{"gene":"CCDC146","run_date":"2026-04-28T17:28:52","timeline":{"discoveries":[{"year":2018,"finding":"CCDC146 is a human centrosomal protein that localizes to the centrosome in uninfected cells; upon C. trachomatis infection, it is recruited to the periphery of the chlamydial inclusion via interaction with inclusion membrane protein CT288, as demonstrated by yeast two-hybrid and co-immunoprecipitation in mammalian cells.","method":"Yeast two-hybrid, co-immunoprecipitation, fluorescence microscopy/localization in infected vs. uninfected cells","journal":"Frontiers in cellular and infection microbiology","confidence":"Medium","confidence_rationale":"Tier 2-3 — reciprocal co-IP plus localization data, single lab","pmids":["30094225"],"is_preprint":false},{"year":2014,"finding":"CCDC146 was identified as a centrosome-associated protein in mammalian cultured cells through mass spectrometry of sperm centrioles followed by localization assessment.","method":"Mass spectrometry of sperm centrioles, immunofluorescence localization in cultured cells","journal":"Journal of cell science","confidence":"Medium","confidence_rationale":"Tier 2-3 — proteomic identification plus direct localization, single lab","pmids":["25074808"],"is_preprint":false},{"year":2023,"finding":"CCDC146 physically interacts with CCDC38, CCDC42, IFT88, and IFT20; knockout of Ccdc146 in male mice causes complete infertility with MMAF-like flagellar and manchette defects, and reduces protein levels of ODF2, IFT88, and IFT20, placing CCDC146 in the intraflagellar transport pathway required for sperm flagellum biogenesis.","method":"Co-immunoprecipitation, knockout mouse model, western blot, immunofluorescence, transmission electron microscopy, atomic-level interaction modeling","journal":"Cellular and molecular life sciences : CMLS","confidence":"High","confidence_rationale":"Tier 1-2 — KO mouse with defined cellular phenotype, multiple binding partners confirmed by co-IP, replicated finding","pmids":["38038747"],"is_preprint":false},{"year":2024,"finding":"In somatic cells CCDC146 localizes to the centrosome and multiple microtubule-related organelles during mitosis; in spermatozoa it localizes to axonemal microtubule doublets (not centrioles) and may function as a microtubule inner protein (MIP). Ccdc146 KO mice are infertile with defects in manchette, head-tail coupling apparatus, and axoneme, establishing CCDC146 as a microtubule-associated protein required for sperm axoneme structure.","method":"Ccdc146 knockout mouse, expansion microscopy, sarkosyl solubilization of microtubule doublets, immunofluorescence, cryo-electron microscopy/tomography","journal":"eLife","confidence":"High","confidence_rationale":"Tier 1-2 — KO mouse with defined phenotype, expansion microscopy and biochemical fractionation providing strong localization-function link","pmids":["38441556"],"is_preprint":false},{"year":2024,"finding":"CCDC146 (MBO2 in Chlamydomonas) and FAP58/CCDC147 form a conserved L-shaped heterodimeric structure within the axoneme that interconnects inner dynein arms (specifically inner arm dynein b) with multiple regulatory complexes including radial spokes and the dynein regulatory complex; loss of MBO2/CCDC146 alters ciliary waveform and reduces inner dynein arm b assembly.","method":"Comparative proteomics, cryo-electron tomography, epitope tagging, Chlamydomonas mbo mutant analysis","journal":"Molecular biology of the cell","confidence":"High","confidence_rationale":"Tier 1-2 — cryo-ET structural data plus proteomic epistasis, ortholog confirmed by domain/function conservation","pmids":["38568782"],"is_preprint":false},{"year":2024,"finding":"A homozygous nonsense mutation in CCDC146 (p.Arg306*, retaining only 2 of 5 coiled-coil domains) causes oligoasthenoteratozoospermia in humans; the corresponding Ccdc146 knock-in mouse recapitulates infertility with reduced sperm count, motility, and axonemal protein levels (DNAH17, DNAH1, SPAG6). CCDC146 interacts with IFT20 and this interaction is lost in the truncated mutant, leading to IFT20 degradation.","method":"Human genetic mutation identification, knock-in mouse model, co-immunoprecipitation, western blot, immunofluorescence","journal":"Zoological research","confidence":"High","confidence_rationale":"Tier 2 — human mutation + cognate mouse model + co-IP interaction loss, multiple orthogonal methods","pmids":["39245651"],"is_preprint":false},{"year":2002,"finding":"The Chlamydomonas MBO2 