{"gene":"CFAP47","run_date":"2026-06-09T22:57:18","timeline":{"discoveries":[{"year":2025,"finding":"Cryo-electron tomography combined with AlphaFold2 resolved the in-cell structure of mouse sperm central apparatus (CA) at sub-nanometer resolution, revealing that CFAP47 is a core structural component of the C1-C2 bridge: its N-terminal domains bind C1 microtubule, its central CFAP47-ring interacts with HYDIN, and its C-terminal region anchors to C2 microtubule. Cfap47-knockout mice display a hollowing bridge in the CA structure and significantly reduced sperm progressive motility, directly confirming CFAP47's role in tethering C1 and C2 within the central apparatus.","method":"In situ cryo-electron tomography, AlphaFold2 atomic modelling, Cfap47-knockout mouse model with sperm motility assay and structural analysis","journal":"Cell research","confidence":"High","confidence_rationale":"Tier 1 / Strong — near-complete atomic model from in-cell cryo-ET, domain-level structural mapping, validated by KO mouse phenotype; replicated across two papers (PMID:40473901 and preprint bio_10.1101_2024.08.06.606614)","pmids":["40473901"],"is_preprint":false},{"year":2024,"finding":"In situ cryo-electron tomography of mouse sperm axoneme identified CFAP47 and HYDIN as the long chain-like ASH-containing proteins responsible for connecting C1 and C2 microtubules in the central apparatus. Sperm from Cfap47-knockout mice displayed a hollowing bridge in the CA structure correlated with reduced progressive motility.","method":"In situ cryo-electron tomography, AlphaFold2 atomic modelling, Cfap47-knockout mouse sperm structural and motility analysis","journal":"bioRxiv","confidence":"High","confidence_rationale":"Tier 1 / Strong — in-cell cryo-ET structure with near-complete atomic model and KO mouse validation; consistent with peer-reviewed companion paper PMID:40473901","pmids":["bio_10.1101_2024.08.06.606614"],"is_preprint":true},{"year":2021,"finding":"Hemizygous loss-of-function missense variants in X-linked CFAP47 cause MMAF and asthenoteratozoospermia in humans. Immunoblotting and immunofluorescence confirmed markedly reduced CFAP47 protein in spermatozoa from affected men. A Cfap47-mutated mouse model recapitulated the phenotype with reduced sperm motility and abnormal flagellar morphology; male mice were sterile but fertility was rescued by ICSI.","method":"Whole-exome sequencing, immunoblotting, immunofluorescence, Cfap47-mutant mouse model, ICSI rescue experiment","journal":"American journal of human genetics","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple orthogonal methods (WES, protein quantification, mouse KO with defined phenotype), replicated across multiple unrelated patients and a mouse model","pmids":["33472045"],"is_preprint":false},{"year":2022,"finding":"CFAP47 physically interacts with WDR87 in the flagellar midpiece of spermatozoa. In CFAP47-mutant men, WDR87 protein was also significantly decreased and mislocalized to a position adjacent to the spermatozoa nuclei rather than the midpiece, indicating that CFAP47 is required for WDR87 transport during spermatozoa flagella biogenesis.","method":"Co-immunoprecipitation (interaction identified), immunofluorescence and immunoblotting in CFAP47-mutant human spermatozoa","journal":"Molecular human reproduction","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — interaction identified by co-IP with functional consequence shown by protein mislocalization in patient material; single lab, two orthogonal methods","pmids":["36571501"],"is_preprint":false},{"year":2023,"finding":"A novel CFAP47 missense mutation (p.V472M) reduces CFAP47 protein in spermatozoa and is associated with disorganized mitochondrial sheath, defective sperm annulus, and abnormal sperm head morphology in addition to MMAF. Mechanism analysis indicated that CFAP47 may regulate expression of CFAP65, CFAP69 and SEPTIN4 through physical interactions, suggesting CFAP47 participates in a protein complex modulating sperm morphogenesis.","method":"Immunofluorescence, western blotting, co-immunoprecipitation (physical interactions with CFAP65, CFAP69, SEPTIN4)","journal":"Frontiers in endocrinology","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single lab, Co-IP interactions reported but limited mechanistic follow-up; interaction data described as 'mechanism analysis' without deep validation","pmids":["37424856"],"is_preprint":false},{"year":2023,"finding":"Hemizygous missense variants of X-linked CFAP47 were identified in two unrelated patients with primary ciliary dyskinesia (PCD). CFAP47 expression was significantly reduced in respiratory epithelial cells of affected individuals both in vivo and in vitro, and a reduction in the number of epithelial ciliary cells and basal bodies was