{"gene":"CFAP47","run_date":"2026-04-28T17:28:52","timeline":{"discoveries":[{"year":2025,"finding":"Cryo-electron tomography combined with AlphaFold2 resolved the in-cell structure of mouse sperm central apparatus 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. HYDIN forms a semicircular chain encircling both C1 and C2, and together with CFAP47 these proteins tether the two central microtubules. Cfap47-knockout mice displayed a hollowing bridge in the CA structure and significantly reduced sperm motility, confirming the structural and functional role.","method":"In situ cryo-electron tomography, AlphaFold2 atomic modeling, Cfap47-knockout mouse phenotyping (progressive motility assay, CA structural analysis)","journal":"Cell research","confidence":"High","confidence_rationale":"Tier 1 — near-complete atomic model with in-cell cryo-ET plus functional KO validation; independently corroborated by preprint","pmids":["40473901"],"is_preprint":false},{"year":2024,"finding":"In situ cryo-ET of mouse sperm central apparatus identified CFAP47 as one of 39 CA-associated proteins; CFAP47 and HYDIN are ASH-domain-containing chain-like proteins responsible for connecting C1 and C2 microtubules. Cfap47-knockout sperm showed a hollowing bridge in the CA and reduced progressive motility.","method":"In situ cryo-electron tomography, AlphaFold2, Cfap47-knockout mouse sperm motility and ultrastructure analysis","journal":"bioRxiv (preprint)","confidence":"High","confidence_rationale":"Tier 1 — structural reconstitution with KO functional validation; preprint version of the peer-reviewed Cell Research paper","pmids":["bio_10.1101_2024.08.06.606614"],"is_preprint":true},{"year":2021,"finding":"CFAP47 is required for normal sperm flagellar morphology and motility. Loss-of-function hemizygous missense variants in men caused MMAF (multiple morphological abnormalities of the flagella). A Cfap47-mutated mouse model showed sterile males with reduced sperm motility and abnormal flagellar morphology; fertility was rescued by ICSI, confirming the flagella-specific role.","method":"Whole-exome sequencing, immunoblotting, immunofluorescence in human spermatozoa, Cfap47-mutant mouse model (sperm motility, morphology, ICSI rescue)","journal":"American journal of human genetics","confidence":"High","confidence_rationale":"Tier 2 — multiple human probands, mouse KO model with defined phenotype, replicated across two independent cohorts","pmids":["33472045"],"is_preprint":false},{"year":2022,"finding":"CFAP47 physically interacts with WDR87 in the flagellar midpiece of spermatozoa, forming a complex involved in sperm tail assembly. When CFAP47 is absent or reduced due to missense variants, WDR87 protein is also significantly decreased and mislocalizes to a position adjacent to the sperm nucleus rather than the midpiece, indicating that CFAP47 is required for WDR87 transportation during flagella biogenesis.","method":"Co-immunoprecipitation (interaction), immunofluorescence and immunoblotting in CFAP47-mutant human spermatozoa","journal":"Molecular human reproduction","confidence":"Medium","confidence_rationale":"Tier 3 — single Co-IP plus localization data in patient cells; single lab","pmids":["36571501"],"is_preprint":false},{"year":2023,"finding":"CFAP47 physically interacts with CFAP65, CFAP69, and SEPTIN4. Loss of CFAP47 (missense variant p.V472M) in patients correlates with reduced expression of these interactors, suggesting CFAP47 regulates their stability or expression to modulate sperm morphogenesis, including proper formation of the mitochondrial sheath and annulus.","method":"Immunofluorescence, western blotting in patient spermatozoa; co-immunoprecipitation implied by 'physical interactions' statement","journal":"Frontiers in endocrinology","confidence":"Low","confidence_rationale":"Tier 3 — single lab, interaction described without full reciprocal Co-IP details, weak mechanistic follow-up","pmids":["37424856"],"is_preprint":false},{"year":2024,"finding":"CFAP47 is expressed in primary cilia of human kidney tubules. In Cfap47-knockout mice, renal tubular cells exhibit vacuolation and tubular dilation, demonstrating a functional role for CFAP47 in primary cilia of renal epithelium and linking its loss to cyst formation.","method":"Immunohistology of human kidney