{"gene":"LRRCC1","run_date":"2026-06-10T02:59:50","timeline":{"discoveries":[{"year":2001,"finding":"The VFL1 protein (Chlamydomonas ortholog of LRRCC1) was cloned via a tagged allele and shown to encode a 128 kDa protein with five N-terminal leucine-rich repeat sequences and a large C-terminal alpha-helical coiled-coil domain. Epitope-tagged Vfl1p copurified with basal body flagellar apparatuses, and immunogold labeling localized it inside the lumen of the basal body at the distal end in a rotationally asymmetric pattern, with most gold particles near the doublet microtubules facing the opposite basal body. This established Vfl1p as the first molecular marker of rotational asymmetry in basal bodies and implicated it in establishing correct rotational orientation.","method":"Tagged-allele cloning, complementation rescue, co-purification with basal body apparatus, immunofluorescence, immunogold electron microscopy","journal":"The Journal of cell biology","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal localization by immunofluorescence and immunogold EM, complementation rescue, co-purification; foundational study replicated conceptually by later work","pmids":["11285274"],"is_preprint":false},{"year":1985,"finding":"The vfl-1 mutation in Chlamydomonas (VFL1/LRRCC1 locus, Chromosome VIII) causes variable flagellar numbers (0–10 per cell), flagella at non-apical positions, uncoupling of flagellar assembly from the cell cycle, unequal cell divisions, and ultrastructural defects including missing/defective striated fibers and reduced rootlet microtubules, establishing the gene's role in controlling basal body number, positioning, and flagellar apparatus integrity.","method":"Genetic mapping, light microscopy, electron microscopy of mutant cells","journal":"The Journal of cell biology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genetic loss-of-function with specific ultrastructural phenotype; single lab but multiple orthogonal readouts","pmids":["3972905"],"is_preprint":false},{"year":1989,"finding":"Examination of the vfl-1 mutant showed it contains approximately normal levels of centrin and possesses a stable nucleus-basal body connector (NBBC), in contrast to vfl-2 which lacks centrin in the NBBC. This negative result establishes that VFL1 function is distinct from centrin/NBBC integrity, placing Vfl1p in a separate pathway controlling basal body number and positioning.","method":"Immunofluorescence with anti-centrin antiserum in mutant strains","journal":"Cell motility and the cytoskeleton","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single immunofluorescence result as part of multi-mutant characterization; negative/comparative finding","pmids":["2696598"],"is_preprint":false},{"year":2008,"finding":"Human CLERC (LRRCC1), the ortholog of Chlamydomonas Vfl1, is a 1032 aa / 120 kDa centrosomal protein with leucine-rich repeat and coiled-coil domains. Endogenous CLERC associates with centrosomes throughout the cell cycle and accumulates during mitosis. RNAi-mediated depletion caused multipolar spindles and centrosome splitting into fractions containing single centrioles, demonstrating that CLERC maintains centrosome structural integrity to support spindle bipolarity during mitosis.","method":"Immunofluorescence localization, RNAi knockdown with spindle morphology and centriole counting readouts","journal":"Cell cycle (Georgetown, Tex.)","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — clean RNAi knockdown with specific mitotic phenotype (multipolar spindles, centriole splitting) plus localization; single lab","pmids":["18728398"],"is_preprint":false},{"year":2019,"finding":"In planarian flatworms, SMED-VFL1 (ortholog of LRRCC1) is required for assembly of centriole appendages that tether cytoskeletal connectors to position centrioles. Loss of SMED-VFL1 disrupts the asymmetric connections between centrioles and impairs alignment of centrioles along polarity fields, contributing to the bilaterally symmetric pattern of the ventral epidermis.","method":"RNAi knockdown in planaria with centriole positioning and polarity readouts","journal":"Developmental cell","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genetic knockdown with specific centriole appendage and polarity phenotype; single study","pmids":["31743665"],"is_preprint":false},{"year":2022,"finding":"Using ultrastructure expansion microscopy (U-ExM), human LRRCC1 was shown to localize preferentially to two consecutive triplet microtubules in the distal lumen of human centrioles, revealing rotationally asymmetric positioning. LRRCC1 