{"gene":"CFAP53","run_date":"2026-06-09T22:57:18","timeline":{"discoveries":[{"year":2012,"finding":"A homozygous deleterious mutation in CCDC11 (CFAP53) results in an abnormally smaller (truncated) protein in patient skin fibroblasts, establishing that loss-of-function of CCDC11 causes autosomal recessive laterality defects.","method":"Homozygosity mapping in a consanguineous family; protein analysis in patient-derived fibroblasts","journal":"Journal of medical genetics","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — direct protein detection in patient cells, single lab, single method confirming truncation","pmids":["22577226"],"is_preprint":false},{"year":2015,"finding":"CCDC11/CFAP53 is a component of centriolar satellites; it interacts with core satellite proteins, and its loss disrupts subcellular organization of satellite proteins and inhibits primary ciliogenesis as well as motile ciliogenesis.","method":"Co-immunoprecipitation, immunofluorescence localization, siRNA knockdown in human tracheal epithelial cells, zebrafish mutant generation (CRISPR/TALEN), Xenopus morpholino depletion","journal":"Molecular biology of the cell","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal Co-IP with satellite components, localization, loss-of-function across three model systems (human cells, Xenopus, zebrafish) with consistent phenotypes","pmids":["26538025"],"is_preprint":false},{"year":2015,"finding":"CFAP53/CCDC11 is an axonemal protein in respiratory cilia but localizes exclusively to basal bodies of cilia in Kupffer's vesicle (the laterality organ); loss of Ccdc11 strongly impairs rotational motion specifically in Kupffer's vesicle cilia while causing only minor defects in kidney cilia motility, demonstrating a differential localization and function in different motile cilia types.","method":"Immunofluorescence localization in zebrafish tissues; high-speed video microscopy of cilia motility in ccdc11-morphant zebrafish; patient mutation analysis","journal":"Human mutation","confidence":"High","confidence_rationale":"Tier 2 / Strong — direct localization with functional readout (cilia motility), replicated in zebrafish in vivo, consistent with patient phenotype","pmids":["25504577"],"is_preprint":false},{"year":2015,"finding":"CFAP53 is specifically required for cilia rotation in Kupffer's vesicle (zebrafish laterality organ), and its loss randomizes asymmetric gene expression and causes laterality defects including dextrocardia and heterotaxy.","method":"CRISPR/Cas9 genome editing in zebrafish to generate cfap53 loss-of-function mutants; cilia motility imaging in Kupffer's vesicle; in situ hybridization for asymmetric gene expression markers","journal":"Human mutation","confidence":"High","confidence_rationale":"Tier 2 / Strong — genetic knockout with defined cellular phenotype (cilia rotation) and molecular readout (asymmetric gene expression), patient mutations corroborating","pmids":["26531781"],"is_preprint":false},{"year":2017,"finding":"CCDC11/CFAP53 localizes to the centriole and actin cytoskeleton in patient-derived cells; cilia in patient cells are longer than controls; in Xenopus, Ccdc11 acts downstream of FoxJ1, and its overexpression or depletion disrupts left-right axial patterning.","method":"Immunofluorescence in patient-derived cells; Xenopus gain- and loss-of-function experiments; cilia length measurement","journal":"The International journal of developmental biology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — localization in patient cells plus epistasis (downstream of FoxJ1) in Xenopus, single lab with two orthogonal methods","pmids":["28621423"],"is_preprint":false},{"year":2020,"finding":"CFAP53 differentially localizes to centriolar satellites at the base of node (9+0) cilia and along the entire axoneme in tracheal (9+2) cilia; CFAP53 associates with microtubules and interacts with axonemal dyneins and TTC25 (a dynein docking complex component); in Cfap53 mutant mice, TTC25 and outer dynein arms are lost from node cilia but largely maintained in tracheal cilia, establishing that CFAP53 at the base facilitates axonemal transport of TTC25 and dyneins into node cilia while axonemal CFAP53 in 9+2 cilia stabilizes dynein binding to microtubules.","method":"Cfap53 knockout mouse; co-immunoprecipitation (CFAP53 with dyneins, TTC25, microtubules); immunofluorescence localization; cilia beat pattern analysis by high-speed imaging; transmission electron microscopy","journal":"PLoS genetics","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal Co-IP, immunofluorescence, genetic knockout mouse with multiple orthogonal functional readouts including TEM and cilia motility analysis","pmids":["33347437"],"is_preprint":false},{"year":2021,"finding":"CFAP53 localizes to the manchette and sperm tail during spermiogenesis; knockout of Cfap53 in male mice causes complete infertility due to impaired sperm flagellum biogenesis; CFAP53 interacts with two manchette- and sperm tail-associated proteins during spermiogenesis.","method":"Cfap53 knockout mouse; immunofluorescence localization during spermiogenesis; co-immunoprecipitation identifying interacting partners; fertility assays","journal":"Frontiers in cell and developmental biology","confidence":"High","confidence_rationale":"Tier 2 / Strong — genetic knockout with defined infertility phenotype, direct localization, and Co-IP identifying interacting partners, single lab but multiple orthogonal methods","pmids":["34124066"],"is_preprint":false},{"year":2022,"finding":"Cfap53, as a centriolar satellite protein deposited in both sperm and oocyte, facilitates proper formation of the zygotic microtubule organizing center (MTOC); loss of