{"gene":"DNAAF5","run_date":"2026-06-09T23:54:42","timeline":{"discoveries":[{"year":2023,"finding":"DNAAF5 functions as a dynein motor assembly factor required for motile cilia function; loss-of-function (null allele homozygosity) is embryonic lethal in mice, and compound heterozygous missense/null animals show severe cilia motor assembly defects with reduced axonemal regulatory and structural proteins detectable by proteomics of isolated airway cilia.","method":"CRISPR-Cas9 genome editing in mice to generate missense and frameshift-null Dnaaf5 alleles; ultrastructure analysis of cilia; proteomic analysis of isolated airway cilia; transcriptional analysis of mouse and human mutant cells","journal":"JCI insight","confidence":"High","confidence_rationale":"Tier 2 / Strong — CRISPR-engineered alleles in vivo with ultrastructural, proteomic, and transcriptional orthogonal readouts; replicated in both peer-reviewed publication and preprint from same group","pmids":["37104040","36712068"],"is_preprint":false},{"year":2023,"finding":"DNAAF5 allele dosage shows allele-specific and tissue-specific effects on cilia motor assembly: the same missense variant allele produces divergent cilia function across different multiciliated tissues, indicating tissue-specific molecular requirements for dynein arm assembly that depend on DNAAF5.","method":"Comparative ultrastructure analysis and proteomic profiling of cilia from multiple multiciliated tissues in Dnaaf5 missense homozygous and compound heterozygous mice","journal":"JCI insight","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — in vivo allelic series with ultrastructure and proteomics, single lab, multiple orthogonal readouts","pmids":["37104040","36712068"],"is_preprint":false},{"year":2022,"finding":"DNAAF5 acts as a scaffold protein that directly binds PFKL (phosphofructokinase, liver type) and recruits the deubiquitinase USP39, forming a ternary complex that stabilizes PFKL protein by promoting its deubiquitination, thereby enhancing glycolysis in hepatocellular carcinoma cells.","method":"Co-immunoprecipitation, mass spectrometry, transcriptome sequencing, stable cell line overexpression/knockout, in vivo xenograft; USP39 knockdown rescue experiment","journal":"Frontiers in oncology","confidence":"Medium","confidence_rationale":"Tier 2–3 / Moderate — reciprocal Co-IP and mass spectrometry with functional rescue, single lab, multiple orthogonal methods; non-ciliary context may represent gain-of-function or off-target role","pmids":["36276075"],"is_preprint":false},{"year":2025,"finding":"dnaaf5 mRNA is expressed in motile ciliated tissues of zebrafish embryos (Kupffer's vesicle, pronephros, floor plate, brain, olfactory placode), and dnaaf5 crispants develop ciliopathic defects, indicating a conserved role in motile cilia biogenesis and function during vertebrate development.","method":"In situ hybridization for spatio-temporal mRNA expression; CRISPR crispant phenotype analysis in zebrafish embryos","journal":"The International journal of developmental biology","confidence":"Medium","confidence_rationale":"Tier 2–3 / Weak — CRISPR loss-of-function in zebrafish with ciliopathic phenotype readout, single lab, single method per finding","pmids":["42029186"],"is_preprint":false}],"current_model":"DNAAF5 is a dynein axonemal assembly factor that acts in the cytoplasm to promote dynein arm assembly prior to axonemal incorporation in motile cilia; loss of DNAAF5 reduces axonemal structural and regulatory proteins and impairs cilia motility in an allele-specific and tissue-specific manner, with complete loss being embryonic lethal in mice, and in a non-ciliary context DNAAF5 also functions as a scaffold that recruits the deubiquitinase USP39 to stabilize PFKL and promote glycolysis in hepatocellular carcinoma cells."