partially co-localizes with the distal centriole component C2CD3 and affects its recruitment. Depletion of LRRCC1 caused defects in centriole structure, ciliary assembly, and ciliary signaling, establishing LRRCC1 as part of a conserved 'acorn' structure at the distal centriole that cooperates with C2CD3 to organize the distal region and promote primary ciliogenesis.","method":"Ultrastructure expansion microscopy (U-ExM), super-resolution imaging, siRNA depletion with ciliary assembly and signaling readouts, co-localization analysis","journal":"eLife","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — multiple orthogonal methods (U-ExM structural localization, functional depletion, co-localization with partner protein); mechanistic placement in distal centriole module","pmids":["35319462"],"is_preprint":false},{"year":2022,"finding":"In Xenopus multiciliated cells, Lrrcc1 encodes a basal body component that localizes proximally at the junction with striated rootlets. Morpholino-mediated knockdown of lrrcc1 caused defects in basal body docking, spacing, and polarization, impaired the apical cytoskeleton, and altered ciliary beating, resulting in greatly reduced cilia-powered fluid flow.","method":"Morpholino knockdown in Xenopus embryonic ciliated epidermis, immunofluorescence localization, high-speed video microscopy of ciliary beating, fluid flow assays","journal":"Journal of cell science","confidence":"High","confidence_rationale":"Tier 2 / Strong — genetic knockdown with multiple specific phenotypic readouts (BB docking, spacing, polarization, apical cytoskeleton, beat, fluid flow) in vertebrate model; replicates functional findings from other organisms","pmids":["35067717"],"is_preprint":false},{"year":2013,"finding":"The vfl1 mutation in Chlamydomonas confers supersensitivity to Taxol, grouping it with other basal body assembly mutants (bld2, bld10, bld12, uni3, vfl2, vfl3), indicating that VFL1 contributes to basal body structural integrity in a manner relevant to microtubule-stabilizing drug sensitivity.","method":"Taxol sensitivity assay in mutant strains, double-mutant genetic analysis","journal":"PloS one","confidence":"Low","confidence_rationale":"Tier 3 / Weak — pharmacological sensitivity assay provides indirect structural inference; vfl1 is one of several mutants tested, no direct mechanism established","pmids":["23320108"],"is_preprint":false},{"year":2025,"finding":"Interactor screening and knockout analysis identified a C2CD3–SSNA1–LRRCC1 hierarchical targeting axis in the distal lumen of human centrioles. LRRCC1 functions downstream of C2CD3 and SSNA1 within this network, placing it in a defined molecular pathway for distal centriole organization and ciliogenesis.","method":"KO-validated antibody immunofluorescence, expansion microscopy, interactor screening, epistasis analysis of targeting hierarchy in human cells","journal":"bioRxiv","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — epistasis/targeting hierarchy established by KO analysis and interactor screening; preprint, not yet peer-reviewed","pmids":["bio_10.1101_2025.04.28.648957"],"is_preprint":true}],"current_model":"LRRCC1 (CLERC/VFL1) encodes a conserved leucine-rich repeat and coiled-coil domain protein that localizes asymmetrically to two consecutive triplet microtubules in the distal lumen of centrioles/basal bodies, where it cooperates with C2CD3 and SSNA1 in a hierarchical targeting network to organize centriole distal structure, maintain centrosome integrity during mitosis, and enable basal body docking/polarization and ciliary assembly and signaling in multiciliated cells."},"narrative":{"mechanistic_narrative":"LRRCC1 (CLERC/VFL1) is a conserved leucine-rich repeat and coiled-coil protein that organizes the distal region of centrioles and basal bodies to control their number, orientation, and competence for ciliogenesis [PMID:11285274, PMID:35319462]. It localizes asymmetrically to two consecutive triplet microtubules in the distal lumen of human centrioles, forming part of a rotationally asymmetric 'acorn' structure, a positioning anticipated by the original Chlamydomonas work showing Vfl1p inside the basal body lumen at the distal end in a rotationally asymmetric pattern [PMID:11285274, PMID:35319462]. Within this distal module LRRCC1 acts downstream of C2CD3 and SSNA1 in a hierarchical targeting axis and contributes to recruiting C2CD3, linking it to a defined molecular pathway for distal centriole organization [PMID:35319462]. Functionally, LRRCC1 maintains centrosome structural integrity through mitosis—its depletion