{"gene":"CFAP57","run_date":"2026-04-28T17:28:52","timeline":{"discoveries":[{"year":2019,"finding":"FAP57/WDR65 (CFAP57 ortholog in Chlamydomonas) is required for targeting assembly of a subset of inner dynein arms (IDAs) to a specific location in the 96 nm axonemal repeat. Using cryo-electron tomography with epitope tagging and gold labeling, FAP57 forms an extended structure that interconnects multiple IDAs and regulatory complexes. High-resolution proteomics confirmed FAP57 forms a discrete complex within the axoneme.","method":"Insertional mutagenesis, cryo-electron tomography, epitope tagging with gold labeling, mass spectrometry proteomics","journal":"Molecular biology of the cell","confidence":"High","confidence_rationale":"Tier 1–2 — multiple orthogonal structural and proteomic methods in a single rigorous study","pmids":["31483737"],"is_preprint":false},{"year":2020,"finding":"CFAP57 localizes throughout the ciliary axoneme in normal human nasal epithelial cells. A PCD-causing nonsense mutation (p.Arg588*) results in skipping of exon 11 (58 amino acids including portions of WD repeats), and the truncated protein fails to incorporate into the axoneme. Loss of CFAP57 causes reduced beat frequency and altered ciliary waveform. In Chlamydomonas fap57 mutants, the 'g' inner dyneins (DHC7 and DHC3) and 'd' inner dynein (DHC2) are reduced, implicating CFAP57 in inner dynein arm assembly.","method":"Whole exome sequencing, immunofluorescence localization, siRNA knockdown in hTECs, tandem mass tag mass spectrometry in Chlamydomonas mutants, high-speed video microscopy","journal":"PLoS genetics","confidence":"High","confidence_rationale":"Tier 2 — multiple orthogonal methods (localization, proteomics, KD phenotype) replicated in human cells and Chlamydomonas","pmids":["32764743"],"is_preprint":false},{"year":2018,"finding":"Fap57p (CFAP57 ortholog in Tetrahymena) is adjacent to the WD-repeat proteins Fap43p and Fap44p and is positioned near the two-headed inner dynein arm IDA I1. Loss of Fap43p or Fap44p alters ciliary waveform and reduces swimming speed, and these proteins are part of a complex adjacent to Fap57p.","method":"Genetic loss-of-function, ciliary motility analysis, immunofluorescence, co-localization in Tetrahymena thermophila","journal":"Cellular and molecular life sciences : CMLS","confidence":"Medium","confidence_rationale":"Tier 3 — localization and motility phenotype in Tetrahymena ortholog; no direct binding assay for FAP57 itself","pmids":["29687140"],"is_preprint":false},{"year":2023,"finding":"CFAP57 loss-of-function mutations (p.R958* and p.R913*) disrupt inner dynein arm (IDA) assembly in sperm flagella, with single-headed IDAs preferentially affected. The long transcript-encoded CFAP57 protein is specifically lost in spermatozoa from affected individuals and Cfap57-mutant mice, while the short transcript product is unaffected, demonstrating isoform-specific function in sperm.","method":"Whole-exome sequencing, CRISPR knock-in mouse model, electron microscopy of sperm ultrastructure, immunofluorescence, Western blot","journal":"JCI insight","confidence":"High","confidence_rationale":"Tier 2 — mouse model recapitulates human phenotype with ultrastructural and molecular validation","pmids":["36752199"],"is_preprint":false},{"year":2025,"finding":"CFAP57 interacts with MYH10 (non-muscle myosin IIB), identified by immunoprecipitation-mass spectrometry. In CFAP57-mutant sperm, MYH10 is mislocalized to the mid-piece and absent from the principal and end pieces. This mislocalization is accompanied by reduced expression of IFT88, a key intraflagellar transport component, establishing CFAP57 as a regulator of MYH10 positioning and IFT88-dependent flagellar assembly.","method":"Immunoprecipitation-mass spectrometry (IP-MS), immunofluorescence, immunoelectron microscopy, CRISPR-Cas9 mouse model","journal":"Human genomics","confidence":"Medium","confidence_rationale":"Tier 2 — IP-MS identification of interaction partner confirmed by immunolocalization and mouse model, single lab","pmids":["41466333"],"is_preprint":false},{"year":2024,"finding":"CFAP57 interacts with CCDC113, which acts as an adaptor protein connecting radial spokes, the nexin-dynein regulatory complex (N-DRC), and doublet microtubules in the sperm axoneme. CCDC113 disruption impairs sperm flagella and head-tail coupling apparatus, and its binding partners include both CFAP57 and CFAP91.","method":"Co-immunoprecipitation, mouse