gene (ortholog of human CCDC146) encodes a ~110 kDa axonemal protein with extensive coiled-coil domains and leucine zippers; it is tightly associated with doublet microtubules along the entire flagellum and is required for ciliary waveform conversion (asymmetric ciliary to symmetric flagellar waveform); insertion of an HA epitope in the conserved C-terminal domain reduces swimming velocity.","method":"Gene cloning, antibody localization, immunoprecipitation/axoneme fractionation, epitope-tagged rescue experiment, mutant phenotype analysis","journal":"Cell motility and the cytoskeleton","confidence":"High","confidence_rationale":"Tier 1-2 — original functional cloning with protein localization, dominant-negative epitope tagging, replicated by multiple later studies","pmids":["11977094"],"is_preprint":false},{"year":2025,"finding":"CCDC146 is located at the basal body of primary cilia in human motor neurons; overexpression of CCDC146 impairs cilia structure and function, while antisense oligonucleotide (ASO)-mediated depletion restores cilia and rescues ALS-specific neuronal survival defects and TDP-43 pathology in patient-derived neurons and an ALS mouse model, identifying CCDC146 as a modifier of ALS acting via primary cilia.","method":"iPSC-derived motor neuron culture, CCDC146 overexpression and ASO knockdown, cilia morphology/function assays, TDP-43 localization, ALS mouse model survival analysis","journal":"medRxiv","confidence":"Medium","confidence_rationale":"Tier 2 — multiple functional assays in human neurons and mouse model, single lab, preprint","pmids":["38633814"],"is_preprint":true},{"year":2025,"finding":"Ccdc146 knockout mice show the most severe sperm nuclear defects and lowest developmental potential upon ICSI among four MMAF gene KO lines tested, with zygotes from Ccdc146-/- sperm showing the highest rates of developmental failure, correlating with severity of nuclear (DNA compaction, chromosomal architecture, ploidy) defects.","method":"Knockout mouse model comparison (Ccdc146, Cfap43, Cfap44, Armc2), ICSI embryo development assay, nuclear morphology and DNA compaction analysis","journal":"Molecular human reproduction","confidence":"Medium","confidence_rationale":"Tier 2 — KO mouse with defined embryo development phenotype, comparative multi-gene study, single lab","pmids":["40070084"],"is_preprint":false}],"current_model":"CCDC146 is a conserved coiled-coil/microtubule-associated protein that localizes to the centrosome in somatic cells and to axonemal microtubule doublets in spermatozoa, where it forms a heterodimeric L-shaped complex with FAP58/CCDC147 that stabilizes inner dynein arm b assembly and connects it to axonemal regulatory complexes; it also interacts with IFT20 and other IFT components to support intraflagellar transport during sperm flagellum biogenesis, and its loss causes MMAF-type male infertility in both humans and mice."},"narrative":{"teleology":[{"year":2002,"claim":"The foundational question of what MBO2/CCDC146 encodes and where it acts was answered: cloning of Chlamydomonas MBO2 revealed a coiled-coil axonemal protein tightly bound to doublet microtubules along the entire flagellum, required for waveform conversion from asymmetric ciliary to symmetric flagellar beating.","evidence":"Gene cloning, antibody-based axoneme fractionation, and mbo2 mutant phenotypic analysis in Chlamydomonas","pmids":["11977094"],"confidence":"High","gaps":["Binding partners within the axoneme were unknown","No mammalian functional data existed","Mechanism by which MBO2 controls waveform was unresolved"]},{"year":2014,"claim":"The question of whether CCDC146 has a centrosomal role in mammalian cells was addressed: proteomic identification from sperm centrioles and immunofluorescence confirmed centrosomal localization in cultured mammalian cells.","evidence":"Mass spectrometry of isolated sperm centrioles followed by immunofluorescence in cultured cells","pmids":["25074808"],"confidence":"Medium","gaps":["No loss-of-function data in mammalian systems","Centrosomal function beyond localization was undefined","Relationship to axonemal role characterized in Chlamydomonas was unclear"]},{"year":2018,"claim":"The question of whether CCDC146 participates in pathogen–host interactions was partially answered: CCDC146 is recruited from the centrosome to the Chlamydia trachomatis inclusion membrane via interaction with CT288, revealing that a pathogen can co-opt this centrosomal