{"gene":"SPEF2","run_date":"2026-06-10T07:46:39","timeline":{"discoveries":[{"year":1999,"finding":"KPL2 (SPEF2) is a novel gene upregulated during ciliogenesis of airway epithelial cells; it encodes a protein >200 kDa containing a calponin homology domain, nuclear localization signals, a P-loop, and a proline-rich region, and is expressed in a stage-specific manner in spermatocytes and round spermatids of the testis.","method":"Differential display, Northern blot, RACE-based cDNA sequencing, Southern blot, protein domain analysis","journal":"American journal of respiratory cell and molecular biology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct cloning and sequence characterization with tissue/stage expression data; single lab, multiple complementary methods","pmids":["10100999"],"is_preprint":false},{"year":2006,"finding":"A retrotransposon insertion within an intron of KPL2 (SPEF2) causes aberrant splicing (exon skipping or intronic sequence inclusion) specifically of a testis-expressed isoform, leading to premature translation termination and the immotile short-tail sperm defect in pigs, demonstrating that SPEF2 is required for correct axonemal development in sperm flagella.","method":"Positional cloning, porcine-human comparative mapping, RT-PCR splice analysis, sequence analysis","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"High","confidence_rationale":"Tier 2 / Strong — positional cloning with molecular characterization of aberrant splicing; replicated in follow-up papers","pmids":["16549801"],"is_preprint":false},{"year":2007,"finding":"The intronic insertion in KPL2 (SPEF2) is a full-length LINE-1 retrotransposon capable of retrotransposition; the aberrant splicing it causes involves interference with intronic splice signals and activation of a cryptic splice site.","method":"Cloning and sequencing of the insertion, junction analysis, characterization of direct target-site repeats","journal":"Molecular genetics and genomics","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — detailed molecular characterization of the insertion mechanism; single lab, multiple sequence-based methods","pmids":["17610085"],"is_preprint":false},{"year":2009,"finding":"SPEF2 protein localizes to the Golgi complex, manchette, basal body, and midpiece of the sperm tail in differentiating germ cells, and physically interacts with the intraflagellar transport protein IFT20 in testis, as demonstrated by yeast two-hybrid assay and co-immunoprecipitation.","method":"Immunofluorescence localization, yeast two-hybrid assay, co-immunoprecipitation","journal":"Biology of reproduction","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — reciprocal interaction confirmed by two orthogonal methods (Y2H + Co-IP); single lab","pmids":["19889948"],"is_preprint":false},{"year":2011,"finding":"Loss of SPEF2 function in mice (bgh mutation, nonsense variant) causes shortened sperm flagella with disorganized axonemal and accessory structures, reduced numbers of elongating spermatids, and reduced cilia beat frequency in respiratory epithelium (with ultrastructurally normal cilia), establishing SPEF2 as required for cilia motility and sperm tail assembly.","method":"Positional cloning, Western blot (protein loss validation), histopathology, immunofluorescence, electron microscopy, video microscopy of cilia beat frequency","journal":"Biology of reproduction","confidence":"High","confidence_rationale":"Tier 2 / Strong — positional cloning of causative mutation validated by Western blot, multiple structural/functional readouts; replicated across species","pmids":["21715716"],"is_preprint":false},{"year":2017,"finding":"SPEF2 functions in microtubule-mediated protein transport during spermatid differentiation: it interacts with cytoplasmic dynein 1 and GOLGA3 (novel interaction partners), co-localizes with dynein 1 in the manchette, and is required for dynein 1-dependent transport of IFT20 from the Golgi to the manchette; loss of SPEF2 also causes basal body duplication and failure of manchette migration, resulting in abnormal sperm head shape.","method":"Male germ cell-specific Spef2 knockout mouse, co-immunoprecipitation, immunofluorescence co-localization, dynein inhibition assay","journal":"Development (Cambridge, England)","confidence":"High","confidence_rationale":"Tier 2 / Strong — cell-type-specific KO with defined phenotype, novel interactions confirmed by Co-IP, functional epistasis via dynein inhibition; multiple orthogonal methods in one study","pmids":["28619825"],"is_preprint":false},{"year":2018,"finding":"SPEF2 is expressed in