observed by immunofluorescence and transmission electron microscopy, establishing CFAP47 as a causative gene for PCD affecting respiratory cilia.","method":"Whole-exome sequencing, Sanger sequencing, qRT-PCR, immunofluorescence, transmission electron microscopy of respiratory epithelial cells","journal":"Molecular genetics & genomic medicine","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple orthogonal methods (TEM, IF, qPCR) in patient-derived cells; single lab","pmids":["37723893"],"is_preprint":false},{"year":2024,"finding":"CFAP47 is expressed in primary cilia of human kidney tubules. Cfap47-knockout mice exhibit vacuolation of tubular cells and tubular dilation, and rare hemizygous missense variants in CFAP47 were identified in male patients with sporadic cystic kidney disease, implicating CFAP47 in cyst formation via its role in renal primary cilia.","method":"Immunohistology of human kidney tissue, Cfap47-knockout mouse model with histological analysis, whole-genome sequencing","journal":"Kidney international reports","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — KO mouse model with defined cellular phenotype plus human tissue localization; single lab, two orthogonal approaches","pmids":["39698362"],"is_preprint":false},{"year":2025,"finding":"A hemizygous missense variant CFAP47 c.3599T>A (p.Phe1200Tyr) in a PCD patient was associated with significantly decreased CFAP47 mRNA levels both in patient-derived sperm and in HEK293 cells transfected with the mutant plasmid compared to controls, suggesting that the variant impairs transcript stability.","method":"qPCR in patient sperm and transfected HEK293 cells expressing mutant vs. wild-type CFAP47 plasmid","journal":"Frontiers in medicine","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single lab, single method (qPCR), no protein-level or structural mechanistic follow-up","pmids":["40636384"],"is_preprint":false},{"year":2026,"finding":"Co-immunoprecipitation experiments confirmed CFAP47 as an interacting protein of androglobin (ADGB) in spermatozoa, placing CFAP47 within an ADGB-associated complex that includes TTC29.","method":"Co-immunoprecipitation (STRING database screen followed by experimental Co-IP validation)","journal":"Journal of Sichuan University. Medical science edition","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single Co-IP experiment, single lab, no further mechanistic characterization of CFAP47 within this complex","pmids":["41834962"],"is_preprint":false}],"current_model":"CFAP47 is a core structural component of the axonemal central apparatus (CA) in motile cilia and sperm flagella: its N-terminal domains anchor to the C1 microtubule, its central CFAP47-ring interacts with HYDIN, and its C-terminal region anchors to C2, thereby bridging C1 and C2; loss of CFAP47 disrupts this bridge, reduces sperm progressive motility, and causes multiple morphological abnormalities of the flagella (MMAF), with additional roles in respiratory cilia (PCD) and renal primary cilia (polycystic kidney disease) established by patient variants and knockout mouse models."},"narrative":{"mechanistic_narrative":"CFAP47 is a core structural component of the axonemal central apparatus (CA) of motile cilia and sperm flagella, where it physically bridges the two central microtubules to maintain flagellar architecture and motility [PMID:40473901]. In situ cryo-electron tomography of mouse sperm resolved CFAP47 as a constituent of the C1–C2 bridge: its N-terminal domains bind the C1 microtubule, its central CFAP47-ring engages HYDIN, and its C-terminal region anchors to the C2 microtubule, and loss of CFAP47 produces a hollowed bridge in the CA with significantly reduced sperm progressive motility [PMID:40473901, PMID:bio_10.1101_2024.08.06.606614]. Consistent with this structural role, hemizygous loss-of-function variants in X-linked CFAP47 in humans reduce CFAP47 protein in spermatozoa and cause multiple morphological abnormalities of the flagella (MMAF) and asthenoteratozoospermia, a phenotype recapitulated in Cfap47-mutant male mice whose sterility is rescued by ICSI [PMID:33472045]. Beyond its CA scaffolding function, CFAP47 supports broader flagellar morphogenesis by enabling correct localization of WDR87 to the midpiece [PMID:36571501]. Loss-of-function variants also cause primary ciliary dyskinesia affecting respiratory cilia [PMID:37723893] and are associated with cystic kidney disease through a role in renal primary cilia, where Cfap47-knockout mice develop tubular vacuolation and dilation [PMID:39698362].","teleology":[{"year":2021,"claim":"Establishing that CFAP47 has an essential function in sperm flagella, this work showed that human loss-of-function variants cause a defined male-infertility syndrome rather than being