{"gene":"DNAAF11","run_date":"2026-06-09T23:54:42","timeline":{"discoveries":[{"year":2013,"finding":"LRRC6 (DNAAF11) physically interacts with ZMYND10 via the LRRC6 CS domain and the ZMYND10 C-terminal domain; certain PCD-causing mutations in either protein abrogate this interaction. Both proteins colocalize with centriole markers SAS6 and PCM1 in the cytoplasm.","method":"Co-immunoprecipitation, domain-mapping, colocalization with centriole markers SAS6/PCM1, zebrafish/Xenopus knockdown models","journal":"American journal of human genetics","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal domain-mapping Co-IP with mutagenesis, colocalization, and in vivo functional validation across two animal models","pmids":["23891469"],"is_preprint":false},{"year":2012,"finding":"Loss-of-function mutations in LRRC6 cause absence of both inner and outer dynein arms from cilia axonemes. Native LRRC6 protein localizes to the cytoplasm and within cilia of airway epithelial cells; it is absent in cells from patients with loss-of-function mutations, which also lack dynein arm protein markers.","method":"Homozygosity mapping, sequencing, transmission electron microscopy, immunofluorescence/immunolocalization in patient airway epithelial cells","journal":"American journal of human genetics","confidence":"High","confidence_rationale":"Tier 2 / Strong — patient cell-based loss-of-function with TEM ultrastructural readout and protein localization, replicated across multiple families and independent labs","pmids":["23122589"],"is_preprint":false},{"year":2013,"finding":"LRRC6 is upregulated during ciliogenesis in human airway epithelial cells in a FOXJ1-dependent fashion. shRNA-mediated silencing of LRRC6 in airway epithelial cells results in absent dynein arms, slowed cilia beat frequency, and mislocalization of dynein arm proteins to the cytoplasm.","method":"shRNA knockdown in human airway epithelial cells, immunofluorescence, cilia beat frequency measurement, FOXJ1-dependent expression analysis","journal":"PloS one","confidence":"High","confidence_rationale":"Tier 2 / Moderate — clean KD with multiple orthogonal readouts (beat frequency, TEM-equivalent protein localization, immunofluorescence), single lab","pmids":["23527195"],"is_preprint":false},{"year":2013,"finding":"Reptin/Ruvbl2 directly interacts with Lrrc6/Seahorse in the cytosol and this interaction is critical for Lrrc6 in vivo function in zebrafish cilia motility; the Reptin–Lrrc6 complex is involved in dynein arm formation, as loss of Reptin reduces axonemal dynein arm density without affecting dynein arm component expression levels.","method":"Co-immunoprecipitation (direct interaction), colocalization in cytosol, zebrafish reptin mutant analysis, dynein arm density quantification","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"High","confidence_rationale":"Tier 2 / Moderate — reciprocal Co-IP demonstrating direct interaction, in vivo genetic rescue, multiple orthogonal readouts in zebrafish","pmids":["23858445"],"is_preprint":false},{"year":2010,"finding":"The Drosophila ortholog TilB (tilB/CG14620) is a cytoplasmic protein required for dynein arm assembly in sperm axonemes and ciliated chordotonal dendrites; tilB mutants lack dynein arms in sperm and sensory neuron dendrites, causing deafness and male sterility, without affecting intraflagellar transport or tubulin modifications.","method":"Deficiency mapping, sequencing, genomic rescue transgene, fluorescently tagged TilB localization, electron microscopy of axonemes","journal":"Genetics","confidence":"High","confidence_rationale":"Tier 2 / Strong — genetic rescue with genomic transgene, in vivo localization, ultrastructural TEM analysis, multiple functional readouts","pmids":["20215474"],"is_preprint":false},{"year":2016,"finding":"In Lrrc6 knockout mice, outer dynein arm (ODA) proteins (DNAH5, DNAH9, IC2) accumulate in the cytoplasm and fail to be transported to the ciliary axoneme, whereas the initial ODA assembly step (IC2–IC1 interaction) remains intact; cilia morphology (9+2 microtubule arrangement) is preserved but motility is completely lost.","method":"Lrrc6 knockout mouse, immunofluorescence, co-immunoprecipitation (IC2-IC1 interaction), transmission electron microscopy","journal":"Genes to cells : devoted to molecular & cellular