causes centrosome splitting and multipolar spindles [PMID:18728398]—and supports ciliary assembly and signaling, with loss producing defects in centriole structure and primary ciliogenesis [PMID:35319462]. In multiciliated cells it localizes proximally at the junction with striated rootlets and is required for basal body docking, spacing, and polarization and for normal ciliary beating and fluid flow [PMID:35067717]. The conserved requirement for the gene in establishing basal body number, positioning, and flagellar apparatus integrity was first defined genetically in Chlamydomonas vfl-1 mutants [PMID:3972905]. The biochemical activity of the leucine-rich repeat and coiled-coil domains has not been characterized in the available corpus.","teleology":[{"year":1985,"claim":"Established that the gene controls basal body number, positioning, and flagellar apparatus integrity, defining the core biological problem before any molecular identity was known.","evidence":"Genetic mapping and light/electron microscopy of Chlamydomonas vfl-1 mutants","pmids":["3972905"],"confidence":"Medium","gaps":["No molecular identity or protein product defined","Mechanism linking the gene to basal body positioning unknown"]},{"year":1989,"claim":"Distinguished VFL1 function from the centrin/nucleus-basal body connector pathway, showing it acts in a separate route to basal body number and positioning.","evidence":"Anti-centrin immunofluorescence comparing vfl-1 and vfl-2 mutants","pmids":["2696598"],"confidence":"Low","gaps":["Single comparative immunofluorescence result","Does not identify the alternative pathway VFL1 operates in"]},{"year":2001,"claim":"Identified the molecular product as a leucine-rich repeat/coiled-coil protein and localized it asymmetrically inside the distal basal body lumen, making it the first molecular marker of basal body rotational asymmetry.","evidence":"Tagged-allele cloning, complementation rescue, basal body co-purification, immunogold EM in Chlamydomonas","pmids":["11285274"],"confidence":"High","gaps":["No molecular partners identified","Biochemical activity of the domains undefined","Mechanism by which it imposes rotational asymmetry unknown"]},{"year":2008,"claim":"Extended the function to human cells, showing the centrosomal ortholog maintains centrosome structural integrity required for mitotic spindle bipolarity.","evidence":"Immunofluorescence and RNAi depletion with spindle and centriole counting readouts in human cells","pmids":["18728398"],"confidence":"Medium","gaps":["Single lab","Molecular basis of centrosome cohesion role not defined","No interaction partners identified"]},{"year":2013,"claim":"Linked vfl1 to basal body structural integrity through shared microtubule-drug sensitivity with other basal body assembly mutants.","evidence":"Taxol sensitivity and double-mutant analysis in Chlamydomonas","pmids":["23320108"],"confidence":"Low","gaps":["Pharmacological inference only, no direct structural mechanism","vfl1 one of several mutants tested"]},{"year":2019,"claim":"Showed the gene is required for centriole appendages that tether cytoskeletal connectors, aligning centrioles along polarity fields during tissue patterning.","evidence":"RNAi knockdown in planaria with centriole positioning and polarity readouts","pmids":["31743665"],"confidence":"Medium","gaps":["Molecular composition of the appendages unknown","Direct binding partners not identified"]},{"year":2022,"claim":"Resolved the precise structural position of human LRRCC1 to two consecutive distal-lumen triplet microtubules and placed it functionally with C2CD3 in an 'acorn' module driving distal centriole organization and primary ciliogenesis.","evidence":"U-ExM super-resolution imaging, co-localization, and siRNA depletion with ciliary assembly and signaling readouts in human cells","pmids":["35319462"],"confidence":"High","gaps":["Direct physical interaction with C2CD3 not demonstrated biochemically","Mechanism of triplet-microtubule selectivity unknown"]},{"year":2022,"claim":"Demonstrated a tissue-level role in multiciliated cells, where the protein localizes near striated rootlets and is required for basal body docking, polarization, and cilia-driven fluid flow.","evidence":"Morpholino knockdown, immunofluorescence, high-speed video and fluid flow assays in Xenopus ciliated epidermis","pmids":["35067717"],"confidence":"High","gaps":["Proximal rootlet-junction localization differs from distal-lumen localization in human centrioles; relationship not reconciled","Direct rootlet-connecting partners not identified"]},{"year":2025,"claim":"Defined