{"gene":"CFAP52","run_date":"2026-06-09T22:57:18","timeline":{"discoveries":[{"year":2005,"finding":"CFAP52 (WDRPUH) protein associates with HSP70, components of the chaperonin-containing TCP-1 (CCT1) complex, and BRCA2, as shown by co-immunoprecipitation in HCC cells. siRNA-mediated knockdown of WDRPUH suppressed growth of HCC cells.","method":"Co-immunoprecipitation (pulldown) and siRNA knockdown with cell proliferation assay","journal":"Neoplasia","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — single Co-IP identifying binding partners, plus functional siRNA knockdown in one study; single lab","pmids":["15967112"],"is_preprint":false},{"year":2007,"finding":"Rat/zebrafish Wdr16 (ortholog of CFAP52) protein expression is restricted to kinocilia-bearing tissues (testis, ependyma, respiratory epithelium) and is upregulated concomitantly with kinocilia formation. Antisense morpholino knockdown of wdr16 in zebrafish causes severe hydrocephalus without altering ependymal morphology or ciliary beat frequency.","method":"In situ hybridization, immunohistochemistry, antisense morpholino knockdown in zebrafish with phenotypic analysis","journal":"Journal of neurochemistry","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — morpholino knockdown with defined hydrocephalus phenotype in zebrafish, replicated across multiple tissues; single lab but multiple orthogonal methods","pmids":["17394468"],"is_preprint":false},{"year":2009,"finding":"The wdr16 (CFAP52) gene is controlled by a bidirectional promoter also responsible for regulating the syntaxin 8 gene; two 100-nucleotide regions critical for promoter activity were identified, containing putative binding sites for transcription factors Foxd1, Sox17, and Spz1.","method":"Lentiviral reporter assay with deletion analysis of the wdr16 promoter in ependymal primary cultures","journal":"Neurochemical research","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single lab, reporter gene assay with deletion constructs; binding sites are putative/computational","pmids":["19191024"],"is_preprint":false},{"year":2020,"finding":"CFAP52 protein localizes to the centrosome/basal body, mitotic spindle poles, transient manchette, and sperm tail (flagellum) in male germ cells, but does NOT localize to the primary cilium. This localization indicates CFAP52 functions in centrosome/basal body matrix and sperm tail constitution beyond motile cilia.","method":"Immunofluorescence microscopy in NIH3T3 cells and male germ cells; subcellular fractionation","journal":"Scientific reports","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct localization by immunofluorescence across multiple cell types with functional interpretation; single lab, multiple structures examined","pmids":["32859975"],"is_preprint":false},{"year":2020,"finding":"Proteomic profiling links CFAP45 and CFAP52 to a shared axonemal module containing dynein ATPases and adenylate kinase (AK8). CFAP45 deficiency reduces CFAP52-associated module activity, and mutations in CFAP52 cause a similar motile ciliopathy (situs inversus and asthenospermia) as CFAP45 deficiency.","method":"Proteomic profiling of CFAP45-deficient cilia/flagella, genetic epistasis via human and mouse mutants with ciliopathy phenotype","journal":"Nature communications","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — proteomic profiling plus human/mouse genetic evidence linking CFAP52 to the same axonemal adenine nucleotide homeostasis module; single study with orthogonal approaches","pmids":["33139725"],"is_preprint":false},{"year":2021,"finding":"HuR (RNA-binding protein) binds Cfap52 mRNA and stabilizes it; HuR deficiency accelerates Cfap52 mRNA degradation, impairs ependymal cell development and motile ciliogenesis. Overexpression of Cfap52 rescues HuR-deficient ependymal cell development, placing CFAP52 as a downstream effector of HuR and of Foxj1/Rfx transcription factors in ependymal ciliogenesis.","method":"Conditional knockout mouse model (brain-specific HuR deletion), transcriptome-wide analysis (RIP/CLIP implied), mRNA stability assay, Cfap52 overexpression rescue experiment","journal":"The Journal of neuroscience","confidence":"High","confidence_rationale":"Tier 2 / Strong — KO mouse with defined ciliogenesis phenotype, mRNA stability assay, and rescue by overexpression; multiple orthogonal methods in a single rigorous study","pmids":["34815315"],"is_preprint":false},{"year":2023,"finding":"CFAP52 interacts with sperm head-tail coupling regulator SPATA6 (by co-immunoprecipitation) and is essential for SPATA6 protein stability; Cfap52 knockout in mice causes acephalic spermatozoa syndrome (ASS) and multiple morphological abnormalities of sperm flagella (MMAF), with failure of connecting piece formation and disruption of the '9+2' axoneme structure. Expression of microtubule inner proteins and radial spoke proteins was reduced after CFAP52 