maternal or paternal Cfap53 arrests zebrafish embryos during the first cell cycle; Cfap53 colocalizes with γ-tubulin at the MTOC, and γ-tubulin localization at the MTOC is impaired in Cfap53-deficient embryos.","method":"Zebrafish maternal and paternal Cfap53 mutants; live imaging and immunofluorescence for γ-tubulin and centrosomal markers; co-localization studies","journal":"Development (Cambridge, England)","confidence":"High","confidence_rationale":"Tier 2 / Strong — genetic loss-of-function with defined cell-cycle arrest phenotype, direct localization, and γ-tubulin mislocalization as molecular readout, in vivo model","pmids":["35980365"],"is_preprint":false},{"year":2024,"finding":"CCDC11/CFAP53 is necessary for successful cytokinesis; during cytokinesis, CCDC11 localizes to the cytokinetic contractile ring overlapping with RhoA, and CCDC11 regulates total RhoA protein levels; depletion of Ccdc11 in Xenopus causes defects in cytokinesis leading to multiciliation in LRO cells, providing a mechanism for LR patterning defects.","method":"Xenopus morpholino depletion; immunofluorescence localization of CCDC11 and RhoA at the contractile ring; Western blot quantification of RhoA protein levels; co-immunoprecipitation; cell division assays","journal":"Cytoskeleton (Hoboken, N.J.)","confidence":"High","confidence_rationale":"Tier 2 / Strong — direct localization to contractile ring, Western blot showing RhoA level regulation, loss-of-function with defined cytokinesis phenotype, multiple orthogonal methods","pmids":["39479942"],"is_preprint":false},{"year":2025,"finding":"FAP53/CFAP53 promotes microtubule doublet (MTD) B-tubule assembly: in vitro reconstitution showed recombinant FAP53 is sufficient to drive MTD formation under physiological tubulin conditions; molecular dynamics simulations revealed FAP53 alleviates steric hindrance from the α-tubulin C-terminal tail and stabilizes B-tubule docking at the A-tubule surface; co-expression of CFAP53 with CFAP20 in HeLa cells induced ectopic MTD-like structures in the cytoplasm.","method":"In vitro reconstitution with recombinant FAP53 and purified tubulin; molecular dynamics simulations; HeLa cell co-expression assay; C. elegans WFAP-53 overexpression in neurons","journal":"bioRxiv","confidence":"High","confidence_rationale":"Tier 1 / Moderate — in vitro reconstitution demonstrating sufficiency for MTD formation, corroborated by structural simulation and cell-based ectopic MTD assay, single lab but multiple orthogonal methods","pmids":["bio_10.1101_2025.08.03.668368"],"is_preprint":true},{"year":2025,"finding":"In silico analysis of a compound heterozygous CFAP53 mutation (c.1013A>T) predicts disruption of the interaction between CFAP53 and TTC25; minigene experiments demonstrated that c.777G>T causes splicing aberrations producing truncated CFAP53 protein.","method":"Whole-exome sequencing; minigene splicing assay; in silico protein interaction prediction","journal":"Journal of applied genetics","confidence":"Low","confidence_rationale":"Tier 3 / Weak — minigene assay confirms splicing, but TTC25 interaction disruption is in silico only; single lab, no direct protein interaction validation","pmids":["39969775"],"is_preprint":false}],"current_model":"CFAP53 (CCDC11) is a centriolar satellite protein that plays multiple mechanistic roles in cilia biogenesis and cell division: it facilitates axonemal transport of outer dynein arms and the dynein docking component TTC25 into node cilia (via its basal localization) while stabilizing dynein binding to axonemal microtubules in 9+2 cilia; it promotes B-tubule nucleation to form microtubule doublets through alleviating steric hindrance at the A-tubule surface; it is required for cytokinesis by localizing to the contractile ring and regulating RhoA protein levels; it is essential for sperm flagellum biogenesis by localizing to the manchette and interacting with flagellar proteins; and it facilitates zygotic MTOC formation by enabling γ-tubulin recruitment to the centrosome, with its loss-of-function collectively causing laterality defects, male infertility, and early embryonic arrest."},"narrative":{"mechanistic_narrative":"CFAP53 (CCDC11) is a centriolar satellite and microtubule-associated protein that operates at several stages of ciliogenesis and cell division, and its loss-of-function causes autosomal recessive laterality defects [PMID:22577226, PMID:26538025]. As a centriolar satellite component it physically associates with core satellite proteins and is required for organizing them, and its depletion blocks both primary and motile ciliogenesis [PMID:26538025]. CFAP53 shows cilia-type-specific deployment: it localizes to basal bodies/centriolar satellites at the base of node (9+0) cilia, where it facilitates axonemal transport of the dynein docking factor TTC25 and outer dynein arms, whereas in tracheal (9+2) cilia it distributes along the axoneme and stabilizes dynein binding to microtubules [PMID:25504577, PMID:33347437]. Consistent with these roles, CFAP53 is specifically required for rotational motility of Kupffer's vesicle cilia, and its loss randomizes asymmetric gene expression to produce heterotaxy [PMID:25504577, PMID:26531781]. At the level of axonemal architecture, CFAP53 promotes microtubule doublet B-tubule assembly by relieving steric hindrance at the A-tubule surface and stabilizing B-tubule docking [PMID:bio_10.1101_2025.08.03.668368]. Beyond cilia, CFAP53 is required for cytokinesis, localizing to the contractile ring alongside RhoA and regulating total RhoA protein levels [PMID:39479942]; it is essential for sperm flagellum biogenesis, localizing to the manchette and sperm tail [PMID:34124066]; and it