{"gene":"IFT56","run_date":"2026-04-28T18:06:53","timeline":{"discoveries":[{"year":2014,"finding":"TTC26/DYF13 (IFT56) is an IFT complex B protein in mammalian cells and Chlamydomonas reinhardtii; loss of TTC26/DYF13 results in short cilia with abnormal motility, but unlike other IFT-B mutants, IFT particle assembly and speed remain normal. Proteomic and biochemical analyses show a specific depletion of motility-related proteins in dyf13 mutant flagella, establishing that IFT56 is required for transport of a distinct cargo subset (motility-related proteins) rather than overall IFT-B assembly.","method":"Live imaging, Co-IP, proteomic analysis of dyf13 mutant flagella, zebrafish morpholino knockdown, Chlamydomonas genetics","journal":"eLife","confidence":"High","confidence_rationale":"Tier 2 — multiple orthogonal methods (live imaging, biochemistry, proteomics, genetic models) across multiple organisms, replicated findings","pmids":["24596149"],"is_preprint":false},{"year":2014,"finding":"TTC26 (IFT56) binds directly to the IFT46 subunit of IFT complex B, as demonstrated by protein-protein interaction assays; this interaction is required for TTC26's participation in IFT-B. In Ttc26 hop mutant mice, Hedgehog signaling is impaired at the step after Gli accumulation at the ciliary tip but before Gli dissociation from its negative regulator Sufu, revealing a specific mechanistic role of IFT56 in Hh signal transduction downstream of ciliary Gli accumulation.","method":"Protein-protein interaction (co-IP/pull-down) assay, Gli activation assay in embryonic fibroblasts, neural tube patterning analysis, mouse genetics","journal":"PLoS genetics","confidence":"High","confidence_rationale":"Tier 2 — direct binding assay combined with epistasis in Hh pathway and genetic mouse model with defined molecular phenotype","pmids":["25340710"],"is_preprint":false},{"year":2017,"finding":"IFT56 is required for the integrity of the IFT-B complex within cilia; in Ift56 mouse mutants, core IFT-B proteins IFT88, IFT81, and IFT27 fail to accumulate normally within cilia, while IFT-A components are unaffected. Loss of IFT56 causes abnormal ciliary microtubule architecture (abnormal positioning and number of microtubule doublets) and impairs efficient accumulation of Gli proteins in cilia, resulting in defective Shh signaling in limb and neural tube.","method":"Ift56 mouse mutant analysis, immunofluorescence/quantification of IFT proteins in cilia, ciliary ultrastructure analysis, Gli accumulation assay","journal":"Development (Cambridge, England)","confidence":"High","confidence_rationale":"Tier 2 — clean KO mouse model with multiple orthogonal readouts (protein accumulation, ultrastructure, signaling) defining a specific mechanistic role for IFT56 within the IFT-B complex","pmids":["28264835"],"is_preprint":false},{"year":2017,"finding":"KIF17, a homodimeric kinesin-2, interacts with the IFT46-IFT56 dimer within the IFT-B complex through its C-terminal sequence immediately upstream of its nuclear localization signal (NLS); this interaction is required for KIF17 entry into cilia but not for its intraciliary trafficking or for IFT-B trafficking itself.","method":"Visible immunoprecipitation (VIP) assay, domain mapping, ciliary entry assays with truncation mutants in mammalian cells","journal":"Molecular biology of the cell","confidence":"High","confidence_rationale":"Tier 2 — direct biochemical interaction mapped to specific domains with functional consequence (ciliary entry), using reciprocal VIP and deletion analysis","pmids":["28077622"],"is_preprint":false},{"year":2012,"finding":"Ttc26 (IFT56) localizes to the transition zone of photoreceptor sensory cilia and primary cilia in mIMCD3 cells; knockdown in mIMCD3 cells produces shortened and defective primary cilia, and morpholino knockdown in zebrafish disrupts ciliogenesis of photoreceptor outer segments and pronephric cilia, establishing a direct role in ciliogenesis.","method":"Immunofluorescence localization, scanning electron microscopy, morpholino knockdown in zebrafish, siRNA knockdown in mIMCD3 cells","journal":"Molecular biology of the cell","confidence":"Medium","confidence_rationale":"Tier 2 — localization with functional consequence confirmed by multiple knockdown models, but no in vitro reconstitution","pmids":["22718903"],"is_preprint":false},{"year":2010,"finding":"In Trypanosoma brucei, the DYF-13/IFT56 orthologue PIFTC3 participates in a ~660 kDa macromolecular complex containing IFT complex B components as well as DYF-1, DYF-3, DYF-11/Elipsa and