a hierarchical targeting axis placing LRRCC1 downstream of C2CD3 and SSNA1 in the distal centriole, establishing its recruitment dependencies.","evidence":"KO-validated immunofluorescence, expansion microscopy, interactor screening, and epistasis analysis in human cells (preprint)","pmids":["bio_10.1101_2025.04.28.648957"],"confidence":"Medium","gaps":["Preprint, not yet peer-reviewed","Direct vs indirect interactions within the axis not distinguished","Stoichiometry and assembly order at molecular resolution unresolved"]},{"year":null,"claim":"The biochemical activity of LRRCC1's leucine-rich repeat and coiled-coil domains and the direct molecular interactions through which it organizes the distal centriole remain undefined.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No in vitro reconstitution of LRRCC1 binding to microtubules or partners","No structural model of the acorn assembly","Mechanism of rotationally asymmetric positioning unexplained"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0008092","term_label":"cytoskeletal protein binding","supporting_discovery_ids":[0,5]}],"localization":[{"term_id":"GO:0005815","term_label":"microtubule organizing center","supporting_discovery_ids":[3,5]},{"term_id":"GO:0005929","term_label":"cilium","supporting_discovery_ids":[5,6]},{"term_id":"GO:0005856","term_label":"cytoskeleton","supporting_discovery_ids":[5,6]}],"pathway":[{"term_id":"R-HSA-1852241","term_label":"Organelle biogenesis and maintenance","supporting_discovery_ids":[5,6]},{"term_id":"R-HSA-1640170","term_label":"Cell Cycle","supporting_discovery_ids":[3]}],"complexes":["distal centriole 'acorn' (C2CD3–SSNA1–LRRCC1 axis)"],"partners":["C2CD3","SSNA1"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q9C099","full_name":"Leucine-rich repeat and coiled-coil domain-containing protein 1","aliases":["Centrosomal leucine-rich repeat and coiled-coil domain-containing protein"],"length_aa":1032,"mass_kda":119.6,"function":"Required for the organization of the mitotic spindle. Maintains the structural integrity of centrosomes during mitosis","subcellular_location":"Cytoplasm, cytoskeleton, microtubule organizing center, centrosome, centriole","url":"https://www.uniprot.org/uniprotkb/Q9C099/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/LRRCC1","classification":"Not Classified","n_dependent_lines":2,"n_total_lines":1208,"dependency_fraction":0.0016556291390728477},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/LRRCC1","total_profiled":1310},"omim":[{"mim_id":"620676","title":"COILED-COIL DOMAIN-CONTAINING PROTEIN 61; CCDC61","url":"https://www.omim.org/entry/620676"},{"mim_id":"617791","title":"LEUCINE-RICH REPEAT- AND COILED-COIL DOMAIN-CONTAINING CENTROSOMAL PROTEIN 1; LRRCC1","url":"https://www.omim.org/entry/617791"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Centrosome","reliability":"Supported"},{"location":"Basal body","reliability":"Supported"},{"location":"Vesicles","reliability":"Additional"},{"location":"Primary cilium","reliability":"Additional"},{"location":"Primary cilium tip","reliability":"Additional"},{"location":"Cytosol","reliability":"Additional"}],"tissue_specificity":"Tissue enhanced","tissue_distribution":"Detected in many","driving_tissues":[{"tissue":"testis","ntpm":31.3}],"url":"https://www.proteinatlas.org/search/LRRCC1"},"hgnc":{"alias_symbol":["KIAA1764","CLERC","VFL1"],"prev_symbol":[]},"alphafold":{"accession":"Q9C099","domains":[{"cath_id":"3.80.10.10","chopping":"26-214","consensus_level":"medium","plddt":88.6515,"start":26,"end":214}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9C099","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q9C099-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q9C099-F1-predicted_aligned_error_v6.png","plddt_mean":73.94},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=LRRCC1","jax_strain_url":"https://www.jax.org/strain/search?query=LRRCC1"},"sequence":{"accession":"Q9C099","fasta_url":"https://rest.uniprot.org/uniprotkb/Q9C099.