{"gene":"DYNC2I1","run_date":"2026-06-09T23:54:42","timeline":{"discoveries":[{"year":2013,"finding":"WDR60 (DYNC2I1) localizes at the base of the primary cilium in human chondrocytes, and loss-of-function mutations cause defects in ciliogenesis and aberrant accumulation of the GLI2 transcription factor at the centrosome/basal body in the absence of an obvious axoneme, establishing WDR60 as required for ciliogenesis and proper Hedgehog pathway execution.","method":"Immunofluorescence localization in wild-type human chondrocytes; analysis of fibroblasts from affected individuals with WDR60 mutations (loss-of-function).","journal":"American journal of human genetics","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct localization experiment tied to functional consequence (GLI2 mislocalization), supported by patient-derived cell analysis; single lab, two orthogonal readouts.","pmids":["23910462"],"is_preprint":false},{"year":2013,"finding":"The Chlamydomonas/planarian ortholog of WDR60 (FAP163/WD60) is an integral component of the retrograde IFT dynein complex: it co-purifies with dynein-1b intermediate chain FAP133 and the LC8 dynein light chain, is present in the flagellar matrix, and is trafficked by IFT. RNAi knockdown in planaria causes severe ciliary assembly defects with IFT particle accumulation, demonstrating that WD60 is absolutely required for retrograde IFT.","method":"Biochemical co-purification from Chlamydomonas flagella; RNAi knockdown in planaria with phenotypic analysis (ciliary morphology, IFT particle accumulation, beat frequency).","journal":"Molecular biology of the cell","confidence":"High","confidence_rationale":"Tier 1-2 / Strong — biochemical co-purification establishing complex membership combined with genetic loss-of-function in an orthologous organism with defined cellular phenotype; multiple orthogonal methods.","pmids":["23864713"],"is_preprint":false},{"year":2018,"finding":"WDR60 forms a distinct dynein-2 subcomplex (WDR60–TCTEX1D2–DYNLT1/DYNLT3) that is separate from the DYNC2H1-DYNC2LI1 and WDR34-DYNLL1/DYNLL2-DYNLRB1/DYNLRB2 subcomplexes. WDR60 directly interacts with the TCTEX1D2-DYNLT1/DYNLT3 dimer. WDR60 knockout causes severe defects in retrograde ciliary protein trafficking and failed assembly of the dynein-2 complex; a WDR60 mutant lacking TCTEX1D2-binding partially restores retrograde trafficking, showing WDR60 plays a major structural and functional role while TCTEX1D2 plays an auxiliary role.","method":"Visible immunoprecipitation (VIP) assay to map interaction modes among dynein-2 subunits; CRISPR/Cas9 knockout of WDR60 and TCTEX1D2; rescue experiments with interaction-deficient WDR60 mutant; ciliary trafficking assays.","journal":"Molecular biology of the cell","confidence":"High","confidence_rationale":"Tier 1-2 / Strong — reciprocal co-IP/VIP assay establishing binary interactions, KO cell lines with defined trafficking phenotype, domain-mapping rescue experiment; multiple orthogonal methods in single study.","pmids":["29742051"],"is_preprint":false},{"year":2022,"finding":"In C. elegans, WDR-60 (the WDR60 ortholog) is the dynein-2-specific intermediate chain required for intraflagellar transport (IFT), while DYCI-1 is the dynein-1-specific intermediate chain required for retrograde axonal transport of synaptic vesicles. Loss of wdr-60 impairs IFT without affecting axonal transport, establishing functional specificity of the two intermediate chains.","method":"Mutational analysis of wdr-60 and dyci-1 alleles in C. elegans with IFT and axonal transport assays.","journal":"Genes to cells","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genetic loss-of-function with defined cellular phenotypes (IFT vs. axonal transport), single lab, two transport assays as orthogonal readouts.","pmids":["36461782"],"is_preprint":false},{"year":2021,"finding":"WDR60 localizes to the microtubule-organizing center (MTOC) in