IFTA-2; co-immunoprecipitation also detected an interaction between DYF-13 and IFT122, a component of IFT complex A, suggesting DYF-13/IFT56 bridges IFT-A and IFT-B complexes.","method":"Affinity purification, mass spectrometry, co-immunoprecipitation","journal":"Molecular microbiology","confidence":"Medium","confidence_rationale":"Tier 2/3 — MS-based interactome and co-IP in trypanosome orthologue; bridging interaction with IFT-A is single co-IP","pmids":["20923419"],"is_preprint":false},{"year":2026,"finding":"TTC26 (IFT56) acts as a scaffold protein in osteoclasts, recruiting the deubiquitinase MINDY3 to promote K48-linked deubiquitination and stabilization of RACK1, which in turn activates NFATc1, the master transcription factor of osteoclastogenesis. Six critical TTC26 residues (N533, T534, E537, R541, K545, K548) are essential for this scaffold activity. Osteoclast-targeted Ttc26 inhibition alleviates bone loss in ovariectomized mice.","method":"Co-immunoprecipitation, RNA sequencing, Western blotting, in vitro osteoclast differentiation assays, protein structural analysis, mouse osteoclast-specific knockout (Lysm-Cre), ovariectomized mouse model","journal":"Journal of orthopaedic translation","confidence":"Medium","confidence_rationale":"Tier 2 — multiple orthogonal methods (Co-IP, in vitro assay, mutagenesis of critical residues, in vivo mouse model) in a single study; not yet replicated","pmids":["42006908"],"is_preprint":false},{"year":2022,"finding":"A CRISPR-replicated point mutation in Ttc26 in mice recapitulates the hop phenotype, including ventral spinal cord fusion and synchronous hindlimb gait, confirming that loss-of-function of TTC26 causes misplaced notochord and reduced induction of ventral progenitor domains during spinal cord development, placing TTC26 upstream of ventral midline patterning.","method":"CRISPR knock-in mouse, fictive locomotion experiments, morphological analysis of spinal cord, in situ hybridization/immunohistochemistry for progenitor markers","journal":"eNeuro","confidence":"Medium","confidence_rationale":"Tier 2 — CRISPR replication of mutation confirms causality, with defined morphological and circuit-level phenotypic readouts","pmids":["35210288"],"is_preprint":false}],"current_model":"IFT56 (TTC26) is an IFT complex B protein that functions primarily as a cargo-selective adaptor and structural scaffold: within cilia it is required for the integrity of the IFT-B complex (enabling accumulation of IFT88, IFT81, IFT27 and proper microtubule architecture), facilitates transport of a specific subset of motility-related cargoes and Gli proteins, mediates ciliary entry of KIF17 through a direct IFT46-IFT56 interaction, and acts downstream of Gli ciliary tip accumulation to enable Gli-Sufu dissociation in Hedgehog signaling; outside cilia, TTC26 additionally functions as a scaffold recruiting MINDY3 to deubiquitinate and stabilize RACK1, thereby activating NFATc1-driven osteoclastogenesis."},"narrative":{"teleology":[{"year":2010,"claim":"Establishing that the DYF-13/IFT56 orthologue resides in a macromolecular complex containing IFT-B subunits and potentially bridges IFT-A and IFT-B provided the first biochemical placement of this protein within the IFT machinery.","evidence":"Affinity purification and mass spectrometry of PIFTC3 complex in Trypanosoma brucei","pmids":["20923419"],"confidence":"Medium","gaps":["IFT-A bridging interaction based on single co-IP without reciprocal validation","Functional consequence of disrupting DYF-13 in trypanosomes not assessed","Whether the ~660 kDa complex composition is conserved in vertebrates was unknown"]},{"year":2012,"claim":"Demonstrating that TTC26 localizes to the ciliary transition zone and is required for ciliogenesis in both mammalian cells and zebrafish established a direct functional role in building primary and sensory cilia.","evidence":"Immunofluorescence localization, siRNA knockdown in mIMCD3 cells, and morpholino knockdown in zebrafish","pmids":["22718903"],"confidence":"Medium","gaps":["Mechanism by which TTC26 at the transition zone supports ciliogenesis was not defined","No biochemical reconstitution of TTC26 function"]},{"year":2014,"claim":"Revealing that IFT56 loss causes short, dysmotile cilia with selective depletion of motility-related proteins — while IFT particle assembly and speed remain normal — redefined IFT56 as a cargo-selective adaptor rather than a core IFT-B assembly factor, and identifying direct binding to IFT46 and a specific block in Gli–Sufu dissociation during Hedgehog signaling placed