incidental polymorphisms.","evidence":"Whole-exome sequencing of MMAF patients with immunoblotting/immunofluorescence protein quantification and a Cfap47-mutant mouse with ICSI rescue","pmids":["33472045"],"confidence":"High","gaps":["Did not resolve the molecular/structural role of CFAP47 within the flagellum","No interacting partners identified","Mechanism linking protein loss to flagellar malformation unknown"]},{"year":2022,"claim":"Moving from phenotype to mechanism, this work identified a physical partner of CFAP47 and showed CFAP47 is required for that partner's correct localization, framing CFAP47 as a transport/assembly factor in the midpiece.","evidence":"Co-immunoprecipitation plus immunofluorescence/immunoblotting in CFAP47-mutant human spermatozoa showing WDR87 depletion and mislocalization","pmids":["36571501"],"confidence":"Medium","gaps":["Single lab; interaction not reciprocally validated","Direct vs indirect nature of CFAP47–WDR87 binding unresolved","Mechanism of WDR87 transport not defined"]},{"year":2023,"claim":"These studies extended CFAP47's disease relevance beyond sperm to motile respiratory cilia, defining it as a PCD gene, while a separate report linked a missense variant to broader sperm structural defects and additional candidate interactions.","evidence":"WES/qRT-PCR/IF/TEM in patient respiratory epithelium (PCD); IF/WB/Co-IP in CFAP47-mutant sperm reporting interactions with CFAP65, CFAP69, SEPTIN4","pmids":["37723893","37424856"],"confidence":"Medium","gaps":["The CFAP65/CFAP69/SEPTIN4 interactions are Low-confidence and lack deep validation","How a CA-bridge protein contributes to mitochondrial sheath and annulus defects is unexplained","Tissue-specific requirements in respiratory vs sperm cilia not dissected"]},{"year":2024,"claim":"This work generalized CFAP47 function to non-motile primary cilia, implicating it in renal cyst formation and broadening its physiological scope beyond motile-cilia syndromes.","evidence":"Immunohistology of human kidney tubules, Cfap47-knockout mouse histology (tubular vacuolation/dilation), and whole-genome sequencing of cystic kidney patients","pmids":["39698362"],"confidence":"Medium","gaps":["Mechanism of CFAP47 action in primary (non-motile) cilia undefined","Causality of patient variants in kidney disease not proven beyond association","Relationship between renal ciliary role and axonemal CA role unclear"]},{"year":2025,"claim":"Cryo-ET with atomic modelling delivered the decisive mechanistic advance, defining CFAP47 as the structural element that tethers C1 to C2 via domain-specific contacts and HYDIN engagement, explaining why its loss collapses the central-apparatus bridge.","evidence":"In situ cryo-electron tomography and AlphaFold2 modelling of mouse sperm CA with Cfap47-knockout structural and motility analysis","pmids":["40473901"],"confidence":"High","gaps":["Atomic contacts inferred partly from AlphaFold2 modelling rather than direct density at side-chain resolution","How the CA-bridge role relates to non-motile renal cilia function unresolved","Regulation/assembly order of CFAP47 into the CA not established"]},{"year":2025,"claim":"A patient-variant study probed the molecular consequence of a specific missense allele, indicating that some CFAP47 mutations act by reducing transcript abundance/stability rather than solely altering protein structure.","evidence":"qPCR in patient sperm and HEK293 cells transfected with mutant vs wild-type CFAP47 plasmid","pmids":["40636384"],"confidence":"Low","gaps":["Single method (qPCR), no protein-level confirmation","Mechanism of reduced transcript stability not defined","Generalizability to other CFAP47 variants unknown"]},{"year":2026,"claim":"This work placed CFAP47 in an additional flagellar protein network, expanding its potential interactome beyond the CA bridge.","evidence":"STRING-guided Co-immunoprecipitation validating CFAP47 as an ADGB (androglobin) interactor in an ADGB/TTC29-associated complex","pmids":["41834962"],"confidence":"Low","gaps":["Single Co-IP, single lab, no reciprocal or in vivo validation","Functional significance of CFAP47–ADGB association unknown","Whether this complex overlaps with the CA-bridge role unresolved"]},{"year":null,"claim":"How CFAP47 is assembled into and recruited to the central apparatus, and how its single molecular scaffold serves both motile (sperm/respiratory) and non-motile (renal) cilia, remains unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["Assembly/recruitment hierarchy of CFAP47 into the CA bridge unknown","Mechanistic basis of renal primary-cilia phenotype not connected to CA structure","Full validated interactome and its functional partitioning undefined"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0005198","term_label":"structural