{"gene":"DNAH6","run_date":"2026-06-09T23:54:42","timeline":{"discoveries":[{"year":2016,"finding":"DNAH6 is required for motile cilia function in Kupffer's vesicle for left-right patterning; dnah6 morpholino knockdown in zebrafish disrupted motile cilia and caused heterotaxy with abnormal cardiac/gut looping. DNAH6 shRNA knockdown also disrupted motile cilia in human and mouse respiratory epithelia.","method":"Morpholino knockdown in zebrafish (ciliary motility, organ looping phenotype); shRNA knockdown in human and mouse respiratory epithelia","journal":"PLoS genetics","confidence":"High","confidence_rationale":"Tier 2 / Strong — loss-of-function in two model systems (zebrafish morpholino and mammalian shRNA) with defined ciliary and organ-laterality phenotypes, replicated across species","pmids":["26918822"],"is_preprint":false},{"year":2016,"finding":"Trans-heterozygous genetic interactions between DNAH6 and other PCD genes (DNAI1, DNAH5) can cause heterotaxy; subthreshold double-morpholino knockdown of dnah6 combined with dnah5 or dnai1 in zebrafish caused heterotaxy, and subthreshold siRNA knockdown of Dnah6 in heterozygous Dnah5 or Dnai1 mutant mouse respiratory epithelia disrupted motile cilia function.","method":"Subthreshold double-morpholino knockdown (epistasis) in zebrafish; subthreshold siRNA knockdown in heterozygous mouse mutant respiratory epithelia","journal":"PLoS genetics","confidence":"High","confidence_rationale":"Tier 2 / Strong — genetic epistasis demonstrated in two model systems with quantitative cilia phenotype readouts, multiple gene pairs tested","pmids":["26918822"],"is_preprint":false},{"year":2018,"finding":"DNAH6 dynein arm motor protein is localized to specific regions of the axoneme in ex vivo human airway ciliary cells, and during in vitro ciliogenesis, DNAH6 progressively moves to the appropriate proximal or distal section of the cilium as waveform development matures.","method":"Immunofluorescence localization of DNAH6 in ex vivo human lung airway cells and primary culture cells undergoing ciliogenesis; correlated with high-speed video microscopy of waveform parameters","journal":"American journal of respiratory cell and molecular biology","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — direct immunofluorescence localization in ex vivo and in vitro human cells with functional waveform correlation, single lab","pmids":["29851510"],"is_preprint":false},{"year":2018,"finding":"DNAH6 is a testis-specific expressed protein localised to the neck region in normal spermatozoa; compound heterozygous variants in DNAH6 result in complete absence of DNAH6 protein and mRNA in patient spermatozoa, associated with sperm head anomaly (acephalic and globozoospermic sperm).","method":"Immunofluorescence staining for localization; quantitative real-time PCR for mRNA expression; whole-exome sequencing for variant identification","journal":"Andrologia","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — direct immunofluorescence localization with loss-of-function patient data, single lab, two orthogonal methods (IF + qPCR)","pmids":["29356036"],"is_preprint":false},{"year":2023,"finding":"DNAH6 variants cause absence of inner dynein arms and radial spokes in sperm flagella, and are associated with deficiencies in acrosome biogenesis, abnormal chromatin compaction, and vacuole-containing sperm heads; decreased levels of component proteins in these defective structures were confirmed by Western blot.","method":"Transmission electron microscopy of sperm ultrastructure; immunofluorescence staining; Western blot analysis; whole-exome sequencing","journal":"Asian journal of andrology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple orthogonal methods (TEM, IF, WB) in patient samples, single lab","pmids":["37594300"],"is_preprint":false},{"year":2023,"finding":"A homozygous frameshift mutation in DNAH6 (c.2823dupT, p.Val942Cysfs*21) causes abnormal DNAH6 mRNA and protein expression in sperm, likely via premature termination codon and mRNA decay, resulting in multiple morphological and ultrastructural abnormalities of sperm flagella (asthenoteratozoospermia).","method":"Whole-exome sequencing and Sanger sequencing; qRT-PCR for mRNA; immunofluorescence for protein; scanning and transmission electron microscopy for ultrastructure","journal":"Frontiers in endocrinology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple orthogonal methods in patient cohort (WES, TEM, IF, qPCR), single lab","pmids":["37424858"],"is_preprint":false},{"year":2024,"finding":"DNAH6 is an inner dynein arm (IDA) heavy chain component in sperm flagella; loss of DNAH3 (another IDA component) in knockout mice and patient spermatozoa results in decreased expression of DNAH6 (along with DNAH1 and DNALI1), indicating DNAH6 is part of the IDA complex whose assembly depends on DNAH3.","method":"Immunofluorescent staining of sperm flagella in DNAH3 KO mice and patient spermatozoa; Western blot","journal":"eLife","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct protein localization and co-expression analysis in KO model and human patients, two orthogonal methods, single lab","pmids":["39503742"],"is_preprint":false},{"year":2024,"finding":"DNAH6 (IDA heavy chain) is conspicuously absent from respiratory ciliary axonemes in patients with disease-causing variants in