mechanisms","confidence":"High","confidence_rationale":"Tier 2 / Moderate — knockout mouse with multiple orthogonal methods (TEM, IF, Co-IP) establishing transport vs. assembly distinction","pmids":["27353389"],"is_preprint":false},{"year":2023,"finding":"LRRC6 promotes nuclear translocation of FOXJ1 (master transcriptional regulator of cilia-associated genes) via an importin-α-dependent mechanism; in Lrrc6 KO mice FOXJ1 remains cytoplasmic, and transcription of ODA/IDA components, dynein axonemal assembly factors, radial spokes, and central apparatus genes is reduced.","method":"Lrrc6 knockout mice, proteomics, transcriptomics, immunofluorescence (FOXJ1 localization), importin-α inhibitor (INI-43), mouse basal cell organoids","journal":"Cell communication and signaling : CCS","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — KO mouse with multiple omics and pharmacological inhibitor evidence; nuclear translocation mechanism supported by inhibitor experiment, single lab","pmids":["37328841"],"is_preprint":false},{"year":2024,"finding":"LRRC6 mutation disrupts interaction with CCDC40, SPAG1, and ZMYND10 as identified by tandem mass tagging proteomics on patient spermatozoa, and reduces expression of dynein arm proteins, linking LRRC6 to a cytoplasmic interactome required for dynein arm assembly.","method":"Tandem mass tagging proteomics on patient spermatozoa, western blotting, immunostaining, transmission electron microscopy","journal":"Andrology","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — proteomics interactome in patient material with orthogonal western blot/IF confirmation, single lab","pmids":["38934611"],"is_preprint":false},{"year":2021,"finding":"A homozygous nonsense variant (p.W250*) in LRRC6 severely impairs LRRC6 protein expression and leads to absence of dynein arm proteins in spermatozoa, confirming that LRRC6 protein is required for dynein arm protein expression/stability in sperm flagella.","method":"Western blotting, immunofluorescence staining, transmission electron microscopy on patient spermatozoa","journal":"Journal of assisted reproduction and genetics","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — patient loss-of-function with TEM and protein-level confirmation, single lab","pmids":["33403504"],"is_preprint":false}],"current_model":"DNAAF11/LRRC6 is a cytoplasmic dynein axonemal assembly factor that forms a complex with ZMYND10 (via CS–C-terminal domain interaction), Reptin/RUVBL2, CCDC40, and SPAG1 to facilitate the pre-assembly and cytoplasm-to-cilia transport of outer and inner dynein arm complexes; independently, LRRC6 promotes importin-α-dependent nuclear translocation of the transcription factor FOXJ1, thereby sustaining transcription of the full cilia gene program, and loss of LRRC6 causes primary ciliary dyskinesia with absent dynein arms, laterality defects, and male infertility."},"narrative":{"mechanistic_narrative":"DNAAF11/LRRC6 is a cytoplasmic dynein axonemal assembly factor required for the pre-assembly and ciliary delivery of outer and inner dynein arm complexes that power motile cilia and sperm flagella [PMID:23122589, PMID:27353389]. It operates within a cytoplasmic interactome, binding ZMYND10 through its CS domain (an interaction abolished by PCD-causing mutations) and associating with Reptin/RUVBL2, CCDC40, and SPAG1; loss of these contacts collapses dynein arm assembly [PMID:23891469, PMID:23858445, PMID:38934611]. Mechanistically, LRRC6 acts downstream of initial dynein arm subunit assembly: in its absence the IC2–IC1 interaction still forms but outer dynein arm proteins (DNAH5, DNAH9, IC2) accumulate in the cytoplasm and fail to reach the axoneme, leaving 9+2 cilia structurally intact but immotile [PMID:27353389]. Independently, LRRC6 promotes importin-α-dependent nuclear translocation of FOXJ1, sustaining transcription of the broader cilia gene program; its own expression is itself FOXJ1-dependent during ciliogenesis [PMID:23527195, PMID:37328841]. Loss-of-function mutations in LRRC6 cause primary ciliary dyskinesia with absent dynein arms and male infertility, a role conserved to the Drosophila ortholog TilB [PMID:23122589, PMID:20215474, PMID:33403504].","teleology":[{"year":2010,"claim":"Established that this gene family encodes a cytoplasmic factor specifically required for axonemal dynein arm assembly rather than for ciliary