facilitates zygotic MTOC formation by enabling γ-tubulin recruitment to the centrosome, with maternal or paternal loss arresting embryos at the first cell cycle [PMID:35980365].","teleology":[{"year":2012,"claim":"Established that CFAP53/CCDC11 loss-of-function is a genetic cause of human laterality defects, linking the gene to left-right axis determination before any molecular mechanism was known.","evidence":"Homozygosity mapping in a consanguineous family with protein analysis in patient fibroblasts","pmids":["22577226"],"confidence":"Medium","gaps":["No subcellular localization or molecular partner identified","Mechanism connecting truncation to laterality defect unresolved"]},{"year":2015,"claim":"Defined CFAP53 as a centriolar satellite protein required for ciliogenesis, providing the first subcellular and interaction context for its function.","evidence":"Reciprocal Co-IP with satellite proteins, immunofluorescence, and loss-of-function in human tracheal cells, Xenopus, and zebrafish","pmids":["26538025"],"confidence":"High","gaps":["Which axonemal cargoes depend on satellite function not yet defined","Distinction between primary and motile cilia roles not mechanistically separated"]},{"year":2015,"claim":"Showed cilia-type-specific localization (axonemal in respiratory cilia, basal-body restricted in the laterality organ) explaining why loss preferentially impairs Kupffer's vesicle motility and produces heterotaxy.","evidence":"Tissue immunofluorescence, high-speed cilia motility imaging, CRISPR/Cas9 zebrafish mutants, and in situ hybridization for asymmetric markers","pmids":["25504577","26531781"],"confidence":"High","gaps":["Molecular basis of differential localization between cilia types unknown","Did not identify the transported axonemal components"]},{"year":2017,"claim":"Placed CFAP53 downstream of the ciliogenic transcription factor FoxJ1 and documented its centriolar and actin-cytoskeleton localization, positioning it within the left-right patterning program.","evidence":"Immunofluorescence in patient cells plus gain- and loss-of-function epistasis in Xenopus","pmids":["28621423"],"confidence":"Medium","gaps":["Functional significance of actin-cytoskeleton localization unresolved","Mechanism of FoxJ1-dependent regulation not defined"]},{"year":2020,"claim":"Resolved the cilia-type-specific mechanism: CFAP53 transports TTC25 and outer dynein arms into node cilia via its basal pool while stabilizing dynein-microtubule binding along 9+2 axonemes.","evidence":"Cfap53 knockout mouse with reciprocal Co-IP (dyneins, TTC25, microtubules), immunofluorescence, TEM, and cilia beat analysis","pmids":["33347437"],"confidence":"High","gaps":["Direct transport machinery linking CFAP53 to TTC25/dynein delivery not identified","Structural basis of dynein-microtubule stabilization unknown"]},{"year":2021,"claim":"Extended CFAP53 function to sperm flagellum biogenesis, demonstrating an axoneme-assembly role distinct from its centriolar satellite activity.","evidence":"Cfap53 knockout mouse with manchette/sperm-tail immunofluorescence, Co-IP of interacting proteins, and fertility assays","pmids":["34124066"],"confidence":"High","gaps":["Identities and roles of the manchette partners not fully characterized","Whether flagellar defect uses the same dynein-transport mechanism as node cilia unclear"]},{"year":2022,"claim":"Revealed a non-ciliary role in zygotic MTOC assembly, showing CFAP53 enables γ-tubulin recruitment to the centrosome and is required maternally and paternally for the first cell cycle.","evidence":"Zebrafish maternal/paternal mutants with live imaging and γ-tubulin colocalization studies","pmids":["35980365"],"confidence":"High","gaps":["Mechanism by which CFAP53 recruits γ-tubulin unresolved","Whether centriolar satellite function underlies the MTOC role not established"]},{"year":2024,"claim":"Identified a cytokinesis requirement, with CFAP53 at the contractile ring regulating RhoA protein levels, providing an alternative route to laterality defects via multiciliation in LRO cells.","evidence":"Xenopus morpholino depletion with contractile-ring immunofluorescence, RhoA Western quantification, Co-IP, and division assays","pmids":["39479942"],"confidence":"High","gaps":["Whether CFAP53 directly binds RhoA or acts indirectly not resolved","Mechanism by which RhoA levels are controlled unknown"]},{"year":2025,"claim":"Demonstrated biochemical sufficiency of CFAP53 to build microtubule doublet B-tubules, defining a direct structural role in axoneme architecture.","evidence":"In vitro reconstitution with recombinant FAP53 and tubulin, molecular dynamics simulations, HeLa co-expression with CFAP20, and C. elegans neuronal overexpression (preprint)","pmids":["bio_10.1101_2025.08.03.668368"],"confidence":"High","gaps":["Preprint, not yet peer-reviewed","Relationship between B-tubule nucleation and dynein-transport roles in vivo not integrated"]},{"year":2025,"claim":"Expanded the disease allelic spectrum by identifying splicing and predicted interaction-disrupting CFAP53 mutations in patients.","evidence":"Whole-exome sequencing, minigene splicing assay, and in silico CFAP53–TTC25 interaction prediction","pmids":["39969775"],"confidence":"Low","gaps":["TTC25 interaction disruption is in silico only with no protein-level validation","Functional consequence of the variants not tested in cells"]},{"year":null,"claim":"How CFAP53's distinct activities—centriolar satellite organization, axonemal dynein transport, B-tubule nucleation, RhoA-dependent cytokinesis, and γ-tubulin recruitment—are coordinated by a single protein remains unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No structural model unifying