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q9C099/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9C099"}},"corpus_meta":[{"pmid":"8244002","id":"PMC_8244002","title":"Cloning of flagellar genes in Chlamydomonas reinhardtii by DNA insertional mutagenesis.","date":"1993","source":"Genetics","url":"https://pubmed.ncbi.nlm.nih.gov/8244002","citation_count":191,"is_preprint":false},{"pmid":"27894351","id":"PMC_27894351","title":"Characterizing the morbid genome of ciliopathies.","date":"2016","source":"Genome biology","url":"https://pubmed.ncbi.nlm.nih.gov/27894351","citation_count":141,"is_preprint":false},{"pmid":"27713108","id":"PMC_27713108","title":"Chronic Exposure to Low Doses of Dioxin Promotes Liver Fibrosis Development in the C57BL/6J Diet-Induced Obesity Mouse Model.","date":"2016","source":"Environmental health perspectives","url":"https://pubmed.ncbi.nlm.nih.gov/27713108","citation_count":97,"is_preprint":false},{"pmid":"11285274","id":"PMC_11285274","title":"The Vfl1 Protein in Chlamydomonas localizes in a rotationally asymmetric pattern at the distal ends of the basal bodies.","date":"2001","source":"The Journal of cell biology","url":"https://pubmed.ncbi.nlm.nih.gov/11285274","citation_count":79,"is_preprint":false},{"pmid":"9006937","id":"PMC_9006937","title":"Identification of two amino acids of the human cholecystokinin-A receptor that interact with the N-terminal moiety of cholecystokinin.","date":"1997","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/9006937","citation_count":67,"is_preprint":false},{"pmid":"2696598","id":"PMC_2696598","title":"Nucleus-basal body connector in Chlamydomonas: evidence for a role in basal body segregation and against essential roles in mitosis or in determining cell polarity.","date":"1989","source":"Cell motility and the cytoskeleton","url":"https://pubmed.ncbi.nlm.nih.gov/2696598","citation_count":59,"is_preprint":false},{"pmid":"1313017","id":"PMC_1313017","title":"Activated cGMP phosphodiesterase of retinal rods. A complex with transducin alpha subunit.","date":"1992","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/1313017","citation_count":58,"is_preprint":false},{"pmid":"8394130","id":"PMC_8394130","title":"G-protein-effector coupling: a real-time light-scattering assay for transducin-phosphodiesterase interaction.","date":"1993","source":"Biochemistry","url":"https://pubmed.ncbi.nlm.nih.gov/8394130","citation_count":57,"is_preprint":false},{"pmid":"35544698","id":"PMC_35544698","title":"The glycosaminoglycan interactome 2.0.","date":"2022","source":"American journal of physiology. 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Epitope-tagged Vfl1p copurified with basal body flagellar apparatuses, and immunogold labeling localized it inside the lumen of the basal body at the distal end in a rotationally asymmetric pattern, with most gold particles near the doublet microtubules facing the opposite basal body. This established Vfl1p as the first molecular marker of rotational asymmetry in basal bodies and implicated it in establishing correct rotational orientation.\",\n      \"method\": \"Tagged-allele cloning, complementation rescue, co-purification with basal body apparatus, immunofluorescence, immunogold electron microscopy\",\n      \"journal\": \"The Journal of cell biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal localization by immunofluorescence and immunogold EM, complementation rescue, co-purification; foundational study replicated conceptually by later work\",\n      \"pmids\": [\"11285274\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1985,\n      \"finding\": \"The vfl-1 mutation in Chlamydomonas (VFL1/LRRCC1 locus, Chromosome VIII) causes variable flagellar numbers (0–10 per cell), flagella at non-apical positions, uncoupling of flagellar assembly from the cell cycle, unequal cell divisions, and ultrastructural defects including missing/defective striated fibers and reduced rootlet microtubules, establishing the gene's role in controlling basal body number, positioning, and flagellar apparatus integrity.\",\n      \"method\": \"Genetic mapping, light microscopy, electron microscopy of mutant cells\",\n      \"journal\": \"The Journal of cell biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic loss-of-function with specific ultrastructural phenotype; single lab but multiple orthogonal readouts\",\n      \"pmids\": [\"3972905\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1989,\n      \"finding\": \"Examination of the vfl-1 mutant showed it contains approximately normal levels of centrin and possesses a stable nucleus-basal body connector (NBBC), in contrast to vfl-2 which lacks centrin in the NBBC. This negative result establishes that VFL1 function is distinct from centrin/NBBC integrity, placing Vfl1p in a separate pathway controlling basal body number and positioning.