neurons and is required for the multipolar-to-bipolar transition of migrating cortical neurons. Knockdown impairs microtubule organization and neuronal migration; this migration defect is rescued by an acetylation-mimicking α-tubulin mutant (K40Q), establishing a non-ciliary role for WDR60 in controlling microtubule acetylation/stability at the MTOC.","method":"shRNA knockdown in embryonic mouse brain (in utero electroporation); immunofluorescence for MTOC localization; rescue with α-TubulinK40Q.","journal":"Cell death & disease","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — KO/KD with defined cellular phenotype plus domain-specific rescue experiment; single lab, two orthogonal readouts (localization + rescue).","pmids":["33436552"],"is_preprint":false},{"year":2023,"finding":"WDR60 interacts with IFT88 (an IFT-B component) by co-immunoprecipitation, whereas WDR34 interacts with both IFT88 and IFT140 (an IFT-A component), revealing differential cargo/adapter interactions within the dynein-2 complex. WDR60 deficiency in mouse embryos downregulates Sonic Hedgehog (SHH) signaling, demonstrating a role in SHH pathway promotion.","method":"Co-immunoprecipitation (CO-IP) from mouse embryo tissue; Wdr60 piggyBac hypomorph mouse model with RNAseq and qRT-PCR of SHH pathway components.","journal":"Frontiers in cell and developmental biology","confidence":"Medium","confidence_rationale":"Tier 2-3 / Moderate — CO-IP establishing IFT88 interaction, supported by in vivo genetic model with transcriptomic readout; single lab, two orthogonal methods.","pmids":["37228654"],"is_preprint":false}],"current_model":"DYNC2I1/WDR60 is a dynein-2-specific intermediate chain that forms a dedicated subcomplex (WDR60–TCTEX1D2–DYNLT1/DYNLT3) within the dynein-2 motor; it is required for retrograde intraflagellar transport (IFT) in cilia, interacts with IFT-B component IFT88, promotes Sonic Hedgehog signaling by enabling proper ciliary trafficking, localizes to the base of primary cilia and the microtubule-organizing center, and also has a non-ciliary role in controlling microtubule organization during neuronal migration."},"narrative":{"mechanistic_narrative":"DYNC2I1/WDR60 is a dynein-2-specific intermediate chain that is essential for retrograde intraflagellar transport (IFT) and ciliary function [PMID:23864713, PMID:36461782]. Within the dynein-2 motor it nucleates a dedicated subcomplex by directly binding the TCTEX1D2–DYNLT1/DYNLT3 dimer, distinct from the DYNC2H1–DYNC2LI1 and WDR34-containing modules; loss of WDR60 abolishes assembly of the dynein-2 complex and severely disrupts retrograde ciliary protein trafficking, with the TCTEX1D2 interaction playing an auxiliary role [PMID:29742051]. WDR60 localizes to the base of the primary cilium and is required for ciliogenesis and proper Hedgehog pathway execution: loss-of-function causes aberrant GLI2 accumulation at the centrosome/basal body and downregulation of Sonic Hedgehog signaling in vivo, consistent with its physical interaction with the IFT-B component IFT88 [PMID:23910462, PMID:37228654]. Beyond cilia, WDR60 localizes to the neuronal microtubule-organizing center and controls the multipolar-to-bipolar transition during cortical neuronal migration through effects on microtubule acetylation/stability, a defect rescued by an acetylation-mimicking α-tubulin K40Q mutant [PMID:33436552].","teleology":[{"year":2013,"claim":"Established WDR60 as a required factor for ciliogenesis and Hedgehog signaling, linking the gene to a defined human ciliopathy phenotype.","evidence":"Immunofluorescence in human chondrocytes and analysis of patient fibroblasts carrying loss-of-function mutations","pmids":["23910462"],"confidence":"Medium","gaps":["Mechanism connecting WDR60 loss to GLI2 mislocalization not resolved","Did not define the molecular complex WDR60 acts within"]},{"year":2013,"claim":"Identified the WDR60 ortholog