osteoblasts and cartilage; Spef2 knockout mice exhibit growth retardation, shorter long bones, reduced bone mineral content, and compromised in vitro osteoblast differentiation, revealing a role for SPEF2 in bone formation and osteoblast differentiation.","method":"Spef2 knockout mouse model, X-ray analysis, bone histology, in vitro osteoblast differentiation assay","journal":"Scientific reports","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — KO mouse with defined skeletal phenotype and in vitro differentiation assay; single lab","pmids":["29339787"],"is_preprint":false},{"year":2019,"finding":"Loss-of-function mutations in SPEF2 (affecting long testis-specific isoforms encoding the IFT20-binding domain) cause multiple morphological abnormalities of the sperm flagella (MMAF) in humans, with disrupted axonemal structure, mitochondrial sheath defects, and reduced SPEF2 protein in spermatozoa.","method":"Whole exome sequencing, transmission electron microscopy, Western blot, immunofluorescence on patient spermatozoa","journal":"Journal of medical genetics","confidence":"High","confidence_rationale":"Tier 2 / Strong — independently identified in two separate cohorts (Chinese and Iranian) with multiple orthogonal functional validation methods","pmids":["31151990","31048344"],"is_preprint":false},{"year":2019,"finding":"SPEF2 deficiency in MMAF patients alters the localization of the axonemal protein CFAP69, indicating that SPEF2 is required for proper targeting of other axonemal proteins in the sperm flagellum.","method":"Immunofluorescence assay on patient spermatozoa","journal":"Journal of medical genetics","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — immunofluorescence in patient cells; replicated across two separate cohorts","pmids":["31048344"],"is_preprint":false},{"year":2020,"finding":"SPEF2 is a central pair (CP)-associated protein in respiratory cilia; in HYDIN-mutant cells, SPEF2 is absent from cilia, demonstrating that SPEF2 localization to the CP apparatus depends on functional HYDIN.","method":"Immunofluorescence microscopy on respiratory epithelial cells from PCD patients with HYDIN and SPEF2 mutations","journal":"American journal of respiratory cell and molecular biology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — large patient cohort (189 individuals) with IF-based protein localization; single lab but broad sample size","pmids":["31545650"],"is_preprint":false},{"year":2022,"finding":"SPEF2 interacts with RSPH9 (radial spoke head component) and IFT20 in vitro; proteomic analysis of SPEF2-mutant patient spermatozoa reveals downregulation of multiple flagellar assembly proteins including SPAG6, DYNLT1, RSPH1, TOM20, EFHC1, MNS1, and IFT20.","method":"Co-immunoprecipitation (in vitro), proteomic analysis (mass spectrometry), Western blot validation","journal":"Asian journal of andrology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP for protein interactions combined with proteomics; single lab","pmids":["34755699"],"is_preprint":false},{"year":2023,"finding":"Pathogenic variants in SPEF2 cause absence or severe reduction of SPEF2 protein in sperm flagella and co-occur with loss of HYDIN in flagella of HYDIN-mutant individuals, providing further evidence for an interaction between HYDIN and SPEF2 in sperm flagella.","method":"Immunofluorescence microscopy on sperm flagella, transmission electron microscopy, high-speed video microscopy, genetic testing","journal":"Frontiers in genetics","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multi-method diagnostic workup across multiple patients; single consortium but cross-validated","pmids":["36873931"],"is_preprint":false},{"year":2024,"finding":"SPEF2 variants cause absence of the central pair complex in sperm flagella, as demonstrated by ultrastructural analysis, and abolish SPEF2 protein in both spermatozoa and respiratory cilia, linking SPEF2 to central pair apparatus integrity.","method":"Whole-exome sequencing, transmission electron microscopy of sperm, immunofluorescence of spermatozoa and nasal cilia, in vitro variant analysis","journal":"Journal of assisted reproduction and genetics","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple orthogonal methods in patient cells; single study","pmids":["38568462"],"is_preprint":false}],"current_model":"SPEF2 is a large ciliary/flagellar protein that localizes to the manchette, basal body, Golgi complex, and sperm tail midpiece during spermatogenesis, where it acts as a linker for cytoplasmic dynein 1-mediated cargo transport (including IFT20) along microtubules; it physically interacts with IFT20, RSPH9, cytoplasmic dynein 1, and GOLGA3, is required for correct axonemal and accessory structure assembly in sperm flagella and for central pair apparatus integrity in motile cilia, and its loss-of-function causes MMAF and primary ciliary dyskinesia in humans and mice, as well as defects in osteoblast differentiation."