molecule activity","supporting_discovery_ids":[0,1]},{"term_id":"GO:0008092","term_label":"cytoskeletal protein binding","supporting_discovery_ids":[0,3]}],"localization":[{"term_id":"GO:0005929","term_label":"cilium","supporting_discovery_ids":[0,5,6]},{"term_id":"GO:0005856","term_label":"cytoskeleton","supporting_discovery_ids":[0,1]}],"pathway":[{"term_id":"R-HSA-1852241","term_label":"Organelle biogenesis and maintenance","supporting_discovery_ids":[0]},{"term_id":"R-HSA-1474165","term_label":"Reproduction","supporting_discovery_ids":[2]}],"complexes":["central apparatus C1-C2 bridge"],"partners":["HYDIN","WDR87","ADGB","TTC29"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q6ZTR5","full_name":"Cilia- and flagella-associated protein 47","aliases":[],"length_aa":3187,"mass_kda":361.6,"function":"Plays a role in flagellar formation and sperm motility","subcellular_location":"Cytoplasm, cytoskeleton, flagellum basal body","url":"https://www.uniprot.org/uniprotkb/Q6ZTR5/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/CFAP47","classification":"Not Classified","n_dependent_lines":0,"n_total_lines":1208,"dependency_fraction":0.0},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/CFAP47","total_profiled":1310},"omim":[{"mim_id":"620274","title":"WD REPEAT-CONTAINING PROTEIN 87; WDR87","url":"https://www.omim.org/entry/620274"},{"mim_id":"614270","title":"CILIA- AND FLAGELLA-ASSOCIATED PROTEIN 65; CFAP65","url":"https://www.omim.org/entry/614270"},{"mim_id":"301059","title":"SPERMATOGENIC FAILURE, X-LINKED, 3; SPGFX3","url":"https://www.omim.org/entry/301059"},{"mim_id":"301057","title":"CILIA- AND FLAGELLA-ASSOCIATED PROTEIN 47; CFAP47","url":"https://www.omim.org/entry/301057"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"","locations":[],"tissue_specificity":"Tissue enhanced","tissue_distribution":"Detected in some","driving_tissues":[{"tissue":"fallopian tube","ntpm":4.4},{"tissue":"pituitary gland","ntpm":1.7},{"tissue":"retina","ntpm":1.4}],"url":"https://www.proteinatlas.org/search/CFAP47"},"hgnc":{"alias_symbol":["FLJ36601","RP13-11B7.1","MGC34831"],"prev_symbol":["CXorf59","CXorf22","CXorf30","CHDC2"]},"alphafold":{"accession":"Q6ZTR5","domains":[],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q6ZTR5","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q6ZTR5-6-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q6ZTR5-6-F1-predicted_aligned_error_v6.png","plddt_mean":71.5},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=CFAP47","jax_strain_url":"https://www.jax.org/strain/search?query=CFAP47"},"sequence":{"accession":"Q6ZTR5","fasta_url":"https://rest.uniprot.org/uniprotkb/Q6ZTR5.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q6ZTR5/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q6ZTR5"}},"corpus_meta":[{"pmid":"33472045","id":"PMC_33472045","title":"Deleterious variants in X-linked CFAP47 induce asthenoteratozoospermia and primary male infertility.","date":"2021","source":"American journal of human genetics","url":"https://pubmed.ncbi.nlm.nih.gov/33472045","citation_count":105,"is_preprint":false},{"pmid":"39267058","id":"PMC_39267058","title":"Whole exome sequencing analysis of 167 men with primary infertility.","date":"2024","source":"BMC medical genomics","url":"https://pubmed.ncbi.nlm.nih.gov/39267058","citation_count":17,"is_preprint":false},{"pmid":"36571501","id":"PMC_36571501","title":"WDR87 interacts with CFAP47 protein in the middle piece of spermatozoa flagella to participate in sperm tail assembly.","date":"2022","source":"Molecular human reproduction","url":"https://pubmed.ncbi.nlm.nih.gov/36571501","citation_count":12,"is_preprint":false},{"pmid":"37424856","id":"PMC_37424856","title":"A novel mutation in CFAP47 causes male infertility due to multiple morphological abnormalities of the sperm flagella.","date":"2023","source":"Frontiers in endocrinology","url":"https://pubmed.ncbi.nlm.nih.gov/37424856","citation_count":11,"is_preprint":false},{"pmid":"40473901","id":"PMC_40473901","title":"In situ structure of the mouse sperm central apparatus reveals mechanistic insights into asthenozoospermia.","date":"2025","source":"Cell research","url":"https://pubmed.ncbi.nlm.nih.gov/40473901","citation_count":11,"is_preprint":false},{"pmid":"37723893","id":"PMC_37723893","title":"Mutations in CFAP47, a previously reported MMAF causative gene, also contribute to the respiratory defects in patients with PCD.","date":"2023","source":"Molecular genetics & genomic medicine","url":"https://pubmed.ncbi.nlm.nih.gov/37723893","citation_count":8,"is_preprint":false},{"pmid":"39698362","id":"PMC_39698362","title":"CFAP47 is Implicated in X-Linked Polycystic Kidney Disease.","date":"2024","source":"Kidney international