intraflagellar transport complex B proteins IFT88, IFT52, and IFT46.","date":"2010","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/20435895","citation_count":68,"is_preprint":false},{"pmid":"28077622","id":"PMC_28077622","title":"Ciliary entry of KIF17 is dependent on its binding to the IFT-B complex via IFT46-IFT56 as well as on its nuclear localization signal.","date":"2017","source":"Molecular biology of the cell","url":"https://pubmed.ncbi.nlm.nih.gov/28077622","citation_count":51,"is_preprint":false},{"pmid":"28298440","id":"PMC_28298440","title":"Structural basis of outer dynein arm intraflagellar transport by the transport adaptor protein ODA16 and the intraflagellar transport protein IFT46.","date":"2017","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/28298440","citation_count":44,"is_preprint":false},{"pmid":"25722189","id":"PMC_25722189","title":"IFT46 plays an essential role in cilia development.","date":"2015","source":"Developmental biology","url":"https://pubmed.ncbi.nlm.nih.gov/25722189","citation_count":38,"is_preprint":false},{"pmid":"28701346","id":"PMC_28701346","title":"The N-terminus of IFT46 mediates intraflagellar transport of outer arm dynein and its cargo-adaptor ODA16.","date":"2017","source":"Molecular biology of the cell","url":"https://pubmed.ncbi.nlm.nih.gov/28701346","citation_count":35,"is_preprint":false},{"pmid":"28302912","id":"PMC_28302912","title":"Intraflagellar transport protein IFT52 recruits IFT46 to the basal body and flagella.","date":"2017","source":"Journal of cell science","url":"https://pubmed.ncbi.nlm.nih.gov/28302912","citation_count":31,"is_preprint":false},{"pmid":"29915351","id":"PMC_29915351","title":"Intraflagellar transport 46 (IFT46) is essential for trafficking IFT proteins between cilia and cytoplasm in Paramecium.","date":"2018","source":"Scientific reports","url":"https://pubmed.ncbi.nlm.nih.gov/29915351","citation_count":13,"is_preprint":false},{"pmid":"27320864","id":"PMC_27320864","title":"IFT46 plays crucial roles in craniofacial and cilia development.","date":"2016","source":"Biochemical and biophysical research communications","url":"https://pubmed.ncbi.nlm.nih.gov/27320864","citation_count":11,"is_preprint":false},{"pmid":"29022313","id":"PMC_29022313","title":"[Prokaryotic expression and purification of Chlamydomonas reinhardtii intraflagellar transport protein 46(IFT46) and preparation of polyclonal antibody].","date":"2016","source":"Sheng wu gong cheng xue bao = Chinese journal of biotechnology","url":"https://pubmed.ncbi.nlm.nih.gov/29022313","citation_count":2,"is_preprint":false},{"pmid":"33628615","id":"PMC_33628615","title":"IFT46 Expression in the Nasal Mucosa of Primary Ciliary Dyskinesia Patients: Preliminary Study.","date":"2021","source":"Allergy & rhinology (Providence, R.I.)","url":"https://pubmed.ncbi.nlm.nih.gov/33628615","citation_count":1,"is_preprint":false},{"pmid":"37363725","id":"PMC_37363725","title":"IFT46 gene promoter-driven ciliopathy disease model in zebrafish.","date":"2023","source":"Frontiers in cell and developmental biology","url":"https://pubmed.ncbi.nlm.nih.gov/37363725","citation_count":0,"is_preprint":false},{"pmid":"41680856","id":"PMC_41680856","title":"Ift46 deficiency causes renal cyst via enhanced Limk2 through lack of autophagy flux.","date":"2026","source":"Cell communication and signaling : CCS","url":"https://pubmed.ncbi.nlm.nih.gov/41680856","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":8485,"output_tokens":2577,"usd":0.032055,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":9721,"output_tokens":3250,"usd":0.064927,"stage2_stop_reason":"end_turn"},"total_usd":0.096982,"stage1_batch_id":"msgbatch_01DUPACZi7AAWwuZiUjseQF4","stage2_batch_id":"msgbatch_018yt7chE3f48PEFtDwtj6AE","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2007,\n      \"finding\": \"IFT46 is a component of IFT complex B in Chlamydomonas reinhardtii; null mutants have greatly reduced levels of most complex B proteins, indicating IFT46 is required for complex B stability. A partial suppressor that restores complex B levels (without restoring IFT46) still fails to transport outer dynein arms into flagella, demonstrating that IFT46 is specifically required for transport of outer dynein arms into flagella.\",\n      \"method\": \"Insertional mutant analysis, suppressor genetics, axonemal ultrastructure (electron microscopy), Western blot for IFT complex B proteins\",\n      \"journal\": \"The Journal of cell biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — genetic epistasis with suppressor screen, multiple orthogonal methods (EM ultrastructure, biochemistry), replicated in follow-up studies\",\n      \"pmids\": [\"17312020\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"IFT46 directly interacts with IFT88 and IFT52 within IFT complex B core, and together these three proteins form a ternary complex. The IFT46 C-terminus (residues within the C-terminal 240 aa) is sufficient to assemble into and stabilize IFT-B, but the N-terminus is required for outer dynein arm transport.