structure or transport machinery generally.","evidence":"Deficiency mapping, genomic rescue transgene, tagged localization and axoneme TEM of the Drosophila ortholog TilB","pmids":["20215474"],"confidence":"High","gaps":["Did not identify mammalian protein partners","Mechanism of how a cytoplasmic protein supports axonemal dynein assembly unresolved"]},{"year":2012,"claim":"Defined LRRC6 as a human PCD gene whose loss removes both inner and outer dynein arms, framing it as an assembly factor acting on dynein arms collectively.","evidence":"Homozygosity mapping, sequencing, TEM, and immunolocalization in patient airway epithelial cells","pmids":["23122589"],"confidence":"High","gaps":["Did not distinguish assembly from transport defect","No molecular partners identified"]},{"year":2013,"claim":"Placed LRRC6 in a defined cytoplasmic assembly network by mapping a direct ZMYND10 interaction and a direct Reptin/RUVBL2 interaction, both required for dynein arm formation.","evidence":"Domain-mapping reciprocal Co-IP with PCD-mutant disruption, centriole-marker colocalization, and zebrafish/Xenopus genetic models","pmids":["23891469","23858445"],"confidence":"High","gaps":["Stoichiometry and assembly order of the complex unknown","How the complex chaperones dynein subunits not resolved"]},{"year":2013,"claim":"Linked LRRC6 to the ciliogenesis transcriptional program and showed knockdown mislocalizes dynein arm proteins to the cytoplasm with loss of beat frequency.","evidence":"shRNA knockdown in human airway epithelium, FOXJ1-dependent expression analysis, immunofluorescence, cilia beat frequency","pmids":["23527195"],"confidence":"High","gaps":["FOXJ1 dependence shown only at expression level, not mechanism","Did not separate transport from assembly"]},{"year":2016,"claim":"Resolved the step at which LRRC6 acts, showing initial ODA subunit assembly (IC2–IC1) is intact but cytoplasm-to-cilia transport of assembled dynein fails.","evidence":"Lrrc6 knockout mouse with immunofluorescence, Co-IP of IC2–IC1, and TEM","pmids":["27353389"],"confidence":"High","gaps":["Molecular machinery linking pre-assembly to transport not defined","Inner dynein arm transport not examined in equivalent detail"]},{"year":2021,"claim":"Confirmed in human sperm that a truncating LRRC6 variant abolishes protein and dynein arm marker expression, extending the assembly role to flagella and infertility.","evidence":"Western blot, immunofluorescence, TEM on patient spermatozoa carrying p.W250*","pmids":["33403504"],"confidence":"Medium","gaps":["Single family","Whether defect is reduced expression versus mislocalization not distinguished"]},{"year":2023,"claim":"Revealed a second, transcriptional axis: LRRC6 drives importin-α-dependent nuclear entry of FOXJ1, so its loss reduces transcription of the full motile-cilia gene set.","evidence":"Lrrc6 KO mice, proteomics/transcriptomics, FOXJ1 immunofluorescence, importin-α inhibitor INI-43, basal cell organoids","pmids":["37328841"],"confidence":"Medium","gaps":["Direct LRRC6–FOXJ1 or LRRC6–importin-α binding not demonstrated","Relationship between cytoplasmic assembly role and nuclear role unclear","Single lab"]},{"year":2024,"claim":"Extended the cytoplasmic interactome to CCDC40 and SPAG1 alongside ZMYND10 in patient material, consolidating LRRC6 as a hub for dynein arm pre-assembly.","evidence":"Tandem mass tagging proteomics on patient spermatozoa with western blot, immunostaining, and TEM","pmids":["38934611"],"confidence":"Medium","gaps":["Interactome inferred from patient material, not reconstituted","Direct versus indirect associations not all distinguished"]},{"year":null,"claim":"How LRRC6 mechanistically couples cytoplasmic dynein pre-assembly to ciliary transport, and how this is reconciled with its FOXJ1 nuclear-translocation role, remains unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No structural model of the assembly complex","Direct LRRC6–importin-α–FOXJ1 binding unproven","Substrate handoff mechanism to transport machinery undefined"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0140096","term_label":"catalytic activity, acting on a protein","supporting_discovery_ids":[0,3,5]},{"term_id":"GO:0060089","term_label":"molecular transducer