CCDC39 or CCDC40 (molecular ruler complex), demonstrating that the CCDC39/CCDC40 96 nm ruler complex is required for axonemal assembly of DNAH6 and other IDA heavy chains (DNAH1, DNAH7) in human respiratory cilia.","method":"Immunofluorescence analyses of respiratory cilia in a cohort of 51 individuals with CCDC39/CCDC40 variants; next-generation sequencing for variant identification","journal":"Cells","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct immunofluorescence in large patient cohort (n=51), single lab, establishes pathway dependency","pmids":["39056782"],"is_preprint":false},{"year":2025,"finding":"In patients with loss-of-function DNAH7 variants (another IDA heavy chain), immunofluorescent staining revealed marked reduction of DNAH6 in spermatozoa alongside DNAH3 reduction, while ODA proteins were unaffected, placing DNAH6 specifically within the inner dynein arm complex of sperm flagella.","method":"Immunofluorescent staining of patient spermatozoa; transmission electron microscopy","journal":"Human genetics","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct protein localization in patient spermatozoa with ultrastructural correlation, single lab","pmids":["40810911"],"is_preprint":false},{"year":2025,"finding":"Brn-3b (POU4F2) transcription factor knockout in mice results in reduced expression of Dnah6, among other genes essential for sperm development, suggesting Dnah6 is transcriptionally regulated by Brn-3b in spermatids.","method":"RNA-seq and qRT-PCR of Brn-3b knockout mouse testes","journal":"Research square (preprint)","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single lab, qRT-PCR/RNA-seq showing expression change in KO, no direct functional rescue or binding evidence for DNAH6 specifically","pmids":["41282076"],"is_preprint":true}],"current_model":"DNAH6 is an inner dynein arm (IDA) heavy chain that localizes to specific axonemal regions in both motile respiratory cilia and sperm flagella; it is required for normal ciliary beating and left-right patterning (with trans-heterozygous interactions with other PCD genes), and for proper sperm flagellar ultrastructure (IDA and radial spoke assembly) and sperm head formation, with its axonemal assembly dependent on the CCDC39/CCDC40 molecular ruler complex."},"narrative":{"mechanistic_narrative":"DNAH6 is an inner dynein arm (IDA) heavy chain that powers motility of both respiratory cilia and sperm flagella and is required for normal ciliary beating and left-right body patterning [PMID:26918822]. Loss of DNAH6 disrupts motile cilia in Kupffer's vesicle and respiratory epithelia across zebrafish and mammalian systems, producing heterotaxy with abnormal cardiac and gut looping, and DNAH6 acts genetically with other primary ciliary dyskinesia genes (DNAI1, DNAH5) such that subthreshold combined reduction causes laterality defects [PMID:26918822]. Within the axoneme DNAH6 occupies defined proximal or distal positions that are progressively established during ciliogenesis as beating waveform matures [PMID:29851510]. Its incorporation into the axoneme depends on the CCDC39/CCDC40 96 nm molecular ruler complex, since DNAH6 is absent from respiratory cilia in patients with CCDC39/CCDC40 variants [PMID:39056782]. In the male germline DNAH6 is a testis-expressed protein localizing to the sperm neck, and its assembly into the sperm flagellar IDA is interdependent with other IDA heavy chains DNAH3 and DNAH7 [PMID:29356036, PMID:39503742, PMID:40810911]. Biallelic DNAH6 variants abolish the protein and cause inner dynein arm and radial spoke loss together with sperm head defects—acephalic, globozoospermic, and vacuolated heads with abnormal acrosome biogenesis and chromatin compaction—and asthenoteratozoospermia [PMID:29356036, PMID:37594300, PMID:37424858].","teleology":[{"year":2016,"claim":"Established that DNAH6 is functionally required for motile cilia and left-right patterning, defining its core role rather than leaving it as an uncharacterized dynein gene.","evidence":"Morpholino knockdown in zebrafish and shRNA knockdown in human/mouse respiratory epithelia with ciliary motility and organ-looping readouts","pmids":["26918822"],"confidence":"High","gaps":["Did not resolve which axonemal substructure DNAH6 builds","Mechanism of motility contribution at the molecular level not defined"]},{"year":2016,"claim":"Showed DNAH6 contributes to laterality as a genetic modifier, explaining how subthreshold defects combine with other PCD genes to cause heterotaxy.","evidence":"Subthreshold double-morpholino epistasis in zebrafish and siRNA knockdown in heterozygous Dnah5/Dnai1 mutant mouse epithelia","pmids":["26918822"],"confidence":"High","gaps":["Physical versus purely genetic interaction with DNAH5/DNAI1 not distinguished","Dosage thresholds in human disease not established"]},{"year":2018,"claim":"Determined that DNAH6 occupies spatially defined axonemal positions set during ciliogenesis, linking its localization to maturation of beating waveform.","evidence":"Immunofluorescence in ex vivo and in vitro human airway cells correlated with high-speed video microscopy","pmids":["29851510"],"confidence":"Medium","gaps":["Single lab","Trafficking mechanism that repositions DNAH6 not identified"]},{"year":2018,"claim":"Extended DNAH6 function to the male germline, identifying it as a testis-specific