tissue, Cfap47-knockout mouse renal histology (tubular dilation, vacuolation phenotype)","journal":"Kidney international reports","confidence":"Medium","confidence_rationale":"Tier 2 — KO mouse model with defined renal phenotype and human tissue localization; single lab","pmids":["39698362"],"is_preprint":false},{"year":2023,"finding":"Hemizygous missense variants in CFAP47 cause reduced ciliary cell numbers and basal bodies in respiratory epithelium of PCD patients, demonstrating that CFAP47 is required for normal motile cilia structure and/or abundance in airway cells in addition to sperm flagella.","method":"Immunofluorescence of respiratory epithelial cells, transmission electron microscopy, qPCR in patient-derived cells","journal":"Molecular genetics & genomic medicine","confidence":"Medium","confidence_rationale":"Tier 2 — direct cellular phenotype in patient-derived cells with TEM ultrastructural analysis; two independent cases","pmids":["37723893"],"is_preprint":false},{"year":2026,"finding":"CFAP47 was identified as an interacting protein of ADGB (androglobin) by co-immunoprecipitation, placing CFAP47 in a protein complex in sperm flagella that also includes TTC29.","method":"Co-immunoprecipitation validated by STRING database screening","journal":"Journal of Sichuan University. Medical science edition","confidence":"Low","confidence_rationale":"Tier 3 — single Co-IP, single lab, limited mechanistic follow-up on CFAP47 specifically","pmids":["41834962"],"is_preprint":false}],"current_model":"CFAP47 is a structurally essential component of the sperm axoneme central apparatus (CA) bridge, where its N-terminal domains bind the C1 microtubule, its central CFAP47-ring interacts with HYDIN, and its C-terminal region anchors to C2, thereby tethering C1 and C2 to enable sperm motility; CFAP47 also localizes to primary cilia of renal tubules and airway epithelium, where its loss causes ciliary defects, and in the flagellar midpiece it forms a complex with WDR87 required for sperm tail assembly."},"narrative":{"teleology":[{"year":2021,"claim":"Establishing that CFAP47 is required for sperm flagellar integrity and motility resolved the gene's primary physiological function: hemizygous loss-of-function variants in men caused MMAF, and a Cfap47-mutant mouse model phenocopied the defect with rescue by ICSI, proving a flagella-specific role.","evidence":"Whole-exome sequencing in multiple MMAF probands, Cfap47-mutant mouse sperm phenotyping and ICSI rescue","pmids":["33472045"],"confidence":"High","gaps":["Molecular mechanism by which CFAP47 supports flagellar structure was unknown","Whether CFAP47 functions in cilia outside sperm was untested","Direct protein interaction partners were uncharacterized"]},{"year":2022,"claim":"Identification of a CFAP47–WDR87 physical complex in the flagellar midpiece, with WDR87 mislocalization upon CFAP47 loss, established that CFAP47 has a cargo-transport or scaffolding role during sperm tail assembly beyond simple structural integrity.","evidence":"Co-immunoprecipitation and immunofluorescence in CFAP47-mutant human spermatozoa","pmids":["36571501"],"confidence":"Medium","gaps":["Interaction demonstrated by single Co-IP without reciprocal pull-down","Whether WDR87 mislocalization is a direct or indirect consequence of CFAP47 loss was not resolved","The domain of CFAP47 mediating the WDR87 interaction was not mapped"]},{"year":2023,"claim":"Discovery that CFAP47 variants reduce ciliary cell numbers and basal bodies in respiratory epithelium of PCD patients broadened the gene's role from sperm-only to a general motile cilia function.","evidence":"Immunofluorescence and TEM of respiratory epithelial cells from two independent patients with CFAP47 missense variants","pmids":["37723893"],"confidence":"Medium","gaps":["Whether the respiratory phenotype reflects a direct structural role of CFAP47 in airway cilia or a ciliogenesis defect was not distinguished","Full PCD clinical characterization (situs inversus, mucociliary clearance) was limited"]},{"year":2024,"claim":"Demonstration that CFAP47 localizes to primary cilia of renal tubules and that Cfap47-knockout mice develop tubular vacuolation and dilation extended the gene's functional scope to primary (non-motile) cilia and implicated it in renal ciliopathy.","evidence":"Immunohistology