IFT56 at a precise epistatic step in Hh transduction.","evidence":"Proteomic analysis of Chlamydomonas dyf13 mutant flagella, live IFT imaging, zebrafish knockdown, co-IP/pull-down of IFT46–TTC26 interaction, Gli activation assays and neural tube patterning in Ttc26 hop mutant mice","pmids":["24596149","25340710"],"confidence":"High","gaps":["Identity of the motility-related cargoes directly bound by IFT56 versus indirectly affected was not resolved","Structural basis of IFT46–IFT56 interaction unknown","Whether the Gli–Sufu dissociation defect reflects a direct IFT56 function at the ciliary tip or an indirect consequence of ciliary architecture defects was unclear"]},{"year":2017,"claim":"Showing that IFT56 loss disrupts ciliary accumulation of core IFT-B proteins (IFT88, IFT81, IFT27) and ciliary microtubule doublet architecture revised the initial model — IFT56 contributes to IFT-B complex integrity within cilia, not only to cargo selection — and mapping the KIF17–IFT46/IFT56 interaction demonstrated that IFT56 gates ciliary entry of a specific kinesin-2 motor.","evidence":"Ift56 knockout mouse analysis with IFT protein quantification and ultrastructure; VIP assays with domain mapping and ciliary entry assays for KIF17 in mammalian cells","pmids":["28264835","28077622"],"confidence":"High","gaps":["How IFT56 supports IFT-B stability inside cilia while being dispensable for cytoplasmic IFT-B assembly is mechanistically unresolved","Structural details of the KIF17–IFT46/IFT56 ternary complex are lacking","Whether KIF17 ciliary entry defect contributes to the Hh signaling phenotype is untested"]},{"year":2022,"claim":"CRISPR replication of the Ttc26 hop mutation confirmed causality for ventral spinal cord patterning defects and synchronous hindlimb gait, extending the developmental consequences of IFT56 loss to neural circuit assembly.","evidence":"CRISPR knock-in mouse, fictive locomotion analysis, morphological and molecular analysis of spinal cord progenitor domains","pmids":["35210288"],"confidence":"Medium","gaps":["Whether the locomotor phenotype is solely a consequence of impaired Hh signaling or involves additional IFT56-dependent pathways was not dissected","No rescue experiment performed"]},{"year":2026,"claim":"Identification of a cilia-independent scaffold function — TTC26 recruits MINDY3 to deubiquitinate and stabilize RACK1, driving NFATc1-dependent osteoclastogenesis — revealed an unexpected non-ciliary role and therapeutic relevance in bone homeostasis.","evidence":"Co-IP, mutagenesis of six critical TTC26 residues, osteoclast-specific Lysm-Cre knockout mice, ovariectomized mouse bone loss model","pmids":["42006908"],"confidence":"Medium","gaps":["Not yet independently replicated","Whether the RACK1-stabilizing scaffold function operates in cell types beyond osteoclasts is unknown","Relationship between ciliary and non-ciliary functions of TTC26 is not addressed"]},{"year":null,"claim":"The structural basis of IFT56's selective cargo recognition, the mechanism by which it maintains IFT-B integrity specifically within the ciliary compartment, and the full extent of its non-ciliary scaffold functions remain unresolved.","evidence":"","pmids":[],"confidence":"High","gaps":["No high-resolution structure of IFT56 alone or in complex with IFT46/KIF17","Mechanism distinguishing IFT56's role in ciliary versus cytoplasmic IFT-B stability is unknown","Full repertoire of cargoes directly dependent on IFT56 for ciliary transport is not defined"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[0,3,6]}],"localization":[{"term_id":"GO:0005929","term_label":"cilium","supporting_discovery_ids":[0,2,4]}],"pathway":[{"term_id":"GO:0005929","term_label":"cilium","supporting_discovery_ids":[0,2,4]},{"term_id":"R-HSA-162582","term_label":"Signal Transduction","supporting_discovery_ids":[1,2]},{"term_id":"R-HSA-1852241","term_label":"Organelle biogenesis and maintenance","supporting_discovery_ids":[0,2,4]}],"complexes":["IFT-B complex"],"partners":["IFT46","KIF17","IFT88","RACK1","MINDY3","IFT81","IFT27"],"other_free_text":[]},"mechanistic_narrative":"IFT56 (TTC26) is a component of the intraflagellar transport complex B (IFT-B) that functions as a cargo-selective adaptor and structural scaffold essential for ciliogenesis, ciliary motility, and Hedgehog signal transduction. IFT56 binds directly to IFT46 within the IFT-B complex and is required for ciliary accumulation of core IFT-B proteins (IFT88, IFT81, IFT27), proper ciliary microtubule architecture, transport of motility-related cargo proteins, and ciliary entry of the kinesin-2 motor KIF17 [PMID:24596149, PMID:25340710, PMID:28264835, PMID:28077622]. In Hedgehog signaling, IFT56 acts downstream of Gli accumulation at the ciliary tip to enable Gli–Sufu dissociation, and its loss causes ventral neural tube patterning defects and limb malformations in mice [PMID:25340710, PMID:28264835, PMID:35210288]. Outside the cilium, TTC26 serves as a scaffold recruiting the deubiquitinase MINDY3 to stabilize RACK1 via K48-linked deubiquitination, thereby activating NFATc1-driven osteoclastogenesis [PMID:42006908]."