neck-localized protein whose loss causes sperm head anomalies.","evidence":"Immunofluorescence, qRT-PCR, and whole-exome sequencing in patients with compound heterozygous variants","pmids":["29356036"],"confidence":"Medium","gaps":["Single lab","Mechanism linking an IDA heavy chain to head formation unresolved"]},{"year":2023,"claim":"Defined the structural consequences of DNAH6 loss in sperm, connecting it to IDA and radial spoke assembly as well as acrosome and chromatin defects.","evidence":"TEM, immunofluorescence, Western blot, and whole-exome sequencing in patient samples; identification of a homozygous frameshift causing asthenoteratozoospermia","pmids":["37594300","37424858"],"confidence":"Medium","gaps":["Single lab cohorts","Causal chain from IDA defect to acrosome/chromatin abnormalities not mechanistically dissected"]},{"year":2024,"claim":"Placed DNAH6 within the sperm flagellar inner dynein arm complex and showed its assembly is interdependent with other IDA heavy chains.","evidence":"Immunofluorescence and Western blot in DNAH3 knockout mice and patient spermatozoa showing co-reduced DNAH6, DNAH1, DNALI1","pmids":["39503742"],"confidence":"Medium","gaps":["Direct physical interaction not demonstrated","Single lab"]},{"year":2024,"claim":"Established that axonemal assembly of DNAH6 requires the CCDC39/CCDC40 96 nm ruler complex, defining its upstream dependency in respiratory cilia.","evidence":"Immunofluorescence of respiratory cilia in a cohort of 51 individuals with CCDC39/CCDC40 variants","pmids":["39056782"],"confidence":"Medium","gaps":["Single lab","Whether DNAH6 binds the ruler directly or assembles downstream not resolved"]},{"year":2025,"claim":"Confirmed DNAH6's IDA membership in sperm via co-dependency with DNAH7, distinguishing it from outer dynein arm components.","evidence":"Immunofluorescent staining and TEM of spermatozoa from patients with loss-of-function DNAH7 variants","pmids":["40810911"],"confidence":"Medium","gaps":["Single lab","Order of IDA heavy chain assembly not established"]},{"year":2025,"claim":"Implicated transcriptional control of DNAH6 expression in spermatids by the POU4F2/Brn-3b factor.","evidence":"RNA-seq and qRT-PCR of Brn-3b knockout mouse testes (preprint)","pmids":["41282076"],"confidence":"Low","gaps":["No direct promoter binding or functional rescue for DNAH6 specifically","Single lab preprint, not peer-reviewed"]},{"year":null,"claim":"How DNAH6 is positioned and anchored at specific axonemal sites and how its loss mechanistically disrupts sperm head and acrosome biogenesis remain unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No structural model of DNAH6 within the IDA","No reconstitution of DNAH6 assembly","Mechanistic link between flagellar IDA loss and head defects undefined"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0003774","term_label":"cytoskeletal motor activity","supporting_discovery_ids":[0,6]},{"term_id":"GO:0140657","term_label":"ATP-dependent activity","supporting_discovery_ids":[0]}],"localization":[{"term_id":"GO:0005929","term_label":"cilium","supporting_discovery_ids":[0,2,7]},{"term_id":"GO:0005856","term_label":"cytoskeleton","supporting_discovery_ids":[2,6]}],"pathway":[{"term_id":"R-HSA-1852241","term_label":"Organelle biogenesis and maintenance","supporting_discovery_ids":[0,7]},{"term_id":"R-HSA-1266738","term_label":"Developmental Biology","supporting_discovery_ids":[0,1]},{"term_id":"R-HSA-1474165","term_label":"Reproduction","supporting_discovery_ids":[3,4]}],"complexes":["inner dynein arm","axoneme"],"partners":["DNAH3","DNAH7","DNAH1","DNALI1","CCDC39","CCDC40","DNAH5","DNAI1"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q9C0G6","full_name":"Dynein axonemal heavy chain 6","aliases":["Axonemal beta dynein heavy chain 6","Ciliary dynein heavy chain 6"],"length_aa":4158,"mass_kda":476.0,"function":"Force generating protein of respiratory cilia. Produces force towards the minus ends of microtubules. Dynein has ATPase activity; the force-producing power stroke is thought to occur on release of ADP (By similarity)","subcellular_location":"Cytoplasm, cytoskeleton, cilium axoneme; Cell projection, cilium, flagellum","url":"https://www.uniprot.org/uniprotkb/Q9C0G6/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/DNAH6","classification":"Not Classified","n_dependent_lines":0,"n_total_lines":1208,"dependency_fraction":0.0},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/DNAH6","total_profiled":1310},"omim":[{"mim_id":"618801","title":"CILIARY DYSKINESIA, PRIMARY, 45; CILD45","url":"https://www.omim.org/entry/618801"},{"mim_id":"618063","title":"CILIARY DYSKINESIA, PRIMARY, 38; CILD38","url":"https://www.omim.org/entry/618063"},{"mim_id":"618058","title":"CILIA- AND FLAGELLA-ASSOCIATED PROTEIN 300; CFAP300","url":"https://www.omim.org/entry/618058"},{"mim_id":"610732","title":"TETRATRICOPEPTIDE REPEAT DOMAIN-CONTAINING PROTEIN 12; TTC12","url":"https://www.omim.org/entry/610732"},{"mim_id":"603336","title":"DYNEIN, AXONEMAL, HEAVY CHAIN 6; DNAH6","url":"https://www.omim.org/entry/603336"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Approved","locations":[{"location":"Plasma membrane","reliability":"Approved"},{"location":"Centriolar satellite","reliability":"Approved"},{"location":"Basal body","reliability":"Approved"},{"location":"Connecting