},"narrative":{"mechanistic_narrative":"SPEF2 is a large (>200 kDa) microtubule-associated protein required for the assembly of motile cilia and sperm flagella, originally identified as a gene upregulated during airway ciliogenesis and expressed stage-specifically in spermatocytes and round spermatids [PMID:10100999]. During spermatid differentiation it localizes to the Golgi complex, manchette, basal body, and sperm tail midpiece and serves as a linker for cytoplasmic dynein 1-mediated cargo transport: it binds cytoplasmic dynein 1 and GOLGA3, co-localizes with dynein in the manchette, and is required for dynein 1-dependent transport of the intraflagellar transport protein IFT20 from the Golgi to the manchette, with its loss causing basal body duplication, failed manchette migration, and abnormal sperm head shape [PMID:19889948, PMID:28619825]. Loss of SPEF2 function disrupts axonemal and accessory-structure assembly, shortens sperm flagella, and reduces ciliary beat frequency in respiratory epithelium [PMID:21715716], and it is needed for correct targeting of other flagellar proteins such as CFAP69 [PMID:31048344]. In motile cilia and sperm flagella SPEF2 is a central pair (CP) apparatus-associated protein whose ciliary localization depends on functional HYDIN, and its loss results in absence of the central pair complex [PMID:31545650, PMID:38568462]. Loss-of-function mutations affecting the long testis-specific, IFT20-binding isoforms cause multiple morphological abnormalities of the sperm flagella (MMAF) in humans, and SPEF2 deficiency is associated with primary ciliary dyskinesia [PMID:31151990, PMID:31048344, PMID:36873931]. Beyond its ciliary roles, SPEF2 also supports osteoblast differentiation and bone formation [PMID:29339787].","teleology":[{"year":1999,"claim":"Established SPEF2 (KPL2) as a ciliogenesis-associated gene, raising the question of what role its large multidomain protein plays in ciliated and germ cells.","evidence":"Differential display and cDNA cloning with stage-specific expression analysis in airway epithelium and testis","pmids":["10100999"],"confidence":"Medium","gaps":["No functional assay linking expression to a ciliary mechanism","Domain functions (CH domain, P-loop) not tested"]},{"year":2006,"claim":"Showed SPEF2 is genetically required for sperm flagellar axoneme development by linking a disruptive intronic insertion to the porcine immotile short-tail sperm defect.","evidence":"Positional cloning and RT-PCR splice analysis in pigs, with comparative mapping","pmids":["16549801"],"confidence":"High","gaps":["Molecular mechanism of SPEF2 in axoneme assembly not defined","Protein-level consequences not characterized"]},{"year":2007,"claim":"Defined the causal lesion as a full-length LINE-1 retrotransposon disrupting splice signals, clarifying how an isoform-specific defect arises.","evidence":"Cloning, junction analysis, and target-site repeat characterization of the insertion","pmids":["17610085"],"confidence":"Medium","gaps":["Does not address SPEF2 protein function","Isoform-specific requirement not mapped to a functional domain"]},{"year":2009,"claim":"Connected SPEF2 to intraflagellar transport by demonstrating it localizes to Golgi, manchette, basal body, and midpiece and binds IFT20.","evidence":"Immunofluorescence, yeast two-hybrid, and co-immunoprecipitation in testis","pmids":["19889948"],"confidence":"Medium","gaps":["Directionality/role of the IFT20 interaction not resolved","No motor or transport mechanism yet identified"]},{"year":2011,"claim":"Established SPEF2 as required for both sperm tail assembly and cilia motility using a loss-of-function mouse with shortened flagella and reduced ciliary beat frequency.","evidence":"Positional cloning of bgh nonsense mutation with histology, EM, and video microscopy","pmids":["21715716"],"confidence":"High","gaps":["Reduced beat frequency despite normal cilia ultrastructure not mechanistically explained","Molecular cargo/transport role still unconfirmed"]},{"year":2017,"claim":"Defined the molecular mechanism: SPEF2 links cytoplasmic dynein 1 and GOLGA3 to drive dynein-dependent IFT20 transport from Golgi to manchette during spermatid differentiation.","evidence":"Germ-cell-specific Spef2 knockout, Co-IP, co-localization, and