reports","url":"https://pubmed.ncbi.nlm.nih.gov/39698362","citation_count":5,"is_preprint":false},{"pmid":"36712874","id":"PMC_36712874","title":"Chronic granulomatous disease associated with Duchenne muscular dystrophy caused by Xp21.1 contiguous gene deletion syndrome: Case report and literature review.","date":"2023","source":"Frontiers in genetics","url":"https://pubmed.ncbi.nlm.nih.gov/36712874","citation_count":4,"is_preprint":false},{"pmid":"38491953","id":"PMC_38491953","title":"Analysis of clinical characteristics and histopathological transcription in 40 patients afflicted by epilepsy stemming from focal cortical dysplasia.","date":"2024","source":"Epilepsia open","url":"https://pubmed.ncbi.nlm.nih.gov/38491953","citation_count":3,"is_preprint":false},{"pmid":"39677330","id":"PMC_39677330","title":"Identification of differentially expressed genes in human testis biopsies with defective spermatogenesis.","date":"2024","source":"Reproductive medicine and biology","url":"https://pubmed.ncbi.nlm.nih.gov/39677330","citation_count":1,"is_preprint":false},{"pmid":"41456035","id":"PMC_41456035","title":"Identification of epileptic hippocampal sclerosis related genes through bulk and single-nucleus RNA sequencing datasets.","date":"2025","source":"Cellular and molecular life sciences : CMLS","url":"https://pubmed.ncbi.nlm.nih.gov/41456035","citation_count":1,"is_preprint":false},{"pmid":"39382080","id":"PMC_39382080","title":"Convergent evolution in high-altitude and marine mammals: Molecular adaptations to pulmonary fibrosis and hypoxia.","date":"2024","source":"Zoological research","url":"https://pubmed.ncbi.nlm.nih.gov/39382080","citation_count":1,"is_preprint":false},{"pmid":"38633811","id":"PMC_38633811","title":"CFAP47 is a novel causative gene implicated in X-linked polycystic kidney disease.","date":"2024","source":"medRxiv : the preprint server for health sciences","url":"https://pubmed.ncbi.nlm.nih.gov/38633811","citation_count":0,"is_preprint":false},{"pmid":"40636384","id":"PMC_40636384","title":"Case Report: Identification of a novel hemizygous CFAP47 variant in a primary ciliary dyskinesia patient with dual ciliary and flagellar defects.","date":"2025","source":"Frontiers in medicine","url":"https://pubmed.ncbi.nlm.nih.gov/40636384","citation_count":0,"is_preprint":false},{"pmid":"41834962","id":"PMC_41834962","title":"[Whole Exome Sequencing Identified Novel Pathogenic Mutations of ADGB in Patients With Oligoasthenozoospermia].","date":"2026","source":"Sichuan da xue xue bao. Yi xue ban = Journal of Sichuan University. Medical science edition","url":"https://pubmed.ncbi.nlm.nih.gov/41834962","citation_count":0,"is_preprint":false},{"pmid":null,"id":"bio_10.1101_2024.08.06.606614","title":"In-cell structural insight into the asymmetric assembly of central apparatus in mammalian sperm axoneme","date":"2024-08-06","source":"bioRxiv","url":"https://doi.org/10.1101/2024.08.06.606614","citation_count":0,"is_preprint":true}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":10745,"output_tokens":2472,"usd":0.034658,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":9619,"output_tokens":2984,"usd":0.061347,"stage2_stop_reason":"end_turn"},"total_usd":0.096005,"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\": 2025,\n      \"finding\": \"Cryo-electron tomography combined with AlphaFold2 resolved the in-cell structure of mouse sperm central apparatus (CA) at sub-nanometer resolution, revealing that CFAP47 is a core structural component of the C1-C2 bridge: its N-terminal domains bind C1 microtubule, its central CFAP47-ring interacts with HYDIN, and its C-terminal region anchors to C2 microtubule. Cfap47-knockout mice display a hollowing bridge in the CA structure and significantly reduced sperm progressive motility, directly confirming CFAP47's role in tethering C1 and C2 within the central apparatus.\",\n      \"method\": \"In situ cryo-electron tomography, AlphaFold2 atomic modelling, Cfap47-knockout mouse model with sperm motility assay and structural analysis\",\n      \"journal\": \"Cell research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — near-complete atomic model from in-cell cryo-ET, domain-level structural mapping, validated by KO mouse phenotype; replicated across two papers (PMID:40473901 and preprint bio_10.1101_2024.08.06.606614)\",\n      \"pmids\": [\"40473901\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"In situ cryo-electron tomography of mouse sperm axoneme identified CFAP47 and HYDIN as the long chain-like ASH-containing proteins responsible for connecting C1 and C2 microtubules in the central apparatus. Sperm from Cfap47-knockout mice displayed a hollowing bridge in the CA structure correlated with reduced progressive motility.