piece","reliability":"Approved"},{"location":"Mid piece","reliability":"Approved"},{"location":"Primary cilium tip","reliability":"Additional"},{"location":"Calyx","reliability":"Additional"}],"tissue_specificity":"Tissue enhanced","tissue_distribution":"Detected in some","driving_tissues":[{"tissue":"choroid plexus","ntpm":5.0},{"tissue":"fallopian tube","ntpm":5.1}],"url":"https://www.proteinatlas.org/search/DNAH6"},"hgnc":{"alias_symbol":["Dnahc6","HL-2","FLJ37357"],"prev_symbol":["DNHL1"]},"alphafold":{"accession":"Q9C0G6","domains":[],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9C0G6","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q9C0G6-4-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q9C0G6-4-F1-predicted_aligned_error_v6.png","plddt_mean":75.62},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=DNAH6","jax_strain_url":"https://www.jax.org/strain/search?query=DNAH6"},"sequence":{"accession":"Q9C0G6","fasta_url":"https://rest.uniprot.org/uniprotkb/Q9C0G6.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q9C0G6/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9C0G6"}},"corpus_meta":[{"pmid":"28206990","id":"PMC_28206990","title":"A familial study of azoospermic men identifies three novel causative mutations in three new human azoospermia genes.","date":"2017","source":"Genetics in medicine : official journal of the American College of Medical Genetics","url":"https://pubmed.ncbi.nlm.nih.gov/28206990","citation_count":111,"is_preprint":false},{"pmid":"26918822","id":"PMC_26918822","title":"DNAH6 and Its Interactions with PCD Genes in Heterotaxy and Primary Ciliary Dyskinesia.","date":"2016","source":"PLoS genetics","url":"https://pubmed.ncbi.nlm.nih.gov/26918822","citation_count":95,"is_preprint":false},{"pmid":"34089056","id":"PMC_34089056","title":"Exome sequencing reveals variants in known and novel candidate genes for severe sperm motility disorders.","date":"2021","source":"Human reproduction (Oxford, England)","url":"https://pubmed.ncbi.nlm.nih.gov/34089056","citation_count":51,"is_preprint":false},{"pmid":"32962729","id":"PMC_32962729","title":"Whole-exome sequencing in patients with premature ovarian insufficiency: early detection and early intervention.","date":"2020","source":"Journal of ovarian research","url":"https://pubmed.ncbi.nlm.nih.gov/32962729","citation_count":47,"is_preprint":false},{"pmid":"29851510","id":"PMC_29851510","title":"Quantifying Ciliary Dynamics during Assembly Reveals Stepwise Waveform Maturation in Airway Cells.","date":"2018","source":"American journal of respiratory cell and molecular biology","url":"https://pubmed.ncbi.nlm.nih.gov/29851510","citation_count":45,"is_preprint":false},{"pmid":"29356036","id":"PMC_29356036","title":"DNAH6 is a novel candidate gene associated with sperm head anomaly.","date":"2018","source":"Andrologia","url":"https://pubmed.ncbi.nlm.nih.gov/29356036","citation_count":43,"is_preprint":false},{"pmid":"24939957","id":"PMC_24939957","title":"Identification of a duplication within the GDF9 gene and novel candidate genes for primary ovarian insufficiency (POI) by a customized high-resolution array comparative genomic hybridization platform.","date":"2014","source":"Human reproduction (Oxford, England)","url":"https://pubmed.ncbi.nlm.nih.gov/24939957","citation_count":40,"is_preprint":false},{"pmid":"34215651","id":"PMC_34215651","title":"Whole-exome sequencing reveals a monogenic cause in 56% of individuals with laterality disorders and associated congenital heart defects.","date":"2021","source":"Journal of medical genetics","url":"https://pubmed.ncbi.nlm.nih.gov/34215651","citation_count":25,"is_preprint":false},{"pmid":"39267058","id":"PMC_39267058","title":"Whole exome sequencing analysis of 167 men with primary infertility.","date":"2024","source":"BMC medical genomics","url":"https://pubmed.ncbi.nlm.nih.gov/39267058","citation_count":17,"is_preprint":false},{"pmid":"39417902","id":"PMC_39417902","title":"Genetic etiological spectrum of sperm morphological abnormalities.","date":"2024","source":"Journal of assisted reproduction and genetics","url":"https://pubmed.ncbi.nlm.nih.gov/39417902","citation_count":17,"is_preprint":false},{"pmid":"37594300","id":"PMC_37594300","title":"Novel variants in DNAH6 cause male infertility associated with multiple morphological abnormalities of the sperm flagella (MMAF) and ICSI outcomes.","date":"2023","source":"Asian journal of andrology","url":"https://pubmed.ncbi.nlm.nih.gov/37594300","citation_count":16,"is_preprint":false},{"pmid":"29323929","id":"PMC_29323929","title":"Variation in Cilia Protein Genes and Progression of Lung Disease in Cystic Fibrosis.","date":"2018","source":"Annals of the American Thoracic Society","url":"https://pubmed.ncbi.nlm.nih.gov/29323929","citation_count":16,"is_preprint":false},{"pmid":"33452591","id":"PMC_33452591","title":"Genetic basis of acephalic spermatozoa syndrome, and intracytoplasmic sperm injection outcomes in infertile men: a systematic scoping review.","date":"2021","source":"Journal of assisted reproduction and genetics","url":"https://pubmed.ncbi.nlm.nih.gov/33452591","citation_count":15,"is_preprint":false},{"pmid":"36623684","id":"PMC_36623684","title":"Identification of Novel Genetic Risk Factors for Focal Segmental Glomerulosclerosis in Children: Results From the Chronic Kidney