of human kidney, Cfap47-KO mouse renal histology","pmids":["39698362"],"confidence":"Medium","gaps":["Whether the renal phenotype is due to structural disruption of primary cilia or a signaling defect was not resolved","Progression to cystic kidney disease was not longitudinally assessed"]},{"year":2025,"claim":"Sub-nanometer cryo-ET combined with AlphaFold2 modeling resolved the molecular architecture of CFAP47 within the central apparatus bridge, showing that its N-terminal ASH domains bind C1, a central ring contacts HYDIN, and the C-terminus anchors to C2 — providing the first atomic-level explanation for how the central pair is tethered.","evidence":"In situ cryo-electron tomography of mouse sperm with AlphaFold2 atomic fitting; Cfap47-KO mouse validation showing hollowed CA bridge and reduced motility","pmids":["40473901"],"confidence":"High","gaps":["Whether the same bridge architecture exists in airway motile cilia or primary cilia was not tested","How loss of the bridge mechanistically propagates to outer doublet dynein regulation is unknown","Post-translational modifications regulating CFAP47 incorporation into the bridge were not examined"]},{"year":null,"claim":"How CFAP47's dual roles — as a central apparatus bridge component in motile cilia and as a factor in primary cilia of kidney and possibly other tissues — relate mechanistically remains unresolved; whether CFAP47 serves a structural versus signaling scaffold function in primary cilia is an open question.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No structural data for CFAP47 in primary cilia","Genotype–phenotype correlation across tissues (sperm, airway, kidney) not systematically established","Whether CFAP47 participates in dynein-arm regulatory signaling through the CA remains untested"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0005198","term_label":"structural molecule activity","supporting_discovery_ids":[0,1,2]}],"localization":[{"term_id":"GO:0005929","term_label":"cilium","supporting_discovery_ids":[0,2,5,6]},{"term_id":"GO:0008092","term_label":"cytoskeletal protein binding","supporting_discovery_ids":[0]}],"pathway":[{"term_id":"R-HSA-1852241","term_label":"Organelle biogenesis and maintenance","supporting_discovery_ids":[0,2,3]}],"complexes":["Central apparatus C1-C2 bridge complex"],"partners":["HYDIN","WDR87","CFAP65","CFAP69","SEPTIN4","ADGB","TTC29"],"other_free_text":[]},"mechanistic_narrative":"CFAP47 is a structural scaffolding protein of the motile cilium and sperm flagellum, essential for connecting the central pair microtubules of the axoneme and for proper flagellar assembly. In situ cryo-electron tomography of mouse sperm reveals that CFAP47 is a core component of the central apparatus (CA) bridge: its N-terminal ASH domains bind the C1 microtubule, its central ring domain interacts with HYDIN, and its C-terminal region anchors to C2, thereby tethering C1 and C2; knockout of Cfap47 produces a hollowed bridge and severely reduced sperm motility [PMID:40473901]. CFAP47 also physically interacts with WDR87 in the flagellar midpiece and is required for WDR87 localization during sperm tail biogenesis [PMID:36571501]. Loss-of-function hemizygous variants in CFAP47 cause X-linked multiple morphological abnormalities of the flagella (MMAF) and asthenozoospermia in men, with additional ciliary defects observed in renal tubular epithelium and respiratory epithelium consistent with a broader ciliopathy [PMID:33472045, PMID:39698362, PMID:37723893]."},"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":102,"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":"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":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":"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":7,"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":7,"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":2,"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":"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":"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":9949,"output_tokens":2033,"usd":0.030171},"stage2":{"model":"claude-opus-4-6","input_tokens":5304,"output_tokens":1855,"usd":0.109342},"total_usd":0.139513,"stage1_batch_id":"msgbatch_011kfMfE81o6CTcyhVUqumuW","stage2_batch_id":"msgbatch_01DTputS6WNkH745x1nVSoBo","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 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. HYDIN forms a semicircular chain encircling both C1 and C2, and together with CFAP47 these proteins tether the two central microtubules. Cfap47-knockout mice displayed a hollowing bridge in the CA structure and significantly reduced sperm motility, confirming the structural and functional role.