activity","supporting_discovery_ids":[6]}],"localization":[{"term_id":"GO:0005829","term_label":"cytosol","supporting_discovery_ids":[1,3,5]},{"term_id":"GO:0005929","term_label":"cilium","supporting_discovery_ids":[1]},{"term_id":"GO:0005815","term_label":"microtubule organizing center","supporting_discovery_ids":[0]}],"pathway":[{"term_id":"R-HSA-1852241","term_label":"Organelle biogenesis and maintenance","supporting_discovery_ids":[1,5]},{"term_id":"R-HSA-1643685","term_label":"Disease","supporting_discovery_ids":[1,8]}],"complexes":[],"partners":["ZMYND10","RUVBL2","CCDC40","SPAG1","FOXJ1"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q86X45","full_name":"Dynein axonemal assembly factor 11","aliases":["Leucine-rich repeat-containing protein 6","Leucine-rich testis-specific protein","Protein tilB homolog","Testis-specific leucine-rich repeat protein"],"length_aa":466,"mass_kda":54.3,"function":"Involved in dynein arm assembly, is important for expression and transporting outer dynein arm (ODA) proteins from the cytoplasm to the cilia (PubMed:23122589, PubMed:23527195, PubMed:33403504). Acts as a crucial component in the formation and motility of spermatozoal flagella (PubMed:33403504)","subcellular_location":"Cytoplasm; Cell projection, cilium; Dynein axonemal particle; Cell projection, cilium, flagellum","url":"https://www.uniprot.org/uniprotkb/Q86X45/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/DNAAF11","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":[],"url":"https://opencell.sf.czbiohub.org/search/DNAAF11","total_profiled":1310},"omim":[{"mim_id":"614935","title":"CILIARY DYSKINESIA, PRIMARY, 19; CILD19","url":"https://www.omim.org/entry/614935"},{"mim_id":"614930","title":"DYNEIN, AXONEMAL, ASSEMBLY FACTOR 11; DNAAF11","url":"https://www.omim.org/entry/614930"},{"mim_id":"244400","title":"CILIARY DYSKINESIA, PRIMARY, 1; CILD1","url":"https://www.omim.org/entry/244400"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Approved","locations":[{"location":"Mid piece","reliability":"Approved"},{"location":"Principal piece","reliability":"Approved"}],"tissue_specificity":"Tissue enhanced","tissue_distribution":"Detected in many","driving_tissues":[{"tissue":"choroid plexus","ntpm":46.5},{"tissue":"testis","ntpm":24.5}],"url":"https://www.proteinatlas.org/search/DNAAF11"},"hgnc":{"alias_symbol":["TSLRP","LRTP","CILD19","tilB"],"prev_symbol":["LRRC6"]},"alphafold":{"accession":"Q86X45","domains":[{"cath_id":"3.80.10.10","chopping":"3-179","consensus_level":"high","plddt":88.2245,"start":3,"end":179},{"cath_id":"2.60.40.790","chopping":"302-380","consensus_level":"high","plddt":90.1706,"start":302,"end":380}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q86X45","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q86X45-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q86X45-F1-predicted_aligned_error_v6.png","plddt_mean":74.31},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=DNAAF11","jax_strain_url":"https://www.jax.org/strain/search?query=DNAAF11"},"sequence":{"accession":"Q86X45","fasta_url":"https://rest.uniprot.org/uniprotkb/Q86X45.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q86X45/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q86X45"}},"corpus_meta":[{"pmid":"23891469","id":"PMC_23891469","title":"ZMYND10 is mutated in primary ciliary dyskinesia and interacts with LRRC6.","date":"2013","source":"American journal of human genetics","url":"https://pubmed.ncbi.nlm.nih.gov/23891469","citation_count":154,"is_preprint":false},{"pmid":"23122589","id":"PMC_23122589","title":"Loss-of-function mutations in LRRC6, a gene essential for proper axonemal assembly of inner and outer dynein arms, cause primary ciliary dyskinesia.","date":"2012","source":"American journal of human genetics","url":"https://pubmed.ncbi.nlm.nih.gov/23122589","citation_count":144,"is_preprint":false},{"pmid":"23527195","id":"PMC_23527195","title":"LRRC6 mutation causes primary ciliary dyskinesia with dynein arm defects.","date":"2013","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/23527195","citation_count":80,"is_preprint":false},{"pmid":"23858445","id":"PMC_23858445","title":"Reptin/Ruvbl2 is a Lrrc6/Seahorse interactor essential for cilia motility.","date":"2013","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/23858445","citation_count":51,"is_preprint":false},{"pmid":"20215474","id":"PMC_20215474","title":"Hearing in Drosophila requires