\",\n      \"method\": \"Yeast two-hybrid, bacterial co-expression, chemical cross-linking, electroporation rescue of ift46 mutant with recombinant IFT46\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — direct protein interaction established by yeast two-hybrid plus bacterial co-expression reconstitution and chemical cross-linking, single lab but multiple orthogonal methods\",\n      \"pmids\": [\"20435895\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"The N-terminus of IFT46 (first 147 residues) is required for interaction with the cargo adaptor ODA16 and for intraflagellar transport of outer dynein arms. The IFT46 C-terminus alone can stabilize IFT-B but cannot support ODA16 import or outer arm dynein transport into flagella.\",\n      \"method\": \"Chlamydomonas suppressor mutant analysis (transposon insertion creating truncated fusion protein), flagellar protein analysis by Western blot, immunofluorescence\",\n      \"journal\": \"Molecular biology of the cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — domain-dissection genetic approach with matched biochemical readouts, consistent with structural data from independent lab (PMID:28298440)\",\n      \"pmids\": [\"28701346\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"Crystal structure of Chlamydomonas ODA16 revealed an 80-residue N-terminal domain and a C-terminal 8-bladed β-propeller domain; both are required for binding the N-terminal 147 residues of IFT46 with a Kd ~200 nM. The C-terminal β-propeller (but not the N-terminal domain) of ODA16 is required for interaction with outer dynein arms, providing an architectural model for ODA16-mediated IFT of ODAs via IFT46.\",\n      \"method\": \"X-ray crystallography (high-resolution crystal structure of CrODA16), binding mapping by truncation/mutagenesis, ITC or equivalent affinity measurement (Kd ~200 nM), co-immunoprecipitation with axonemal ODAs\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — crystal structure plus domain mutagenesis plus affinity measurement, single lab but multiple orthogonal methods\",\n      \"pmids\": [\"28298440\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"IFT52 recruits IFT46 to the basal body via direct interaction with residues L285 and L286 in the C-terminal sequence (residues 246–321, BBTS3) of IFT46; this sequence is both necessary and sufficient for basal body and ciliary targeting. Ectopic nuclear expression of the IFT52 C-terminal domain re-routes IFT46 to nuclei, confirming the IFT52–IFT46 interaction drives localization.\",\n      \"method\": \"Expression of IFT46 truncation constructs in ift46-1 mutant, site-directed mutagenesis (L285/L286), co-immunoprecipitation, IFT/motor mutant epistasis, ectopic nuclear targeting experiment\",\n      \"journal\": \"Journal of cell science\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — mutagenesis of specific residues combined with localization rescue and epistasis in multiple IFT/motor mutants, single lab but multiple orthogonal approaches\",\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 the IFT-B complex through KIF17's C-terminal sequence immediately upstream of its nuclear localization signal (NLS). This IFT-B binding (via IFT46–IFT56) is required for KIF17 entry into cilia across the permeability barrier, whereas KIF17 is dispensable for ciliogenesis and IFT-B trafficking itself.\",\n      \"method\": \"Visible immunoprecipitation (VIP) assay, deletion mapping of KIF17 C-terminus, RNAi/rescue in mammalian cells\",\n      \"journal\": \"Molecular biology of the cell\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — reciprocal interaction shown by VIP assay with domain mapping, single lab, single primary method for the interaction\",\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 of ift46 causes shortened/absent cilia in kidney and spinal canal, and Ift46 knockout mice show randomized heart looping (defective left-right axis patterning), establishing an essential role for IFT46 in vertebrate ciliogenesis.\",\n      \"method\": \"Morpholino knockdown in zebrafish, Ift46 knockout mice, immunofluorescence localization, electron microscopy of cilia\",\n      \"journal\": \"Developmental biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — loss-of-function in two vertebrate models with specific ciliary phenotype readout, but no molecular mechanism beyond IFT-B role established\",\n      \"pmids\": [\"25722189\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"In Paramecium, IFT46 depletion (RNAi) causes IFT57-GFP to abnormally accumulate in the cortex and cytoplasm rather than enter cilia, demonstrating that IFT46 is essential for trafficking IFT-B proteins between the cytoplasm and cilia.