\",\n      \"method\": \"Immunofluorescence with anti-centrin antiserum in mutant strains\",\n      \"journal\": \"Cell motility and the cytoskeleton\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single immunofluorescence result as part of multi-mutant characterization; negative/comparative finding\",\n      \"pmids\": [\"2696598\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"Human CLERC (LRRCC1), the ortholog of Chlamydomonas Vfl1, is a 1032 aa / 120 kDa centrosomal protein with leucine-rich repeat and coiled-coil domains. Endogenous CLERC associates with centrosomes throughout the cell cycle and accumulates during mitosis. RNAi-mediated depletion caused multipolar spindles and centrosome splitting into fractions containing single centrioles, demonstrating that CLERC maintains centrosome structural integrity to support spindle bipolarity during mitosis.\",\n      \"method\": \"Immunofluorescence localization, RNAi knockdown with spindle morphology and centriole counting readouts\",\n      \"journal\": \"Cell cycle (Georgetown, Tex.)\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — clean RNAi knockdown with specific mitotic phenotype (multipolar spindles, centriole splitting) plus localization; single lab\",\n      \"pmids\": [\"18728398\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"In planarian flatworms, SMED-VFL1 (ortholog of LRRCC1) is required for assembly of centriole appendages that tether cytoskeletal connectors to position centrioles. Loss of SMED-VFL1 disrupts the asymmetric connections between centrioles and impairs alignment of centrioles along polarity fields, contributing to the bilaterally symmetric pattern of the ventral epidermis.\",\n      \"method\": \"RNAi knockdown in planaria with centriole positioning and polarity readouts\",\n      \"journal\": \"Developmental cell\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic knockdown with specific centriole appendage and polarity phenotype; single study\",\n      \"pmids\": [\"31743665\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"Using ultrastructure expansion microscopy (U-ExM), human LRRCC1 was shown to localize preferentially to two consecutive triplet microtubules in the distal lumen of human centrioles, revealing rotationally asymmetric positioning. LRRCC1 partially co-localizes with the distal centriole component C2CD3 and affects its recruitment. Depletion of LRRCC1 caused defects in centriole structure, ciliary assembly, and ciliary signaling, establishing LRRCC1 as part of a conserved 'acorn' structure at the distal centriole that cooperates with C2CD3 to organize the distal region and promote primary ciliogenesis.\",\n      \"method\": \"Ultrastructure expansion microscopy (U-ExM), super-resolution imaging, siRNA depletion with ciliary assembly and signaling readouts, co-localization analysis\",\n      \"journal\": \"eLife\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — multiple orthogonal methods (U-ExM structural localization, functional depletion, co-localization with partner protein); mechanistic placement in distal centriole module\",\n      \"pmids\": [\"35319462\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"In Xenopus multiciliated cells, Lrrcc1 encodes a basal body component that localizes proximally at the junction with striated rootlets. Morpholino-mediated knockdown of lrrcc1 caused defects in basal body docking, spacing, and polarization, impaired the apical cytoskeleton, and altered ciliary beating, resulting in greatly reduced cilia-powered fluid flow.\",\n      \"method\": \"Morpholino knockdown in Xenopus embryonic ciliated epidermis, immunofluorescence localization, high-speed video microscopy of ciliary beating, fluid flow assays\",\n      \"journal\": \"Journal of cell science\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — genetic knockdown with multiple specific phenotypic readouts (BB docking, spacing, polarization, apical cytoskeleton, beat, fluid flow) in vertebrate model; replicates functional findings from other organisms\",\n      \"pmids\": [\"35067717\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"The vfl1 mutation in Chlamydomonas confers supersensitivity to Taxol, grouping it with other basal body assembly mutants (bld2, bld10, bld12, uni3, vfl2, vfl3), indicating that VFL1 contributes to basal body structural integrity in a manner relevant to microtubule-stabilizing drug sensitivity.\",\n      \"method\": \"Taxol sensitivity assay in mutant strains, double-mutant genetic analysis\",\n      \"journal\": \"PloS one\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — pharmacological sensitivity assay provides indirect structural inference; vfl1 is one of several mutants tested, no direct mechanism established\",\n      \"pmids\": [\"23320108\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"Interactor screening and knockout analysis identified a C2CD3–SSNA1–LRRCC1 hierarchical targeting axis in the distal lumen of human centrioles. LRRCC1 functions downstream of C2CD3 and SSNA1 within this network, placing it in a defined molecular pathway for distal centriole organization and ciliogenesis.