as an integral retrograde IFT dynein component, establishing its role in retrograde transport at the biochemical and genetic level.","evidence":"Co-purification from Chlamydomonas flagella with dynein-1b intermediate chain FAP133 and LC8; RNAi knockdown in planaria with ciliary phenotyping","pmids":["23864713"],"confidence":"High","gaps":["Used invertebrate/algal orthologs rather than human protein","Did not map the human dynein-2 subcomplex architecture"]},{"year":2018,"claim":"Resolved the architecture of the dynein-2 motor, showing WDR60 forms a discrete subcomplex with TCTEX1D2–DYNLT1/DYNLT3 and is structurally required for complex assembly and retrograde trafficking.","evidence":"Visible immunoprecipitation interaction mapping, CRISPR/Cas9 knockout of WDR60 and TCTEX1D2, and interaction-deficient rescue with trafficking assays","pmids":["29742051"],"confidence":"High","gaps":["No structural model of the assembled subcomplex","Cargo-adapter interactions of WDR60 not yet defined"]},{"year":2021,"claim":"Revealed a non-ciliary function for WDR60 at the neuronal MTOC controlling microtubule acetylation and neuronal migration, broadening its role beyond IFT.","evidence":"shRNA knockdown by in utero electroporation in mouse cortex with MTOC localization and rescue by α-tubulin K40Q","pmids":["33436552"],"confidence":"Medium","gaps":["Molecular mechanism linking WDR60 to tubulin acetylation unknown","Whether this role depends on dynein-2 complex assembly unclear"]},{"year":2022,"claim":"Demonstrated functional specificity of the intermediate chains, showing WDR60 serves dynein-2/IFT exclusively while DYCI-1 serves dynein-1/axonal transport.","evidence":"Mutational analysis of wdr-60 and dyci-1 alleles in C. elegans with IFT and axonal transport assays","pmids":["36461782"],"confidence":"Medium","gaps":["Performed in C. elegans; human specificity inferred","Does not address overlap with the MTOC/migration role"]},{"year":2023,"claim":"Defined differential IFT adapter interactions, showing WDR60 binds IFT-B component IFT88 and that its deficiency downregulates SHH signaling in vivo.","evidence":"Co-immunoprecipitation from mouse embryo tissue and Wdr60 hypomorph mouse with RNAseq/qRT-PCR of SHH pathway components","pmids":["37228654"],"confidence":"Medium","gaps":["Single Co-IP without reciprocal/structural validation of IFT88 binding","Direct cargo specificity for retrograde transport not established"]},{"year":null,"claim":"How WDR60 mechanistically couples retrograde IFT cargo selection to Hedgehog output, and how its ciliary versus MTOC/microtubule-acetylation roles are coordinated, remain open.","evidence":"No direct experimental evidence in the available corpus","pmids":[],"confidence":"Low","gaps":["No structural model of WDR60 within the assembled dynein-2 motor","Mechanism of WDR60-dependent tubulin acetylation unknown","Direct retrograde cargoes of WDR60 not identified"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0008092","term_label":"cytoskeletal protein binding","supporting_discovery_ids":[1,2,4]},{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[2,5]}],"localization":[{"term_id":"GO:0005929","term_label":"cilium","supporting_discovery_ids":[0,1]},{"term_id":"GO:0005815","term_label":"microtubule organizing center","supporting_discovery_ids":[4]}],"pathway":[{"term_id":"R-HSA-5653656","term_label":"Vesicle-mediated transport","supporting_discovery_ids":[1,2,3]},{"term_id":"R-HSA-162582","term_label":"Signal Transduction","supporting_discovery_ids":[0,5]},{"term_id":"R-HSA-1266738","term_label":"Developmental Biology","supporting_discovery_ids":[4]}],"complexes":["dynein-2 (cytoplasmic dynein 2) motor complex","WDR60–TCTEX1D2–DYNLT1/DYNLT3 subcomplex"],"partners":["TCTEX1D2","DYNLT1","DYNLT3","IFT88"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q8WVS4","full_name":"Cytoplasmic dynein 2 intermediate chain 1","aliases":["Dynein 2 