\",\n      \"method\": \"RNAi knockdown in Paramecium, GFP-tagged IFT57 localization by fluorescence microscopy\",\n      \"journal\": \"Scientific reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — clean RNAi KD with specific fluorescent cargo-trafficking readout, single lab, single organism model\",\n      \"pmids\": [\"29915351\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"In mouse collecting duct cells, Ift46 deficiency impairs autophagy flux, which leads to increased Limk2 protein translation. Limk2 directly interacts with the autophagy receptor p62/SQSTM1 (verified by co-immunoprecipitation). The resulting elevated Limk2 promotes partial epithelial-to-mesenchymal transition and contributes to renal cyst formation. This 'Ift46-autophagy-Limk2' axis was validated in collecting duct-specific Ift46-knockout mice and in human ADPKD samples.\",\n      \"method\": \"RNA-seq of Ift46 knockdown cells, co-immunoprecipitation (Limk2–p62 interaction), 3D culture cyst model, collecting duct-specific Ift46 knockout mice, autophagy flux assays with pharmacological modulators\",\n      \"journal\": \"Cell communication and signaling : CCS\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — Co-IP for Limk2-p62 interaction, KO mouse model with phenotype, multiple methods but single lab and novel pathway not yet independently replicated\",\n      \"pmids\": [\"41680856\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"IFT46 is a core IFT complex B protein whose N-terminus directly binds the cargo adaptor ODA16 (Kd ~200 nM, structurally defined) to mediate intraflagellar transport of outer dynein arms into cilia, while its C-terminus (residues 246–321) interacts with IFT52 (at L285/L286) to stabilize the complex B core and mediate basal body/ciliary targeting; IFT46 also forms part of an IFT46–IFT56 dimer that recruits KIF17 into cilia, and beyond ciliogenesis, IFT46 regulates autophagy flux to control Limk2 stability and partial EMT in renal epithelial cells.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"IFT46 is a core subunit of intraflagellar transport (IFT) complex B that is essential for ciliogenesis and for the selective import of axonemal cargoes into cilia and flagella [#0, #6]. Its function is structurally bipartite: the C-terminal region (residues 246–321, including L285/L286) docks onto IFT52 to assemble and stabilize the IFT-B core and to drive basal-body and ciliary targeting, such that loss of IFT46 destabilizes most complex B proteins [#0, #1, #4]; ectopic nuclear-tethered IFT52 re-routes IFT46 to the nucleus, confirming IFT52 directs IFT46 localization [#4]. The N-terminal 147 residues are functionally dedicated to cargo handling, binding the cargo adaptor ODA16 with ~200 nM affinity to mediate intraflagellar transport of outer dynein arms—a role genetically separable from the protein's structural role, since an IFT46 fragment that restores complex B stability still cannot import ODA16 or outer dynein arms [#0, #2, #3]. IFT46 also participates in an IFT46–IFT56 dimer that binds the homodimeric kinesin KIF17 and licenses its entry into cilia across the ciliary permeability barrier [#5]. Across organisms IFT46 is required for trafficking of IFT-B proteins between cytoplasm and cilia, and its loss in vertebrates produces shortened or absent cilia and randomized left-right axis patterning [#6, #7]. Beyond ciliogenesis, IFT46 deficiency in renal collecting-duct cells impairs autophagy flux, elevating Limk2 (a p62/SQSTM1 interactor) to promote partial epithelial-to-mesenchymal transition and renal cyst formation [#8].\",\n  \"teleology\": [\n    {\n      \"year\": 2007,\n      \"claim\": \"Established that IFT46 is a required structural component of IFT complex B and, separately, that it carries out a specific cargo function for outer dynein arm import—the first evidence that one IFT subunit couples assembly to selective cargo transport.\",\n      \"evidence\": \"Insertional null mutants and a suppressor that restores complex B without IFT46, with axonemal EM and Western blots in Chlamydomonas\",\n      \"pmids\": [\"17312020\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not map which IFT46 domains mediate structural versus cargo functions\", \"Direct cargo adaptor for outer dynein arms not yet identified\"]\n    },\n    {\n      \"year\": 2010,\n      \"claim\": \"Defined the molecular basis of IFT46's structural role by showing it forms a ternary core with IFT88 and IFT52, and localized the assembly determinant to the C-terminus while assigning cargo transport to the N-terminus.\",\n      \"evidence\": \"Yeast two-hybrid, bacterial co-expression, chemical cross-linking, and electroporation rescue of ift46 mutants\",\n      \"pmids\": [\"20435895\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not identify the N-terminal binding partner mediating dynein arm transport\", \"Precise residues contacting IFT52 not yet defined\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Resolved how IFT46 selects outer dynein arm cargo: its N-terminal 147 residues bind the cargo adaptor ODA16, and structural work defined the ODA16 architecture (N-terminal domain plus 8-bladed β-propeller) and the ~200 nM affinity of the interaction, linking adaptor binding to ODA recognition.