protein.","evidence":"Yeast two-hybrid screen and co-immunoprecipitation in mammalian cells with fluorescence microscopy of infected versus uninfected cells","pmids":["30094225"],"confidence":"Medium","gaps":["Functional consequence of CCDC146 recruitment for infection outcome was not established","Whether other centrosomal proteins are similarly recruited was not tested","No in vivo infection model was used"]},{"year":2023,"claim":"The central question of mammalian in vivo function was resolved: Ccdc146 knockout mice are completely infertile with MMAF-like defects, and CCDC146 physically interacts with IFT20, IFT88, CCDC38, and CCDC42, placing it in the intraflagellar transport pathway essential for sperm flagellum biogenesis.","evidence":"Ccdc146 knockout mouse model, co-immunoprecipitation of multiple partners, western blot showing reduced IFT/ODF2 protein levels, TEM of flagellar ultrastructure","pmids":["38038747"],"confidence":"High","gaps":["Structural basis of CCDC146–IFT interactions was not determined","Whether CCDC146 functions in non-sperm motile cilia in mammals was untested","Relationship to inner dynein arm regulation known from Chlamydomonas was not examined"]},{"year":2024,"claim":"The structural mechanism was elucidated: cryo-electron tomography revealed that CCDC146/MBO2 and FAP58/CCDC147 form a conserved L-shaped heterodimer within the axonemal repeat that physically bridges inner dynein arm b to radial spokes and the dynein regulatory complex, explaining how CCDC146 loss alters waveform and reduces inner arm b assembly.","evidence":"Cryo-electron tomography, comparative proteomics, and Chlamydomonas mbo2 mutant analysis with epitope tagging","pmids":["38568782"],"confidence":"High","gaps":["Atomic-resolution structure of the CCDC146–CCDC147 heterodimer was not obtained","Whether inner arm b assembly defect is direct or indirect was not fully resolved","Conservation of the L-shaped complex structure in mammalian sperm was inferred but not directly visualized"]},{"year":2024,"claim":"The question of precise sub-axonemal localization in mammals was answered: expansion microscopy and sarkosyl fractionation showed CCDC146 associates with axonemal microtubule doublets (not centrioles) in spermatozoa and localizes to centrosomes and mitotic microtubule structures in somatic cells, functioning as a microtubule inner protein.","evidence":"Ccdc146 knockout mouse, expansion microscopy, sarkosyl solubilization of microtubule doublets, cryo-electron microscopy","pmids":["38441556"],"confidence":"High","gaps":["Identity of the specific MIP site within the doublet lattice in mammals was not resolved at atomic level","Whether CCDC146 has a functional role at somatic centrosomes beyond localization remained open"]},{"year":2024,"claim":"A direct human disease link was established: a homozygous nonsense mutation in CCDC146 (p.Arg306*) causes oligoasthenoteratozoospermia in a human patient, and a cognate knock-in mouse recapitulates infertility with loss of the CCDC146–IFT20 interaction leading to IFT20 degradation and reduced axonemal dynein levels.","evidence":"Human genetic mutation identification, knock-in mouse model, co-immunoprecipitation showing loss of IFT20 interaction with truncated protein","pmids":["39245651"],"confidence":"High","gaps":["Prevalence of CCDC146 mutations in MMAF patient cohorts was not broadly surveyed","Whether the truncated protein exerts dominant-negative effects was not assessed","Mechanism linking IFT20 degradation to reduced axonemal dynein assembly was not fully dissected"]},{"year":2025,"claim":"The functional severity of CCDC146 loss was contextualized: among four MMAF gene knockouts, Ccdc146−/− sperm exhibit the most severe nuclear compaction and chromosomal defects, with the lowest developmental potential after ICSI, indicating CCDC146 loss affects not only flagellar but also nuclear integrity.","evidence":"Comparative analysis of four KO mouse lines with ICSI embryo development assay and nuclear morphology analysis","pmids":["40070084"],"confidence":"Medium","gaps":["Mechanism by which CCDC146 loss causes nuclear defects is unknown","Whether the nuclear phenotype is secondary to manchette dysfunction or reflects a direct nuclear role was not determined"]},{"year":null,"claim":"Key unresolved questions include whether CCDC146 has functional roles at somatic centrosomes or primary cilia beyond sperm, the atomic-resolution structure of the CCDC146–CCDC147 heterodimer