deficiency.","method":"Co-immunoprecipitation, Cfap52 knockout mouse model, transmission electron microscopy, Western blot for downstream proteins","journal":"eLife","confidence":"High","confidence_rationale":"Tier 2 / Strong — KO mouse with defined ultrastructural sperm phenotype, co-IP identifying SPATA6 interaction and stability dependence, downstream protein expression analysis; multiple orthogonal methods in one rigorous study","pmids":["38126872"],"is_preprint":false},{"year":2023,"finding":"CFAP52 interacts directly with CFAP45 (confirmed by co-immunoprecipitation); Cfap52 knockout in mice reduces CFAP45 protein levels in the sperm flagellum and disrupts microtubule sliding produced by dynein ATPase, causing decreased sperm motility and male infertility without altering axoneme ultrastructure. The midpiece-principal piece junction of the sperm tail is disorganized upon Cfap52 loss.","method":"Co-immunoprecipitation, Cfap52 knockout mouse model, sperm motility assay, transmission electron microscopy, dynein-driven microtubule sliding assay","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — in vitro microtubule sliding assay plus co-IP plus KO mouse with defined motility and ultrastructural phenotype; multiple orthogonal methods in one study","pmids":["37236356"],"is_preprint":false},{"year":2022,"finding":"CRISPR/Cas9 F0 crispant targeting of cfap52 in zebrafish recapitulates ciliary phenotypes consistent with zygotic null mutants, confirming CFAP52 has a functional role in cilia.","method":"Multiple-guide CRISPR/Cas9 F0 crispant analysis in zebrafish with ciliary phenotype readout","journal":"Disease models & mechanisms","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — CRISPR crispant phenotype confirmed in zebrafish; ciliary phenotype established but limited mechanistic detail; single study","pmids":["36533556"],"is_preprint":false}],"current_model":"CFAP52 (also known as WDR16/WDRPUH) is a WD40-repeat protein that localizes to the centrosome/basal body, mitotic spindle poles, manchette, and sperm flagellum in male germ cells; it functions as a component of an axonemal adenine nucleotide homeostasis module alongside CFAP45, dynein ATPases, and adenylate kinase, where it interacts directly with CFAP45 (stabilizing it in the flagellum) and with SPATA6 (stabilizing it for connecting piece formation), thereby supporting dynein-driven microtubule sliding, axoneme '9+2' integrity, and sperm head-tail coupling; additionally, CFAP52 mRNA is post-transcriptionally stabilized by the RNA-binding protein HuR downstream of Foxj1/Rfx transcription factors to drive ependymal ciliogenesis, and loss of CFAP52 in mice and humans causes asthenospermia, acephalic spermatozoa, MMAF, and laterality defects consistent with a motile ciliopathy."},"narrative":{"mechanistic_narrative":"CFAP52 (WDR16/WDRPUH) is a WD40-repeat protein that supports the assembly and motility of motile cilia and sperm flagella across vertebrate germ and ciliated cells [PMID:33139725, PMID:37236356]. In male germ cells it localizes to the centrosome/basal body, mitotic spindle poles, the transient manchette, and the sperm flagellum, but is excluded from primary cilia, marking it as a constituent of the basal-body matrix and the sperm tail rather than a general ciliary protein [PMID:32859975]. Functionally it acts as a scaffold/stabilizing partner: it binds CFAP45 directly and maintains CFAP45 levels in the flagellum to sustain dynein-ATPase-driven microtubule sliding, placing it within a shared axonemal module containing dynein ATPases and adenylate kinase (AK8) [PMID:33139725, PMID:37236356]. It also interacts with the head-tail coupling regulator SPATA6 and is required for SPATA6 protein stability and connecting-piece formation, so that its loss in mice produces acephalic spermatozoa, MMAF, disrupted '9+2' axoneme integrity, and reduced microtubule-inner and radial-spoke protein levels [PMID:38126872]. Loss of CFAP52 causes a motile ciliopathy with situs inversus, hydrocephalus, and asthenospermia in animal models and humans [PMID:17394468, PMID:33139725, PMID:37236356]. In ependymal ciliogenesis, Cfap52 mRNA is post-transcriptionally stabilized by the RNA-binding protein HuR acting downstream of Foxj1/Rfx, and CFAP52 overexpression rescues HuR-deficient ependymal development [PMID:34815315].","teleology":[{"year":2005,"claim":"Established the first protein interactions of CFAP52, linking it to chaperone machinery and a proliferative role before its ciliary function was known.","evidence":"Co-immunoprecipitation and siRNA knockdown in HCC cells","pmids":["15967112"],"confidence":"Medium","gaps":["HSP70/CCT1/BRCA2 associations not validated reciprocally or in ciliated cells","Relationship between proliferation phenotype and later-defined ciliary roles unresolved"]},{"year":2007,"claim":"Connected CFAP52 to motile-ciliated tissues by showing its ortholog is expressed with kinocilia and that its loss causes