Disease in Children (CKiD) Cohort.","date":"2023","source":"American journal of kidney diseases : the official journal of the National Kidney Foundation","url":"https://pubmed.ncbi.nlm.nih.gov/36623684","citation_count":13,"is_preprint":false},{"pmid":"39503742","id":"PMC_39503742","title":"DNAH3 deficiency causes flagellar inner dynein arm loss and male infertility in humans and mice.","date":"2024","source":"eLife","url":"https://pubmed.ncbi.nlm.nih.gov/39503742","citation_count":12,"is_preprint":false},{"pmid":"36965814","id":"PMC_36965814","title":"High-Resolution Genomic Profiling of Liver Cancer Links Etiology With Mutation and Epigenetic Signatures.","date":"2023","source":"Cellular and molecular gastroenterology and hepatology","url":"https://pubmed.ncbi.nlm.nih.gov/36965814","citation_count":11,"is_preprint":false},{"pmid":"37424858","id":"PMC_37424858","title":"A novel frameshift mutation in DNAH6 associated with male infertility and asthenoteratozoospermia.","date":"2023","source":"Frontiers in endocrinology","url":"https://pubmed.ncbi.nlm.nih.gov/37424858","citation_count":10,"is_preprint":false},{"pmid":"39056782","id":"PMC_39056782","title":"Primary Ciliary Dyskinesia Associated Disease-Causing Variants in CCDC39 and CCDC40 Cause Axonemal Absence of Inner Dynein Arm Heavy Chains DNAH1, DNAH6, and DNAH7.","date":"2024","source":"Cells","url":"https://pubmed.ncbi.nlm.nih.gov/39056782","citation_count":9,"is_preprint":false},{"pmid":"32582379","id":"PMC_32582379","title":"Identification of a novel deletion mutation in DPY19L2 from an infertile patient with globozoospermia: a case report.","date":"2020","source":"Molecular cytogenetics","url":"https://pubmed.ncbi.nlm.nih.gov/32582379","citation_count":8,"is_preprint":false},{"pmid":"39256880","id":"PMC_39256880","title":"Association of novel DNAH11 variants with asthenoteratozoospermia lead to male infertility.","date":"2024","source":"Human genomics","url":"https://pubmed.ncbi.nlm.nih.gov/39256880","citation_count":7,"is_preprint":false},{"pmid":"26030606","id":"PMC_26030606","title":"Targeted resequencing of the pericentromere of chromosome 2 linked to constitutional delay of growth and puberty.","date":"2015","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/26030606","citation_count":4,"is_preprint":false},{"pmid":"40269853","id":"PMC_40269853","title":"Genetic and transcriptional insights into immune checkpoint blockade response and survival: lessons from melanoma and beyond.","date":"2025","source":"Journal of translational medicine","url":"https://pubmed.ncbi.nlm.nih.gov/40269853","citation_count":3,"is_preprint":false},{"pmid":"40810911","id":"PMC_40810911","title":"Biallelic loss-of-function variants of DNAH7 cause male infertility associated with asthenozoospermia in humans.","date":"2025","source":"Human genetics","url":"https://pubmed.ncbi.nlm.nih.gov/40810911","citation_count":2,"is_preprint":false},{"pmid":"39192248","id":"PMC_39192248","title":"Molecular characterization of DNAH6 and ATPase6 (Mitochondrial DNA) genes in asthenozoospermia patients in the northern region of India.","date":"2024","source":"BMC urology","url":"https://pubmed.ncbi.nlm.nih.gov/39192248","citation_count":1,"is_preprint":false},{"pmid":"41115892","id":"PMC_41115892","title":"Identifying potential genetic biomarkers for sperm dysfunction through whole-genome sequencing.","date":"2025","source":"Scientific reports","url":"https://pubmed.ncbi.nlm.nih.gov/41115892","citation_count":1,"is_preprint":false},{"pmid":"41264116","id":"PMC_41264116","title":"The essential role of cytoskeleton and ciliary abnormalities in the development of congenital pulmonary airway malformations.","date":"2025","source":"Pediatric surgery international","url":"https://pubmed.ncbi.nlm.nih.gov/41264116","citation_count":0,"is_preprint":false},{"pmid":"40550064","id":"PMC_40550064","title":"Molecular insights into gender-specific differences in rheumatoid arthritis: A study using high-throughput sequencing and Mendelian randomization.","date":"2025","source":"Medicine","url":"https://pubmed.ncbi.nlm.nih.gov/40550064","citation_count":0,"is_preprint":false},{"pmid":"40694934","id":"PMC_40694934","title":"Gonadal sex differentiation in Eleutheronema tetradactylum: Histological features and transcriptomic insights from mature gonads.","date":"2025","source":"Comparative biochemistry and physiology. Part D, Genomics & proteomics","url":"https://pubmed.ncbi.nlm.nih.gov/40694934","citation_count":0,"is_preprint":false},{"pmid":"41282076","id":"PMC_41282076","title":"POU4F2/Brn-3b is Essential for Spermatogenesis and its Disruption is Linked to Male Infertility in Mice and Humans.","date":"2025","source":"Research square","url":"https://pubmed.ncbi.nlm.nih.gov/41282076","citation_count":0,"is_preprint":false},{"pmid":"42074143","id":"PMC_42074143","title":"The Molecular Landscape of CASTLE: A Rare Thymus-like Head and Neck Cancer.","date":"2026","source":"International journal of molecular sciences","url":"https://pubmed.ncbi.nlm.nih.gov/42074143","citation_count":0,"is_preprint":false},{"pmid":"40004451","id":"PMC_40004451","title":"Identification of Alterations in the Expression of Genes Related to the Implant Failure in Spanish Patients with Down Syndrome and Periodontal