microtubule binding, dynein interaction, and B-tubule docking","Domain mapping of the multiple interaction surfaces not reported","Direct versus indirect nature of RhoA and γ-tubulin regulation undetermined"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0008092","term_label":"cytoskeletal protein binding","supporting_discovery_ids":[5,9]},{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[5]},{"term_id":"GO:0005198","term_label":"structural molecule activity","supporting_discovery_ids":[9]}],"localization":[{"term_id":"GO:0005929","term_label":"cilium","supporting_discovery_ids":[2,5]},{"term_id":"GO:0005856","term_label":"cytoskeleton","supporting_discovery_ids":[4,5]},{"term_id":"GO:0005815","term_label":"microtubule organizing center","supporting_discovery_ids":[7]}],"pathway":[{"term_id":"R-HSA-1852241","term_label":"Organelle biogenesis and maintenance","supporting_discovery_ids":[1,5]},{"term_id":"R-HSA-1266738","term_label":"Developmental Biology","supporting_discovery_ids":[3,4]},{"term_id":"R-HSA-1640170","term_label":"Cell Cycle","supporting_discovery_ids":[8,7]}],"complexes":["centriolar satellites"],"partners":["TTC25","CFAP20","RHOA","AXONEMAL DYNEIN"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q96M91","full_name":"Cilia- and flagella-associated protein 53","aliases":["Coiled-coil domain-containing protein 11"],"length_aa":514,"mass_kda":61.8,"function":"Microtubule inner protein (MIP) part of the dynein-decorated doublet microtubules (DMTs) in cilia axoneme, which is required for motile cilia beating (PubMed:36191189). Regulates motility patterns of both 9+0 and 9+2 motile cilia through differential localization and recruitment of axonemal dynein components (By similarity). Required for centriolar satellite integrity and non-motile cilium assembly (PubMed:26538025). Required for motile cilium formation (PubMed:26538025). Through its role in the beating of primary cilia, involved in the establishment of organ laterality during embryogenesis (PubMed:26531781). Required for sperm flagellum biogenesis and is essential for male fertility (By similarity)","subcellular_location":"Cytoplasm, cytoskeleton, cilium axoneme; Cytoplasm, cytoskeleton, flagellum axoneme; Cytoplasm, cytoskeleton, microtubule organizing center, centrosome, centriole; Cytoplasm, cytoskeleton, microtubule organizing center, centrosome, centriolar satellite; Cytoplasm, cytoskeleton, spindle pole; Cytoplasm, cytoskeleton; Cell projection, cilium","url":"https://www.uniprot.org/uniprotkb/Q96M91/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/CFAP53","classification":"Not Classified","n_dependent_lines":1,"n_total_lines":1208,"dependency_fraction":0.0008278145695364238},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/CFAP53","total_profiled":1310},"omim":[{"mim_id":"621139","title":"COILED-COIL DOMAIN-CONTAINING PROTEIN 178; CCDC178","url":"https://www.omim.org/entry/621139"},{"mim_id":"619669","title":"PIERCER OF MICROTUBULE WALL 2; PIERCE2","url":"https://www.omim.org/entry/619669"},{"mim_id":"614779","title":"HETEROTAXY, VISCERAL, 6, AUTOSOMAL; HTX6","url":"https://www.omim.org/entry/614779"},{"mim_id":"614759","title":"CILIA- AND FLAGELLA-ASSOCIATED PROTEIN 53; CFAP53","url":"https://www.omim.org/entry/614759"},{"mim_id":"614502","title":"PIERCER OF MICROTUBULE WALL 1; PIERCE1","url":"https://www.omim.org/entry/614502"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Approved","locations":[{"location":"Basal body","reliability":"Approved"},{"location":"Cytosol","reliability":"Approved"},{"location":"Nucleoplasm","reliability":"Additional"},{"location":"Nuclear membrane","reliability":"Additional"}],"tissue_specificity":"Group enriched","tissue_distribution":"Detected in many","driving_tissues":[{"tissue":"choroid plexus","ntpm":19.4},{"tissue":"fallopian tube","ntpm":26.8},{"tissue":"testis","ntpm":76.5}],"url":"https://www.proteinatlas.org/search/CFAP53"},"hgnc":{"alias_symbol":["FLJ32743"],"prev_symbol":["CCDC11"]},"alphafold":{"accession":"Q96M91","domains":[{"cath_id":"1.20.5","chopping":"40-120","consensus_level":"medium","plddt":94.6628,"start":40,"end":120}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q96M91","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q96M91-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q96M91-F1-predicted_aligned_error_v6.png","plddt_mean":86.0},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=CFAP53","jax_strain_url":"https://www.jax.org/strain/search?query=CFAP53"},"sequence":{"accession":"Q96M91","fasta_url":"https://rest.uniprot.org/uniprotkb/Q96M91.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q96M91/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q96M91"}},"corpus_meta":[{"pmid":"22577226","id":"PMC_22577226","title":"A human laterality disorder associated with recessive CCDC11 mutation.","date":"2012","source":"Journal of medical genetics","url":"https://pubmed.ncbi.nlm.nih.gov/22577226","citation_count":46,"is_preprint":false},{"pmid":"26538025","id":"PMC_26538025","title":"Ccdc11 is a novel centriolar satellite protein essential for ciliogenesis and establishment of left-right asymmetry.","date":"2015","source":"Molecular biology of the cell","url":"https://pubmed.ncbi.nlm.nih.gov/26538025","citation_count":45,"is_preprint":false},{"pmid":"25504577","id":"PMC_25504577","title":"Mutations in CCDC11, which encodes a coiled-coil containing ciliary protein, causes situs inversus due to dysmotility of monocilia in the left-right organizer.","date":"2015","source":"Human mutation","url":"https://pubmed.ncbi.nlm.nih.gov/25504577","citation_count":44,"is_preprint":false},{"pmid":"26531781","id":"PMC_26531781","title":"A Zebrafish