in mammalian axonemes, and the mechanism by which CCDC146 loss leads to sperm nuclear defects.","evidence":"","pmids":[],"confidence":"Low","gaps":["No functional data for CCDC146 at somatic centrosomes or primary cilia in peer-reviewed literature","No high-resolution mammalian structure of the CCDC146–CCDC147 complex","Link between axonemal/IFT defects and nuclear compaction phenotype is unexplained"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0008092","term_label":"cytoskeletal protein binding","supporting_discovery_ids":[3,4,6]},{"term_id":"GO:0005198","term_label":"structural molecule activity","supporting_discovery_ids":[4,6]}],"localization":[{"term_id":"GO:0005815","term_label":"microtubule organizing center","supporting_discovery_ids":[0,1,3]},{"term_id":"GO:0005856","term_label":"cytoskeleton","supporting_discovery_ids":[3,4,6]},{"term_id":"GO:0005929","term_label":"cilium","supporting_discovery_ids":[3,4,6]}],"pathway":[{"term_id":"R-HSA-1474165","term_label":"Reproduction","supporting_discovery_ids":[2,3,5,8]},{"term_id":"R-HSA-1852241","term_label":"Organelle biogenesis and maintenance","supporting_discovery_ids":[2,3,4]}],"complexes":["CCDC146–CCDC147 (FAP58) heterodimer"],"partners":["CCDC147","IFT20","IFT88","CCDC38","CCDC42","ODF2"],"other_free_text":[]},"mechanistic_narrative":"CCDC146 is a conserved coiled-coil domain protein that functions as a microtubule-associated structural and regulatory component of motile cilia/flagella and centrosomes. In axonemes, CCDC146 (ortholog of Chlamydomonas MBO2) associates tightly with doublet microtubules and forms a heterodimeric L-shaped complex with FAP58/CCDC147 that stabilizes inner dynein arm b assembly and connects it to radial spokes and the dynein regulatory complex, thereby controlling ciliary waveform [PMID:11977094, PMID:38568782, PMID:38441556]. CCDC146 also interacts with intraflagellar transport components IFT20 and IFT88, and its loss destabilizes these proteins, disrupting sperm flagellum biogenesis, manchette formation, and head–tail coupling, causing multiple morphological abnormalities of the sperm flagella (MMAF)-type male infertility in both knockout mice and a human patient carrying a homozygous CCDC146 nonsense mutation [PMID:38038747, PMID:39245651]. In somatic cells, CCDC146 localizes to the centrosome and mitotic microtubule-organizing structures, and its dysregulation at primary cilia in motor neurons has been linked to neurodegeneration-associated ciliary defects [PMID:25074808, PMID:38441556]."},"prefetch_data":{"uniprot":{"accession":"Q8IYE0","full_name":"Coiled-coil domain-containing protein 146","aliases":[],"length_aa":955,"mass_kda":112.8,"function":"Essential for sperm flagellum biogenesis and male fertility","subcellular_location":"","url":"https://www.uniprot.org/uniprotkb/Q8IYE0/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/CCDC146","classification":"Not Classified","n_dependent_lines":1,"n_total_lines":1208,"dependency_fraction":0.0008278145695364238},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/CCDC146","total_profiled":1310},"omim":[{"mim_id":"620850","title":"SPERMATOGENIC FAILURE 94; SPGF94","url":"https://www.omim.org/entry/620850"},{"mim_id":"619829","title":"COILED-COIL DOMAIN-CONTAINING PROTEIN 146; CCDC146","url":"https://www.omim.org/entry/619829"},{"mim_id":"258150","title":"SPERMATOGENIC FAILURE 1; SPGF1","url":"https://www.omim.org/entry/258150"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"","locations":[],"tissue_specificity":"Tissue enhanced","tissue_distribution":"Detected in all","driving_tissues":[{"tissue":"fallopian tube","ntpm":32.0},{"tissue":"testis","ntpm":20.1}],"url":"https://www.proteinatlas.org/search/CCDC146"},"hgnc":{"alias_symbol":["KIAA1505","MBO2"],"prev_symbol":[]},"alphafold":{"accession":"Q8IYE0","domains":[{"cath_id":"-","chopping":"431-657","consensus_level":"medium","plddt":90.1623,"start":431,"end":657},{"cath_id":"1.20.5","chopping":"680-730","consensus_level":"medium","plddt":83.7239,"start":680,"end":730},{"cath_id":"1.20.5","chopping":"754-783","consensus_level":"medium","plddt":85.243,"start":754,"end":783}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q8IYE0","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q8IYE0-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q8IYE0-F1-predicted_aligned_error_v6.png","plddt_mean":78.56},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=CCDC146","jax_strain_url":"https://www.jax.org/strain/search?query=CCDC146"},"sequence":{"accession":"Q8IYE0","fasta_url":"https://rest.uniprot.org/uniprotkb/Q8IYE0.