intermediate chain 1","WD repeat-containing protein 60"],"length_aa":1066,"mass_kda":122.6,"function":"Acts as one of several non-catalytic accessory components of the cytoplasmic dynein 2 complex (dynein-2 complex), a motor protein complex that drives the movement of cargos along microtubules within cilia and flagella in concert with the intraflagellar transport (IFT) system (PubMed:23910462, PubMed:25205765, PubMed:29742051, PubMed:31451806). DYNC2I1 plays a major role in retrograde ciliary protein trafficking in cilia and flagella (PubMed:29742051, PubMed:30320547, PubMed:30649997). Also requires to maintain a functional transition zone (PubMed:30320547)","subcellular_location":"Cell projection, cilium; Cytoplasm, cytoskeleton, microtubule organizing center, centrosome","url":"https://www.uniprot.org/uniprotkb/Q8WVS4/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/DYNC2I1","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":"DYNC2LI1","stoichiometry":4.0},{"gene":"DYNLL1","stoichiometry":0.2},{"gene":"DYNLL2","stoichiometry":0.2},{"gene":"RACK1","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/search/DYNC2I1","total_profiled":1310},"omim":[{"mim_id":"615503","title":"SHORT-RIB THORACIC DYSPLASIA 8 WITH OR WITHOUT POLYDACTYLY; SRTD8","url":"https://www.omim.org/entry/615503"},{"mim_id":"615462","title":"DYNEIN, CYTOPLASMIC 2, INTERMEDIATE CHAIN 1; DYNC2I1","url":"https://www.omim.org/entry/615462"},{"mim_id":"610772","title":"NK6 HOMEOBOX 3; NKX6-3","url":"https://www.omim.org/entry/610772"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Centrosome","reliability":"Supported"},{"location":"Basal body","reliability":"Supported"},{"location":"Primary cilium","reliability":"Additional"},{"location":"Cytosol","reliability":"Additional"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/DYNC2I1"},"hgnc":{"alias_symbol":["FLJ10300","FAP163","CFAP163","DIC6"],"prev_symbol":["WDR60"]},"alphafold":{"accession":"Q8WVS4","domains":[],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q8WVS4","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q8WVS4-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q8WVS4-F1-predicted_aligned_error_v6.png","plddt_mean":63.47},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=DYNC2I1","jax_strain_url":"https://www.jax.org/strain/search?query=DYNC2I1"},"sequence":{"accession":"Q8WVS4","fasta_url":"https://rest.uniprot.org/uniprotkb/Q8WVS4.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q8WVS4/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q8WVS4"}},"corpus_meta":[{"pmid":"23910462","id":"PMC_23910462","title":"Short-rib polydactyly and Jeune syndromes are caused by mutations in WDR60.","date":"2013","source":"American journal of human genetics","url":"https://pubmed.ncbi.nlm.nih.gov/23910462","citation_count":98,"is_preprint":false},{"pmid":"29742051","id":"PMC_29742051","title":"Interaction of WDR60 intermediate chain with TCTEX1D2 light chain of the dynein-2 complex is crucial for ciliary protein trafficking.","date":"2018","source":"Molecular biology of the cell","url":"https://pubmed.ncbi.nlm.nih.gov/29742051","citation_count":54,"is_preprint":false},{"pmid":"23864713","id":"PMC_23864713","title":"WD60/FAP163 is a dynein intermediate chain required for retrograde intraflagellar transport in cilia.","date":"2013","source":"Molecular biology of the cell","url":"https://pubmed.ncbi.nlm.nih.gov/23864713","citation_count":43,"is_preprint":false},{"pmid":"9354844","id":"PMC_9354844","title":"Spondylocostal dysostosis associated with a 46, XX,+15,dic(6;15)(q25;q11.2) translocation.","date":"1997","source":"Clinical dysmorphology","url":"https://pubmed.ncbi.nlm.nih.gov/9354844","citation_count":12,"is_preprint":false},{"pmid":"29271569","id":"PMC_29271569","title":"Expanding the phenotype associated with biallelic WDR60 mutations: Siblings with retinal degeneration and polydactyly lacking other