Disease.","date":"2025","source":"Genes","url":"https://pubmed.ncbi.nlm.nih.gov/40004451","citation_count":0,"is_preprint":false},{"pmid":null,"id":"bio_10.1101_2024.06.28.24309634","title":"Transcriptomics-Driven Machine Learning Models Accurately Predict Chemotherapy Response in Muscle-invasive Bladder Cancer","date":"2024-06-28","source":"bioRxiv","url":"https://doi.org/10.1101/2024.06.28.24309634","citation_count":0,"is_preprint":true}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":20917,"output_tokens":2469,"usd":0.049893,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":9630,"output_tokens":2985,"usd":0.061387,"stage2_stop_reason":"end_turn"},"total_usd":0.11128,"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\": 2016,\n      \"finding\": \"DNAH6 is required for motile cilia function in Kupffer's vesicle for left-right patterning; dnah6 morpholino knockdown in zebrafish disrupted motile cilia and caused heterotaxy with abnormal cardiac/gut looping. DNAH6 shRNA knockdown also disrupted motile cilia in human and mouse respiratory epithelia.\",\n      \"method\": \"Morpholino knockdown in zebrafish (ciliary motility, organ looping phenotype); shRNA knockdown in human and mouse respiratory epithelia\",\n      \"journal\": \"PLoS genetics\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — loss-of-function in two model systems (zebrafish morpholino and mammalian shRNA) with defined ciliary and organ-laterality phenotypes, replicated across species\",\n      \"pmids\": [\"26918822\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"Trans-heterozygous genetic interactions between DNAH6 and other PCD genes (DNAI1, DNAH5) can cause heterotaxy; subthreshold double-morpholino knockdown of dnah6 combined with dnah5 or dnai1 in zebrafish caused heterotaxy, and subthreshold siRNA knockdown of Dnah6 in heterozygous Dnah5 or Dnai1 mutant mouse respiratory epithelia disrupted motile cilia function.\",\n      \"method\": \"Subthreshold double-morpholino knockdown (epistasis) in zebrafish; subthreshold siRNA knockdown in heterozygous mouse mutant respiratory epithelia\",\n      \"journal\": \"PLoS genetics\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — genetic epistasis demonstrated in two model systems with quantitative cilia phenotype readouts, multiple gene pairs tested\",\n      \"pmids\": [\"26918822\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"DNAH6 dynein arm motor protein is localized to specific regions of the axoneme in ex vivo human airway ciliary cells, and during in vitro ciliogenesis, DNAH6 progressively moves to the appropriate proximal or distal section of the cilium as waveform development matures.\",\n      \"method\": \"Immunofluorescence localization of DNAH6 in ex vivo human lung airway cells and primary culture cells undergoing ciliogenesis; correlated with high-speed video microscopy of waveform parameters\",\n      \"journal\": \"American journal of respiratory cell and molecular biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — direct immunofluorescence localization in ex vivo and in vitro human cells with functional waveform correlation, single lab\",\n      \"pmids\": [\"29851510\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"DNAH6 is a testis-specific expressed protein localised to the neck region in normal spermatozoa; compound heterozygous variants in DNAH6 result in complete absence of DNAH6 protein and mRNA in patient spermatozoa, associated with sperm head anomaly (acephalic and globozoospermic sperm).\",\n      \"method\": \"Immunofluorescence staining for localization; quantitative real-time PCR for mRNA expression; whole-exome sequencing for variant identification\",\n      \"journal\": \"Andrologia\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — direct immunofluorescence localization with loss-of-function patient data, single lab, two orthogonal methods (IF + qPCR)\",\n      \"pmids\": [\"29356036\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"DNAH6 variants cause absence of inner dynein arms and radial spokes in sperm flagella, and are associated with deficiencies in acrosome biogenesis, abnormal chromatin compaction, and vacuole-containing sperm heads; decreased levels of component proteins in these defective structures were confirmed by Western blot.\",\n      \"method\": \"Transmission electron microscopy of sperm ultrastructure; immunofluorescence staining; Western blot analysis; whole-exome sequencing\",\n      \"journal\": \"Asian journal of andrology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple orthogonal methods (TEM, IF, WB) in patient samples, single lab\",\n      \"pmids\": [\"37594300\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"A homozygous frameshift mutation in DNAH6 (c.2823dupT, p.Val942Cysfs*21) causes abnormal DNAH6 mRNA and protein expression in sperm, likely via premature termination codon and mRNA decay, resulting in multiple morphological and ultrastructural abnormalities of sperm flagella (asthenoteratozoospermia).\",\n      \"method\": \"Whole-exome sequencing and Sanger sequencing; qRT-PCR for mRNA; immunofluorescence for protein; scanning and transmission electron microscopy for ultrastructure\",\n      \"journal\": \"Frontiers in endocrinology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple orthogonal methods in patient cohort (WES, TEM, IF, qPCR), single lab\",\n      \"pmids\": [\"37424858\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"DNAH6 is an inner dynein arm (IDA) heavy chain component in sperm flagella; loss of DNAH3 (another IDA component) in knockout mice and patient spermatozoa results in decreased expression of DNAH6 (along with DNAH1 and DNALI1), indicating DNAH6 is part of the IDA complex whose assembly depends on DNAH3.