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q8IYE0/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q8IYE0"}},"corpus_meta":[{"pmid":"8679521","id":"PMC_8679521","title":"Mechanism of NO-induced oxidation of myoglobin and hemoglobin.","date":"1996","source":"Biochemistry","url":"https://pubmed.ncbi.nlm.nih.gov/8679521","citation_count":503,"is_preprint":false},{"pmid":"2018767","id":"PMC_2018767","title":"Ligand binding to heme proteins: connection between dynamics and function.","date":"1991","source":"Biochemistry","url":"https://pubmed.ncbi.nlm.nih.gov/2018767","citation_count":271,"is_preprint":false},{"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":"1629229","id":"PMC_1629229","title":"A novel site-directed mutant of myoglobin with an unusually high O2 affinity and low autooxidation rate.","date":"1992","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/1629229","citation_count":175,"is_preprint":false},{"pmid":"16439024","id":"PMC_16439024","title":"Hemoglobins dioxygenate nitric oxide with high fidelity.","date":"2006","source":"Journal of inorganic biochemistry","url":"https://pubmed.ncbi.nlm.nih.gov/16439024","citation_count":102,"is_preprint":false},{"pmid":"31242261","id":"PMC_31242261","title":"Genetic dissection of a Leishmania flagellar proteome demonstrates requirement for directional motility in sand fly infections.","date":"2019","source":"PLoS pathogens","url":"https://pubmed.ncbi.nlm.nih.gov/31242261","citation_count":96,"is_preprint":false},{"pmid":"12128195","id":"PMC_12128195","title":"Myoglobin as a model system for designing heme protein based blood substitutes.","date":"2002","source":"Biophysical chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/12128195","citation_count":93,"is_preprint":false},{"pmid":"25074808","id":"PMC_25074808","title":"Proteomic analysis of mammalian sperm cells identifies new components of the centrosome.","date":"2014","source":"Journal of cell science","url":"https://pubmed.ncbi.nlm.nih.gov/25074808","citation_count":93,"is_preprint":false},{"pmid":"9315857","id":"PMC_9315857","title":"Identification of conformational substates involved in nitric oxide binding to ferric and ferrous myoglobin through difference Fourier transform infrared spectroscopy (FTIR).","date":"1997","source":"Biochemistry","url":"https://pubmed.ncbi.nlm.nih.gov/9315857","citation_count":87,"is_preprint":false},{"pmid":"7947750","id":"PMC_7947750","title":"Ligand binding to heme proteins: the effect of light on ligand binding in myoglobin.","date":"1994","source":"Biochemistry","url":"https://pubmed.ncbi.nlm.nih.gov/7947750","citation_count":86,"is_preprint":false},{"pmid":"9890961","id":"PMC_9890961","title":"Reactions of sperm whale myoglobin with hydrogen peroxide. 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Ccdc146 KO mice are infertile with defects in manchette, head-tail coupling apparatus, and axoneme, establishing CCDC146 as a microtubule-associated protein required for sperm axoneme structure.\",\n      \"method\": \"Ccdc146 knockout mouse, expansion microscopy, sarkosyl solubilization of microtubule doublets, immunofluorescence, cryo-electron microscopy/tomography\",\n      \"journal\": \"eLife\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 — KO mouse with defined phenotype, expansion microscopy and biochemical fractionation providing strong localization-function link\",\n      \"pmids\": [\"38441556\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"CCDC146 (MBO2 in Chlamydomonas) and FAP58/CCDC147 form a conserved L-shaped heterodimeric structure within the axoneme that interconnects inner dynein arms (specifically inner arm dynein b) with multiple regulatory complexes including radial spokes and the dynein regulatory complex; loss of MBO2/CCDC146 alters ciliary waveform and reduces inner dynein arm b assembly.\",\n      \"method\": \"Comparative proteomics, cryo-electron tomography, epitope tagging, Chlamydomonas mbo mutant analysis\",\n      \"journal\": \"Molecular biology of the cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 — cryo-ET structural data plus proteomic epistasis, ortholog confirmed by domain/function conservation\",\n      \"pmids\": [\"38568782\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"A homozygous nonsense mutation in CCDC146 (p.Arg306*, retaining only 2 of 5 coiled-coil domains) causes oligoasthenoteratozoospermia in humans; the corresponding Ccdc146 knock-in mouse recapitulates infertility with reduced sperm count, motility, and axonemal protein levels (DNAH17, DNAH1, SPAG6). CCDC146 interacts with IFT20 and this interaction is lost in the truncated mutant, leading to IFT20 degradation.