TilB, a conserved protein associated with ciliary motility.","date":"2010","source":"Genetics","url":"https://pubmed.ncbi.nlm.nih.gov/20215474","citation_count":40,"is_preprint":false},{"pmid":"27353389","id":"PMC_27353389","title":"Transport of the outer dynein arm complex to cilia requires a cytoplasmic protein Lrrc6.","date":"2016","source":"Genes to cells : devoted to molecular & cellular mechanisms","url":"https://pubmed.ncbi.nlm.nih.gov/27353389","citation_count":26,"is_preprint":false},{"pmid":"29511670","id":"PMC_29511670","title":"Whole-Exome Sequencing Identified a Novel Compound Heterozygous Mutation of LRRC6 in a Chinese Primary Ciliary Dyskinesia Patient.","date":"2018","source":"BioMed research international","url":"https://pubmed.ncbi.nlm.nih.gov/29511670","citation_count":21,"is_preprint":false},{"pmid":"33403504","id":"PMC_33403504","title":"The effect of a novel LRRC6 mutation on the flagellar ultrastructure in a primary ciliary dyskinesia patient.","date":"2021","source":"Journal of assisted reproduction and genetics","url":"https://pubmed.ncbi.nlm.nih.gov/33403504","citation_count":10,"is_preprint":false},{"pmid":"37328841","id":"PMC_37328841","title":"LRRC6 regulates biogenesis of motile cilia by aiding FOXJ1 translocation into the nucleus.","date":"2023","source":"Cell communication and signaling : CCS","url":"https://pubmed.ncbi.nlm.nih.gov/37328841","citation_count":7,"is_preprint":false},{"pmid":"36515799","id":"PMC_36515799","title":"Identification of novel biallelic LRRC6 variants in male Chinese patients with primary ciliary dyskinesia and infertility.","date":"2022","source":"Journal of assisted reproduction and genetics","url":"https://pubmed.ncbi.nlm.nih.gov/36515799","citation_count":7,"is_preprint":false},{"pmid":"38934611","id":"PMC_38934611","title":"A novel homozygous LRRC6 mutation causes male infertility with asthenozoospermia and primary ciliary dyskinesia in humans.","date":"2024","source":"Andrology","url":"https://pubmed.ncbi.nlm.nih.gov/38934611","citation_count":6,"is_preprint":false},{"pmid":"39875006","id":"PMC_39875006","title":"Histone modification-based functional characterization and genetic association of polymorphisms in LRRC6 and MTMR10 within CRC susceptibility regions 8q24 and 15q13.3.","date":"2025","source":"Gene","url":"https://pubmed.ncbi.nlm.nih.gov/39875006","citation_count":2,"is_preprint":false},{"pmid":"31774527","id":"PMC_31774527","title":"The Loci of Behavioral Evolution: Evidence That Fas2 and tilB Underlie Differences in Pupation Site Choice Behavior between Drosophila melanogaster and D. simulans.","date":"2020","source":"Molecular biology and evolution","url":"https://pubmed.ncbi.nlm.nih.gov/31774527","citation_count":1,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":8856,"output_tokens":2306,"usd":0.030579,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":9444,"output_tokens":2858,"usd":0.059335,"stage2_stop_reason":"end_turn"},"total_usd":0.089914,"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\": \"LRRC6 (DNAAF11) physically interacts with ZMYND10 via the LRRC6 CS domain and the ZMYND10 C-terminal domain; certain PCD-causing mutations in either protein abrogate this interaction. Both proteins colocalize with centriole markers SAS6 and PCM1 in the cytoplasm.\",\n      \"method\": \"Co-immunoprecipitation, domain-mapping, colocalization with centriole markers SAS6/PCM1, zebrafish/Xenopus knockdown models\",\n      \"journal\": \"American journal of human genetics\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal domain-mapping Co-IP with mutagenesis, colocalization, and in vivo functional validation across two animal models\",\n      \"pmids\": [\"23891469\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"Loss-of-function mutations in LRRC6 cause absence of both inner and outer dynein arms from cilia axonemes. Native LRRC6 protein localizes to the cytoplasm and within cilia of airway epithelial cells; it is absent in cells from patients with loss-of-function mutations, which also lack dynein arm protein markers.