hydrocephalus, defining cilia as the relevant context.","evidence":"In situ hybridization, immunohistochemistry and antisense morpholino knockdown in zebrafish","pmids":["17394468"],"confidence":"Medium","gaps":["Hydrocephalus arises without altered beat frequency, leaving the cellular mechanism unexplained","Molecular function of the protein not addressed"]},{"year":2009,"claim":"Characterized transcriptional control of the gene, identifying a shared bidirectional promoter with syntaxin 8.","evidence":"Lentiviral reporter and deletion analysis in ependymal primary cultures","pmids":["19191024"],"confidence":"Low","gaps":["Foxd1/Sox17/Spz1 sites are computational, not experimentally bound","No connection to in vivo regulation demonstrated"]},{"year":2020,"claim":"Defined the subcellular distribution of CFAP52, distinguishing it from primary-cilium proteins and localizing it to basal body, spindle poles, manchette, and flagellum.","evidence":"Immunofluorescence in NIH3T3 and germ cells plus subcellular fractionation","pmids":["32859975"],"confidence":"Medium","gaps":["Molecular activity at each structure not resolved","No interaction partners identified in this study"]},{"year":2020,"claim":"Placed CFAP52 in a defined axonemal adenine-nucleotide homeostasis module with CFAP45, dynein ATPases, and adenylate kinase, explaining its ciliopathy phenotype.","evidence":"Proteomic profiling of CFAP45-deficient cilia and human/mouse genetic epistasis","pmids":["33139725"],"confidence":"Medium","gaps":["Direct biochemical activity of CFAP52 within the module not measured","Order of assembly within the module unresolved"]},{"year":2021,"claim":"Identified post-transcriptional control of Cfap52 by HuR as a key step in ependymal ciliogenesis, with overexpression rescue establishing it as a downstream effector.","evidence":"Brain-specific HuR conditional knockout, mRNA stability assay, and Cfap52 overexpression rescue in mouse","pmids":["34815315"],"confidence":"High","gaps":["Direct HuR-binding site on Cfap52 mRNA not mapped","How CFAP52 levels translate to ciliogenesis at the protein level unresolved"]},{"year":2022,"claim":"Confirmed CFAP52's functional requirement in cilia through a rapid in vivo genetic approach recapitulating null phenotypes.","evidence":"Multiple-guide CRISPR/Cas9 F0 crispant analysis in zebrafish","pmids":["36533556"],"confidence":"Medium","gaps":["Limited mechanistic resolution beyond phenotype confirmation","No molecular partners assessed"]},{"year":2023,"claim":"Resolved CFAP52's role in dynein-driven motility by showing it binds and stabilizes CFAP45 in the flagellum to enable microtubule sliding.","evidence":"Co-IP, Cfap52 knockout mouse, sperm motility and dynein-driven microtubule sliding assays, TEM","pmids":["37236356"],"confidence":"High","gaps":["Sliding defect occurs without axonemal ultrastructure change, mechanism of force loss not fully defined","Stoichiometry of the CFAP52-CFAP45 interaction unknown"]},{"year":2023,"claim":"Established CFAP52 in sperm head-tail coupling via SPATA6 stabilization, explaining acephalic spermatozoa and MMAF phenotypes.","evidence":"Co-IP, Cfap52 knockout mouse, TEM, and Western blot of downstream axonemal proteins","pmids":["38126872"],"confidence":"High","gaps":["Mechanism by which CFAP52 stabilizes SPATA6 (direct vs scaffolding) not defined","Reduction of MIPs and radial spoke proteins is correlative, not mechanistically linked"]},{"year":null,"claim":"How CFAP52 coordinates its distinct roles across basal body, manchette, head-tail junction, and flagellar axoneme through a single WD40 scaffold remains unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No structural model of CFAP52 or its complexes","Unclear whether the CFAP45 and SPATA6 interactions are mutually exclusive or temporally separated","Biochemical activity beyond protein stabilization not established"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0008092","term_label":"cytoskeletal protein binding","supporting_discovery_ids":[4,6,7]},{"term_id":"GO:0140313","term_label":"molecular sequestering activity","supporting_discovery_ids":[6,7]}],"localization":[{"term_id":"GO:0005815","term_label":"microtubule organizing center","supporting_discovery_ids":[3]},{"term_id":"GO:0005929","term_label":"cilium","supporting_discovery_ids":[1,4,8]},{"term_id":"GO:0005856","term_label":"cytoskeleton","supporting_discovery_ids":[3,7]}],"pathway":[{"term_id":"R-HSA-1852241","term_label":"Organelle biogenesis and maintenance","supporting_discovery_ids":[4,5,7]},{"term_id":"R-HSA-1474165","term_label":"Reproduction","supporting_discovery_ids":[6,7]}],"complexes":["axonemal dynein/adenylate kinase module"],"partners":["CFAP45","SPATA6","AK8","HUR","HSP70","BRCA2"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q8N1V2","full_name":"Cilia- and flagella-associated protein 52","aliases":["WD repeat-containing protein 16","WD40-repeat protein