\",\n      \"method\": \"In situ cryo-electron tomography, AlphaFold2 atomic modelling, Cfap47-knockout mouse sperm structural and motility analysis\",\n      \"journal\": \"bioRxiv\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — in-cell cryo-ET structure with near-complete atomic model and KO mouse validation; consistent with peer-reviewed companion paper PMID:40473901\",\n      \"pmids\": [\"bio_10.1101_2024.08.06.606614\"],\n      \"is_preprint\": true\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"Hemizygous loss-of-function missense variants in X-linked CFAP47 cause MMAF and asthenoteratozoospermia in humans. Immunoblotting and immunofluorescence confirmed markedly reduced CFAP47 protein in spermatozoa from affected men. A Cfap47-mutated mouse model recapitulated the phenotype with reduced sperm motility and abnormal flagellar morphology; male mice were sterile but fertility was rescued by ICSI.\",\n      \"method\": \"Whole-exome sequencing, immunoblotting, immunofluorescence, Cfap47-mutant mouse model, ICSI rescue experiment\",\n      \"journal\": \"American journal of human genetics\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple orthogonal methods (WES, protein quantification, mouse KO with defined phenotype), replicated across multiple unrelated patients and a mouse model\",\n      \"pmids\": [\"33472045\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"CFAP47 physically interacts with WDR87 in the flagellar midpiece of spermatozoa. In CFAP47-mutant men, WDR87 protein was also significantly decreased and mislocalized to a position adjacent to the spermatozoa nuclei rather than the midpiece, indicating that CFAP47 is required for WDR87 transport during spermatozoa flagella biogenesis.\",\n      \"method\": \"Co-immunoprecipitation (interaction identified), immunofluorescence and immunoblotting in CFAP47-mutant human spermatozoa\",\n      \"journal\": \"Molecular human reproduction\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — interaction identified by co-IP with functional consequence shown by protein mislocalization in patient material; single lab, two orthogonal methods\",\n      \"pmids\": [\"36571501\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"A novel CFAP47 missense mutation (p.V472M) reduces CFAP47 protein in spermatozoa and is associated with disorganized mitochondrial sheath, defective sperm annulus, and abnormal sperm head morphology in addition to MMAF. Mechanism analysis indicated that CFAP47 may regulate expression of CFAP65, CFAP69 and SEPTIN4 through physical interactions, suggesting CFAP47 participates in a protein complex modulating sperm morphogenesis.\",\n      \"method\": \"Immunofluorescence, western blotting, co-immunoprecipitation (physical interactions with CFAP65, CFAP69, SEPTIN4)\",\n      \"journal\": \"Frontiers in endocrinology\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single lab, Co-IP interactions reported but limited mechanistic follow-up; interaction data described as 'mechanism analysis' without deep validation\",\n      \"pmids\": [\"37424856\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"Hemizygous missense variants of X-linked CFAP47 were identified in two unrelated patients with primary ciliary dyskinesia (PCD). CFAP47 expression was significantly reduced in respiratory epithelial cells of affected individuals both in vivo and in vitro, and a reduction in the number of epithelial ciliary cells and basal bodies was observed by immunofluorescence and transmission electron microscopy, establishing CFAP47 as a causative gene for PCD affecting respiratory cilia.\",\n      \"method\": \"Whole-exome sequencing, Sanger sequencing, qRT-PCR, immunofluorescence, transmission electron microscopy of respiratory epithelial cells\",\n      \"journal\": \"Molecular genetics & genomic medicine\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple orthogonal methods (TEM, IF, qPCR) in patient-derived cells; single lab\",\n      \"pmids\": [\"37723893\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"CFAP47 is expressed in primary cilia of human kidney tubules. Cfap47-knockout mice exhibit vacuolation of tubular cells and tubular dilation, and rare hemizygous missense variants in CFAP47 were identified in male patients with sporadic cystic kidney disease, implicating CFAP47 in cyst formation via its role in renal primary cilia.\",\n      \"method\": \"Immunohistology of human kidney tissue, Cfap47-knockout mouse model with histological analysis, whole-genome sequencing\",\n      \"journal\": \"Kidney international reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — KO mouse model with defined cellular phenotype plus human tissue localization; single lab, two orthogonal approaches\",\n      \"pmids\": [\"39698362\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"A hemizygous missense variant CFAP47 c.3599T>A (p.Phe1200Tyr) in a PCD patient was associated with significantly decreased CFAP47 mRNA levels both in patient-derived sperm and in HEK293 cells transfected with the mutant plasmid compared to controls, suggesting that the variant impairs transcript stability.