knockout model, electron microscopy, immunofluorescence","journal":"eLife","confidence":"Medium","confidence_rationale":"Tier 2 — reciprocal co-IP with mouse KO validation; CFAP57 is binding partner, not primary subject","pmids":["39671309"],"is_preprint":false},{"year":2025,"finding":"DNAH10 (inner arm dynein heavy chain) interacts with CFAP57 as part of the inner dynein arm f (IDAf) complex, confirmed by co-immunoprecipitation. Loss of DNAH10 leads to reduced expression of CFAP57 in patient cells and Dnah10 KO mice, indicating CFAP57 is a component of the IDAf complex.","method":"Co-immunoprecipitation, immunostaining, mouse knockout model, proteomics","journal":"Orphanet journal of rare diseases","confidence":"Medium","confidence_rationale":"Tier 2 — co-IP confirmed interaction; CFAP57 is a binding partner within IDAf complex context","pmids":["40898283"],"is_preprint":false},{"year":2022,"finding":"CRISPR/Cas9 F0 crispant zebrafish targeting cfap57 recapitulates ciliary phenotypes consistent with loss of ciliary function, validating CFAP57 as a cilia-associated gene required for normal ciliary function in vivo.","method":"CRISPR/Cas9 F0 crispant zebrafish, ciliary phenotype analysis","journal":"Disease models & mechanisms","confidence":"Low","confidence_rationale":"Tier 3 — phenotypic screen without detailed mechanistic follow-up for CFAP57 specifically","pmids":["36533556"],"is_preprint":false}],"current_model":"CFAP57 is a conserved WD-repeat/coiled-coil domain protein that localizes along the ciliary and flagellar axoneme, where it forms an extended structural complex that docks and targets a subset of inner dynein arms (particularly single-headed IDAs and the 'g'- and 'd'-type dyneins) to specific positions within the 96 nm axonemal repeat, interacts with regulatory hubs including DNAH10 (IDAf complex), CCDC113, and MYH10, and is required for intraflagellar transport (IFT88 regulation) during flagellogenesis; loss of its long isoform disrupts IDA assembly causing reduced ciliary beat frequency, altered waveform, and MMAF-associated male infertility."},"narrative":{"teleology":[{"year":2018,"claim":"Positioning CFAP57 within the axonemal repeat architecture: Fap57p in Tetrahymena was shown to reside adjacent to the WD-repeat proteins Fap43p/Fap44p near the two-headed IDA I1, establishing that it occupies a defined structural niche within the 96 nm repeat.","evidence":"Genetic loss-of-function and immunofluorescence co-localization in Tetrahymena thermophila","pmids":["29687140"],"confidence":"Medium","gaps":["No direct binding assay for FAP57 itself; adjacency inferred from Fap43/44 studies","Precise molecular contacts between FAP57 and neighboring complexes unresolved","Functional consequences of FAP57 loss not tested in this organism"]},{"year":2019,"claim":"Defining the structural and molecular function of CFAP57: cryo-ET with gold labeling in Chlamydomonas revealed that FAP57 forms an extended structure interconnecting multiple IDAs and regulatory complexes, and proteomics identified it as a discrete axonemal complex, establishing its role as a structural scaffold for IDA targeting within the 96 nm repeat.","evidence":"Insertional mutagenesis, cryo-electron tomography with epitope tagging and gold labeling, mass spectrometry proteomics in Chlamydomonas","pmids":["31483737"],"confidence":"High","gaps":["Identity of all direct binding partners within the extended FAP57 structure not resolved","Whether the scaffold function is conserved in mammalian cilia not yet tested"]},{"year":2020,"claim":"Translating the scaffold function to human disease: CFAP57 localizes along the human ciliary axoneme, and a PCD-causing nonsense mutation prevents axonemal incorporation of the truncated protein, leading to reduced beat frequency and loss of specific IDAs ('g' and 'd' type), directly linking the Chlamydomonas mechanism to human ciliary disease.","evidence":"Whole-exome sequencing, immunofluorescence in human nasal epithelial cells, siRNA knockdown in hTECs, TMT-MS in Chlamydomonas mutants, high-speed video microscopy","pmids":["32764743"],"confidence":"High","gaps":["Whether all single-headed IDA subtypes are equally dependent on CFAP57 remains unclear","Mechanism by which the truncated protein fails to incorporate into the axoneme is unknown"]},{"year":2022,"claim":"In vivo validation in vertebrates: CRISPR F0 crispant zebrafish targeting cfap57 displayed ciliary phenotypes, providing