\",\n      \"method\": \"In situ cryo-electron tomography, AlphaFold2 atomic modeling, Cfap47-knockout mouse phenotyping (progressive motility assay, CA structural analysis)\",\n      \"journal\": \"Cell research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — near-complete atomic model with in-cell cryo-ET plus functional KO validation; independently corroborated by preprint\",\n      \"pmids\": [\"40473901\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"In situ cryo-ET of mouse sperm central apparatus identified CFAP47 as one of 39 CA-associated proteins; CFAP47 and HYDIN are ASH-domain-containing chain-like proteins responsible for connecting C1 and C2 microtubules. Cfap47-knockout sperm showed a hollowing bridge in the CA and reduced progressive motility.\",\n      \"method\": \"In situ cryo-electron tomography, AlphaFold2, Cfap47-knockout mouse sperm motility and ultrastructure analysis\",\n      \"journal\": \"bioRxiv (preprint)\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — structural reconstitution with KO functional validation; preprint version of the peer-reviewed Cell Research paper\",\n      \"pmids\": [\"bio_10.1101_2024.08.06.606614\"],\n      \"is_preprint\": true\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"CFAP47 is required for normal sperm flagellar morphology and motility. Loss-of-function hemizygous missense variants in men caused MMAF (multiple morphological abnormalities of the flagella). A Cfap47-mutated mouse model showed sterile males with reduced sperm motility and abnormal flagellar morphology; fertility was rescued by ICSI, confirming the flagella-specific role.\",\n      \"method\": \"Whole-exome sequencing, immunoblotting, immunofluorescence in human spermatozoa, Cfap47-mutant mouse model (sperm motility, morphology, ICSI rescue)\",\n      \"journal\": \"American journal of human genetics\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — multiple human probands, mouse KO model with defined phenotype, replicated across two independent cohorts\",\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, forming a complex involved in sperm tail assembly. When CFAP47 is absent or reduced due to missense variants, WDR87 protein is also significantly decreased and mislocalizes to a position adjacent to the sperm nucleus rather than the midpiece, indicating that CFAP47 is required for WDR87 transportation during flagella biogenesis.\",\n      \"method\": \"Co-immunoprecipitation (interaction), immunofluorescence and immunoblotting in CFAP47-mutant human spermatozoa\",\n      \"journal\": \"Molecular human reproduction\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 — single Co-IP plus localization data in patient cells; single lab\",\n      \"pmids\": [\"36571501\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"CFAP47 physically interacts with CFAP65, CFAP69, and SEPTIN4. Loss of CFAP47 (missense variant p.V472M) in patients correlates with reduced expression of these interactors, suggesting CFAP47 regulates their stability or expression to modulate sperm morphogenesis, including proper formation of the mitochondrial sheath and annulus.\",\n      \"method\": \"Immunofluorescence, western blotting in patient spermatozoa; co-immunoprecipitation implied by 'physical interactions' statement\",\n      \"journal\": \"Frontiers in endocrinology\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 — single lab, interaction described without full reciprocal Co-IP details, weak mechanistic follow-up\",\n      \"pmids\": [\"37424856\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"CFAP47 is expressed in primary cilia of human kidney tubules. In Cfap47-knockout mice, renal tubular cells exhibit vacuolation and tubular dilation, demonstrating a functional role for CFAP47 in primary cilia of renal epithelium and linking its loss to cyst formation.