},"prefetch_data":{"uniprot":{"accession":"A0AVF1","full_name":"Intraflagellar transport protein 56","aliases":["Tetratricopeptide repeat protein 26","TPR repeat protein 26"],"length_aa":554,"mass_kda":64.2,"function":"Component of the intraflagellar transport (IFT) complex B required for transport of proteins in the motile cilium. Required for transport of specific ciliary cargo proteins related to motility, while it is neither required for IFT complex B assembly or motion nor for cilium assembly. Required for efficient coupling between the accumulation of GLI2 and GLI3 at the ciliary tips and their dissociation from the negative regulator SUFU. Plays a key role in maintaining the integrity of the IFT complex B and the proper ciliary localization of the IFT complex B components. Not required for IFT complex A ciliary localization or function. Essential for maintaining proper microtubule organization within the ciliary axoneme","subcellular_location":"Cell projection, cilium","url":"https://www.uniprot.org/uniprotkb/A0AVF1/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/IFT56","classification":"Not Classified","n_dependent_lines":0,"n_total_lines":1208,"dependency_fraction":0.0},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[{"gene":"HSPB11","stoichiometry":10.0},{"gene":"FKBP5","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/search/IFT56","total_profiled":1310},"omim":[{"mim_id":"617453","title":"TETRATRICOPEPTIDE REPEAT DOMAIN-CONTAINING PROTEIN 26; TTC26","url":"https://www.omim.org/entry/617453"}],"hpa":{"profiled":true,"resolved_as":"TTC26","reliability":"Approved","locations":[{"location":"Nucleoplasm","reliability":"Approved"},{"location":"Primary cilium","reliability":"Additional"},{"location":"Mitochondria","reliability":"Additional"},{"location":"Cytosol","reliability":"Additional"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/TTC26"},"hgnc":{"alias_symbol":["FLJ12571","dyf-13","DYF13"],"prev_symbol":["TTC26"]},"alphafold":{"accession":"A0AVF1","domains":[{"cath_id":"1.25.40.10","chopping":"149-270","consensus_level":"medium","plddt":91.6932,"start":149,"end":270},{"cath_id":"1.25.40,1.25.40","chopping":"276-386","consensus_level":"medium","plddt":95.6531,"start":276,"end":386},{"cath_id":"1.25.40,1.25.40","chopping":"390-475","consensus_level":"medium","plddt":96.7972,"start":390,"end":475},{"cath_id":"-","chopping":"476-554","consensus_level":"medium","plddt":93.4666,"start":476,"end":554}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/A0AVF1","model_url":"https://alphafold.ebi.ac.uk/files/AF-A0AVF1-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-A0AVF1-F1-predicted_aligned_error_v6.png","plddt_mean":91.56},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=IFT56","jax_strain_url":"https://www.jax.org/strain/search?query=IFT56"},"sequence":{"accession":"A0AVF1","fasta_url":"https://rest.uniprot.org/uniprotkb/A0AVF1.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/A0AVF1/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/A0AVF1"}},"corpus_meta":[{"pmid":"24596149","id":"PMC_24596149","title":"TTC26/DYF13 is an intraflagellar transport protein required for transport of motility-related proteins into flagella.","date":"2014","source":"eLife","url":"https://pubmed.ncbi.nlm.nih.gov/24596149","citation_count":61,"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":50,"is_preprint":false},{"pmid":"28264835","id":"PMC_28264835","title":"IFT56 regulates vertebrate developmental patterning by maintaining IFTB complex integrity and ciliary microtubule architecture.","date":"2017","source":"Development (Cambridge, England)","url":"https://pubmed.ncbi.nlm.nih.gov/28264835","citation_count":32,"is_preprint":false},{"pmid":"22718903","id":"PMC_22718903","title":"Knockdown of ttc26 disrupts ciliogenesis of the photoreceptor cells and the pronephros in zebrafish.","date":"2012","source":"Molecular biology of the cell","url":"https://pubmed.ncbi.nlm.nih.gov/22718903","citation_count":25,"is_preprint":false},{"pmid":"25340710","id":"PMC_25340710","title":"A