Loss-of-Function Model for Human CFAP53 Mutations Reveals Its Specific Role in Laterality Organ Function.","date":"2015","source":"Human mutation","url":"https://pubmed.ncbi.nlm.nih.gov/26531781","citation_count":23,"is_preprint":false},{"pmid":"33347437","id":"PMC_33347437","title":"CFAP53 regulates mammalian cilia-type motility patterns through differential localization and recruitment of axonemal dynein components.","date":"2020","source":"PLoS genetics","url":"https://pubmed.ncbi.nlm.nih.gov/33347437","citation_count":21,"is_preprint":false},{"pmid":"34124066","id":"PMC_34124066","title":"Essential Role of CFAP53 in Sperm Flagellum Biogenesis.","date":"2021","source":"Frontiers in cell and developmental biology","url":"https://pubmed.ncbi.nlm.nih.gov/34124066","citation_count":20,"is_preprint":false},{"pmid":"28621423","id":"PMC_28621423","title":"Roles of the cilium-associated gene CCDC11 in left-right patterning and in laterality disorders in humans.","date":"2017","source":"The International journal of developmental biology","url":"https://pubmed.ncbi.nlm.nih.gov/28621423","citation_count":11,"is_preprint":false},{"pmid":"35980365","id":"PMC_35980365","title":"The centriolar satellite protein Cfap53 facilitates formation of the zygotic microtubule organizing center in the zebrafish embryo.","date":"2022","source":"Development (Cambridge, England)","url":"https://pubmed.ncbi.nlm.nih.gov/35980365","citation_count":3,"is_preprint":false},{"pmid":"39479942","id":"PMC_39479942","title":"The Heterotaxy Gene CCDC11 Is Important for Cytokinesis via RhoA Regulation.","date":"2024","source":"Cytoskeleton (Hoboken, N.J.)","url":"https://pubmed.ncbi.nlm.nih.gov/39479942","citation_count":3,"is_preprint":false},{"pmid":"37041101","id":"PMC_37041101","title":"Prenatal CFAP53-related laterality defect: case report and review of the literature.","date":"2023","source":"The journal of maternal-fetal & neonatal medicine : the official journal of the European Association of Perinatal Medicine, the Federation of Asia and Oceania Perinatal Societies, the International Society of Perinatal Obstetricians","url":"https://pubmed.ncbi.nlm.nih.gov/37041101","citation_count":2,"is_preprint":false},{"pmid":"39969775","id":"PMC_39969775","title":"Identification of novel biallelic mutations in CFAP53 associated with fetal situs inversus totalis and literature review.","date":"2025","source":"Journal of applied genetics","url":"https://pubmed.ncbi.nlm.nih.gov/39969775","citation_count":1,"is_preprint":false},{"pmid":null,"id":"bio_10.1101_2025.08.03.668368","title":"Physiological Reconstitution of Microtubule Doublets","date":"2025-08-04","source":"bioRxiv","url":"https://doi.org/10.1101/2025.08.03.668368","citation_count":0,"is_preprint":true}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":7317,"output_tokens":3084,"usd":0.034105,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":10459,"output_tokens":3705,"usd":0.07246,"stage2_stop_reason":"end_turn"},"total_usd":0.106565,"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\": 2012,\n      \"finding\": \"A homozygous deleterious mutation in CCDC11 (CFAP53) results in an abnormally smaller (truncated) protein in patient skin fibroblasts, establishing that loss-of-function of CCDC11 causes autosomal recessive laterality defects.\",\n      \"method\": \"Homozygosity mapping in a consanguineous family; protein analysis in patient-derived fibroblasts\",\n      \"journal\": \"Journal of medical genetics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — direct protein detection in patient cells, single lab, single method confirming truncation\",\n      \"pmids\": [\"22577226\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"CCDC11/CFAP53 is a component of centriolar satellites; it interacts with core satellite proteins, and its loss disrupts subcellular organization of satellite proteins and inhibits primary ciliogenesis as well as motile ciliogenesis.\",\n      \"method\": \"Co-immunoprecipitation, immunofluorescence localization, siRNA knockdown in human tracheal epithelial cells, zebrafish mutant generation (CRISPR/TALEN), Xenopus morpholino depletion\",\n      \"journal\": \"Molecular biology of the cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal Co-IP with satellite components, localization, loss-of-function across three model systems (human cells, Xenopus, zebrafish) with consistent phenotypes\",\n      \"pmids\": [\"26538025\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"CFAP53/CCDC11 is an axonemal protein in respiratory cilia but localizes exclusively to basal bodies of cilia in Kupffer's vesicle (the laterality organ); loss of Ccdc11 strongly impairs rotational motion specifically in Kupffer's vesicle cilia while causing only minor defects in kidney cilia motility, demonstrating a differential localization and function in different motile cilia types.\",\n      \"method\": \"Immunofluorescence localization in zebrafish tissues; high-speed video microscopy of cilia motility in ccdc11-morphant zebrafish; patient mutation analysis\",\n      \"journal\": \"Human mutation\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — direct localization with functional readout (cilia motility), replicated in zebrafish in vivo, consistent with patient phenotype\",\n      \"pmids\": [\"25504577\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"CFAP53 is specifically required for cilia rotation in Kupffer's vesicle (zebrafish laterality organ), and its loss randomizes asymmetric gene expression and causes laterality defects including dextrocardia and heterotaxy.