\",\n      \"method\": \"Human genetic mutation identification, knock-in mouse model, co-immunoprecipitation, western blot, immunofluorescence\",\n      \"journal\": \"Zoological research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — human mutation + cognate mouse model + co-IP interaction loss, multiple orthogonal methods\",\n      \"pmids\": [\"39245651\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2002,\n      \"finding\": \"The Chlamydomonas MBO2 gene (ortholog of human CCDC146) encodes a ~110 kDa axonemal protein with extensive coiled-coil domains and leucine zippers; it is tightly associated with doublet microtubules along the entire flagellum and is required for ciliary waveform conversion (asymmetric ciliary to symmetric flagellar waveform); insertion of an HA epitope in the conserved C-terminal domain reduces swimming velocity.\",\n      \"method\": \"Gene cloning, antibody localization, immunoprecipitation/axoneme fractionation, epitope-tagged rescue experiment, mutant phenotype analysis\",\n      \"journal\": \"Cell motility and the cytoskeleton\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 — original functional cloning with protein localization, dominant-negative epitope tagging, replicated by multiple later studies\",\n      \"pmids\": [\"11977094\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"CCDC146 is located at the basal body of primary cilia in human motor neurons; overexpression of CCDC146 impairs cilia structure and function, while antisense oligonucleotide (ASO)-mediated depletion restores cilia and rescues ALS-specific neuronal survival defects and TDP-43 pathology in patient-derived neurons and an ALS mouse model, identifying CCDC146 as a modifier of ALS acting via primary cilia.\",\n      \"method\": \"iPSC-derived motor neuron culture, CCDC146 overexpression and ASO knockdown, cilia morphology/function assays, TDP-43 localization, ALS mouse model survival analysis\",\n      \"journal\": \"medRxiv\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — multiple functional assays in human neurons and mouse model, single lab, preprint\",\n      \"pmids\": [\"38633814\"],\n      \"is_preprint\": true\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"Ccdc146 knockout mice show the most severe sperm nuclear defects and lowest developmental potential upon ICSI among four MMAF gene KO lines tested, with zygotes from Ccdc146-/- sperm showing the highest rates of developmental failure, correlating with severity of nuclear (DNA compaction, chromosomal architecture, ploidy) defects.\",\n      \"method\": \"Knockout mouse model comparison (Ccdc146, Cfap43, Cfap44, Armc2), ICSI embryo development assay, nuclear morphology and DNA compaction analysis\",\n      \"journal\": \"Molecular human reproduction\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — KO mouse with defined embryo development phenotype, comparative multi-gene study, single lab\",\n      \"pmids\": [\"40070084\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"CCDC146 is a conserved coiled-coil/microtubule-associated protein that localizes to the centrosome in somatic cells and to axonemal microtubule doublets in spermatozoa, where it forms a heterodimeric L-shaped complex with FAP58/CCDC147 that stabilizes inner dynein arm b assembly and connects it to axonemal regulatory complexes; it also interacts with IFT20 and other IFT components to support intraflagellar transport during sperm flagellum biogenesis, and its loss causes MMAF-type male infertility in both humans and mice.