features of short rib thoracic dystrophies.","date":"2017","source":"American journal of medical genetics. Part A","url":"https://pubmed.ncbi.nlm.nih.gov/29271569","citation_count":8,"is_preprint":false},{"pmid":"25426168","id":"PMC_25426168","title":"Delineation variable genotype/phenotype correlations of 6q27 terminal deletion derived from dic(6;18)(q27;p10).","date":"2014","source":"Molecular cytogenetics","url":"https://pubmed.ncbi.nlm.nih.gov/25426168","citation_count":7,"is_preprint":false},{"pmid":"36461782","id":"PMC_36461782","title":"Dynein intermediate chains DYCI-1 and WDR-60 have specific functions in Caenorhabditis elegans.","date":"2022","source":"Genes to cells : devoted to molecular & cellular mechanisms","url":"https://pubmed.ncbi.nlm.nih.gov/36461782","citation_count":6,"is_preprint":false},{"pmid":"33436552","id":"PMC_33436552","title":"SRPS associated protein WDR60 regulates the multipolar-to-bipolar transition of migrating neurons during cortical development.","date":"2021","source":"Cell death & disease","url":"https://pubmed.ncbi.nlm.nih.gov/33436552","citation_count":3,"is_preprint":false},{"pmid":"37228654","id":"PMC_37228654","title":"Deficiency of Wdr60 and Wdr34 cause distinct neural tube malformation phenotypes in early embryos.","date":"2023","source":"Frontiers in cell and developmental biology","url":"https://pubmed.ncbi.nlm.nih.gov/37228654","citation_count":3,"is_preprint":false},{"pmid":"36381051","id":"PMC_36381051","title":"A novel WDR60 variant contributes to a late diagnosis of Jeune asphyxiating thoracic dystrophy in a Chinese patient: A case report.","date":"2022","source":"Clinical case reports","url":"https://pubmed.ncbi.nlm.nih.gov/36381051","citation_count":1,"is_preprint":false},{"pmid":"14697641","id":"PMC_14697641","title":"Characterization of psu dic(6;5)(p21.3;q13) with reverse chromosome painting in a patient with secondary myelodysplastic syndrome following treatment for multiple myeloma.","date":"2004","source":"Cancer genetics and cytogenetics","url":"https://pubmed.ncbi.nlm.nih.gov/14697641","citation_count":1,"is_preprint":false},{"pmid":"41269779","id":"PMC_41269779","title":"Ciliogenesis in pancreatic neuroendocrine tumors: insight into the role of WDR60.","date":"2025","source":"Endocrine-related cancer","url":"https://pubmed.ncbi.nlm.nih.gov/41269779","citation_count":0,"is_preprint":false},{"pmid":"42256993","id":"PMC_42256993","title":"Prenatal Diagnosis of Short Rib-Polydactyly Syndrome (SRPS), DYNC2I1-Related: Identification of a Novel Homozygous Missense Variant by Clinical Exome Sequencing.","date":"2026","source":"Clinical case reports","url":"https://pubmed.ncbi.nlm.nih.gov/42256993","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":7806,"output_tokens":1971,"usd":0.026492,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":8871,"output_tokens":2606,"usd":0.054753,"stage2_stop_reason":"end_turn"},"total_usd":0.081245,"stage1_batch_id":"msgbatch_01AsR7g8dGTEiEw9U83bJeWn","stage2_batch_id":"msgbatch_01YV5ZyxtFNUZEjxRcpd9jzb","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2013,\n      \"finding\": \"WDR60 (DYNC2I1) localizes at the base of the primary cilium in human chondrocytes, and loss-of-function mutations cause defects in ciliogenesis and aberrant accumulation of the GLI2 transcription factor at the centrosome/basal body in the absence of an obvious axoneme, establishing WDR60 as required for ciliogenesis and proper Hedgehog pathway execution.\",\n      \"method\": \"Immunofluorescence localization in wild-type human chondrocytes; analysis of fibroblasts from affected individuals with WDR60 mutations (loss-of-function).\",\n      \"journal\": \"American journal of human genetics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct localization experiment tied to functional consequence (GLI2 mislocalization), supported by patient-derived cell analysis; single lab, two orthogonal readouts.