cross-species confirmation that CFAP57 is required for normal ciliary function in a vertebrate model.","evidence":"CRISPR/Cas9 F0 crispant zebrafish phenotype screen","pmids":["36533556"],"confidence":"Low","gaps":["Screening-level validation without detailed mechanistic or ultrastructural analysis of cfap57 specifically","Mosaicism inherent to F0 crispants limits interpretation of severity","No IDA-specific assessment performed"]},{"year":2023,"claim":"Resolving isoform-specific function: the long CFAP57 isoform is specifically required for single-headed IDA assembly in sperm, as patient mutations and a CRISPR knock-in mouse model showed selective loss of the long isoform protein with corresponding IDA defects, while the short isoform remained intact.","evidence":"Whole-exome sequencing, CRISPR knock-in mouse model, electron microscopy, Western blot, immunofluorescence","pmids":["36752199"],"confidence":"High","gaps":["Function of the short CFAP57 isoform is undefined","Whether isoform-specific requirements extend to respiratory cilia is untested","Structural basis for why the long isoform is selectively needed for single-headed IDAs is unknown"]},{"year":2024,"claim":"Identifying CFAP57 as part of a regulatory hub connecting axonemal sub-structures: CCDC113 was shown to bind CFAP57 and serve as an adaptor linking radial spokes, N-DRC, and doublet microtubules, placing CFAP57 within a multi-component regulatory network.","evidence":"Co-immunoprecipitation, mouse knockout model, electron microscopy, immunofluorescence","pmids":["39671309"],"confidence":"Medium","gaps":["Whether CFAP57-CCDC113 interaction is direct or mediated by additional subunits not determined","Functional consequence of specifically disrupting the CFAP57-CCDC113 interface is unknown"]},{"year":2025,"claim":"Placing CFAP57 within the IDAf complex and expanding its interaction network: CFAP57 was confirmed as a DNAH10/IDAf complex component by co-IP, and separately shown to interact with MYH10 and regulate IFT88 expression, broadening its role from a static scaffold to a regulator of flagellar assembly and cargo transport.","evidence":"Co-immunoprecipitation, IP-mass spectrometry, immunoelectron microscopy, mouse knockout models, proteomics","pmids":["40898283","41466333"],"confidence":"Medium","gaps":["Mechanism by which CFAP57 regulates IFT88 expression is unknown (transcriptional vs. post-translational)","Whether MYH10 interaction is direct or within a larger complex is unresolved","CFAP57's role in IDAf complex assembly vs. stability not distinguished"]},{"year":null,"claim":"The structural basis for how CFAP57 selectively targets specific IDA subtypes to defined positions within the 96 nm repeat, the function of its short isoform, and whether its IFT-regulatory role extends beyond spermatogenesis to respiratory and nodal cilia remain open questions.","evidence":"","pmids":[],"confidence":"High","gaps":["No high-resolution structure of mammalian CFAP57 or its complexes","Short isoform function entirely uncharacterized","Tissue-specific requirements beyond sperm and respiratory cilia untested"]}],"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":[0,2,5]}],"localization":[{"term_id":"GO:0005929","term_label":"cilium","supporting_discovery_ids":[0,1,2,3]},{"term_id":"GO:0005856","term_label":"cytoskeleton","supporting_discovery_ids":[0,1,5]}],"pathway":[{"term_id":"R-HSA-1852241","term_label":"Organelle biogenesis and maintenance","supporting_discovery_ids":[0,1,3,4]}],"complexes":["Inner dynein arm f (IDAf) complex"],"partners":["DNAH10","CCDC113","MYH10","IFT88","CFAP91","FAP43","FAP44"],"other_free_text":[]},"mechanistic_narrative":"CFAP57 is a conserved WD-repeat protein that functions as an extended axonemal scaffold required for the targeted assembly and docking of inner dynein arms within the 96 nm repeat of motile cilia and flagella. Cryo-electron tomography in Chlamydomonas shows that CFAP57 forms an elongated structure interconnecting multiple inner dynein arms (IDAs) and regulatory complexes, and its loss preferentially depletes single-headed IDAs including the 'g'-type (DHC7, DHC3) and 'd'-type (DHC2) dyneins [PMID:31483737, PMID:32764743]. CFAP57 is a component of the inner dynein arm f (IDAf) complex through interaction with DNAH10, physically associates with the adaptor CCDC113 linking radial spokes and the nexin-dynein regulatory complex, and regulates MYH10 positioning and IFT88-dependent intraflagellar transport during flagellogenesis [PMID:40898283, PMID:39671309, PMID:41466333]. Loss-of-function mutations in CFAP57—specifically disrupting its long isoform—cause reduced ciliary beat frequency, altered waveform, primary ciliary dyskinesia, and multiple morphological abnormalities of the sperm flagella (MMAF)-associated male infertility in humans and mice [PMID:32764743, PMID:36752199]."