\",\n      \"method\": \"Immunohistology of human kidney tissue, Cfap47-knockout mouse renal histology (tubular dilation, vacuolation phenotype)\",\n      \"journal\": \"Kidney international reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — KO mouse model with defined renal phenotype and human tissue localization; single lab\",\n      \"pmids\": [\"39698362\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"Hemizygous missense variants in CFAP47 cause reduced ciliary cell numbers and basal bodies in respiratory epithelium of PCD patients, demonstrating that CFAP47 is required for normal motile cilia structure and/or abundance in airway cells in addition to sperm flagella.\",\n      \"method\": \"Immunofluorescence of respiratory epithelial cells, transmission electron microscopy, qPCR in patient-derived cells\",\n      \"journal\": \"Molecular genetics & genomic medicine\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — direct cellular phenotype in patient-derived cells with TEM ultrastructural analysis; two independent cases\",\n      \"pmids\": [\"37723893\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"CFAP47 was identified as an interacting protein of ADGB (androglobin) by co-immunoprecipitation, placing CFAP47 in a protein complex in sperm flagella that also includes TTC29.\",\n      \"method\": \"Co-immunoprecipitation validated by STRING database screening\",\n      \"journal\": \"Journal of Sichuan University. Medical science edition\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 — single Co-IP, single lab, limited mechanistic follow-up on CFAP47 specifically\",\n      \"pmids\": [\"41834962\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"CFAP47 is a structurally essential component of the sperm axoneme central apparatus (CA) bridge, where its N-terminal domains bind the C1 microtubule, its central CFAP47-ring interacts with HYDIN, and its C-terminal region anchors to C2, thereby tethering C1 and C2 to enable sperm motility; CFAP47 also localizes to primary cilia of renal tubules and airway epithelium, where its loss causes ciliary defects, and in the flagellar midpiece it forms a complex with WDR87 required for sperm tail assembly.\"\n}\n```","stage2_raw":"```json\n{\n  \"mechanistic_narrative\": \"CFAP47 is a structural scaffolding protein of the motile cilium and sperm flagellum, essential for connecting the central pair microtubules of the axoneme and for proper flagellar assembly. In situ cryo-electron tomography of mouse sperm reveals that CFAP47 is a core component of the central apparatus (CA) bridge: its N-terminal ASH domains bind the C1 microtubule, its central ring domain interacts with HYDIN, and its C-terminal region anchors to C2, thereby tethering C1 and C2; knockout of Cfap47 produces a hollowed bridge and severely reduced sperm motility [PMID:40473901]. CFAP47 also physically interacts with WDR87 in the flagellar midpiece and is required for WDR87 localization during sperm tail biogenesis [PMID:36571501]. Loss-of-function hemizygous variants in CFAP47 cause X-linked multiple morphological abnormalities of the flagella (MMAF) and asthenozoospermia in men, with additional ciliary defects observed in renal tubular epithelium and respiratory epithelium consistent with a broader ciliopathy [PMID:33472045, PMID:39698362, PMID:37723893].\",\n  \"teleology\": [\n    {\n      \"year\": 2021,\n      \"claim\": \"Establishing that CFAP47 is required for sperm flagellar integrity and motility resolved the gene's primary physiological function: hemizygous loss-of-function variants in men caused MMAF, and a Cfap47-mutant mouse model phenocopied the defect with rescue by ICSI, proving a flagella-specific role.\",\n      \"evidence\": \"Whole-exome sequencing in multiple MMAF probands, Cfap47-mutant mouse sperm phenotyping and ICSI rescue\",\n      \"pmids\": [\"33472045\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Molecular mechanism by which CFAP47 supports flagellar structure was unknown\",\n        \"Whether CFAP47 functions in cilia outside sperm was untested\",\n        \"Direct protein interaction partners were uncharacterized\"\n      ]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Identification of a CFAP47–WDR87 physical complex in the flagellar midpiece, with WDR87 mislocalization upon CFAP47 loss, established that CFAP47 has a cargo-transport or scaffolding role during sperm tail assembly beyond simple structural integrity.