up-regulated in HCC"],"length_aa":620,"mass_kda":68.3,"function":"Microtubule inner protein (MIP) part of the dynein-decorated doublet microtubules (DMTs) in cilia axoneme (PubMed:36191189). Important for proper ciliary and flagellar beating. May act in cooperation with CFAP45 and axonemal dynein subunit DNAH11 (PubMed:33139725). May play a role in cell growth and/or survival (PubMed:15967112)","subcellular_location":"Cytoplasm; Cytoplasm, cytoskeleton, cilium axoneme; Cytoplasm, cytoskeleton, flagellum axoneme","url":"https://www.uniprot.org/uniprotkb/Q8N1V2/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/CFAP52","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/CFAP52","total_profiled":1310},"omim":[{"mim_id":"619607","title":"HETEROTAXY, VISCERAL, 10, AUTOSOMAL, WITH MALE INFERTILITY; HTX10","url":"https://www.omim.org/entry/619607"},{"mim_id":"609804","title":"CILIA- AND FLAGELLA-ASSOCIATED PROTEIN 52; CFAP52","url":"https://www.omim.org/entry/609804"},{"mim_id":"605152","title":"CILIA- AND FLAGELLA-ASSOCIATED PROTEIN 45; CFAP45","url":"https://www.omim.org/entry/605152"},{"mim_id":"603339","title":"DYNEIN, AXONEMAL, HEAVY CHAIN 11; DNAH11","url":"https://www.omim.org/entry/603339"},{"mim_id":"306955","title":"HETEROTAXY, VISCERAL, 1, X-LINKED; HTX1","url":"https://www.omim.org/entry/306955"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Approved","locations":[{"location":"Microtubules","reliability":"Approved"},{"location":"Primary cilium","reliability":"Additional"},{"location":"Centriolar satellite","reliability":"Additional"},{"location":"Basal body","reliability":"Additional"}],"tissue_specificity":"Tissue enhanced","tissue_distribution":"Detected in some","driving_tissues":[{"tissue":"choroid plexus","ntpm":37.4},{"tissue":"fallopian tube","ntpm":54.4}],"url":"https://www.proteinatlas.org/search/CFAP52"},"hgnc":{"alias_symbol":["WDRPUH","FLJ37528"],"prev_symbol":["WDR16"]},"alphafold":{"accession":"Q8N1V2","domains":[{"cath_id":"2.130.10.10","chopping":"28-256","consensus_level":"medium","plddt":92.4636,"start":28,"end":256},{"cath_id":"2.130.10.10","chopping":"336-616","consensus_level":"medium","plddt":93.8782,"start":336,"end":616}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q8N1V2","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q8N1V2-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q8N1V2-F1-predicted_aligned_error_v6.png","plddt_mean":93.44},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=CFAP52","jax_strain_url":"https://www.jax.org/strain/search?query=CFAP52"},"sequence":{"accession":"Q8N1V2","fasta_url":"https://rest.uniprot.org/uniprotkb/Q8N1V2.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q8N1V2/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q8N1V2"}},"corpus_meta":[{"pmid":"33139725","id":"PMC_33139725","title":"CFAP45 deficiency causes situs abnormalities and asthenospermia by disrupting an axonemal adenine nucleotide homeostasis module.","date":"2020","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/33139725","citation_count":56,"is_preprint":false},{"pmid":"32686114","id":"PMC_32686114","title":"Single cell transcriptomes of normal endometrial derived organoids uncover novel cell type markers and cryptic differentiation of primary tumours.","date":"2020","source":"The Journal of pathology","url":"https://pubmed.ncbi.nlm.nih.gov/32686114","citation_count":50,"is_preprint":false},{"pmid":"25469542","id":"PMC_25469542","title":"A human laterality disorder associated with a homozygous WDR16 deletion.","date":"2014","source":"European journal of human genetics : EJHG","url":"https://pubmed.ncbi.nlm.nih.gov/25469542","citation_count":45,"is_preprint":false},{"pmid":"17394468","id":"PMC_17394468","title":"Biosynthesis of Wdr16, a marker protein for kinocilia-bearing cells, starts at the time of kinocilia formation in rat, and wdr16 gene knockdown causes hydrocephalus in zebrafish.","date":"2007","source":"Journal of neurochemistry","url":"https://pubmed.ncbi.nlm.nih.gov/17394468","citation_count":29,"is_preprint":false},{"pmid":"15967112","id":"PMC_15967112","title":"WDRPUH, a novel WD-repeat-containing protein, is highly expressed in human hepatocellular carcinoma and involved in cell proliferation.","date":"2005","source":"Neoplasia (New York, N.Y.)","url":"https://pubmed.ncbi.nlm.nih.gov/15967112","citation_count":26,"is_preprint":false},{"pmid":"33525928","id":"PMC_33525928","title":"Phase I studies of peptide vaccine cocktails derived from GPC3, WDRPUH and NEIL3 for advanced hepatocellular carcinoma.","date":"2021","source":"Immunotherapy","url":"https://pubmed.ncbi.nlm.nih.gov/33525928","citation_count":22,"is_preprint":false},{"pmid":"23434627","id":"PMC_23434627","title":"Identification of chromosomal copy number variations and novel candidate loci in hereditary nonpolyposis colorectal cancer with mismatch repair