},"prefetch_data":{"uniprot":{"accession":"Q96MR6","full_name":"Cilia- and flagella-associated protein 57","aliases":["WD repeat-containing protein 65"],"length_aa":1250,"mass_kda":145.0,"function":"Associates with components of the nexin-dynein regulatory complex (N-DRC), a key regulator of ciliary/flagellar motility, and might act as an inner dynein arm (IDA) hub or linkage","subcellular_location":"Cytoplasm, cytoskeleton, cilium axoneme","url":"https://www.uniprot.org/uniprotkb/Q96MR6/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/CFAP57","classification":"Not Classified","n_dependent_lines":27,"n_total_lines":1208,"dependency_fraction":0.022350993377483443},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/CFAP57","total_profiled":1310},"omim":[{"mim_id":"620917","title":"SPERMATOGENIC FAILURE 95; SPGF95","url":"https://www.omim.org/entry/620917"},{"mim_id":"614259","title":"CILIA- AND FLAGELLA-ASSOCIATED PROTEIN 57; CFAP57","url":"https://www.omim.org/entry/614259"},{"mim_id":"258150","title":"SPERMATOGENIC FAILURE 1; SPGF1","url":"https://www.omim.org/entry/258150"},{"mim_id":"244400","title":"CILIARY DYSKINESIA, PRIMARY, 1; CILD1","url":"https://www.omim.org/entry/244400"},{"mim_id":"119300","title":"VAN DER WOUDE SYNDROME 1; VWS1","url":"https://www.omim.org/entry/119300"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Primary cilium","reliability":"Supported"},{"location":"Cytosol","reliability":"Supported"}],"tissue_specificity":"Group enriched","tissue_distribution":"Detected in some","driving_tissues":[{"tissue":"choroid plexus","ntpm":13.2},{"tissue":"fallopian tube","ntpm":22.0},{"tissue":"testis","ntpm":14.8}],"url":"https://www.proteinatlas.org/search/CFAP57"},"hgnc":{"alias_symbol":["FLJ32000"],"prev_symbol":["WDR65"]},"alphafold":{"accession":"Q96MR6","domains":[{"cath_id":"2.130.10.10","chopping":"54-192","consensus_level":"medium","plddt":90.422,"start":54,"end":192},{"cath_id":"2.40.10.480","chopping":"521-592","consensus_level":"medium","plddt":91.5871,"start":521,"end":592},{"cath_id":"1.20.5","chopping":"1084-1144","consensus_level":"medium","plddt":67.7751,"start":1084,"end":1144}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q96MR6","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q96MR6-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q96MR6-F1-predicted_aligned_error_v6.png","plddt_mean":78.5},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=CFAP57","jax_strain_url":"https://www.jax.org/strain/search?query=CFAP57"},"sequence":{"accession":"Q96MR6","fasta_url":"https://rest.uniprot.org/uniprotkb/Q96MR6.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q96MR6/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q96MR6"}},"corpus_meta":[{"pmid":"29687140","id":"PMC_29687140","title":"Ciliary proteins Fap43 and Fap44 interact with each other and are essential for proper cilia and flagella beating.","date":"2018","source":"Cellular and molecular life sciences : CMLS","url":"https://pubmed.ncbi.nlm.nih.gov/29687140","citation_count":42,"is_preprint":false},{"pmid":"32764743","id":"PMC_32764743","title":"Mutation of CFAP57, a protein required for the asymmetric targeting of a subset of inner dynein arms in Chlamydomonas, causes primary ciliary dyskinesia.","date":"2020","source":"PLoS genetics","url":"https://pubmed.ncbi.nlm.nih.gov/32764743","citation_count":39,"is_preprint":false},{"pmid":"31483737","id":"PMC_31483737","title":"FAP57/WDR65 targets assembly of a subset of inner arm dyneins and connects to regulatory hubs in cilia.","date":"2019","source":"Molecular biology of the cell","url":"https://pubmed.ncbi.nlm.nih.gov/31483737","citation_count":32,"is_preprint":false},{"pmid":"34400346","id":"PMC_34400346","title":"Proteomic Signature of Host Response to SARS-CoV-2 Infection in the Nasopharynx.","date":"2021","source":"Molecular & cellular proteomics : MCP","url":"https://pubmed.ncbi.nlm.nih.gov/34400346","citation_count":30,"is_preprint":false},{"pmid":"36752199","id":"PMC_36752199","title":"Loss-of-function mutations in CFAP57 cause