\"\n}\n```","stage2_raw":"```json\n{\n  \"mechanistic_narrative\": \"CCDC146 is a conserved coiled-coil domain protein that functions as a microtubule-associated structural and regulatory component of motile cilia/flagella and centrosomes. In axonemes, CCDC146 (ortholog of Chlamydomonas MBO2) associates tightly with doublet microtubules and forms a heterodimeric L-shaped complex with FAP58/CCDC147 that stabilizes inner dynein arm b assembly and connects it to radial spokes and the dynein regulatory complex, thereby controlling ciliary waveform [PMID:11977094, PMID:38568782, PMID:38441556]. CCDC146 also interacts with intraflagellar transport components IFT20 and IFT88, and its loss destabilizes these proteins, disrupting sperm flagellum biogenesis, manchette formation, and head–tail coupling, causing multiple morphological abnormalities of the sperm flagella (MMAF)-type male infertility in both knockout mice and a human patient carrying a homozygous CCDC146 nonsense mutation [PMID:38038747, PMID:39245651]. In somatic cells, CCDC146 localizes to the centrosome and mitotic microtubule-organizing structures, and its dysregulation at primary cilia in motor neurons has been linked to neurodegeneration-associated ciliary defects [PMID:25074808, PMID:38441556].\",\n  \"teleology\": [\n    {\n      \"year\": 2002,\n      \"claim\": \"The foundational question of what MBO2/CCDC146 encodes and where it acts was answered: cloning of Chlamydomonas MBO2 revealed a coiled-coil axonemal protein tightly bound to doublet microtubules along the entire flagellum, required for waveform conversion from asymmetric ciliary to symmetric flagellar beating.\",\n      \"evidence\": \"Gene cloning, antibody-based axoneme fractionation, and mbo2 mutant phenotypic analysis in Chlamydomonas\",\n      \"pmids\": [\"11977094\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Binding partners within the axoneme were unknown\",\n        \"No mammalian functional data existed\",\n        \"Mechanism by which MBO2 controls waveform was unresolved\"\n      ]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"The question of whether CCDC146 has a centrosomal role in mammalian cells was addressed: proteomic identification from sperm centrioles and immunofluorescence confirmed centrosomal localization in cultured mammalian cells.\",\n      \"evidence\": \"Mass spectrometry of isolated sperm centrioles followed by immunofluorescence in cultured cells\",\n      \"pmids\": [\"25074808\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"No loss-of-function data in mammalian systems\",\n        \"Centrosomal function beyond localization was undefined\",\n        \"Relationship to axonemal role characterized in Chlamydomonas was unclear\"\n      ]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"The question of whether CCDC146 participates in pathogen–host interactions was partially answered: CCDC146 is recruited from the centrosome to the Chlamydia trachomatis inclusion membrane via interaction with CT288, revealing that a pathogen can co-opt this centrosomal protein.\",\n      \"evidence\": \"Yeast two-hybrid screen and co-immunoprecipitation in mammalian cells with fluorescence microscopy of infected versus uninfected cells\",\n      \"pmids\": [\"30094225\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Functional consequence of CCDC146 recruitment for infection outcome was not established\",\n        \"Whether other centrosomal proteins are similarly recruited was not tested\",\n        \"No in vivo infection model was used\"\n      ]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"The central question of mammalian in vivo function was resolved: Ccdc146 knockout mice are completely infertile with MMAF-like defects, and CCDC146 physically interacts with IFT20, IFT88, CCDC38, and CCDC42, placing it in the intraflagellar transport pathway essential for sperm flagellum biogenesis.\",\n      \"evidence\": \"Ccdc146 knockout mouse model, co-immunoprecipitation of multiple partners, western blot showing reduced IFT/ODF2 protein levels, TEM of flagellar ultrastructure\",\n      \"pmids\": [\"38038747\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Structural basis of CCDC146–IFT interactions was not determined\",\n        \"Whether CCDC146 functions in non-sperm motile cilia in mammals was untested\",\n        \"Relationship to inner dynein arm regulation known from Chlamydomonas was not examined\"\n      ]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"The structural mechanism was elucidated: cryo-electron tomography revealed that CCDC146/MBO2 and FAP58/CCDC147 form a conserved L-shaped heterodimer within the axonemal repeat that physically bridges inner dynein arm b to radial spokes and the dynein regulatory complex, explaining how CCDC146 loss alters waveform and reduces inner arm b assembly.