\",\n      \"method\": \"Homozygosity mapping, sequencing, transmission electron microscopy, immunofluorescence/immunolocalization in patient airway epithelial cells\",\n      \"journal\": \"American journal of human genetics\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — patient cell-based loss-of-function with TEM ultrastructural readout and protein localization, replicated across multiple families and independent labs\",\n      \"pmids\": [\"23122589\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"LRRC6 is upregulated during ciliogenesis in human airway epithelial cells in a FOXJ1-dependent fashion. shRNA-mediated silencing of LRRC6 in airway epithelial cells results in absent dynein arms, slowed cilia beat frequency, and mislocalization of dynein arm proteins to the cytoplasm.\",\n      \"method\": \"shRNA knockdown in human airway epithelial cells, immunofluorescence, cilia beat frequency measurement, FOXJ1-dependent expression analysis\",\n      \"journal\": \"PloS one\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — clean KD with multiple orthogonal readouts (beat frequency, TEM-equivalent protein localization, immunofluorescence), single lab\",\n      \"pmids\": [\"23527195\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"Reptin/Ruvbl2 directly interacts with Lrrc6/Seahorse in the cytosol and this interaction is critical for Lrrc6 in vivo function in zebrafish cilia motility; the Reptin–Lrrc6 complex is involved in dynein arm formation, as loss of Reptin reduces axonemal dynein arm density without affecting dynein arm component expression levels.\",\n      \"method\": \"Co-immunoprecipitation (direct interaction), colocalization in cytosol, zebrafish reptin mutant analysis, dynein arm density quantification\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal Co-IP demonstrating direct interaction, in vivo genetic rescue, multiple orthogonal readouts in zebrafish\",\n      \"pmids\": [\"23858445\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"The Drosophila ortholog TilB (tilB/CG14620) is a cytoplasmic protein required for dynein arm assembly in sperm axonemes and ciliated chordotonal dendrites; tilB mutants lack dynein arms in sperm and sensory neuron dendrites, causing deafness and male sterility, without affecting intraflagellar transport or tubulin modifications.\",\n      \"method\": \"Deficiency mapping, sequencing, genomic rescue transgene, fluorescently tagged TilB localization, electron microscopy of axonemes\",\n      \"journal\": \"Genetics\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — genetic rescue with genomic transgene, in vivo localization, ultrastructural TEM analysis, multiple functional readouts\",\n      \"pmids\": [\"20215474\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"In Lrrc6 knockout mice, outer dynein arm (ODA) proteins (DNAH5, DNAH9, IC2) accumulate in the cytoplasm and fail to be transported to the ciliary axoneme, whereas the initial ODA assembly step (IC2–IC1 interaction) remains intact; cilia morphology (9+2 microtubule arrangement) is preserved but motility is completely lost.\",\n      \"method\": \"Lrrc6 knockout mouse, immunofluorescence, co-immunoprecipitation (IC2-IC1 interaction), transmission electron microscopy\",\n      \"journal\": \"Genes to cells : devoted to molecular & cellular mechanisms\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — knockout mouse with multiple orthogonal methods (TEM, IF, Co-IP) establishing transport vs. assembly distinction\",\n      \"pmids\": [\"27353389\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"LRRC6 promotes nuclear translocation of FOXJ1 (master transcriptional regulator of cilia-associated genes) via an importin-α-dependent mechanism; in Lrrc6 KO mice FOXJ1 remains cytoplasmic, and transcription of ODA/IDA components, dynein axonemal assembly factors, radial spokes, and central apparatus genes is reduced.\",\n      \"method\": \"Lrrc6 knockout mice, proteomics, transcriptomics, immunofluorescence (FOXJ1 localization), importin-α inhibitor (INI-43), mouse basal cell organoids\",\n      \"journal\": \"Cell communication and signaling : CCS\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — KO mouse with multiple omics and pharmacological inhibitor evidence; nuclear translocation mechanism supported by inhibitor experiment, single lab\",\n      \"pmids\": [\"37328841\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"LRRC6 mutation disrupts interaction with CCDC40, SPAG1, and ZMYND10 as identified by tandem mass tagging proteomics on patient spermatozoa, and reduces expression of dynein arm proteins, linking LRRC6 to a cytoplasmic interactome required for dynein arm assembly.