multiple morphological abnormalities of the flagella in humans and mice.","date":"2023","source":"JCI insight","url":"https://pubmed.ncbi.nlm.nih.gov/36752199","citation_count":26,"is_preprint":false},{"pmid":"27486773","id":"PMC_27486773","title":"Integrated analysis miRNA and mRNA profiling in patients with severe oligozoospermia reveals miR-34c-3p downregulates PLCXD3 expression.","date":"2016","source":"Oncotarget","url":"https://pubmed.ncbi.nlm.nih.gov/27486773","citation_count":21,"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":"21574244","id":"PMC_21574244","title":"Genomic strategy identifies a missense mutation in WD-repeat domain 65 (WDR65) in an individual with Van der Woude syndrome.","date":"2011","source":"American journal of medical genetics. Part A","url":"https://pubmed.ncbi.nlm.nih.gov/21574244","citation_count":12,"is_preprint":false},{"pmid":"39671309","id":"PMC_39671309","title":"CCDC113 stabilizes sperm axoneme and head-tail coupling apparatus to ensure male fertility.","date":"2024","source":"eLife","url":"https://pubmed.ncbi.nlm.nih.gov/39671309","citation_count":7,"is_preprint":false},{"pmid":"22447971","id":"PMC_22447971","title":"Transcriptional targeting in the airway using novel gene regulatory elements.","date":"2012","source":"American journal of respiratory cell and molecular biology","url":"https://pubmed.ncbi.nlm.nih.gov/22447971","citation_count":5,"is_preprint":false},{"pmid":"41466333","id":"PMC_41466333","title":"Mutations in CFAP57 disrupt the localization of MYH10 and IFT88, leading to flagellogenesis failure in humans and mice.","date":"2025","source":"Human genomics","url":"https://pubmed.ncbi.nlm.nih.gov/41466333","citation_count":0,"is_preprint":false},{"pmid":"41793497","id":"PMC_41793497","title":"A novel CFAP57 nonsense mutation causes asthenozoospermia in a consanguineous Emirati family.","date":"2026","source":"Molecular biology reports","url":"https://pubmed.ncbi.nlm.nih.gov/41793497","citation_count":0,"is_preprint":false},{"pmid":"40898283","id":"PMC_40898283","title":"DNAH10 mutation cause primary ciliary dyskinesia with defects of IDAf complex assembly and lung fibrosis manifestation.","date":"2025","source":"Orphanet journal of rare diseases","url":"https://pubmed.ncbi.nlm.nih.gov/40898283","citation_count":0,"is_preprint":false},{"pmid":"40431640","id":"PMC_40431640","title":"Anthraquinone-2-Carboxylic Acid Is a Potential Antiviral Candidate Against Influenza Viruses In Vitro and In Vivo.","date":"2025","source":"Viruses","url":"https://pubmed.ncbi.nlm.nih.gov/40431640","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":8754,"output_tokens":2161,"usd":0.029338},"stage2":{"model":"claude-opus-4-6","input_tokens":5434,"output_tokens":2388,"usd":0.130305},"total_usd":0.159643,"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\": 2019,\n      \"finding\": \"FAP57/WDR65 (CFAP57 ortholog in Chlamydomonas) is required for targeting assembly of a subset of inner dynein arms (IDAs) to a specific location in the 96 nm axonemal repeat. Using cryo-electron tomography with epitope tagging and gold labeling, FAP57 forms an extended structure that interconnects multiple IDAs and regulatory complexes. High-resolution proteomics confirmed FAP57 forms a discrete complex within the axoneme.\",\n      \"method\": \"Insertional mutagenesis, cryo-electron tomography, epitope tagging with gold labeling, mass spectrometry proteomics\",\n      \"journal\": \"Molecular biology of the cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 — multiple orthogonal structural and proteomic methods in a single rigorous study\",\n      \"pmids\": [\"31483737\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"CFAP57 localizes throughout the ciliary axoneme in normal human nasal epithelial cells. A PCD-causing nonsense mutation (p.Arg588*) results in skipping of exon 11 (58 amino acids including portions of WD repeats), and the truncated protein fails to incorporate into the axoneme. Loss of CFAP57 causes reduced beat frequency and altered ciliary waveform. In Chlamydomonas fap57 mutants, the 'g' inner dyneins (DHC7 and DHC3) and 'd' inner dynein (DHC2) are reduced, implicating CFAP57 in inner dynein arm assembly.