proficiency.","date":"2013","source":"Genomics","url":"https://pubmed.ncbi.nlm.nih.gov/23434627","citation_count":20,"is_preprint":false},{"pmid":"36533556","id":"PMC_36533556","title":"Variable phenotypes and penetrance between and within different zebrafish ciliary transition zone mutants.","date":"2022","source":"Disease models & mechanisms","url":"https://pubmed.ncbi.nlm.nih.gov/36533556","citation_count":17,"is_preprint":false},{"pmid":"32859975","id":"PMC_32859975","title":"The WD40-protein CFAP52/WDR16 is a centrosome/basal body protein and localizes to the manchette and the flagellum in male germ cells.","date":"2020","source":"Scientific reports","url":"https://pubmed.ncbi.nlm.nih.gov/32859975","citation_count":16,"is_preprint":false},{"pmid":"34815315","id":"PMC_34815315","title":"Loss of RNA-Binding Protein HuR Leads to Defective Ependymal Cells and Hydrocephalus.","date":"2021","source":"The Journal of neuroscience : the official journal of the Society for Neuroscience","url":"https://pubmed.ncbi.nlm.nih.gov/34815315","citation_count":13,"is_preprint":false},{"pmid":"38126872","id":"PMC_38126872","title":"Identification of CFAP52 as a novel diagnostic target of male infertility with defects of sperm head-tail connection and flagella development.","date":"2023","source":"eLife","url":"https://pubmed.ncbi.nlm.nih.gov/38126872","citation_count":12,"is_preprint":false},{"pmid":"37118964","id":"PMC_37118964","title":"Differential Proteomic Analysis of Human Sperm: A Systematic Review to Identify Candidate Targets to Monitor Sperm Quality.","date":"2023","source":"The world journal of men's health","url":"https://pubmed.ncbi.nlm.nih.gov/37118964","citation_count":8,"is_preprint":false},{"pmid":"37236356","id":"PMC_37236356","title":"The cilia and flagella associated protein CFAP52 orchestrated with CFAP45 is required for sperm motility in mice.","date":"2023","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/37236356","citation_count":6,"is_preprint":false},{"pmid":"36106701","id":"PMC_36106701","title":"Identification of candidate sex-specific genomic regions in male and female Asian arowana genomes.","date":"2022","source":"GigaScience","url":"https://pubmed.ncbi.nlm.nih.gov/36106701","citation_count":4,"is_preprint":false},{"pmid":"40565529","id":"PMC_40565529","title":"Identification of Novel Genetic Loci Involved in Testis Traits of the Jiangxi Local Breed Based on GWAS Analyses.","date":"2025","source":"Genes","url":"https://pubmed.ncbi.nlm.nih.gov/40565529","citation_count":4,"is_preprint":false},{"pmid":"19191024","id":"PMC_19191024","title":"Lentiviral transfection of ependymal primary cultures facilitates the characterisation of kinocilia-specific promoters.","date":"2009","source":"Neurochemical research","url":"https://pubmed.ncbi.nlm.nih.gov/19191024","citation_count":1,"is_preprint":false},{"pmid":"41214700","id":"PMC_41214700","title":"Analysis of the associations between DNA methylation and clinical features reveals the potential oncogenic effect of CFAP52 in esophageal squamous cell cancer.","date":"2025","source":"Cancer cell international","url":"https://pubmed.ncbi.nlm.nih.gov/41214700","citation_count":0,"is_preprint":false},{"pmid":"40166594","id":"PMC_40166594","title":"Distinct and Shared Molecular Mechanisms in Pediatric Antrochoanal Polyps and Chronic Rhinosinusitis with Nasal Polyps: A Proteomic and Metabolomic Integrative Analysis.","date":"2025","source":"Journal of inflammation research","url":"https://pubmed.ncbi.nlm.nih.gov/40166594","citation_count":0,"is_preprint":false},{"pmid":"39755840","id":"PMC_39755840","title":"Genetic landscape in undiagnosed patients with syndromic hearing loss revealed by whole exome sequencing and phenotype similarity search.","date":"2025","source":"Human genetics","url":"https://pubmed.ncbi.nlm.nih.gov/39755840","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":11470,"output_tokens":2469,"usd":0.035722,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":9642,"output_tokens":3051,"usd":0.062242,"stage2_stop_reason":"end_turn"},"total_usd":0.097964,"stage1_batch_id":"msgbatch_01ACAxJQabDsht39JXeWG22d","stage2_batch_id":"msgbatch_01QEU22A9U5sbPTgsMzTmvSf","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2005,\n      \"finding\": \"CFAP52 (WDRPUH) protein associates with HSP70, components of the chaperonin-containing TCP-1 (CCT1) complex, and BRCA2, as shown by co-immunoprecipitation in HCC cells. siRNA-mediated knockdown of WDRPUH suppressed growth of HCC cells.\",\n      \"method\": \"Co-immunoprecipitation (pulldown) and siRNA knockdown with cell proliferation assay\",\n      \"journal\": \"Neoplasia\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — single Co-IP identifying binding partners, plus functional siRNA knockdown in one study; single lab\",\n      \"pmids\": [\"15967112\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2007,\n      \"finding\": \"Rat/zebrafish Wdr16 (ortholog of CFAP52) protein expression is restricted to kinocilia-bearing tissues (testis, ependyma, respiratory epithelium) and is upregulated concomitantly with kinocilia formation. Antisense morpholino knockdown of wdr16 in zebrafish causes severe hydrocephalus without altering ependymal morphology or ciliary beat frequency.