\",\n      \"method\": \"Immunofluorescent staining of sperm flagella in DNAH3 KO mice and patient spermatozoa; Western blot\",\n      \"journal\": \"eLife\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct protein localization and co-expression analysis in KO model and human patients, two orthogonal methods, single lab\",\n      \"pmids\": [\"39503742\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"DNAH6 (IDA heavy chain) is conspicuously absent from respiratory ciliary axonemes in patients with disease-causing variants in CCDC39 or CCDC40 (molecular ruler complex), demonstrating that the CCDC39/CCDC40 96 nm ruler complex is required for axonemal assembly of DNAH6 and other IDA heavy chains (DNAH1, DNAH7) in human respiratory cilia.\",\n      \"method\": \"Immunofluorescence analyses of respiratory cilia in a cohort of 51 individuals with CCDC39/CCDC40 variants; next-generation sequencing for variant identification\",\n      \"journal\": \"Cells\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct immunofluorescence in large patient cohort (n=51), single lab, establishes pathway dependency\",\n      \"pmids\": [\"39056782\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"In patients with loss-of-function DNAH7 variants (another IDA heavy chain), immunofluorescent staining revealed marked reduction of DNAH6 in spermatozoa alongside DNAH3 reduction, while ODA proteins were unaffected, placing DNAH6 specifically within the inner dynein arm complex of sperm flagella.\",\n      \"method\": \"Immunofluorescent staining of patient spermatozoa; transmission electron microscopy\",\n      \"journal\": \"Human genetics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct protein localization in patient spermatozoa with ultrastructural correlation, single lab\",\n      \"pmids\": [\"40810911\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"Brn-3b (POU4F2) transcription factor knockout in mice results in reduced expression of Dnah6, among other genes essential for sperm development, suggesting Dnah6 is transcriptionally regulated by Brn-3b in spermatids.\",\n      \"method\": \"RNA-seq and qRT-PCR of Brn-3b knockout mouse testes\",\n      \"journal\": \"Research square (preprint)\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single lab, qRT-PCR/RNA-seq showing expression change in KO, no direct functional rescue or binding evidence for DNAH6 specifically\",\n      \"pmids\": [\"41282076\"],\n      \"is_preprint\": true\n    }\n  ],\n  \"current_model\": \"DNAH6 is an inner dynein arm (IDA) heavy chain that localizes to specific axonemal regions in both motile respiratory cilia and sperm flagella; it is required for normal ciliary beating and left-right patterning (with trans-heterozygous interactions with other PCD genes), and for proper sperm flagellar ultrastructure (IDA and radial spoke assembly) and sperm head formation, with its axonemal assembly dependent on the CCDC39/CCDC40 molecular ruler complex.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"DNAH6 is an inner dynein arm (IDA) heavy chain that powers motility of both respiratory cilia and sperm flagella and is required for normal ciliary beating and left-right body patterning [#0]. Loss of DNAH6 disrupts motile cilia in Kupffer's vesicle and respiratory epithelia across zebrafish and mammalian systems, producing heterotaxy with abnormal cardiac and gut looping, and DNAH6 acts genetically with other primary ciliary dyskinesia genes (DNAI1, DNAH5) such that subthreshold combined reduction causes laterality defects [#0, #1]. Within the axoneme DNAH6 occupies defined proximal or distal positions that are progressively established during ciliogenesis as beating waveform matures [#2]. Its incorporation into the axoneme depends on the CCDC39/CCDC40 96 nm molecular ruler complex, since DNAH6 is absent from respiratory cilia in patients with CCDC39/CCDC40 variants [#7]. In the male germline DNAH6 is a testis-expressed protein localizing to the sperm neck, and its assembly into the sperm flagellar IDA is interdependent with other IDA heavy chains DNAH3 and DNAH7 [#3, #6, #8]. Biallelic DNAH6 variants abolish the protein and cause inner dynein arm and radial spoke loss together with sperm head defects—acephalic, globozoospermic, and vacuolated heads with abnormal acrosome biogenesis and chromatin compaction—and asthenoteratozoospermia [#3, #4, #5].\",\n  \"teleology\": [\n    {\n      \"year\": 2016,\n      \"claim\": \"Established that DNAH6 is functionally required for motile cilia and left-right patterning, defining its core role rather than leaving it as an uncharacterized dynein gene.\",\n      \"evidence\": \"Morpholino knockdown in zebrafish and shRNA knockdown in human/mouse respiratory epithelia with ciliary motility and organ-looping readouts\",\n      \"pmids\": [\"26918822\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not resolve which axonemal substructure DNAH6 builds\", \"Mechanism of motility contribution at the molecular level not defined\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"Showed DNAH6 contributes to laterality as a genetic modifier, explaining how subthreshold defects combine with other PCD genes to cause heterotaxy.