mutation in the mouse ttc26 gene leads to impaired hedgehog signaling.","date":"2014","source":"PLoS genetics","url":"https://pubmed.ncbi.nlm.nih.gov/25340710","citation_count":24,"is_preprint":false},{"pmid":"20923419","id":"PMC_20923419","title":"Biochemical analysis of PIFTC3, the Trypanosoma brucei orthologue of nematode DYF-13, reveals interactions with established and putative intraflagellar transport components.","date":"2010","source":"Molecular microbiology","url":"https://pubmed.ncbi.nlm.nih.gov/20923419","citation_count":19,"is_preprint":false},{"pmid":"32617964","id":"PMC_32617964","title":"Pituitary stalk interruption syndrome broadens the clinical spectrum of the TTC26 ciliopathy.","date":"2020","source":"Clinical genetics","url":"https://pubmed.ncbi.nlm.nih.gov/32617964","citation_count":12,"is_preprint":false},{"pmid":"34177428","id":"PMC_34177428","title":"Identification of the TTC26 Splice Variant in a Novel Complex Ciliopathy Syndrome with Biliary, Renal, Neurological, and Skeletal Manifestations.","date":"2021","source":"Molecular syndromology","url":"https://pubmed.ncbi.nlm.nih.gov/34177428","citation_count":10,"is_preprint":false},{"pmid":"35210288","id":"PMC_35210288","title":"Hop Mice Display Synchronous Hindlimb Locomotion and a Ventrally Fused Lumbar Spinal Cord Caused by a Point Mutation in Ttc26.","date":"2022","source":"eNeuro","url":"https://pubmed.ncbi.nlm.nih.gov/35210288","citation_count":3,"is_preprint":false},{"pmid":"38135897","id":"PMC_38135897","title":"A novel TTC26 variant in a patient with hexadactyly, pituitary stalk interruption, hepatopathy, nephropathy, and bilateral lip-palate cleft: A case report and expansion of the phenotype.","date":"2023","source":"American journal of medical genetics. Part A","url":"https://pubmed.ncbi.nlm.nih.gov/38135897","citation_count":3,"is_preprint":false},{"pmid":"41352382","id":"PMC_41352382","title":"Genetic background influences the extent and severity of cilia-related congenital anomalies in Ift56/Ttc26 mutant mice.","date":"2025","source":"Developmental biology","url":"https://pubmed.ncbi.nlm.nih.gov/41352382","citation_count":0,"is_preprint":false},{"pmid":"42006908","id":"PMC_42006908","title":"TTC26 scaffolds MINDY3-mediated RACK1 deubiquitination to drive osteoclastogenesis and pathological bone resorption.","date":"2026","source":"Journal of orthopaedic translation","url":"https://pubmed.ncbi.nlm.nih.gov/42006908","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":7129,"output_tokens":2408,"usd":0.028754},"stage2":{"model":"claude-opus-4-6","input_tokens":5679,"output_tokens":2298,"usd":0.128768},"total_usd":0.157522,"stage1_batch_id":"msgbatch_01DzrsgVgYngY1hvM3DU1yF2","stage2_batch_id":"msgbatch_01KA9b7iRzKFdhoBUT7vCvSe","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2014,\n      \"finding\": \"TTC26/DYF13 (IFT56) is an IFT complex B protein in mammalian cells and Chlamydomonas reinhardtii; loss of TTC26/DYF13 results in short cilia with abnormal motility, but unlike other IFT-B mutants, IFT particle assembly and speed remain normal. Proteomic and biochemical analyses show a specific depletion of motility-related proteins in dyf13 mutant flagella, establishing that IFT56 is required for transport of a distinct cargo subset (motility-related proteins) rather than overall IFT-B assembly.\",\n      \"method\": \"Live imaging, Co-IP, proteomic analysis of dyf13 mutant flagella, zebrafish morpholino knockdown, Chlamydomonas genetics\",\n      \"journal\": \"eLife\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — multiple orthogonal methods (live imaging, biochemistry, proteomics, genetic models) across multiple organisms, replicated findings\",\n      \"pmids\": [\"24596149\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"TTC26 (IFT56) binds directly to the IFT46 subunit of IFT complex B, as demonstrated by protein-protein interaction assays; this interaction is required for TTC26's participation in IFT-B. In Ttc26 hop mutant mice, Hedgehog signaling is impaired at the step after Gli accumulation at the ciliary tip but before Gli dissociation from its negative regulator Sufu, revealing a specific mechanistic role of IFT56 in Hh signal transduction downstream of ciliary Gli accumulation.