\",\n      \"method\": \"In situ hybridization, immunohistochemistry, antisense morpholino knockdown in zebrafish with phenotypic analysis\",\n      \"journal\": \"Journal of neurochemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — morpholino knockdown with defined hydrocephalus phenotype in zebrafish, replicated across multiple tissues; single lab but multiple orthogonal methods\",\n      \"pmids\": [\"17394468\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"The wdr16 (CFAP52) gene is controlled by a bidirectional promoter also responsible for regulating the syntaxin 8 gene; two 100-nucleotide regions critical for promoter activity were identified, containing putative binding sites for transcription factors Foxd1, Sox17, and Spz1.\",\n      \"method\": \"Lentiviral reporter assay with deletion analysis of the wdr16 promoter in ependymal primary cultures\",\n      \"journal\": \"Neurochemical research\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single lab, reporter gene assay with deletion constructs; binding sites are putative/computational\",\n      \"pmids\": [\"19191024\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"CFAP52 protein localizes to the centrosome/basal body, mitotic spindle poles, transient manchette, and sperm tail (flagellum) in male germ cells, but does NOT localize to the primary cilium. This localization indicates CFAP52 functions in centrosome/basal body matrix and sperm tail constitution beyond motile cilia.\",\n      \"method\": \"Immunofluorescence microscopy in NIH3T3 cells and male germ cells; subcellular fractionation\",\n      \"journal\": \"Scientific reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct localization by immunofluorescence across multiple cell types with functional interpretation; single lab, multiple structures examined\",\n      \"pmids\": [\"32859975\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"Proteomic profiling links CFAP45 and CFAP52 to a shared axonemal module containing dynein ATPases and adenylate kinase (AK8). CFAP45 deficiency reduces CFAP52-associated module activity, and mutations in CFAP52 cause a similar motile ciliopathy (situs inversus and asthenospermia) as CFAP45 deficiency.\",\n      \"method\": \"Proteomic profiling of CFAP45-deficient cilia/flagella, genetic epistasis via human and mouse mutants with ciliopathy phenotype\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — proteomic profiling plus human/mouse genetic evidence linking CFAP52 to the same axonemal adenine nucleotide homeostasis module; single study with orthogonal approaches\",\n      \"pmids\": [\"33139725\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"HuR (RNA-binding protein) binds Cfap52 mRNA and stabilizes it; HuR deficiency accelerates Cfap52 mRNA degradation, impairs ependymal cell development and motile ciliogenesis. Overexpression of Cfap52 rescues HuR-deficient ependymal cell development, placing CFAP52 as a downstream effector of HuR and of Foxj1/Rfx transcription factors in ependymal ciliogenesis.\",\n      \"method\": \"Conditional knockout mouse model (brain-specific HuR deletion), transcriptome-wide analysis (RIP/CLIP implied), mRNA stability assay, Cfap52 overexpression rescue experiment\",\n      \"journal\": \"The Journal of neuroscience\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — KO mouse with defined ciliogenesis phenotype, mRNA stability assay, and rescue by overexpression; multiple orthogonal methods in a single rigorous study\",\n      \"pmids\": [\"34815315\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"CFAP52 interacts with sperm head-tail coupling regulator SPATA6 (by co-immunoprecipitation) and is essential for SPATA6 protein stability; Cfap52 knockout in mice causes acephalic spermatozoa syndrome (ASS) and multiple morphological abnormalities of sperm flagella (MMAF), with failure of connecting piece formation and disruption of the '9+2' axoneme structure. Expression of microtubule inner proteins and radial spoke proteins was reduced after CFAP52 deficiency.\",\n      \"method\": \"Co-immunoprecipitation, Cfap52 knockout mouse model, transmission electron microscopy, Western blot for downstream proteins\",\n      \"journal\": \"eLife\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — KO mouse with defined ultrastructural sperm phenotype, co-IP identifying SPATA6 interaction and stability dependence, downstream protein expression analysis; multiple orthogonal methods in one rigorous study\",\n      \"pmids\": [\"38126872\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"CFAP52 interacts directly with CFAP45 (confirmed by co-immunoprecipitation); Cfap52 knockout in mice reduces CFAP45 protein levels in the sperm flagellum and disrupts microtubule sliding produced by dynein ATPase, causing decreased sperm motility and male infertility without altering axoneme ultrastructure. The midpiece-principal piece junction of the sperm tail is disorganized upon Cfap52 loss.