\",\n      \"method\": \"KO-validated antibody immunofluorescence, expansion microscopy, interactor screening, epistasis analysis of targeting hierarchy in human cells\",\n      \"journal\": \"bioRxiv\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — epistasis/targeting hierarchy established by KO analysis and interactor screening; preprint, not yet peer-reviewed\",\n      \"pmids\": [\"bio_10.1101_2025.04.28.648957\"],\n      \"is_preprint\": true\n    }\n  ],\n  \"current_model\": \"LRRCC1 (CLERC/VFL1) encodes a conserved leucine-rich repeat and coiled-coil domain protein that localizes asymmetrically to two consecutive triplet microtubules in the distal lumen of centrioles/basal bodies, where it cooperates with C2CD3 and SSNA1 in a hierarchical targeting network to organize centriole distal structure, maintain centrosome integrity during mitosis, and enable basal body docking/polarization and ciliary assembly and signaling in multiciliated cells.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"LRRCC1 (CLERC/VFL1) is a conserved leucine-rich repeat and coiled-coil protein that organizes the distal region of centrioles and basal bodies to control their number, orientation, and competence for ciliogenesis [#0, #5]. It localizes asymmetrically to two consecutive triplet microtubules in the distal lumen of human centrioles, forming part of a rotationally asymmetric 'acorn' structure, a positioning anticipated by the original Chlamydomonas work showing Vfl1p inside the basal body lumen at the distal end in a rotationally asymmetric pattern [#0, #5]. Within this distal module LRRCC1 acts downstream of C2CD3 and SSNA1 in a hierarchical targeting axis and contributes to recruiting C2CD3, linking it to a defined molecular pathway for distal centriole organization [#5]. Functionally, LRRCC1 maintains centrosome structural integrity through mitosis—its depletion causes centrosome splitting and multipolar spindles [#3]—and supports ciliary assembly and signaling, with loss producing defects in centriole structure and primary ciliogenesis [#5]. In multiciliated cells it localizes proximally at the junction with striated rootlets and is required for basal body docking, spacing, and polarization and for normal ciliary beating and fluid flow [#6]. The conserved requirement for the gene in establishing basal body number, positioning, and flagellar apparatus integrity was first defined genetically in Chlamydomonas vfl-1 mutants [#1]. The biochemical activity of the leucine-rich repeat and coiled-coil domains has not been characterized in the available corpus.\",\n  \"teleology\": [\n    {\n      \"year\": 1985,\n      \"claim\": \"Established that the gene controls basal body number, positioning, and flagellar apparatus integrity, defining the core biological problem before any molecular identity was known.\",\n      \"evidence\": \"Genetic mapping and light/electron microscopy of Chlamydomonas vfl-1 mutants\",\n      \"pmids\": [\"3972905\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No molecular identity or protein product defined\", \"Mechanism linking the gene to basal body positioning unknown\"]\n    },\n    {\n      \"year\": 1989,\n      \"claim\": \"Distinguished VFL1 function from the centrin/nucleus-basal body connector pathway, showing it acts in a separate route to basal body number and positioning.\",\n      \"evidence\": \"Anti-centrin immunofluorescence comparing vfl-1 and vfl-2 mutants\",\n      \"pmids\": [\"2696598\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"Single comparative immunofluorescence result\", \"Does not identify the alternative pathway VFL1 operates in\"]\n    },\n    {\n      \"year\": 2001,\n      \"claim\": \"Identified the molecular product as a leucine-rich repeat/coiled-coil protein and localized it asymmetrically inside the distal basal body lumen, making it the first molecular marker of basal body rotational asymmetry.\",\n      \"evidence\": \"Tagged-allele cloning, complementation rescue, basal body co-purification, immunogold EM in Chlamydomonas\",\n      \"pmids\": [\"11285274\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"No molecular partners identified\", \"Biochemical activity of the domains undefined\", \"Mechanism by which it imposes rotational asymmetry unknown\"]\n    },\n    {\n      \"year\": 2008,\n      \"claim\": \"Extended the function to human cells, showing the centrosomal ortholog maintains centrosome structural integrity required for mitotic spindle bipolarity.