\",\n      \"method\": \"Whole exome sequencing, immunofluorescence localization, siRNA knockdown in hTECs, tandem mass tag mass spectrometry in Chlamydomonas mutants, high-speed video microscopy\",\n      \"journal\": \"PLoS genetics\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — multiple orthogonal methods (localization, proteomics, KD phenotype) replicated in human cells and Chlamydomonas\",\n      \"pmids\": [\"32764743\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"Fap57p (CFAP57 ortholog in Tetrahymena) is adjacent to the WD-repeat proteins Fap43p and Fap44p and is positioned near the two-headed inner dynein arm IDA I1. Loss of Fap43p or Fap44p alters ciliary waveform and reduces swimming speed, and these proteins are part of a complex adjacent to Fap57p.\",\n      \"method\": \"Genetic loss-of-function, ciliary motility analysis, immunofluorescence, co-localization in Tetrahymena thermophila\",\n      \"journal\": \"Cellular and molecular life sciences : CMLS\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 — localization and motility phenotype in Tetrahymena ortholog; no direct binding assay for FAP57 itself\",\n      \"pmids\": [\"29687140\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"CFAP57 loss-of-function mutations (p.R958* and p.R913*) disrupt inner dynein arm (IDA) assembly in sperm flagella, with single-headed IDAs preferentially affected. The long transcript-encoded CFAP57 protein is specifically lost in spermatozoa from affected individuals and Cfap57-mutant mice, while the short transcript product is unaffected, demonstrating isoform-specific function in sperm.\",\n      \"method\": \"Whole-exome sequencing, CRISPR knock-in mouse model, electron microscopy of sperm ultrastructure, immunofluorescence, Western blot\",\n      \"journal\": \"JCI insight\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — mouse model recapitulates human phenotype with ultrastructural and molecular validation\",\n      \"pmids\": [\"36752199\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"CFAP57 interacts with MYH10 (non-muscle myosin IIB), identified by immunoprecipitation-mass spectrometry. In CFAP57-mutant sperm, MYH10 is mislocalized to the mid-piece and absent from the principal and end pieces. This mislocalization is accompanied by reduced expression of IFT88, a key intraflagellar transport component, establishing CFAP57 as a regulator of MYH10 positioning and IFT88-dependent flagellar assembly.\",\n      \"method\": \"Immunoprecipitation-mass spectrometry (IP-MS), immunofluorescence, immunoelectron microscopy, CRISPR-Cas9 mouse model\",\n      \"journal\": \"Human genomics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — IP-MS identification of interaction partner confirmed by immunolocalization and mouse model, single lab\",\n      \"pmids\": [\"41466333\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"CFAP57 interacts with CCDC113, which acts as an adaptor protein connecting radial spokes, the nexin-dynein regulatory complex (N-DRC), and doublet microtubules in the sperm axoneme. CCDC113 disruption impairs sperm flagella and head-tail coupling apparatus, and its binding partners include both CFAP57 and CFAP91.\",\n      \"method\": \"Co-immunoprecipitation, mouse knockout model, electron microscopy, immunofluorescence\",\n      \"journal\": \"eLife\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — reciprocal co-IP with mouse KO validation; CFAP57 is binding partner, not primary subject\",\n      \"pmids\": [\"39671309\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"DNAH10 (inner arm dynein heavy chain) interacts with CFAP57 as part of the inner dynein arm f (IDAf) complex, confirmed by co-immunoprecipitation. Loss of DNAH10 leads to reduced expression of CFAP57 in patient cells and Dnah10 KO mice, indicating CFAP57 is a component of the IDAf complex.\",\n      \"method\": \"Co-immunoprecipitation, immunostaining, mouse knockout model, proteomics\",\n      \"journal\": \"Orphanet journal of rare diseases\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — co-IP confirmed interaction; CFAP57 is a binding partner within IDAf complex context\",\n      \"pmids\": [\"40898283\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"CRISPR/Cas9 F0 crispant zebrafish targeting cfap57 recapitulates ciliary phenotypes consistent with loss of ciliary function, validating CFAP57 as a cilia-associated gene required for normal ciliary function in vivo.