\",\n      \"method\": \"Co-immunoprecipitation, Cfap52 knockout mouse model, sperm motility assay, transmission electron microscopy, dynein-driven microtubule sliding assay\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — in vitro microtubule sliding assay plus co-IP plus KO mouse with defined motility and ultrastructural phenotype; multiple orthogonal methods in one study\",\n      \"pmids\": [\"37236356\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"CRISPR/Cas9 F0 crispant targeting of cfap52 in zebrafish recapitulates ciliary phenotypes consistent with zygotic null mutants, confirming CFAP52 has a functional role in cilia.\",\n      \"method\": \"Multiple-guide CRISPR/Cas9 F0 crispant analysis in zebrafish with ciliary phenotype readout\",\n      \"journal\": \"Disease models & mechanisms\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — CRISPR crispant phenotype confirmed in zebrafish; ciliary phenotype established but limited mechanistic detail; single study\",\n      \"pmids\": [\"36533556\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"CFAP52 (also known as WDR16/WDRPUH) is a WD40-repeat protein that localizes to the centrosome/basal body, mitotic spindle poles, manchette, and sperm flagellum in male germ cells; it functions as a component of an axonemal adenine nucleotide homeostasis module alongside CFAP45, dynein ATPases, and adenylate kinase, where it interacts directly with CFAP45 (stabilizing it in the flagellum) and with SPATA6 (stabilizing it for connecting piece formation), thereby supporting dynein-driven microtubule sliding, axoneme '9+2' integrity, and sperm head-tail coupling; additionally, CFAP52 mRNA is post-transcriptionally stabilized by the RNA-binding protein HuR downstream of Foxj1/Rfx transcription factors to drive ependymal ciliogenesis, and loss of CFAP52 in mice and humans causes asthenospermia, acephalic spermatozoa, MMAF, and laterality defects consistent with a motile ciliopathy.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"CFAP52 (WDR16/WDRPUH) is a WD40-repeat protein that supports the assembly and motility of motile cilia and sperm flagella across vertebrate germ and ciliated cells [#4, #7]. In male germ cells it localizes to the centrosome/basal body, mitotic spindle poles, the transient manchette, and the sperm flagellum, but is excluded from primary cilia, marking it as a constituent of the basal-body matrix and the sperm tail rather than a general ciliary protein [#3]. Functionally it acts as a scaffold/stabilizing partner: it binds CFAP45 directly and maintains CFAP45 levels in the flagellum to sustain dynein-ATPase-driven microtubule sliding, placing it within a shared axonemal module containing dynein ATPases and adenylate kinase (AK8) [#4, #7]. It also interacts with the head-tail coupling regulator SPATA6 and is required for SPATA6 protein stability and connecting-piece formation, so that its loss in mice produces acephalic spermatozoa, MMAF, disrupted '9+2' axoneme integrity, and reduced microtubule-inner and radial-spoke protein levels [#6]. Loss of CFAP52 causes a motile ciliopathy with situs inversus, hydrocephalus, and asthenospermia in animal models and humans [#1, #4, #7]. In ependymal ciliogenesis, Cfap52 mRNA is post-transcriptionally stabilized by the RNA-binding protein HuR acting downstream of Foxj1/Rfx, and CFAP52 overexpression rescues HuR-deficient ependymal development [#5].\",\n  \"teleology\": [\n    {\n      \"year\": 2005,\n      \"claim\": \"Established the first protein interactions of CFAP52, linking it to chaperone machinery and a proliferative role before its ciliary function was known.\",\n      \"evidence\": \"Co-immunoprecipitation and siRNA knockdown in HCC cells\",\n      \"pmids\": [\"15967112\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"HSP70/CCT1/BRCA2 associations not validated reciprocally or in ciliated cells\", \"Relationship between proliferation phenotype and later-defined ciliary roles unresolved\"]\n    },\n    {\n      \"year\": 2007,\n      \"claim\": \"Connected CFAP52 to motile-ciliated tissues by showing its ortholog is expressed with kinocilia and that its loss causes hydrocephalus, defining cilia as the relevant context.\",\n      \"evidence\": \"In situ hybridization, immunohistochemistry and antisense morpholino knockdown in zebrafish\",\n      \"pmids\": [\"17394468\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Hydrocephalus arises without altered beat frequency, leaving the cellular mechanism unexplained\", \"Molecular function of the protein not addressed\"]\n    },\n    {\n      \"year\": 2009,\n      \"claim\": \"Characterized transcriptional control of the gene, identifying a shared bidirectional promoter with syntaxin 8.