\",\n      \"method\": \"Tandem mass tagging proteomics on patient spermatozoa, western blotting, immunostaining, transmission electron microscopy\",\n      \"journal\": \"Andrology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — proteomics interactome in patient material with orthogonal western blot/IF confirmation, single lab\",\n      \"pmids\": [\"38934611\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"A homozygous nonsense variant (p.W250*) in LRRC6 severely impairs LRRC6 protein expression and leads to absence of dynein arm proteins in spermatozoa, confirming that LRRC6 protein is required for dynein arm protein expression/stability in sperm flagella.\",\n      \"method\": \"Western blotting, immunofluorescence staining, transmission electron microscopy on patient spermatozoa\",\n      \"journal\": \"Journal of assisted reproduction and genetics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — patient loss-of-function with TEM and protein-level confirmation, single lab\",\n      \"pmids\": [\"33403504\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"DNAAF11/LRRC6 is a cytoplasmic dynein axonemal assembly factor that forms a complex with ZMYND10 (via CS–C-terminal domain interaction), Reptin/RUVBL2, CCDC40, and SPAG1 to facilitate the pre-assembly and cytoplasm-to-cilia transport of outer and inner dynein arm complexes; independently, LRRC6 promotes importin-α-dependent nuclear translocation of the transcription factor FOXJ1, thereby sustaining transcription of the full cilia gene program, and loss of LRRC6 causes primary ciliary dyskinesia with absent dynein arms, laterality defects, and male infertility.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"DNAAF11/LRRC6 is a cytoplasmic dynein axonemal assembly factor required for the pre-assembly and ciliary delivery of outer and inner dynein arm complexes that power motile cilia and sperm flagella [#1, #5]. It operates within a cytoplasmic interactome, binding ZMYND10 through its CS domain (an interaction abolished by PCD-causing mutations) and associating with Reptin/RUVBL2, CCDC40, and SPAG1; loss of these contacts collapses dynein arm assembly [#0, #3, #7]. Mechanistically, LRRC6 acts downstream of initial dynein arm subunit assembly: in its absence the IC2\\u2013IC1 interaction still forms but outer dynein arm proteins (DNAH5, DNAH9, IC2) accumulate in the cytoplasm and fail to reach the axoneme, leaving 9+2 cilia structurally intact but immotile [#5]. Independently, LRRC6 promotes importin-\\u03b1-dependent nuclear translocation of FOXJ1, sustaining transcription of the broader cilia gene program; its own expression is itself FOXJ1-dependent during ciliogenesis [#2, #6]. Loss-of-function mutations in LRRC6 cause primary ciliary dyskinesia with absent dynein arms and male infertility, a role conserved to the Drosophila ortholog TilB [#1, #4, #8].\",\n  \"teleology\": [\n    {\n      \"year\": 2010,\n      \"claim\": \"Established that this gene family encodes a cytoplasmic factor specifically required for axonemal dynein arm assembly rather than for ciliary structure or transport machinery generally.\",\n      \"evidence\": \"Deficiency mapping, genomic rescue transgene, tagged localization and axoneme TEM of the Drosophila ortholog TilB\",\n      \"pmids\": [\"20215474\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not identify mammalian protein partners\", \"Mechanism of how a cytoplasmic protein supports axonemal dynein assembly unresolved\"]\n    },\n    {\n      \"year\": 2012,\n      \"claim\": \"Defined LRRC6 as a human PCD gene whose loss removes both inner and outer dynein arms, framing it as an assembly factor acting on dynein arms collectively.\",\n      \"evidence\": \"Homozygosity mapping, sequencing, TEM, and immunolocalization in patient airway epithelial cells\",\n      \"pmids\": [\"23122589\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not distinguish assembly from transport defect\", \"No molecular partners identified\"]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"Placed LRRC6 in a defined cytoplasmic assembly network by mapping a direct ZMYND10 interaction and a direct Reptin/RUVBL2 interaction, both required for dynein arm formation.