\",\n      \"method\": \"CRISPR/Cas9 F0 crispant zebrafish, ciliary phenotype analysis\",\n      \"journal\": \"Disease models & mechanisms\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 — phenotypic screen without detailed mechanistic follow-up for CFAP57 specifically\",\n      \"pmids\": [\"36533556\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"CFAP57 is a conserved WD-repeat/coiled-coil domain protein that localizes along the ciliary and flagellar axoneme, where it forms an extended structural complex that docks and targets a subset of inner dynein arms (particularly single-headed IDAs and the 'g'- and 'd'-type dyneins) to specific positions within the 96 nm axonemal repeat, interacts with regulatory hubs including DNAH10 (IDAf complex), CCDC113, and MYH10, and is required for intraflagellar transport (IFT88 regulation) during flagellogenesis; loss of its long isoform disrupts IDA assembly causing reduced ciliary beat frequency, altered waveform, and MMAF-associated male infertility.\"\n}\n```","stage2_raw":"```json\n{\n  \"mechanistic_narrative\": \"CFAP57 is a conserved WD-repeat protein that functions as an extended axonemal scaffold required for the targeted assembly and docking of inner dynein arms within the 96 nm repeat of motile cilia and flagella. Cryo-electron tomography in Chlamydomonas shows that CFAP57 forms an elongated structure interconnecting multiple inner dynein arms (IDAs) and regulatory complexes, and its loss preferentially depletes single-headed IDAs including the 'g'-type (DHC7, DHC3) and 'd'-type (DHC2) dyneins [PMID:31483737, PMID:32764743]. CFAP57 is a component of the inner dynein arm f (IDAf) complex through interaction with DNAH10, physically associates with the adaptor CCDC113 linking radial spokes and the nexin-dynein regulatory complex, and regulates MYH10 positioning and IFT88-dependent intraflagellar transport during flagellogenesis [PMID:40898283, PMID:39671309, PMID:41466333]. Loss-of-function mutations in CFAP57—specifically disrupting its long isoform—cause reduced ciliary beat frequency, altered waveform, primary ciliary dyskinesia, and multiple morphological abnormalities of the sperm flagella (MMAF)-associated male infertility in humans and mice [PMID:32764743, PMID:36752199].\",\n  \"teleology\": [\n    {\n      \"year\": 2018,\n      \"claim\": \"Positioning CFAP57 within the axonemal repeat architecture: Fap57p in Tetrahymena was shown to reside adjacent to the WD-repeat proteins Fap43p/Fap44p near the two-headed IDA I1, establishing that it occupies a defined structural niche within the 96 nm repeat.\",\n      \"evidence\": \"Genetic loss-of-function and immunofluorescence co-localization in Tetrahymena thermophila\",\n      \"pmids\": [\"29687140\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"No direct binding assay for FAP57 itself; adjacency inferred from Fap43/44 studies\",\n        \"Precise molecular contacts between FAP57 and neighboring complexes unresolved\",\n        \"Functional consequences of FAP57 loss not tested in this organism\"\n      ]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Defining the structural and molecular function of CFAP57: cryo-ET with gold labeling in Chlamydomonas revealed that FAP57 forms an extended structure interconnecting multiple IDAs and regulatory complexes, and proteomics identified it as a discrete axonemal complex, establishing its role as a structural scaffold for IDA targeting within the 96 nm repeat.\",\n      \"evidence\": \"Insertional mutagenesis, cryo-electron tomography with epitope tagging and gold labeling, mass spectrometry proteomics in Chlamydomonas\",\n      \"pmids\": [\"31483737\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Identity of all direct binding partners within the extended FAP57 structure not resolved\",\n        \"Whether the scaffold function is conserved in mammalian cilia not yet tested\"\n      ]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Translating the scaffold function to human disease: CFAP57 localizes along the human ciliary axoneme, and a PCD-causing nonsense mutation prevents axonemal incorporation of the truncated protein, leading to reduced beat frequency and loss of specific IDAs ('g' and 'd' type), directly linking the Chlamydomonas mechanism to human ciliary disease.\",\n      \"evidence\": \"Whole-exome sequencing, immunofluorescence in human nasal epithelial cells, siRNA knockdown in hTECs, TMT-MS in Chlamydomonas mutants, high-speed video microscopy\",\n      \"pmids\": [\"32764743\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Whether all single-headed IDA subtypes are equally dependent on CFAP57 remains unclear\",\n        \"Mechanism by which the truncated protein fails to incorporate into the axoneme is unknown\"\n      ]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"In vivo validation in vertebrates: CRISPR F0 crispant zebrafish targeting cfap57 displayed ciliary phenotypes, providing cross-species confirmation that CFAP57 is required for normal ciliary function in a vertebrate model.