},"narrative":{"mechanistic_narrative":"DNAAF5 is a cytoplasmic dynein axonemal assembly factor required for the function of motile cilia [PMID:37104040, PMID:36712068]. It promotes the assembly of dynein motor complexes prior to their incorporation into the axoneme, such that its loss reduces both axonemal regulatory and structural proteins and produces severe cilia motor assembly defects; complete loss-of-function is embryonic lethal in mice [PMID:37104040, PMID:36712068]. The requirement for DNAAF5 is allele- and tissue-specific: the same missense variant yields divergent cilia function across different multiciliated tissues, indicating tissue-specific molecular requirements for dynein arm assembly [PMID:37104040, PMID:36712068]. This role is conserved in vertebrate development, where dnaaf5 is expressed in motile ciliated tissues of zebrafish embryos and its loss produces ciliopathic phenotypes [PMID:42029186]. In a non-ciliary context, DNAAF5 acts as a scaffold that directly binds PFKL and recruits the deubiquitinase USP39, forming a ternary complex that stabilizes PFKL by promoting its deubiquitination and thereby enhancing glycolysis in hepatocellular carcinoma cells [PMID:36276075].","teleology":[{"year":2022,"claim":"Identified a non-ciliary, scaffolding function for DNAAF5, establishing that it can bridge a substrate to a deubiquitinase to control protein stability and metabolic output.","evidence":"Co-IP, mass spectrometry, knockout/overexpression cell lines, xenografts, and USP39 knockdown rescue in hepatocellular carcinoma cells","pmids":["36276075"],"confidence":"Medium","gaps":["Single lab, non-ciliary context may represent a gain-of-function or context-restricted role","Structural basis of the DNAAF5–PFKL–USP39 ternary complex not resolved","Relationship between this glycolytic scaffold role and the cilia assembly function unknown"]},{"year":2023,"claim":"Established DNAAF5 as a dynein motor assembly factor essential for motile cilia, defining its in vivo requirement and the proteomic consequences of its loss.","evidence":"CRISPR-Cas9 engineered missense and frameshift-null Dnaaf5 alleles in mice, with cilia ultrastructure, proteomics of isolated airway cilia, and transcriptional readouts","pmids":["37104040","36712068"],"confidence":"High","gaps":["Precise biochemical step in dynein arm preassembly catalyzed or scaffolded by DNAAF5 not defined","Direct dynein-chain or co-chaperone partners not identified"]},{"year":2023,"claim":"Revealed that DNAAF5 dependence is allele- and tissue-specific, explaining how a single variant can produce divergent cilia phenotypes across multiciliated tissues.","evidence":"Comparative ultrastructure and proteomic profiling of cilia from multiple multiciliated tissues in Dnaaf5 missense homozygous and compound heterozygous mice","pmids":["37104040","36712068"],"confidence":"Medium","gaps":["Molecular basis of tissue-specific dynein arm assembly requirements not identified","Single-lab allelic series"]},{"year":2025,"claim":"Demonstrated evolutionary conservation of the motile cilia role, showing DNAAF5 acts in motile ciliated tissues during vertebrate development.","evidence":"In situ hybridization expression mapping and CRISPR crispant phenotyping in zebrafish embryos","pmids":["42029186"],"confidence":"Medium","gaps":["Single method per finding; crispant rescue not described","Molecular partners in zebrafish not defined"]},{"year":null,"claim":"How DNAAF5 reconciles its cytoplasmic dynein preassembly role with the non-ciliary glycolytic scaffold function, and the precise biochemical step it performs in dynein arm assembly, remain unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No structural model of DNAAF5 or its complexes","Direct dynein assembly substrates/co-factors unidentified","Whether scaffolding for deubiquitination is a general DNAAF5 mechanism is unknown"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[2]}],"localization":[{"term_id":"GO:0005929","term_label":"cilium","supporting_discovery_ids":[0,3]},{"term_id":"GO:0005829","term_label":"cytosol","supporting_discovery_ids":[2]}],"pathway":[{"term_id":"R-HSA-1852241","term_label":"Organelle biogenesis and maintenance","supporting_discovery_ids":[0]},{"term_id":"R-HSA-1266738","term_label":"Developmental Biology","supporting_discovery_ids":[3]}],"complexes":[],"partners":["PFKL","USP39"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q86Y56","full_name":"Dynein axonemal assembly factor 5","aliases":["HEAT repeat-containing protein 2"],"length_aa":855,"mass_kda":93.5,"function":"Cytoplasmic protein involved in the delivery of the dynein machinery to the motile cilium. It is required for the assembly of the axonemal dynein inner and outer arms, two structures attached to the peripheral outer doublet A microtubule of the axoneme, that play a crucial role in cilium motility","subcellular_location":"Cytoplasm; Dynein axonemal particle","url":"https://www.uniprot.org/uniprotkb/Q86Y56/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/DNAAF5","classification":"Not