\",\n      \"evidence\": \"Chlamydomonas suppressor domain dissection plus X-ray crystallography of ODA16, truncation/mutagenesis binding maps, affinity measurement, and Co-IP with axonemal ODAs\",\n      \"pmids\": [\"28701346\", \"28298440\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Stoichiometry of the IFT46–ODA16–ODA assembly during transit not resolved\", \"How cargo is released at the ciliary tip unknown\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Pinpointed the targeting mechanism by showing IFT52 recruits IFT46 to the basal body through L285/L286 in a C-terminal sequence (246–321) that is necessary and sufficient for ciliary localization, with ectopic nuclear IFT52 mislocalizing IFT46.\",\n      \"evidence\": \"IFT46 truncation/site-directed mutagenesis, Co-IP, motor-mutant epistasis, and ectopic nuclear targeting in Chlamydomonas\",\n      \"pmids\": [\"28302912\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether targeting precedes or follows IFT-B core assembly not resolved\", \"Regulation of IFT52–IFT46 docking unknown\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Extended IFT46's adaptor role beyond dynein arms by showing an IFT46–IFT56 dimer binds KIF17 and is required for KIF17 entry into cilia across the permeability barrier.\",\n      \"evidence\": \"Visible immunoprecipitation assay, KIF17 C-terminal deletion mapping, and RNAi/rescue in mammalian cells\",\n      \"pmids\": [\"28077622\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Interaction shown by a single primary method (VIP) from one lab\", \"Structural basis of the IFT46–IFT56–KIF17 interaction not defined\"]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Demonstrated the physiological requirement for IFT46 in vertebrate ciliogenesis and left-right patterning, generalizing the Chlamydomonas findings to development.\",\n      \"evidence\": \"Morpholino knockdown in zebrafish and Ift46 knockout mice with IF localization and ciliary EM\",\n      \"pmids\": [\"25722189\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No molecular mechanism beyond the IFT-B role established in vertebrates\", \"Tissue-specific cargo dependencies not dissected\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Confirmed IFT46's conserved role in shuttling IFT-B proteins between cytoplasm and cilia by showing IFT57 mislocalizes upon IFT46 depletion.\",\n      \"evidence\": \"RNAi knockdown in Paramecium with GFP-tagged IFT57 fluorescence localization\",\n      \"pmids\": [\"29915351\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single organism, single cargo readout\", \"Whether IFT46 acts on IFT57 directly or via complex B integrity not distinguished\"]\n    },\n    {\n      \"year\": 2026,\n      \"claim\": \"Uncovered a non-ciliary function in which IFT46 deficiency impairs autophagy flux to stabilize Limk2 and drive partial EMT, linking IFT46 loss to renal cyst formation.\",\n      \"evidence\": \"RNA-seq, Limk2–p62 Co-IP, 3D cyst culture, collecting-duct-specific Ift46 knockout mice, and autophagy flux assays, with human ADPKD validation\",\n      \"pmids\": [\"41680856\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Co-IP for Limk2–p62 without reciprocal/structural validation\", \"How IFT46 mechanistically controls autophagy flux not defined\", \"Novel axis not yet independently replicated\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How IFT46's ciliary transport function mechanistically connects to its regulation of autophagy and Limk2 stability remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether the autophagy phenotype is a direct IFT46 activity or a downstream consequence of cilia loss is unknown\", \"No structural model of the IFT46 N-terminus bound to ODA16 in the full IFT-B context\", \"Mechanism of cargo loading and release during transit not defined\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [2, 3, 5]},\n      {\"term_id\": \"GO:0005198\", \"supporting_discovery_ids\": [0, 1]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005929\", \"supporting_discovery_ids\": [4, 6, 7]},\n      {\"term_id\": \"GO:0005815\", \"supporting_discovery_ids\": [4, 6]},\n      {\"term_id\": \"GO:0005829\", \"supporting_discovery_ids\": [7]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-5653656\", \"supporting_discovery_ids\": [0, 2, 5, 7]},\n      {\"term_id\": \"R-HSA-1852241\", \"supporting_discovery_ids\": [6]},\n      {\"term_id\": \"R-HSA-9612973\", \"supporting_discovery_ids\": [8]}\n    ],\n    \"complexes\": [\"IFT complex B\"],\n    \"partners\": [\"IFT52\", \"IFT88\", \"ODA16\", \"IFT56\", \"KIF17\", \"IFT57\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":6,"faith_total":6,"faith_pct":100.0}}