\",\n      \"evidence\": \"CRISPR/Cas9 F0 crispant zebrafish phenotype screen\",\n      \"pmids\": [\"36533556\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"Screening-level validation without detailed mechanistic or ultrastructural analysis of cfap57 specifically\",\n        \"Mosaicism inherent to F0 crispants limits interpretation of severity\",\n        \"No IDA-specific assessment performed\"\n      ]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Resolving isoform-specific function: the long CFAP57 isoform is specifically required for single-headed IDA assembly in sperm, as patient mutations and a CRISPR knock-in mouse model showed selective loss of the long isoform protein with corresponding IDA defects, while the short isoform remained intact.\",\n      \"evidence\": \"Whole-exome sequencing, CRISPR knock-in mouse model, electron microscopy, Western blot, immunofluorescence\",\n      \"pmids\": [\"36752199\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Function of the short CFAP57 isoform is undefined\",\n        \"Whether isoform-specific requirements extend to respiratory cilia is untested\",\n        \"Structural basis for why the long isoform is selectively needed for single-headed IDAs is unknown\"\n      ]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Identifying CFAP57 as part of a regulatory hub connecting axonemal sub-structures: CCDC113 was shown to bind CFAP57 and serve as an adaptor linking radial spokes, N-DRC, and doublet microtubules, placing CFAP57 within a multi-component regulatory network.\",\n      \"evidence\": \"Co-immunoprecipitation, mouse knockout model, electron microscopy, immunofluorescence\",\n      \"pmids\": [\"39671309\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Whether CFAP57-CCDC113 interaction is direct or mediated by additional subunits not determined\",\n        \"Functional consequence of specifically disrupting the CFAP57-CCDC113 interface is unknown\"\n      ]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Placing CFAP57 within the IDAf complex and expanding its interaction network: CFAP57 was confirmed as a DNAH10/IDAf complex component by co-IP, and separately shown to interact with MYH10 and regulate IFT88 expression, broadening its role from a static scaffold to a regulator of flagellar assembly and cargo transport.\",\n      \"evidence\": \"Co-immunoprecipitation, IP-mass spectrometry, immunoelectron microscopy, mouse knockout models, proteomics\",\n      \"pmids\": [\"40898283\", \"41466333\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Mechanism by which CFAP57 regulates IFT88 expression is unknown (transcriptional vs. post-translational)\",\n        \"Whether MYH10 interaction is direct or within a larger complex is unresolved\",\n        \"CFAP57's role in IDAf complex assembly vs. stability not distinguished\"\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"The structural basis for how CFAP57 selectively targets specific IDA subtypes to defined positions within the 96 nm repeat, the function of its short isoform, and whether its IFT-regulatory role extends beyond spermatogenesis to respiratory and nodal cilia remain open questions.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"No high-resolution structure of mammalian CFAP57 or its complexes\",\n        \"Short isoform function entirely uncharacterized\",\n        \"Tissue-specific requirements beyond sperm and respiratory cilia untested\"\n      ]\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, 2, 5]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005929\", \"supporting_discovery_ids\": [0, 1, 2, 3]},\n      {\"term_id\": \"GO:0005856\", \"supporting_discovery_ids\": [0, 1, 5]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-1852241\", \"supporting_discovery_ids\": [0, 1, 3, 4]}\n    ],\n    \"complexes\": [\n      \"Inner dynein arm f (IDAf) complex\"\n    ],\n    \"partners\": [\n      \"DNAH10\",\n      \"CCDC113\",\n      \"MYH10\",\n      \"IFT88\",\n      \"CFAP91\",\n      \"FAP43\",\n      \"FAP44\"\n    ],\n    \"other_free_text\": []\n  }\n}\n```"}