\",\n      \"evidence\": \"Domain-mapping reciprocal Co-IP with PCD-mutant disruption, centriole-marker colocalization, and zebrafish/Xenopus genetic models\",\n      \"pmids\": [\"23891469\", \"23858445\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Stoichiometry and assembly order of the complex unknown\", \"How the complex chaperones dynein subunits not resolved\"]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"Linked LRRC6 to the ciliogenesis transcriptional program and showed knockdown mislocalizes dynein arm proteins to the cytoplasm with loss of beat frequency.\",\n      \"evidence\": \"shRNA knockdown in human airway epithelium, FOXJ1-dependent expression analysis, immunofluorescence, cilia beat frequency\",\n      \"pmids\": [\"23527195\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"FOXJ1 dependence shown only at expression level, not mechanism\", \"Did not separate transport from assembly\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"Resolved the step at which LRRC6 acts, showing initial ODA subunit assembly (IC2\\u2013IC1) is intact but cytoplasm-to-cilia transport of assembled dynein fails.\",\n      \"evidence\": \"Lrrc6 knockout mouse with immunofluorescence, Co-IP of IC2\\u2013IC1, and TEM\",\n      \"pmids\": [\"27353389\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Molecular machinery linking pre-assembly to transport not defined\", \"Inner dynein arm transport not examined in equivalent detail\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Confirmed in human sperm that a truncating LRRC6 variant abolishes protein and dynein arm marker expression, extending the assembly role to flagella and infertility.\",\n      \"evidence\": \"Western blot, immunofluorescence, TEM on patient spermatozoa carrying p.W250*\",\n      \"pmids\": [\"33403504\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single family\", \"Whether defect is reduced expression versus mislocalization not distinguished\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Revealed a second, transcriptional axis: LRRC6 drives importin-\\u03b1-dependent nuclear entry of FOXJ1, so its loss reduces transcription of the full motile-cilia gene set.\",\n      \"evidence\": \"Lrrc6 KO mice, proteomics/transcriptomics, FOXJ1 immunofluorescence, importin-\\u03b1 inhibitor INI-43, basal cell organoids\",\n      \"pmids\": [\"37328841\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct LRRC6\\u2013FOXJ1 or LRRC6\\u2013importin-\\u03b1 binding not demonstrated\", \"Relationship between cytoplasmic assembly role and nuclear role unclear\", \"Single lab\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Extended the cytoplasmic interactome to CCDC40 and SPAG1 alongside ZMYND10 in patient material, consolidating LRRC6 as a hub for dynein arm pre-assembly.\",\n      \"evidence\": \"Tandem mass tagging proteomics on patient spermatozoa with western blot, immunostaining, and TEM\",\n      \"pmids\": [\"38934611\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Interactome inferred from patient material, not reconstituted\", \"Direct versus indirect associations not all distinguished\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How LRRC6 mechanistically couples cytoplasmic dynein pre-assembly to ciliary transport, and how this is reconciled with its FOXJ1 nuclear-translocation role, remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No structural model of the assembly complex\", \"Direct LRRC6\\u2013importin-\\u03b1\\u2013FOXJ1 binding unproven\", \"Substrate handoff mechanism to transport machinery undefined\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0140096\", \"supporting_discovery_ids\": [0, 3, 5]},\n      {\"term_id\": \"GO:0060089\", \"supporting_discovery_ids\": [6]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005829\", \"supporting_discovery_ids\": [1, 3, 5]},\n      {\"term_id\": \"GO:0005929\", \"supporting_discovery_ids\": [1]},\n      {\"term_id\": \"GO:0005815\", \"supporting_discovery_ids\": [0]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-1852241\", \"supporting_discovery_ids\": [1, 5]},\n      {\"term_id\": \"R-HSA-1643685\", \"supporting_discovery_ids\": [1, 8]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\"ZMYND10\", \"RUVBL2\", \"CCDC40\", \"SPAG1\", \"FOXJ1\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":5,"faith_total":5,"faith_pct":100.0}}