\",\n      \"method\": \"Protein-protein interaction (co-IP/pull-down) assay, Gli activation assay in embryonic fibroblasts, neural tube patterning analysis, mouse genetics\",\n      \"journal\": \"PLoS genetics\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — direct binding assay combined with epistasis in Hh pathway and genetic mouse model with defined molecular phenotype\",\n      \"pmids\": [\"25340710\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"IFT56 is required for the integrity of the IFT-B complex within cilia; in Ift56 mouse mutants, core IFT-B proteins IFT88, IFT81, and IFT27 fail to accumulate normally within cilia, while IFT-A components are unaffected. Loss of IFT56 causes abnormal ciliary microtubule architecture (abnormal positioning and number of microtubule doublets) and impairs efficient accumulation of Gli proteins in cilia, resulting in defective Shh signaling in limb and neural tube.\",\n      \"method\": \"Ift56 mouse mutant analysis, immunofluorescence/quantification of IFT proteins in cilia, ciliary ultrastructure analysis, Gli accumulation assay\",\n      \"journal\": \"Development (Cambridge, England)\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — clean KO mouse model with multiple orthogonal readouts (protein accumulation, ultrastructure, signaling) defining a specific mechanistic role for IFT56 within the IFT-B complex\",\n      \"pmids\": [\"28264835\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"KIF17, a homodimeric kinesin-2, interacts with the IFT46-IFT56 dimer within the IFT-B complex through its C-terminal sequence immediately upstream of its nuclear localization signal (NLS); this interaction is required for KIF17 entry into cilia but not for its intraciliary trafficking or for IFT-B trafficking itself.\",\n      \"method\": \"Visible immunoprecipitation (VIP) assay, domain mapping, ciliary entry assays with truncation mutants in mammalian cells\",\n      \"journal\": \"Molecular biology of the cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — direct biochemical interaction mapped to specific domains with functional consequence (ciliary entry), using reciprocal VIP and deletion analysis\",\n      \"pmids\": [\"28077622\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"Ttc26 (IFT56) localizes to the transition zone of photoreceptor sensory cilia and primary cilia in mIMCD3 cells; knockdown in mIMCD3 cells produces shortened and defective primary cilia, and morpholino knockdown in zebrafish disrupts ciliogenesis of photoreceptor outer segments and pronephric cilia, establishing a direct role in ciliogenesis.\",\n      \"method\": \"Immunofluorescence localization, scanning electron microscopy, morpholino knockdown in zebrafish, siRNA knockdown in mIMCD3 cells\",\n      \"journal\": \"Molecular biology of the cell\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — localization with functional consequence confirmed by multiple knockdown models, but no in vitro reconstitution\",\n      \"pmids\": [\"22718903\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"In Trypanosoma brucei, the DYF-13/IFT56 orthologue PIFTC3 participates in a ~660 kDa macromolecular complex containing IFT complex B components as well as DYF-1, DYF-3, DYF-11/Elipsa and IFTA-2; co-immunoprecipitation also detected an interaction between DYF-13 and IFT122, a component of IFT complex A, suggesting DYF-13/IFT56 bridges IFT-A and IFT-B complexes.\",\n      \"method\": \"Affinity purification, mass spectrometry, co-immunoprecipitation\",\n      \"journal\": \"Molecular microbiology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2/3 — MS-based interactome and co-IP in trypanosome orthologue; bridging interaction with IFT-A is single co-IP\",\n      \"pmids\": [\"20923419\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"TTC26 (IFT56) acts as a scaffold protein in osteoclasts, recruiting the deubiquitinase MINDY3 to promote K48-linked deubiquitination and stabilization of RACK1, which in turn activates NFATc1, the master transcription factor of osteoclastogenesis. Six critical TTC26 residues (N533, T534, E537, R541, K545, K548) are essential for this scaffold activity. Osteoclast-targeted Ttc26 inhibition alleviates bone loss in ovariectomized mice.\",\n      \"method\": \"Co-immunoprecipitation, RNA sequencing, Western blotting, in vitro osteoclast differentiation assays, protein structural analysis, mouse osteoclast-specific knockout (Lysm-Cre), ovariectomized mouse model\",\n      \"journal\": \"Journal of orthopaedic translation\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — multiple orthogonal methods (Co-IP, in vitro assay, mutagenesis of critical residues, in vivo mouse model) in a single study; not yet replicated\",\n      \"pmids\": [\"42006908\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"A CRISPR-replicated point mutation in Ttc26 in mice recapitulates the hop phenotype, including ventral spinal cord fusion and synchronous hindlimb gait, confirming that loss-of-function of TTC26 causes misplaced notochord and reduced induction of ventral progenitor domains during spinal cord development, placing TTC26 upstream of ventral midline patterning.