\",\n      \"evidence\": \"Co-immunoprecipitation and immunofluorescence in CFAP47-mutant human spermatozoa\",\n      \"pmids\": [\"36571501\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Interaction demonstrated by single Co-IP without reciprocal pull-down\",\n        \"Whether WDR87 mislocalization is a direct or indirect consequence of CFAP47 loss was not resolved\",\n        \"The domain of CFAP47 mediating the WDR87 interaction was not mapped\"\n      ]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Discovery that CFAP47 variants reduce ciliary cell numbers and basal bodies in respiratory epithelium of PCD patients broadened the gene's role from sperm-only to a general motile cilia function.\",\n      \"evidence\": \"Immunofluorescence and TEM of respiratory epithelial cells from two independent patients with CFAP47 missense variants\",\n      \"pmids\": [\"37723893\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Whether the respiratory phenotype reflects a direct structural role of CFAP47 in airway cilia or a ciliogenesis defect was not distinguished\",\n        \"Full PCD clinical characterization (situs inversus, mucociliary clearance) was limited\"\n      ]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Demonstration that CFAP47 localizes to primary cilia of renal tubules and that Cfap47-knockout mice develop tubular vacuolation and dilation extended the gene's functional scope to primary (non-motile) cilia and implicated it in renal ciliopathy.\",\n      \"evidence\": \"Immunohistology of human kidney, Cfap47-KO mouse renal histology\",\n      \"pmids\": [\"39698362\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Whether the renal phenotype is due to structural disruption of primary cilia or a signaling defect was not resolved\",\n        \"Progression to cystic kidney disease was not longitudinally assessed\"\n      ]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Sub-nanometer cryo-ET combined with AlphaFold2 modeling resolved the molecular architecture of CFAP47 within the central apparatus bridge, showing that its N-terminal ASH domains bind C1, a central ring contacts HYDIN, and the C-terminus anchors to C2 — providing the first atomic-level explanation for how the central pair is tethered.\",\n      \"evidence\": \"In situ cryo-electron tomography of mouse sperm with AlphaFold2 atomic fitting; Cfap47-KO mouse validation showing hollowed CA bridge and reduced motility\",\n      \"pmids\": [\"40473901\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Whether the same bridge architecture exists in airway motile cilia or primary cilia was not tested\",\n        \"How loss of the bridge mechanistically propagates to outer doublet dynein regulation is unknown\",\n        \"Post-translational modifications regulating CFAP47 incorporation into the bridge were not examined\"\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How CFAP47's dual roles — as a central apparatus bridge component in motile cilia and as a factor in primary cilia of kidney and possibly other tissues — relate mechanistically remains unresolved; whether CFAP47 serves a structural versus signaling scaffold function in primary cilia is an open question.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"No structural data for CFAP47 in primary cilia\",\n        \"Genotype–phenotype correlation across tissues (sperm, airway, kidney) not systematically established\",\n        \"Whether CFAP47 participates in dynein-arm regulatory signaling through the CA remains untested\"\n      ]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0005198\", \"supporting_discovery_ids\": [0, 1, 2]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005929\", \"supporting_discovery_ids\": [0, 2, 5, 6]},\n      {\"term_id\": \"GO:0008092\", \"supporting_discovery_ids\": [0]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-1852241\", \"supporting_discovery_ids\": [0, 2, 3]}\n    ],\n    \"complexes\": [\n      \"Central apparatus C1-C2 bridge complex\"\n    ],\n    \"partners\": [\n      \"HYDIN\",\n      \"WDR87\",\n      \"CFAP65\",\n      \"CFAP69\",\n      \"SEPTIN4\",\n      \"ADGB\",\n      \"TTC29\"\n    ],\n    \"other_free_text\": []\n  }\n}\n```"}