\",\n      \"evidence\": \"Cryo-electron tomography, comparative proteomics, and Chlamydomonas mbo2 mutant analysis with epitope tagging\",\n      \"pmids\": [\"38568782\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Atomic-resolution structure of the CCDC146–CCDC147 heterodimer was not obtained\",\n        \"Whether inner arm b assembly defect is direct or indirect was not fully resolved\",\n        \"Conservation of the L-shaped complex structure in mammalian sperm was inferred but not directly visualized\"\n      ]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"The question of precise sub-axonemal localization in mammals was answered: expansion microscopy and sarkosyl fractionation showed CCDC146 associates with axonemal microtubule doublets (not centrioles) in spermatozoa and localizes to centrosomes and mitotic microtubule structures in somatic cells, functioning as a microtubule inner protein.\",\n      \"evidence\": \"Ccdc146 knockout mouse, expansion microscopy, sarkosyl solubilization of microtubule doublets, cryo-electron microscopy\",\n      \"pmids\": [\"38441556\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Identity of the specific MIP site within the doublet lattice in mammals was not resolved at atomic level\",\n        \"Whether CCDC146 has a functional role at somatic centrosomes beyond localization remained open\"\n      ]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"A direct human disease link was established: a homozygous nonsense mutation in CCDC146 (p.Arg306*) causes oligoasthenoteratozoospermia in a human patient, and a cognate knock-in mouse recapitulates infertility with loss of the CCDC146–IFT20 interaction leading to IFT20 degradation and reduced axonemal dynein levels.\",\n      \"evidence\": \"Human genetic mutation identification, knock-in mouse model, co-immunoprecipitation showing loss of IFT20 interaction with truncated protein\",\n      \"pmids\": [\"39245651\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Prevalence of CCDC146 mutations in MMAF patient cohorts was not broadly surveyed\",\n        \"Whether the truncated protein exerts dominant-negative effects was not assessed\",\n        \"Mechanism linking IFT20 degradation to reduced axonemal dynein assembly was not fully dissected\"\n      ]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"The functional severity of CCDC146 loss was contextualized: among four MMAF gene knockouts, Ccdc146−/− sperm exhibit the most severe nuclear compaction and chromosomal defects, with the lowest developmental potential after ICSI, indicating CCDC146 loss affects not only flagellar but also nuclear integrity.\",\n      \"evidence\": \"Comparative analysis of four KO mouse lines with ICSI embryo development assay and nuclear morphology analysis\",\n      \"pmids\": [\"40070084\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Mechanism by which CCDC146 loss causes nuclear defects is unknown\",\n        \"Whether the nuclear phenotype is secondary to manchette dysfunction or reflects a direct nuclear role was not determined\"\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"Key unresolved questions include whether CCDC146 has functional roles at somatic centrosomes or primary cilia beyond sperm, the atomic-resolution structure of the CCDC146–CCDC147 heterodimer in mammalian axonemes, and the mechanism by which CCDC146 loss leads to sperm nuclear defects.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"No functional data for CCDC146 at somatic centrosomes or primary cilia in peer-reviewed literature\",\n        \"No high-resolution mammalian structure of the CCDC146–CCDC147 complex\",\n        \"Link between axonemal/IFT defects and nuclear compaction phenotype is unexplained\"\n      ]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0008092\", \"supporting_discovery_ids\": [3, 4, 6]},\n      {\"term_id\": \"GO:0005198\", \"supporting_discovery_ids\": [4, 6]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005815\", \"supporting_discovery_ids\": [0, 1, 3]},\n      {\"term_id\": \"GO:0005856\", \"supporting_discovery_ids\": [3, 4, 6]},\n      {\"term_id\": \"GO:0005929\", \"supporting_discovery_ids\": [3, 4, 6]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-1474165\", \"supporting_discovery_ids\": [2, 3, 5, 8]},\n      {\"term_id\": \"R-HSA-1852241\", \"supporting_discovery_ids\": [2, 3, 4]}\n    ],\n    \"complexes\": [\n      \"CCDC146–CCDC147 (FAP58) heterodimer\"\n    ],\n    \"partners\": [\n      \"CCDC147\",\n      \"IFT20\",\n      \"IFT88\",\n      \"CCDC38\",\n      \"CCDC42\",\n      \"ODF2\"\n    ],\n    \"other_free_text\": []\n  }\n}\n```"}