\",\n      \"evidence\": \"Subthreshold double-morpholino epistasis in zebrafish and siRNA knockdown in heterozygous Dnah5/Dnai1 mutant mouse epithelia\",\n      \"pmids\": [\"26918822\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Physical versus purely genetic interaction with DNAH5/DNAI1 not distinguished\", \"Dosage thresholds in human disease not established\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Determined that DNAH6 occupies spatially defined axonemal positions set during ciliogenesis, linking its localization to maturation of beating waveform.\",\n      \"evidence\": \"Immunofluorescence in ex vivo and in vitro human airway cells correlated with high-speed video microscopy\",\n      \"pmids\": [\"29851510\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single lab\", \"Trafficking mechanism that repositions DNAH6 not identified\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Extended DNAH6 function to the male germline, identifying it as a testis-specific neck-localized protein whose loss causes sperm head anomalies.\",\n      \"evidence\": \"Immunofluorescence, qRT-PCR, and whole-exome sequencing in patients with compound heterozygous variants\",\n      \"pmids\": [\"29356036\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single lab\", \"Mechanism linking an IDA heavy chain to head formation unresolved\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Defined the structural consequences of DNAH6 loss in sperm, connecting it to IDA and radial spoke assembly as well as acrosome and chromatin defects.\",\n      \"evidence\": \"TEM, immunofluorescence, Western blot, and whole-exome sequencing in patient samples; identification of a homozygous frameshift causing asthenoteratozoospermia\",\n      \"pmids\": [\"37594300\", \"37424858\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single lab cohorts\", \"Causal chain from IDA defect to acrosome/chromatin abnormalities not mechanistically dissected\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Placed DNAH6 within the sperm flagellar inner dynein arm complex and showed its assembly is interdependent with other IDA heavy chains.\",\n      \"evidence\": \"Immunofluorescence and Western blot in DNAH3 knockout mice and patient spermatozoa showing co-reduced DNAH6, DNAH1, DNALI1\",\n      \"pmids\": [\"39503742\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct physical interaction not demonstrated\", \"Single lab\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Established that axonemal assembly of DNAH6 requires the CCDC39/CCDC40 96 nm ruler complex, defining its upstream dependency in respiratory cilia.\",\n      \"evidence\": \"Immunofluorescence of respiratory cilia in a cohort of 51 individuals with CCDC39/CCDC40 variants\",\n      \"pmids\": [\"39056782\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single lab\", \"Whether DNAH6 binds the ruler directly or assembles downstream not resolved\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Confirmed DNAH6's IDA membership in sperm via co-dependency with DNAH7, distinguishing it from outer dynein arm components.\",\n      \"evidence\": \"Immunofluorescent staining and TEM of spermatozoa from patients with loss-of-function DNAH7 variants\",\n      \"pmids\": [\"40810911\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single lab\", \"Order of IDA heavy chain assembly not established\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Implicated transcriptional control of DNAH6 expression in spermatids by the POU4F2/Brn-3b factor.\",\n      \"evidence\": \"RNA-seq and qRT-PCR of Brn-3b knockout mouse testes (preprint)\",\n      \"pmids\": [\"41282076\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No direct promoter binding or functional rescue for DNAH6 specifically\", \"Single lab preprint, not peer-reviewed\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How DNAH6 is positioned and anchored at specific axonemal sites and how its loss mechanistically disrupts sperm head and acrosome biogenesis remain unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No structural model of DNAH6 within the IDA\", \"No reconstitution of DNAH6 assembly\", \"Mechanistic link between flagellar IDA loss and head defects undefined\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0003774\", \"supporting_discovery_ids\": [0, 6]},\n      {\"term_id\": \"GO:0140657\", \"supporting_discovery_ids\": [0]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005929\", \"supporting_discovery_ids\": [0, 2, 7]},\n      {\"term_id\": \"GO:0005856\", \"supporting_discovery_ids\": [2, 6]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-1852241\", \"supporting_discovery_ids\": [0, 7]},\n      {\"term_id\": \"R-HSA-1266738\", \"supporting_discovery_ids\": [0, 1]},\n      {\"term_id\": \"R-HSA-1474165\", \"supporting_discovery_ids\": [3, 4]}\n    ],\n    \"complexes\": [\"inner dynein arm\", \"axoneme\"],\n    \"partners\": [\"DNAH3\", \"DNAH7\", \"DNAH1\", \"DNALI1\", \"CCDC39\", \"CCDC40\", \"DNAH5\", \"DNAI1\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":6,"faith_total":6,"faith_pct":100.0}}