Classified","n_dependent_lines":187,"n_total_lines":1208,"dependency_fraction":0.15480132450331127},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/DNAAF5","total_profiled":1310},"omim":[{"mim_id":"614874","title":"CILIARY DYSKINESIA, PRIMARY, 18; CILD18","url":"https://www.omim.org/entry/614874"},{"mim_id":"614864","title":"DYNEIN, AXONEMAL, ASSEMBLY FACTOR 5; DNAAF5","url":"https://www.omim.org/entry/614864"},{"mim_id":"244400","title":"CILIARY DYSKINESIA, PRIMARY, 1; CILD1","url":"https://www.omim.org/entry/244400"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Cytosol","reliability":"Supported"},{"location":"Nucleoli","reliability":"Additional"},{"location":"Microtubules","reliability":"Additional"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/DNAAF5"},"hgnc":{"alias_symbol":["FLJ20397","FLJ31671","FLJ39381","FLJ25564","CILD18"],"prev_symbol":["HEATR2"]},"alphafold":{"accession":"Q86Y56","domains":[{"cath_id":"1.25.10,1.25.40","chopping":"241-326_344-422","consensus_level":"medium","plddt":97.5335,"start":241,"end":422},{"cath_id":"1.25.40,1.20.930","chopping":"736-855","consensus_level":"medium","plddt":90.4667,"start":736,"end":855},{"cath_id":"1.25.40","chopping":"433-553","consensus_level":"medium","plddt":95.8406,"start":433,"end":553},{"cath_id":"1.25.40","chopping":"577-734","consensus_level":"medium","plddt":93.8901,"start":577,"end":734}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q86Y56","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q86Y56-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q86Y56-F1-predicted_aligned_error_v6.png","plddt_mean":92.44},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=DNAAF5","jax_strain_url":"https://www.jax.org/strain/search?query=DNAAF5"},"sequence":{"accession":"Q86Y56","fasta_url":"https://rest.uniprot.org/uniprotkb/Q86Y56.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q86Y56/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q86Y56"}},"corpus_meta":[{"pmid":"37104040","id":"PMC_37104040","title":"The effect of Dnaaf5 gene dosage on primary ciliary dyskinesia phenotypes.","date":"2023","source":"JCI insight","url":"https://pubmed.ncbi.nlm.nih.gov/37104040","citation_count":17,"is_preprint":false},{"pmid":"36276075","id":"PMC_36276075","title":"DNAAF5 promotes hepatocellular carcinoma malignant progression by recruiting USP39 to improve PFKL protein stability.","date":"2022","source":"Frontiers in oncology","url":"https://pubmed.ncbi.nlm.nih.gov/36276075","citation_count":17,"is_preprint":false},{"pmid":"37539664","id":"PMC_37539664","title":"Genome-Wide Meta-Analysis of Cerebrospinal Fluid Biomarkers in Alzheimer's Disease and Parkinson's Disease Cohorts.","date":"2023","source":"Movement disorders : official journal of the Movement Disorder Society","url":"https://pubmed.ncbi.nlm.nih.gov/37539664","citation_count":9,"is_preprint":false},{"pmid":"38350390","id":"PMC_38350390","title":"Identification of candidate genes affecting the tibia quality in Nonghua duck.","date":"2024","source":"Poultry science","url":"https://pubmed.ncbi.nlm.nih.gov/38350390","citation_count":3,"is_preprint":false},{"pmid":"37398091","id":"PMC_37398091","title":"Genome-wide meta-analysis of CSF biomarkers in Alzheimer's disease and Parkinson's disease cohorts.","date":"2023","source":"medRxiv : the preprint server for health sciences","url":"https://pubmed.ncbi.nlm.nih.gov/37398091","citation_count":1,"is_preprint":false},{"pmid":"36712068","id":"PMC_36712068","title":"The effect of Dnaaf5 gene dosage on primary ciliary dyskinesia phenotypes.","date":"2023","source":"bioRxiv : the preprint server for biology","url":"https://pubmed.ncbi.nlm.nih.gov/36712068","citation_count":0,"is_preprint":false},{"pmid":"40205804","id":"PMC_40205804","title":"Comprehensive Proteomics and Machine Learning Analysis to Distinguish Follicular Adenoma and Follicular Thyroid Carcinoma from Indeterminate Thyroid Nodules.","date":"2025","source":"Endocrinology and metabolism (Seoul, Korea)","url":"https://pubmed.ncbi.nlm.nih.gov/40205804","citation_count":0,"is_preprint":false},{"pmid":"42029186","id":"PMC_42029186","title":"Dynein axonemal assembly factors (dnaaf) 5 and 9 are expressed in ciliated organs of zebrafish embryos.","date":"2025","source":"The International journal of developmental biology","url":"https://pubmed.ncbi.nlm.nih.gov/42029186","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":6662,"output_tokens":1160,"usd":0.018693,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":7764,"output_tokens":1897,"usd":0.043123,"stage2_stop_reason":"end_turn"},"total_usd":0.061816,"stage1_batch_id":"msgbatch_01AsR7g8dGTEiEw9U83bJeWn","stage2_batch_id":"msgbatch_01YV5ZyxtFNUZEjxRcpd9jzb","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2023,\n      \"finding\": \"DNAAF5 functions as a dynein motor assembly factor required for motile cilia function; loss-of-function (null allele homozygosity) is embryonic lethal in mice, and compound heterozygous missense/null animals show severe cilia motor assembly defects with reduced axonemal regulatory and structural proteins detectable by proteomics of isolated airway cilia.