\",\n      \"method\": \"CRISPR/Cas9 genome editing in zebrafish to generate cfap53 loss-of-function mutants; cilia motility imaging in Kupffer's vesicle; in situ hybridization for asymmetric gene expression markers\",\n      \"journal\": \"Human mutation\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — genetic knockout with defined cellular phenotype (cilia rotation) and molecular readout (asymmetric gene expression), patient mutations corroborating\",\n      \"pmids\": [\"26531781\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"CCDC11/CFAP53 localizes to the centriole and actin cytoskeleton in patient-derived cells; cilia in patient cells are longer than controls; in Xenopus, Ccdc11 acts downstream of FoxJ1, and its overexpression or depletion disrupts left-right axial patterning.\",\n      \"method\": \"Immunofluorescence in patient-derived cells; Xenopus gain- and loss-of-function experiments; cilia length measurement\",\n      \"journal\": \"The International journal of developmental biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — localization in patient cells plus epistasis (downstream of FoxJ1) in Xenopus, single lab with two orthogonal methods\",\n      \"pmids\": [\"28621423\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"CFAP53 differentially localizes to centriolar satellites at the base of node (9+0) cilia and along the entire axoneme in tracheal (9+2) cilia; CFAP53 associates with microtubules and interacts with axonemal dyneins and TTC25 (a dynein docking complex component); in Cfap53 mutant mice, TTC25 and outer dynein arms are lost from node cilia but largely maintained in tracheal cilia, establishing that CFAP53 at the base facilitates axonemal transport of TTC25 and dyneins into node cilia while axonemal CFAP53 in 9+2 cilia stabilizes dynein binding to microtubules.\",\n      \"method\": \"Cfap53 knockout mouse; co-immunoprecipitation (CFAP53 with dyneins, TTC25, microtubules); immunofluorescence localization; cilia beat pattern analysis by high-speed imaging; transmission electron microscopy\",\n      \"journal\": \"PLoS genetics\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal Co-IP, immunofluorescence, genetic knockout mouse with multiple orthogonal functional readouts including TEM and cilia motility analysis\",\n      \"pmids\": [\"33347437\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"CFAP53 localizes to the manchette and sperm tail during spermiogenesis; knockout of Cfap53 in male mice causes complete infertility due to impaired sperm flagellum biogenesis; CFAP53 interacts with two manchette- and sperm tail-associated proteins during spermiogenesis.\",\n      \"method\": \"Cfap53 knockout mouse; immunofluorescence localization during spermiogenesis; co-immunoprecipitation identifying interacting partners; fertility assays\",\n      \"journal\": \"Frontiers in cell and developmental biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — genetic knockout with defined infertility phenotype, direct localization, and Co-IP identifying interacting partners, single lab but multiple orthogonal methods\",\n      \"pmids\": [\"34124066\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"Cfap53, as a centriolar satellite protein deposited in both sperm and oocyte, facilitates proper formation of the zygotic microtubule organizing center (MTOC); loss of maternal or paternal Cfap53 arrests zebrafish embryos during the first cell cycle; Cfap53 colocalizes with γ-tubulin at the MTOC, and γ-tubulin localization at the MTOC is impaired in Cfap53-deficient embryos.\",\n      \"method\": \"Zebrafish maternal and paternal Cfap53 mutants; live imaging and immunofluorescence for γ-tubulin and centrosomal markers; co-localization studies\",\n      \"journal\": \"Development (Cambridge, England)\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — genetic loss-of-function with defined cell-cycle arrest phenotype, direct localization, and γ-tubulin mislocalization as molecular readout, in vivo model\",\n      \"pmids\": [\"35980365\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"CCDC11/CFAP53 is necessary for successful cytokinesis; during cytokinesis, CCDC11 localizes to the cytokinetic contractile ring overlapping with RhoA, and CCDC11 regulates total RhoA protein levels; depletion of Ccdc11 in Xenopus causes defects in cytokinesis leading to multiciliation in LRO cells, providing a mechanism for LR patterning defects.\",\n      \"method\": \"Xenopus morpholino depletion; immunofluorescence localization of CCDC11 and RhoA at the contractile ring; Western blot quantification of RhoA protein levels; co-immunoprecipitation; cell division assays\",\n      \"journal\": \"Cytoskeleton (Hoboken, N.J.)\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — direct localization to contractile ring, Western blot showing RhoA level regulation, loss-of-function with defined cytokinesis phenotype, multiple orthogonal methods\",\n      \"pmids\": [\"39479942\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"FAP53/CFAP53 promotes microtubule doublet (MTD) B-tubule assembly: in vitro reconstitution showed recombinant FAP53 is sufficient to drive MTD formation under physiological tubulin conditions; molecular dynamics simulations revealed FAP53 alleviates steric hindrance from the α-tubulin C-terminal tail and stabilizes B-tubule docking at the A-tubule surface; co-expression of CFAP53 with CFAP20 in HeLa cells induced ectopic MTD-like structures in the cytoplasm.