\",\n      \"method\": \"CRISPR knock-in mouse, fictive locomotion experiments, morphological analysis of spinal cord, in situ hybridization/immunohistochemistry for progenitor markers\",\n      \"journal\": \"eNeuro\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — CRISPR replication of mutation confirms causality, with defined morphological and circuit-level phenotypic readouts\",\n      \"pmids\": [\"35210288\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"IFT56 (TTC26) is an IFT complex B protein that functions primarily as a cargo-selective adaptor and structural scaffold: within cilia it is required for the integrity of the IFT-B complex (enabling accumulation of IFT88, IFT81, IFT27 and proper microtubule architecture), facilitates transport of a specific subset of motility-related cargoes and Gli proteins, mediates ciliary entry of KIF17 through a direct IFT46-IFT56 interaction, and acts downstream of Gli ciliary tip accumulation to enable Gli-Sufu dissociation in Hedgehog signaling; outside cilia, TTC26 additionally functions as a scaffold recruiting MINDY3 to deubiquitinate and stabilize RACK1, thereby activating NFATc1-driven osteoclastogenesis.\"\n}\n```","stage2_raw":"```json\n{\n  \"mechanistic_narrative\": \"IFT56 (TTC26) is a component of the intraflagellar transport complex B (IFT-B) that functions as a cargo-selective adaptor and structural scaffold essential for ciliogenesis, ciliary motility, and Hedgehog signal transduction. IFT56 binds directly to IFT46 within the IFT-B complex and is required for ciliary accumulation of core IFT-B proteins (IFT88, IFT81, IFT27), proper ciliary microtubule architecture, transport of motility-related cargo proteins, and ciliary entry of the kinesin-2 motor KIF17 [PMID:24596149, PMID:25340710, PMID:28264835, PMID:28077622]. In Hedgehog signaling, IFT56 acts downstream of Gli accumulation at the ciliary tip to enable Gli–Sufu dissociation, and its loss causes ventral neural tube patterning defects and limb malformations in mice [PMID:25340710, PMID:28264835, PMID:35210288]. Outside the cilium, TTC26 serves as a scaffold recruiting the deubiquitinase MINDY3 to stabilize RACK1 via K48-linked deubiquitination, thereby activating NFATc1-driven osteoclastogenesis [PMID:42006908].\",\n  \"teleology\": [\n    {\n      \"year\": 2010,\n      \"claim\": \"Establishing that the DYF-13/IFT56 orthologue resides in a macromolecular complex containing IFT-B subunits and potentially bridges IFT-A and IFT-B provided the first biochemical placement of this protein within the IFT machinery.\",\n      \"evidence\": \"Affinity purification and mass spectrometry of PIFTC3 complex in Trypanosoma brucei\",\n      \"pmids\": [\"20923419\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"IFT-A bridging interaction based on single co-IP without reciprocal validation\",\n        \"Functional consequence of disrupting DYF-13 in trypanosomes not assessed\",\n        \"Whether the ~660 kDa complex composition is conserved in vertebrates was unknown\"\n      ]\n    },\n    {\n      \"year\": 2012,\n      \"claim\": \"Demonstrating that TTC26 localizes to the ciliary transition zone and is required for ciliogenesis in both mammalian cells and zebrafish established a direct functional role in building primary and sensory cilia.\",\n      \"evidence\": \"Immunofluorescence localization, siRNA knockdown in mIMCD3 cells, and morpholino knockdown in zebrafish\",\n      \"pmids\": [\"22718903\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Mechanism by which TTC26 at the transition zone supports ciliogenesis was not defined\",\n        \"No biochemical reconstitution of TTC26 function\"\n      ]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Revealing that IFT56 loss causes short, dysmotile cilia with selective depletion of motility-related proteins — while IFT particle assembly and speed remain normal — redefined IFT56 as a cargo-selective adaptor rather than a core IFT-B assembly factor, and identifying direct binding to IFT46 and a specific block in Gli–Sufu dissociation during Hedgehog signaling placed IFT56 at a precise epistatic step in Hh transduction.