\",\n      \"method\": \"CRISPR-Cas9 genome editing in mice to generate missense and frameshift-null Dnaaf5 alleles; ultrastructure analysis of cilia; proteomic analysis of isolated airway cilia; transcriptional analysis of mouse and human mutant cells\",\n      \"journal\": \"JCI insight\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — CRISPR-engineered alleles in vivo with ultrastructural, proteomic, and transcriptional orthogonal readouts; replicated in both peer-reviewed publication and preprint from same group\",\n      \"pmids\": [\"37104040\", \"36712068\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"DNAAF5 allele dosage shows allele-specific and tissue-specific effects on cilia motor assembly: the same missense variant allele produces divergent cilia function across different multiciliated tissues, indicating tissue-specific molecular requirements for dynein arm assembly that depend on DNAAF5.\",\n      \"method\": \"Comparative ultrastructure analysis and proteomic profiling of cilia from multiple multiciliated tissues in Dnaaf5 missense homozygous and compound heterozygous mice\",\n      \"journal\": \"JCI insight\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — in vivo allelic series with ultrastructure and proteomics, single lab, multiple orthogonal readouts\",\n      \"pmids\": [\"37104040\", \"36712068\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"DNAAF5 acts as a scaffold protein that directly binds PFKL (phosphofructokinase, liver type) and recruits the deubiquitinase USP39, forming a ternary complex that stabilizes PFKL protein by promoting its deubiquitination, thereby enhancing glycolysis in hepatocellular carcinoma cells.\",\n      \"method\": \"Co-immunoprecipitation, mass spectrometry, transcriptome sequencing, stable cell line overexpression/knockout, in vivo xenograft; USP39 knockdown rescue experiment\",\n      \"journal\": \"Frontiers in oncology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2–3 / Moderate — reciprocal Co-IP and mass spectrometry with functional rescue, single lab, multiple orthogonal methods; non-ciliary context may represent gain-of-function or off-target role\",\n      \"pmids\": [\"36276075\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"dnaaf5 mRNA is expressed in motile ciliated tissues of zebrafish embryos (Kupffer's vesicle, pronephros, floor plate, brain, olfactory placode), and dnaaf5 crispants develop ciliopathic defects, indicating a conserved role in motile cilia biogenesis and function during vertebrate development.\",\n      \"method\": \"In situ hybridization for spatio-temporal mRNA expression; CRISPR crispant phenotype analysis in zebrafish embryos\",\n      \"journal\": \"The International journal of developmental biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2–3 / Weak — CRISPR loss-of-function in zebrafish with ciliopathic phenotype readout, single lab, single method per finding\",\n      \"pmids\": [\"42029186\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"DNAAF5 is a dynein axonemal assembly factor that acts in the cytoplasm to promote dynein arm assembly prior to axonemal incorporation in motile cilia; loss of DNAAF5 reduces axonemal structural and regulatory proteins and impairs cilia motility in an allele-specific and tissue-specific manner, with complete loss being embryonic lethal in mice, and in a non-ciliary context DNAAF5 also functions as a scaffold that recruits the deubiquitinase USP39 to stabilize PFKL and promote glycolysis in hepatocellular carcinoma cells.