\",\n      \"evidence\": \"Lentiviral reporter and deletion analysis in ependymal primary cultures\",\n      \"pmids\": [\"19191024\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"Foxd1/Sox17/Spz1 sites are computational, not experimentally bound\", \"No connection to in vivo regulation demonstrated\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Defined the subcellular distribution of CFAP52, distinguishing it from primary-cilium proteins and localizing it to basal body, spindle poles, manchette, and flagellum.\",\n      \"evidence\": \"Immunofluorescence in NIH3T3 and germ cells plus subcellular fractionation\",\n      \"pmids\": [\"32859975\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Molecular activity at each structure not resolved\", \"No interaction partners identified in this study\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Placed CFAP52 in a defined axonemal adenine-nucleotide homeostasis module with CFAP45, dynein ATPases, and adenylate kinase, explaining its ciliopathy phenotype.\",\n      \"evidence\": \"Proteomic profiling of CFAP45-deficient cilia and human/mouse genetic epistasis\",\n      \"pmids\": [\"33139725\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct biochemical activity of CFAP52 within the module not measured\", \"Order of assembly within the module unresolved\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Identified post-transcriptional control of Cfap52 by HuR as a key step in ependymal ciliogenesis, with overexpression rescue establishing it as a downstream effector.\",\n      \"evidence\": \"Brain-specific HuR conditional knockout, mRNA stability assay, and Cfap52 overexpression rescue in mouse\",\n      \"pmids\": [\"34815315\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Direct HuR-binding site on Cfap52 mRNA not mapped\", \"How CFAP52 levels translate to ciliogenesis at the protein level unresolved\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Confirmed CFAP52's functional requirement in cilia through a rapid in vivo genetic approach recapitulating null phenotypes.\",\n      \"evidence\": \"Multiple-guide CRISPR/Cas9 F0 crispant analysis in zebrafish\",\n      \"pmids\": [\"36533556\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Limited mechanistic resolution beyond phenotype confirmation\", \"No molecular partners assessed\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Resolved CFAP52's role in dynein-driven motility by showing it binds and stabilizes CFAP45 in the flagellum to enable microtubule sliding.\",\n      \"evidence\": \"Co-IP, Cfap52 knockout mouse, sperm motility and dynein-driven microtubule sliding assays, TEM\",\n      \"pmids\": [\"37236356\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Sliding defect occurs without axonemal ultrastructure change, mechanism of force loss not fully defined\", \"Stoichiometry of the CFAP52-CFAP45 interaction unknown\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Established CFAP52 in sperm head-tail coupling via SPATA6 stabilization, explaining acephalic spermatozoa and MMAF phenotypes.\",\n      \"evidence\": \"Co-IP, Cfap52 knockout mouse, TEM, and Western blot of downstream axonemal proteins\",\n      \"pmids\": [\"38126872\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Mechanism by which CFAP52 stabilizes SPATA6 (direct vs scaffolding) not defined\", \"Reduction of MIPs and radial spoke proteins is correlative, not mechanistically linked\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How CFAP52 coordinates its distinct roles across basal body, manchette, head-tail junction, and flagellar axoneme through a single WD40 scaffold remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No structural model of CFAP52 or its complexes\", \"Unclear whether the CFAP45 and SPATA6 interactions are mutually exclusive or temporally separated\", \"Biochemical activity beyond protein stabilization not established\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0008092\", \"supporting_discovery_ids\": [4, 6, 7]},\n      {\"term_id\": \"GO:0140313\", \"supporting_discovery_ids\": [6, 7]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005815\", \"supporting_discovery_ids\": [3]},\n      {\"term_id\": \"GO:0005929\", \"supporting_discovery_ids\": [1, 4, 8]},\n      {\"term_id\": \"GO:0005856\", \"supporting_discovery_ids\": [3, 7]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-1852241\", \"supporting_discovery_ids\": [4, 5, 7]},\n      {\"term_id\": \"R-HSA-1474165\", \"supporting_discovery_ids\": [6, 7]}\n    ],\n    \"complexes\": [\"axonemal dynein/adenylate kinase module\"],\n    \"partners\": [\"CFAP45\", \"SPATA6\", \"AK8\", \"HuR\", \"HSP70\", \"BRCA2\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":6,"faith_total":6,"faith_pct":100.0}}