\",\n      \"method\": \"qPCR in patient sperm and transfected HEK293 cells expressing mutant vs. wild-type CFAP47 plasmid\",\n      \"journal\": \"Frontiers in medicine\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single lab, single method (qPCR), no protein-level or structural mechanistic follow-up\",\n      \"pmids\": [\"40636384\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"Co-immunoprecipitation experiments confirmed CFAP47 as an interacting protein of androglobin (ADGB) in spermatozoa, placing CFAP47 within an ADGB-associated complex that includes TTC29.\",\n      \"method\": \"Co-immunoprecipitation (STRING database screen followed by experimental Co-IP validation)\",\n      \"journal\": \"Journal of Sichuan University. Medical science edition\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single Co-IP experiment, single lab, no further mechanistic characterization of CFAP47 within this complex\",\n      \"pmids\": [\"41834962\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"CFAP47 is a core structural component of the axonemal central apparatus (CA) in motile cilia and sperm flagella: its N-terminal domains anchor to the C1 microtubule, its central CFAP47-ring interacts with HYDIN, and its C-terminal region anchors to C2, thereby bridging C1 and C2; loss of CFAP47 disrupts this bridge, reduces sperm progressive motility, and causes multiple morphological abnormalities of the flagella (MMAF), with additional roles in respiratory cilia (PCD) and renal primary cilia (polycystic kidney disease) established by patient variants and knockout mouse models.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"CFAP47 is a core structural component of the axonemal central apparatus (CA) of motile cilia and sperm flagella, where it physically bridges the two central microtubules to maintain flagellar architecture and motility [#0]. In situ cryo-electron tomography of mouse sperm resolved CFAP47 as a constituent of the C1–C2 bridge: its N-terminal domains bind the C1 microtubule, its central CFAP47-ring engages HYDIN, and its C-terminal region anchors to the C2 microtubule, and loss of CFAP47 produces a hollowed bridge in the CA with significantly reduced sperm progressive motility [#0, #1]. Consistent with this structural role, hemizygous loss-of-function variants in X-linked CFAP47 in humans reduce CFAP47 protein in spermatozoa and cause multiple morphological abnormalities of the flagella (MMAF) and asthenoteratozoospermia, a phenotype recapitulated in Cfap47-mutant male mice whose sterility is rescued by ICSI [#2]. Beyond its CA scaffolding function, CFAP47 supports broader flagellar morphogenesis by enabling correct localization of WDR87 to the midpiece [#3]. Loss-of-function variants also cause primary ciliary dyskinesia affecting respiratory cilia [#5] and are associated with cystic kidney disease through a role in renal primary cilia, where Cfap47-knockout mice develop tubular vacuolation and dilation [#6].\",\n  \"teleology\": [\n    {\n      \"year\": 2021,\n      \"claim\": \"Establishing that CFAP47 has an essential function in sperm flagella, this work showed that human loss-of-function variants cause a defined male-infertility syndrome rather than being incidental polymorphisms.\",\n      \"evidence\": \"Whole-exome sequencing of MMAF patients with immunoblotting/immunofluorescence protein quantification and a Cfap47-mutant mouse with ICSI rescue\",\n      \"pmids\": [\"33472045\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not resolve the molecular/structural role of CFAP47 within the flagellum\", \"No interacting partners identified\", \"Mechanism linking protein loss to flagellar malformation unknown\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Moving from phenotype to mechanism, this work identified a physical partner of CFAP47 and showed CFAP47 is required for that partner's correct localization, framing CFAP47 as a transport/assembly factor in the midpiece.\",\n      \"evidence\": \"Co-immunoprecipitation plus immunofluorescence/immunoblotting in CFAP47-mutant human spermatozoa showing WDR87 depletion and mislocalization\",\n      \"pmids\": [\"36571501\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single lab; interaction not reciprocally validated\", \"Direct vs indirect nature of CFAP47–WDR87 binding unresolved\", \"Mechanism of WDR87 transport not defined\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"These studies extended CFAP47's disease relevance beyond sperm to motile respiratory cilia, defining it as a PCD gene, while a separate report linked a missense variant to broader sperm structural defects and additional candidate interactions.