\",\n      \"pmids\": [\"23910462\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"The Chlamydomonas/planarian ortholog of WDR60 (FAP163/WD60) is an integral component of the retrograde IFT dynein complex: it co-purifies with dynein-1b intermediate chain FAP133 and the LC8 dynein light chain, is present in the flagellar matrix, and is trafficked by IFT. RNAi knockdown in planaria causes severe ciliary assembly defects with IFT particle accumulation, demonstrating that WD60 is absolutely required for retrograde IFT.\",\n      \"method\": \"Biochemical co-purification from Chlamydomonas flagella; RNAi knockdown in planaria with phenotypic analysis (ciliary morphology, IFT particle accumulation, beat frequency).\",\n      \"journal\": \"Molecular biology of the cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 / Strong — biochemical co-purification establishing complex membership combined with genetic loss-of-function in an orthologous organism with defined cellular phenotype; multiple orthogonal methods.\",\n      \"pmids\": [\"23864713\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"WDR60 forms a distinct dynein-2 subcomplex (WDR60–TCTEX1D2–DYNLT1/DYNLT3) that is separate from the DYNC2H1-DYNC2LI1 and WDR34-DYNLL1/DYNLL2-DYNLRB1/DYNLRB2 subcomplexes. WDR60 directly interacts with the TCTEX1D2-DYNLT1/DYNLT3 dimer. WDR60 knockout causes severe defects in retrograde ciliary protein trafficking and failed assembly of the dynein-2 complex; a WDR60 mutant lacking TCTEX1D2-binding partially restores retrograde trafficking, showing WDR60 plays a major structural and functional role while TCTEX1D2 plays an auxiliary role.\",\n      \"method\": \"Visible immunoprecipitation (VIP) assay to map interaction modes among dynein-2 subunits; CRISPR/Cas9 knockout of WDR60 and TCTEX1D2; rescue experiments with interaction-deficient WDR60 mutant; ciliary trafficking assays.\",\n      \"journal\": \"Molecular biology of the cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 / Strong — reciprocal co-IP/VIP assay establishing binary interactions, KO cell lines with defined trafficking phenotype, domain-mapping rescue experiment; multiple orthogonal methods in single study.\",\n      \"pmids\": [\"29742051\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"In C. elegans, WDR-60 (the WDR60 ortholog) is the dynein-2-specific intermediate chain required for intraflagellar transport (IFT), while DYCI-1 is the dynein-1-specific intermediate chain required for retrograde axonal transport of synaptic vesicles. Loss of wdr-60 impairs IFT without affecting axonal transport, establishing functional specificity of the two intermediate chains.\",\n      \"method\": \"Mutational analysis of wdr-60 and dyci-1 alleles in C. elegans with IFT and axonal transport assays.\",\n      \"journal\": \"Genes to cells\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic loss-of-function with defined cellular phenotypes (IFT vs. axonal transport), single lab, two transport assays as orthogonal readouts.\",\n      \"pmids\": [\"36461782\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"WDR60 localizes to the microtubule-organizing center (MTOC) in neurons and is required for the multipolar-to-bipolar transition of migrating cortical neurons. Knockdown impairs microtubule organization and neuronal migration; this migration defect is rescued by an acetylation-mimicking α-tubulin mutant (K40Q), establishing a non-ciliary role for WDR60 in controlling microtubule acetylation/stability at the MTOC.\",\n      \"method\": \"shRNA knockdown in embryonic mouse brain (in utero electroporation); immunofluorescence for MTOC localization; rescue with α-TubulinK40Q.\",\n      \"journal\": \"Cell death & disease\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — KO/KD with defined cellular phenotype plus domain-specific rescue experiment; single lab, two orthogonal readouts (localization + rescue).