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"DNAAF5 is a cytoplasmic dynein axonemal assembly factor required for the function of motile cilia [#0]. It promotes the assembly of dynein motor complexes prior to their incorporation into the axoneme, such that its loss reduces both axonemal regulatory and structural proteins and produces severe cilia motor assembly defects; complete loss-of-function is embryonic lethal in mice [#0]. The requirement for DNAAF5 is allele- and tissue-specific: the same missense variant yields divergent cilia function across different multiciliated tissues, indicating tissue-specific molecular requirements for dynein arm assembly [#1]. This role is conserved in vertebrate development, where dnaaf5 is expressed in motile ciliated tissues of zebrafish embryos and its loss produces ciliopathic phenotypes [#3]. In a non-ciliary context, DNAAF5 acts as a scaffold that directly binds PFKL and recruits the deubiquitinase USP39, forming a ternary complex that stabilizes PFKL by promoting its deubiquitination and thereby enhancing glycolysis in hepatocellular carcinoma cells [#2].\",\n  \"teleology\": [\n    {\n      \"year\": 2022,\n      \"claim\": \"Identified a non-ciliary, scaffolding function for DNAAF5, establishing that it can bridge a substrate to a deubiquitinase to control protein stability and metabolic output.\",\n      \"evidence\": \"Co-IP, mass spectrometry, knockout/overexpression cell lines, xenografts, and USP39 knockdown rescue in hepatocellular carcinoma cells\",\n      \"pmids\": [\"36276075\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Single lab, non-ciliary context may represent a gain-of-function or context-restricted role\",\n        \"Structural basis of the DNAAF5–PFKL–USP39 ternary complex not resolved\",\n        \"Relationship between this glycolytic scaffold role and the cilia assembly function unknown\"\n      ]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Established DNAAF5 as a dynein motor assembly factor essential for motile cilia, defining its in vivo requirement and the proteomic consequences of its loss.\",\n      \"evidence\": \"CRISPR-Cas9 engineered missense and frameshift-null Dnaaf5 alleles in mice, with cilia ultrastructure, proteomics of isolated airway cilia, and transcriptional readouts\",\n      \"pmids\": [\"37104040\", \"36712068\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Precise biochemical step in dynein arm preassembly catalyzed or scaffolded by DNAAF5 not defined\",\n        \"Direct dynein-chain or co-chaperone partners not identified\"\n      ]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Revealed that DNAAF5 dependence is allele- and tissue-specific, explaining how a single variant can produce divergent cilia phenotypes across multiciliated tissues.\",\n      \"evidence\": \"Comparative ultrastructure and proteomic profiling of cilia from multiple multiciliated tissues in Dnaaf5 missense homozygous and compound heterozygous mice\",\n      \"pmids\": [\"37104040\", \"36712068\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Molecular basis of tissue-specific dynein arm assembly requirements not identified\",\n        \"Single-lab allelic series\"\n      ]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Demonstrated evolutionary conservation of the motile cilia role, showing DNAAF5 acts in motile ciliated tissues during vertebrate development.\",\n      \"evidence\": \"In situ hybridization expression mapping and CRISPR crispant phenotyping in zebrafish embryos\",\n      \"pmids\": [\"42029186\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Single method per finding; crispant rescue not described\",\n        \"Molecular partners in zebrafish not defined\"\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How DNAAF5 reconciles its cytoplasmic dynein preassembly role with the non-ciliary glycolytic scaffold function, and the precise biochemical step it performs in dynein arm assembly, remain unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"No structural model of DNAAF5 or its complexes\",\n        \"Direct dynein assembly substrates/co-factors unidentified\",\n        \"Whether scaffolding for deubiquitination is a general DNAAF5 mechanism is unknown\"\n      ]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [2]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005929\", \"supporting_discovery_ids\": [0, 3]},\n      {\"term_id\": \"GO:0005829\", \"supporting_discovery_ids\": [2]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-1852241\", \"supporting_discovery_ids\": [0]},\n      {\"term_id\": \"R-HSA-1266738\", \"supporting_discovery_ids\": [3]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\"PFKL\", \"USP39\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":5,"faith_total":5,"faith_pct":100.0}}