\",\n      \"method\": \"In vitro reconstitution with recombinant FAP53 and purified tubulin; molecular dynamics simulations; HeLa cell co-expression assay; C. elegans WFAP-53 overexpression in neurons\",\n      \"journal\": \"bioRxiv\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — in vitro reconstitution demonstrating sufficiency for MTD formation, corroborated by structural simulation and cell-based ectopic MTD assay, single lab but multiple orthogonal methods\",\n      \"pmids\": [\"bio_10.1101_2025.08.03.668368\"],\n      \"is_preprint\": true\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"In silico analysis of a compound heterozygous CFAP53 mutation (c.1013A>T) predicts disruption of the interaction between CFAP53 and TTC25; minigene experiments demonstrated that c.777G>T causes splicing aberrations producing truncated CFAP53 protein.\",\n      \"method\": \"Whole-exome sequencing; minigene splicing assay; in silico protein interaction prediction\",\n      \"journal\": \"Journal of applied genetics\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — minigene assay confirms splicing, but TTC25 interaction disruption is in silico only; single lab, no direct protein interaction validation\",\n      \"pmids\": [\"39969775\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"CFAP53 (CCDC11) is a centriolar satellite protein that plays multiple mechanistic roles in cilia biogenesis and cell division: it facilitates axonemal transport of outer dynein arms and the dynein docking component TTC25 into node cilia (via its basal localization) while stabilizing dynein binding to axonemal microtubules in 9+2 cilia; it promotes B-tubule nucleation to form microtubule doublets through alleviating steric hindrance at the A-tubule surface; it is required for cytokinesis by localizing to the contractile ring and regulating RhoA protein levels; it is essential for sperm flagellum biogenesis by localizing to the manchette and interacting with flagellar proteins; and it facilitates zygotic MTOC formation by enabling γ-tubulin recruitment to the centrosome, with its loss-of-function collectively causing laterality defects, male infertility, and early embryonic arrest.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"CFAP53 (CCDC11) is a centriolar satellite and microtubule-associated protein that operates at several stages of ciliogenesis and cell division, and its loss-of-function causes autosomal recessive laterality defects [#0, #1]. As a centriolar satellite component it physically associates with core satellite proteins and is required for organizing them, and its depletion blocks both primary and motile ciliogenesis [#1]. CFAP53 shows cilia-type-specific deployment: it localizes to basal bodies/centriolar satellites at the base of node (9+0) cilia, where it facilitates axonemal transport of the dynein docking factor TTC25 and outer dynein arms, whereas in tracheal (9+2) cilia it distributes along the axoneme and stabilizes dynein binding to microtubules [#2, #5]. Consistent with these roles, CFAP53 is specifically required for rotational motility of Kupffer's vesicle cilia, and its loss randomizes asymmetric gene expression to produce heterotaxy [#2, #3]. At the level of axonemal architecture, CFAP53 promotes microtubule doublet B-tubule assembly by relieving steric hindrance at the A-tubule surface and stabilizing B-tubule docking [#9]. Beyond cilia, CFAP53 is required for cytokinesis, localizing to the contractile ring alongside RhoA and regulating total RhoA protein levels [#8]; it is essential for sperm flagellum biogenesis, localizing to the manchette and sperm tail [#6]; and it facilitates zygotic MTOC formation by enabling \\u03b3-tubulin recruitment to the centrosome, with maternal or paternal loss arresting embryos at the first cell cycle [#7].\",\n  \"teleology\": [\n    {\n      \"year\": 2012,\n      \"claim\": \"Established that CFAP53/CCDC11 loss-of-function is a genetic cause of human laterality defects, linking the gene to left-right axis determination before any molecular mechanism was known.\",\n      \"evidence\": \"Homozygosity mapping in a consanguineous family with protein analysis in patient fibroblasts\",\n      \"pmids\": [\"22577226\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"No subcellular localization or molecular partner identified\",\n        \"Mechanism connecting truncation to laterality defect unresolved\"\n      ]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Defined CFAP53 as a centriolar satellite protein required for ciliogenesis, providing the first subcellular and interaction context for its function.\",\n      \"evidence\": \"Reciprocal Co-IP with satellite proteins, immunofluorescence, and loss-of-function in human tracheal cells, Xenopus, and zebrafish\",\n      \"pmids\": [\"26538025\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Which axonemal cargoes depend on satellite function not yet defined\",\n        \"Distinction between primary and motile cilia roles not mechanistically separated\"\n      ]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Showed cilia-type-specific localization (axonemal in respiratory cilia, basal-body restricted in the laterality organ) explaining why loss preferentially impairs Kupffer's vesicle motility and produces heterotaxy.\",\n      \"evidence\": \"Tissue immunofluorescence, high-speed cilia motility imaging, CRISPR/Cas9 zebrafish mutants, and in situ hybridization for asymmetric markers\",\n      \"pmids\": [\"25504577\", \"26531781\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Molecular basis of differential localization between cilia types unknown\",\n        \"Did not identify the transported axonemal components\"\n      ]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Placed CFAP53 downstream of the ciliogenic transcription factor FoxJ1 and documented its centriolar and actin-cytoskeleton localization, positioning it within the left-right patterning program.