\",\n      \"pmids\": [\"33436552\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"WDR60 interacts with IFT88 (an IFT-B component) by co-immunoprecipitation, whereas WDR34 interacts with both IFT88 and IFT140 (an IFT-A component), revealing differential cargo/adapter interactions within the dynein-2 complex. WDR60 deficiency in mouse embryos downregulates Sonic Hedgehog (SHH) signaling, demonstrating a role in SHH pathway promotion.\",\n      \"method\": \"Co-immunoprecipitation (CO-IP) from mouse embryo tissue; Wdr60 piggyBac hypomorph mouse model with RNAseq and qRT-PCR of SHH pathway components.\",\n      \"journal\": \"Frontiers in cell and developmental biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 / Moderate — CO-IP establishing IFT88 interaction, supported by in vivo genetic model with transcriptomic readout; single lab, two orthogonal methods.\",\n      \"pmids\": [\"37228654\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"DYNC2I1/WDR60 is a dynein-2-specific intermediate chain that forms a dedicated subcomplex (WDR60–TCTEX1D2–DYNLT1/DYNLT3) within the dynein-2 motor; it is required for retrograde intraflagellar transport (IFT) in cilia, interacts with IFT-B component IFT88, promotes Sonic Hedgehog signaling by enabling proper ciliary trafficking, localizes to the base of primary cilia and the microtubule-organizing center, and also has a non-ciliary role in controlling microtubule organization during neuronal migration.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"DYNC2I1/WDR60 is a dynein-2-specific intermediate chain that is essential for retrograde intraflagellar transport (IFT) and ciliary function [#1, #3]. Within the dynein-2 motor it nucleates a dedicated subcomplex by directly binding the TCTEX1D2\\u2013DYNLT1/DYNLT3 dimer, distinct from the DYNC2H1\\u2013DYNC2LI1 and WDR34-containing modules; loss of WDR60 abolishes assembly of the dynein-2 complex and severely disrupts retrograde ciliary protein trafficking, with the TCTEX1D2 interaction playing an auxiliary role [#2]. WDR60 localizes to the base of the primary cilium and is required for ciliogenesis and proper Hedgehog pathway execution: loss-of-function causes aberrant GLI2 accumulation at the centrosome/basal body and downregulation of Sonic Hedgehog signaling in vivo, consistent with its physical interaction with the IFT-B component IFT88 [#0, #5]. Beyond cilia, WDR60 localizes to the neuronal microtubule-organizing center and controls the multipolar-to-bipolar transition during cortical neuronal migration through effects on microtubule acetylation/stability, a defect rescued by an acetylation-mimicking \\u03b1-tubulin K40Q mutant [#4].\",\n  \"teleology\": [\n    {\n      \"year\": 2013,\n      \"claim\": \"Established WDR60 as a required factor for ciliogenesis and Hedgehog signaling, linking the gene to a defined human ciliopathy phenotype.\",\n      \"evidence\": \"Immunofluorescence in human chondrocytes and analysis of patient fibroblasts carrying loss-of-function mutations\",\n      \"pmids\": [\"23910462\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Mechanism connecting WDR60 loss to GLI2 mislocalization not resolved\",\n        \"Did not define the molecular complex WDR60 acts within\"\n      ]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"Identified the WDR60 ortholog as an integral retrograde IFT dynein component, establishing its role in retrograde transport at the biochemical and genetic level.\",\n      \"evidence\": \"Co-purification from Chlamydomonas flagella with dynein-1b intermediate chain FAP133 and LC8; RNAi knockdown in planaria with ciliary phenotyping\",\n      \"pmids\": [\"23864713\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Used invertebrate/algal orthologs rather than human protein\",\n        \"Did not map the human dynein-2 subcomplex architecture\"\n      ]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Resolved the architecture of the dynein-2 motor, showing WDR60 forms a discrete subcomplex with TCTEX1D2\\u2013DYNLT1/DYNLT3 and is structurally required for complex assembly and retrograde trafficking.