\",\n      \"evidence\": \"WES/qRT-PCR/IF/TEM in patient respiratory epithelium (PCD); IF/WB/Co-IP in CFAP47-mutant sperm reporting interactions with CFAP65, CFAP69, SEPTIN4\",\n      \"pmids\": [\"37723893\", \"37424856\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"The CFAP65/CFAP69/SEPTIN4 interactions are Low-confidence and lack deep validation\", \"How a CA-bridge protein contributes to mitochondrial sheath and annulus defects is unexplained\", \"Tissue-specific requirements in respiratory vs sperm cilia not dissected\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"This work generalized CFAP47 function to non-motile primary cilia, implicating it in renal cyst formation and broadening its physiological scope beyond motile-cilia syndromes.\",\n      \"evidence\": \"Immunohistology of human kidney tubules, Cfap47-knockout mouse histology (tubular vacuolation/dilation), and whole-genome sequencing of cystic kidney patients\",\n      \"pmids\": [\"39698362\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanism of CFAP47 action in primary (non-motile) cilia undefined\", \"Causality of patient variants in kidney disease not proven beyond association\", \"Relationship between renal ciliary role and axonemal CA role unclear\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Cryo-ET with atomic modelling delivered the decisive mechanistic advance, defining CFAP47 as the structural element that tethers C1 to C2 via domain-specific contacts and HYDIN engagement, explaining why its loss collapses the central-apparatus bridge.\",\n      \"evidence\": \"In situ cryo-electron tomography and AlphaFold2 modelling of mouse sperm CA with Cfap47-knockout structural and motility analysis\",\n      \"pmids\": [\"40473901\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Atomic contacts inferred partly from AlphaFold2 modelling rather than direct density at side-chain resolution\", \"How the CA-bridge role relates to non-motile renal cilia function unresolved\", \"Regulation/assembly order of CFAP47 into the CA not established\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"A patient-variant study probed the molecular consequence of a specific missense allele, indicating that some CFAP47 mutations act by reducing transcript abundance/stability rather than solely altering protein structure.\",\n      \"evidence\": \"qPCR in patient sperm and HEK293 cells transfected with mutant vs wild-type CFAP47 plasmid\",\n      \"pmids\": [\"40636384\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"Single method (qPCR), no protein-level confirmation\", \"Mechanism of reduced transcript stability not defined\", \"Generalizability to other CFAP47 variants unknown\"]\n    },\n    {\n      \"year\": 2026,\n      \"claim\": \"This work placed CFAP47 in an additional flagellar protein network, expanding its potential interactome beyond the CA bridge.\",\n      \"evidence\": \"STRING-guided Co-immunoprecipitation validating CFAP47 as an ADGB (androglobin) interactor in an ADGB/TTC29-associated complex\",\n      \"pmids\": [\"41834962\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"Single Co-IP, single lab, no reciprocal or in vivo validation\", \"Functional significance of CFAP47–ADGB association unknown\", \"Whether this complex overlaps with the CA-bridge role unresolved\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How CFAP47 is assembled into and recruited to the central apparatus, and how its single molecular scaffold serves both motile (sperm/respiratory) and non-motile (renal) cilia, remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Assembly/recruitment hierarchy of CFAP47 into the CA bridge unknown\", \"Mechanistic basis of renal primary-cilia phenotype not connected to CA structure\", \"Full validated interactome and its functional partitioning undefined\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0005198\", \"supporting_discovery_ids\": [0, 1]},\n      {\"term_id\": \"GO:0008092\", \"supporting_discovery_ids\": [0, 3]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005929\", \"supporting_discovery_ids\": [0, 5, 6]},\n      {\"term_id\": \"GO:0005856\", \"supporting_discovery_ids\": [0, 1]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-1852241\", \"supporting_discovery_ids\": [0]},\n      {\"term_id\": \"R-HSA-1474165\", \"supporting_discovery_ids\": [2]}\n    ],\n    \"complexes\": [\"central apparatus C1-C2 bridge\"],\n    \"partners\": [\"HYDIN\", \"WDR87\", \"ADGB\", \"TTC29\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"faith_supported":5,"faith_total":5,"faith_pct":100.0}}