\",\n      \"evidence\": \"Proteomic analysis of Chlamydomonas dyf13 mutant flagella, live IFT imaging, zebrafish knockdown, co-IP/pull-down of IFT46–TTC26 interaction, Gli activation assays and neural tube patterning in Ttc26 hop mutant mice\",\n      \"pmids\": [\"24596149\", \"25340710\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Identity of the motility-related cargoes directly bound by IFT56 versus indirectly affected was not resolved\",\n        \"Structural basis of IFT46–IFT56 interaction unknown\",\n        \"Whether the Gli–Sufu dissociation defect reflects a direct IFT56 function at the ciliary tip or an indirect consequence of ciliary architecture defects was unclear\"\n      ]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Showing that IFT56 loss disrupts ciliary accumulation of core IFT-B proteins (IFT88, IFT81, IFT27) and ciliary microtubule doublet architecture revised the initial model — IFT56 contributes to IFT-B complex integrity within cilia, not only to cargo selection — and mapping the KIF17–IFT46/IFT56 interaction demonstrated that IFT56 gates ciliary entry of a specific kinesin-2 motor.\",\n      \"evidence\": \"Ift56 knockout mouse analysis with IFT protein quantification and ultrastructure; VIP assays with domain mapping and ciliary entry assays for KIF17 in mammalian cells\",\n      \"pmids\": [\"28264835\", \"28077622\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"How IFT56 supports IFT-B stability inside cilia while being dispensable for cytoplasmic IFT-B assembly is mechanistically unresolved\",\n        \"Structural details of the KIF17–IFT46/IFT56 ternary complex are lacking\",\n        \"Whether KIF17 ciliary entry defect contributes to the Hh signaling phenotype is untested\"\n      ]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"CRISPR replication of the Ttc26 hop mutation confirmed causality for ventral spinal cord patterning defects and synchronous hindlimb gait, extending the developmental consequences of IFT56 loss to neural circuit assembly.\",\n      \"evidence\": \"CRISPR knock-in mouse, fictive locomotion analysis, morphological and molecular analysis of spinal cord progenitor domains\",\n      \"pmids\": [\"35210288\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Whether the locomotor phenotype is solely a consequence of impaired Hh signaling or involves additional IFT56-dependent pathways was not dissected\",\n        \"No rescue experiment performed\"\n      ]\n    },\n    {\n      \"year\": 2026,\n      \"claim\": \"Identification of a cilia-independent scaffold function — TTC26 recruits MINDY3 to deubiquitinate and stabilize RACK1, driving NFATc1-dependent osteoclastogenesis — revealed an unexpected non-ciliary role and therapeutic relevance in bone homeostasis.\",\n      \"evidence\": \"Co-IP, mutagenesis of six critical TTC26 residues, osteoclast-specific Lysm-Cre knockout mice, ovariectomized mouse bone loss model\",\n      \"pmids\": [\"42006908\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Not yet independently replicated\",\n        \"Whether the RACK1-stabilizing scaffold function operates in cell types beyond osteoclasts is unknown\",\n        \"Relationship between ciliary and non-ciliary functions of TTC26 is not addressed\"\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"The structural basis of IFT56's selective cargo recognition, the mechanism by which it maintains IFT-B integrity specifically within the ciliary compartment, and the full extent of its non-ciliary scaffold functions remain unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"No high-resolution structure of IFT56 alone or in complex with IFT46/KIF17\",\n        \"Mechanism distinguishing IFT56's role in ciliary versus cytoplasmic IFT-B stability is unknown\",\n        \"Full repertoire of cargoes directly dependent on IFT56 for ciliary transport is not defined\"\n      ]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [0, 3, 6]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005929\", \"supporting_discovery_ids\": [0, 2, 4]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"GO:0005929\", \"supporting_discovery_ids\": [0, 2, 4]},\n      {\"term_id\": \"R-HSA-162582\", \"supporting_discovery_ids\": [1, 2]},\n      {\"term_id\": \"R-HSA-1852241\", \"supporting_discovery_ids\": [0, 2, 4]}\n    ],\n    \"complexes\": [\n      \"IFT-B complex\"\n    ],\n    \"partners\": [\n      \"IFT46\",\n      \"KIF17\",\n      \"IFT88\",\n      \"RACK1\",\n      \"MINDY3\",\n      \"IFT81\",\n      \"IFT27\"\n    ],\n    \"other_free_text\": []\n  }\n}\n```"}