\",\n      \"evidence\": \"Visible immunoprecipitation interaction mapping, CRISPR/Cas9 knockout of WDR60 and TCTEX1D2, and interaction-deficient rescue with trafficking assays\",\n      \"pmids\": [\"29742051\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"No structural model of the assembled subcomplex\",\n        \"Cargo-adapter interactions of WDR60 not yet defined\"\n      ]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Revealed a non-ciliary function for WDR60 at the neuronal MTOC controlling microtubule acetylation and neuronal migration, broadening its role beyond IFT.\",\n      \"evidence\": \"shRNA knockdown by in utero electroporation in mouse cortex with MTOC localization and rescue by \\u03b1-tubulin K40Q\",\n      \"pmids\": [\"33436552\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Molecular mechanism linking WDR60 to tubulin acetylation unknown\",\n        \"Whether this role depends on dynein-2 complex assembly unclear\"\n      ]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Demonstrated functional specificity of the intermediate chains, showing WDR60 serves dynein-2/IFT exclusively while DYCI-1 serves dynein-1/axonal transport.\",\n      \"evidence\": \"Mutational analysis of wdr-60 and dyci-1 alleles in C. elegans with IFT and axonal transport assays\",\n      \"pmids\": [\"36461782\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Performed in C. elegans; human specificity inferred\",\n        \"Does not address overlap with the MTOC/migration role\"\n      ]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Defined differential IFT adapter interactions, showing WDR60 binds IFT-B component IFT88 and that its deficiency downregulates SHH signaling in vivo.\",\n      \"evidence\": \"Co-immunoprecipitation from mouse embryo tissue and Wdr60 hypomorph mouse with RNAseq/qRT-PCR of SHH pathway components\",\n      \"pmids\": [\"37228654\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Single Co-IP without reciprocal/structural validation of IFT88 binding\",\n        \"Direct cargo specificity for retrograde transport not established\"\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How WDR60 mechanistically couples retrograde IFT cargo selection to Hedgehog output, and how its ciliary versus MTOC/microtubule-acetylation roles are coordinated, remain open.\",\n      \"evidence\": \"No direct experimental evidence in the available corpus\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"No structural model of WDR60 within the assembled dynein-2 motor\",\n        \"Mechanism of WDR60-dependent tubulin acetylation unknown\",\n        \"Direct retrograde cargoes of WDR60 not identified\"\n      ]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0008092\", \"supporting_discovery_ids\": [1, 2, 4]},\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [2, 5]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005929\", \"supporting_discovery_ids\": [0, 1]},\n      {\"term_id\": \"GO:0005815\", \"supporting_discovery_ids\": [4]},\n      {\"term_id\": \"GO:0005813\", \"supporting_discovery_ids\": [0]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-5653656\", \"supporting_discovery_ids\": [1, 2, 3]},\n      {\"term_id\": \"R-HSA-162582\", \"supporting_discovery_ids\": [0, 5]},\n      {\"term_id\": \"R-HSA-1266738\", \"supporting_discovery_ids\": [4]}\n    ],\n    \"complexes\": [\"dynein-2 (cytoplasmic dynein 2) motor complex\", \"WDR60\\u2013TCTEX1D2\\u2013DYNLT1/DYNLT3 subcomplex\"],\n    \"partners\": [\"TCTEX1D2\", \"DYNLT1\", \"DYNLT3\", \"IFT88\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"tie","faith_supported":4,"faith_total":4,"faith_pct":100.0}}