\",\n      \"evidence\": \"Immunofluorescence and RNAi depletion with spindle and centriole counting readouts in human cells\",\n      \"pmids\": [\"18728398\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single lab\", \"Molecular basis of centrosome cohesion role not defined\", \"No interaction partners identified\"]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"Linked vfl1 to basal body structural integrity through shared microtubule-drug sensitivity with other basal body assembly mutants.\",\n      \"evidence\": \"Taxol sensitivity and double-mutant analysis in Chlamydomonas\",\n      \"pmids\": [\"23320108\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"Pharmacological inference only, no direct structural mechanism\", \"vfl1 one of several mutants tested\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Showed the gene is required for centriole appendages that tether cytoskeletal connectors, aligning centrioles along polarity fields during tissue patterning.\",\n      \"evidence\": \"RNAi knockdown in planaria with centriole positioning and polarity readouts\",\n      \"pmids\": [\"31743665\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Molecular composition of the appendages unknown\", \"Direct binding partners not identified\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Resolved the precise structural position of human LRRCC1 to two consecutive distal-lumen triplet microtubules and placed it functionally with C2CD3 in an 'acorn' module driving distal centriole organization and primary ciliogenesis.\",\n      \"evidence\": \"U-ExM super-resolution imaging, co-localization, and siRNA depletion with ciliary assembly and signaling readouts in human cells\",\n      \"pmids\": [\"35319462\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Direct physical interaction with C2CD3 not demonstrated biochemically\", \"Mechanism of triplet-microtubule selectivity unknown\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Demonstrated a tissue-level role in multiciliated cells, where the protein localizes near striated rootlets and is required for basal body docking, polarization, and cilia-driven fluid flow.\",\n      \"evidence\": \"Morpholino knockdown, immunofluorescence, high-speed video and fluid flow assays in Xenopus ciliated epidermis\",\n      \"pmids\": [\"35067717\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Proximal rootlet-junction localization differs from distal-lumen localization in human centrioles; relationship not reconciled\", \"Direct rootlet-connecting partners not identified\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Defined a hierarchical targeting axis placing LRRCC1 downstream of C2CD3 and SSNA1 in the distal centriole, establishing its recruitment dependencies.\",\n      \"evidence\": \"KO-validated immunofluorescence, expansion microscopy, interactor screening, and epistasis analysis in human cells (preprint)\",\n      \"pmids\": [\"bio_10.1101_2025.04.28.648957\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Preprint, not yet peer-reviewed\", \"Direct vs indirect interactions within the axis not distinguished\", \"Stoichiometry and assembly order at molecular resolution unresolved\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"The biochemical activity of LRRCC1's leucine-rich repeat and coiled-coil domains and the direct molecular interactions through which it organizes the distal centriole remain undefined.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No in vitro reconstitution of LRRCC1 binding to microtubules or partners\", \"No structural model of the acorn assembly\", \"Mechanism of rotationally asymmetric positioning unexplained\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0008092\", \"supporting_discovery_ids\": [0, 5]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005815\", \"supporting_discovery_ids\": [3, 5]},\n      {\"term_id\": \"GO:0005929\", \"supporting_discovery_ids\": [5, 6]},\n      {\"term_id\": \"GO:0005856\", \"supporting_discovery_ids\": [5, 6]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-1852241\", \"supporting_discovery_ids\": [5, 6]},\n      {\"term_id\": \"R-HSA-1640170\", \"supporting_discovery_ids\": [3]}\n    ],\n    \"complexes\": [\"distal centriole 'acorn' (C2CD3–SSNA1–LRRCC1 axis)\"],\n    \"partners\": [\"C2CD3\", \"SSNA1\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":6,"faith_total":6,"faith_pct":100.0}}