\",\n      \"evidence\": \"Immunofluorescence in patient cells plus gain- and loss-of-function epistasis in Xenopus\",\n      \"pmids\": [\"28621423\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Functional significance of actin-cytoskeleton localization unresolved\",\n        \"Mechanism of FoxJ1-dependent regulation not defined\"\n      ]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Resolved the cilia-type-specific mechanism: CFAP53 transports TTC25 and outer dynein arms into node cilia via its basal pool while stabilizing dynein-microtubule binding along 9+2 axonemes.\",\n      \"evidence\": \"Cfap53 knockout mouse with reciprocal Co-IP (dyneins, TTC25, microtubules), immunofluorescence, TEM, and cilia beat analysis\",\n      \"pmids\": [\"33347437\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Direct transport machinery linking CFAP53 to TTC25/dynein delivery not identified\",\n        \"Structural basis of dynein-microtubule stabilization unknown\"\n      ]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Extended CFAP53 function to sperm flagellum biogenesis, demonstrating an axoneme-assembly role distinct from its centriolar satellite activity.\",\n      \"evidence\": \"Cfap53 knockout mouse with manchette/sperm-tail immunofluorescence, Co-IP of interacting proteins, and fertility assays\",\n      \"pmids\": [\"34124066\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Identities and roles of the manchette partners not fully characterized\",\n        \"Whether flagellar defect uses the same dynein-transport mechanism as node cilia unclear\"\n      ]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Revealed a non-ciliary role in zygotic MTOC assembly, showing CFAP53 enables \\u03b3-tubulin recruitment to the centrosome and is required maternally and paternally for the first cell cycle.\",\n      \"evidence\": \"Zebrafish maternal/paternal mutants with live imaging and \\u03b3-tubulin colocalization studies\",\n      \"pmids\": [\"35980365\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Mechanism by which CFAP53 recruits \\u03b3-tubulin unresolved\",\n        \"Whether centriolar satellite function underlies the MTOC role not established\"\n      ]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Identified a cytokinesis requirement, with CFAP53 at the contractile ring regulating RhoA protein levels, providing an alternative route to laterality defects via multiciliation in LRO cells.\",\n      \"evidence\": \"Xenopus morpholino depletion with contractile-ring immunofluorescence, RhoA Western quantification, Co-IP, and division assays\",\n      \"pmids\": [\"39479942\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Whether CFAP53 directly binds RhoA or acts indirectly not resolved\",\n        \"Mechanism by which RhoA levels are controlled unknown\"\n      ]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Demonstrated biochemical sufficiency of CFAP53 to build microtubule doublet B-tubules, defining a direct structural role in axoneme architecture.\",\n      \"evidence\": \"In vitro reconstitution with recombinant FAP53 and tubulin, molecular dynamics simulations, HeLa co-expression with CFAP20, and C. elegans neuronal overexpression (preprint)\",\n      \"pmids\": [\"bio_10.1101_2025.08.03.668368\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Preprint, not yet peer-reviewed\",\n        \"Relationship between B-tubule nucleation and dynein-transport roles in vivo not integrated\"\n      ]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Expanded the disease allelic spectrum by identifying splicing and predicted interaction-disrupting CFAP53 mutations in patients.\",\n      \"evidence\": \"Whole-exome sequencing, minigene splicing assay, and in silico CFAP53\\u2013TTC25 interaction prediction\",\n      \"pmids\": [\"39969775\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"TTC25 interaction disruption is in silico only with no protein-level validation\",\n        \"Functional consequence of the variants not tested in cells\"\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How CFAP53's distinct activities\\u2014centriolar satellite organization, axonemal dynein transport, B-tubule nucleation, RhoA-dependent cytokinesis, and \\u03b3-tubulin recruitment\\u2014are coordinated by a single protein remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"No structural model unifying microtubule binding, dynein interaction, and B-tubule docking\",\n        \"Domain mapping of the multiple interaction surfaces not reported\",\n        \"Direct versus indirect nature of RhoA and \\u03b3-tubulin regulation undetermined\"\n      ]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0008092\", \"supporting_discovery_ids\": [5, 9]},\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [5]},\n      {\"term_id\": \"GO:0005198\", \"supporting_discovery_ids\": [9]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005814\", \"supporting_discovery_ids\": [1, 4]},\n      {\"term_id\": \"GO:0005929\", \"supporting_discovery_ids\": [2, 5]},\n      {\"term_id\": \"GO:0005856\", \"supporting_discovery_ids\": [4, 5]},\n      {\"term_id\": \"GO:0005815\", \"supporting_discovery_ids\": [7]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-1852241\", \"supporting_discovery_ids\": [1, 5]},\n      {\"term_id\": \"R-HSA-1266738\", \"supporting_discovery_ids\": [3, 4]},\n      {\"term_id\": \"R-HSA-1640170\", \"supporting_discovery_ids\": [8, 7]}\n    ],\n    \"complexes\": [\n      \"centriolar satellites\"\n    ],\n    \"partners\": [\n      \"TTC25\",\n      \"CFAP20\",\n      \"RhoA\",\n      \"axonemal dynein\"\n    ],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":5,"faith_total":5,"faith_pct":100.0}}