dynein inhibition assay","pmids":["28619825"],"confidence":"High","gaps":["Whether SPEF2 transports cargoes beyond IFT20 not established","Structural basis of dynein/GOLGA3 binding unknown"]},{"year":2018,"claim":"Revealed a non-ciliary role for SPEF2 in osteoblast differentiation and bone formation.","evidence":"Spef2 knockout mouse with X-ray, bone histology, and in vitro osteoblast differentiation assays","pmids":["29339787"],"confidence":"Medium","gaps":["Molecular pathway linking SPEF2 to osteoblast differentiation unknown","Whether the bone phenotype is cilia-dependent not determined"]},{"year":2019,"claim":"Established SPEF2 as a human MMAF gene and showed it is needed for correct targeting of other axonemal proteins.","evidence":"Whole-exome sequencing in two cohorts, TEM, Western blot, and CFAP69 immunofluorescence on patient sperm","pmids":["31151990","31048344"],"confidence":"High","gaps":["Mechanism by which SPEF2 directs CFAP69 localization unknown","Genotype-phenotype relationship across isoforms incompletely mapped"]},{"year":2020,"claim":"Placed SPEF2 within the central pair apparatus of respiratory cilia and showed its ciliary localization depends on HYDIN.","evidence":"Immunofluorescence on respiratory epithelium from HYDIN- and SPEF2-mutant PCD patients","pmids":["31545650"],"confidence":"Medium","gaps":["Direct HYDIN-SPEF2 physical interaction not demonstrated here","Hierarchy of central pair assembly not fully resolved"]},{"year":2022,"claim":"Broadened the interaction network to RSPH9 and confirmed IFT20 binding, while proteomics revealed downstream flagellar assembly proteins depleted upon SPEF2 loss.","evidence":"In vitro Co-IP plus mass spectrometry and Western blot on SPEF2-mutant sperm","pmids":["34755699"],"confidence":"Medium","gaps":["Direct versus indirect nature of proteomic changes not separated","RSPH9 interaction not validated in vivo"]},{"year":2023,"claim":"Reinforced a SPEF2-HYDIN relationship in sperm flagella by showing co-loss of the two proteins in mutant flagella.","evidence":"Immunofluorescence, TEM, and high-speed video microscopy across multiple patients","pmids":["36873931"],"confidence":"Medium","gaps":["Does not establish direct physical interaction","Whether co-loss reflects shared assembly pathway or mutual stabilization unclear"]},{"year":2024,"claim":"Linked SPEF2 directly to central pair complex integrity by showing variants abolish the central pair in sperm flagella and deplete SPEF2 in both sperm and respiratory cilia.","evidence":"Whole-exome sequencing, sperm TEM, immunofluorescence of spermatozoa and nasal cilia, in vitro variant analysis","pmids":["38568462"],"confidence":"Medium","gaps":["Whether SPEF2 is structural to or assembles the central pair not distinguished","Mechanistic link between central pair loss and motility defect not detailed"]},{"year":null,"claim":"How SPEF2 mechanistically connects its dynein/IFT20 cargo-transport role in the manchette to its central pair apparatus role within the assembled axoneme remains unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No structural model of SPEF2 or its binding interfaces","Whether central pair and transport functions are separable across isoforms unknown","Molecular basis of the osteoblast phenotype uncharacterized"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[3,5]},{"term_id":"GO:0008092","term_label":"cytoskeletal protein binding","supporting_discovery_ids":[5]},{"term_id":"GO:0005198","term_label":"structural molecule activity","supporting_discovery_ids":[9,12]}],"localization":[{"term_id":"GO:0005929","term_label":"cilium","supporting_discovery_ids":[4,9,12]},{"term_id":"GO:0005794","term_label":"Golgi apparatus","supporting_discovery_ids":[3,5]},{"term_id":"GO:0005815","term_label":"microtubule organizing center","supporting_discovery_ids":[3,5]},{"term_id":"GO:0005856","term_label":"cytoskeleton","supporting_discovery_ids":[3,5]}],"pathway":[{"term_id":"R-HSA-1852241","term_label":"Organelle biogenesis and maintenance","supporting_discovery_ids":[4,9,12]},{"term_id":"R-HSA-9609507","term_label":"Protein localization","supporting_discovery_ids":[5]},{"term_id":"R-HSA-1474165","term_label":"Reproduction","supporting_discovery_ids":[7]},{"term_id":"R-HSA-1643685","term_label":"Disease","supporting_discovery_ids":[7,11]}],"complexes":["central pair apparatus","manchette"],"partners":["IFT20","DYNC1H1","GOLGA3","RSPH9","HYDIN","CFAP69"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q9C093","full_name":"Sperm flagellar protein 2","aliases":["Protein KPL2"],"length_aa":1822,"mass_kda":209.8,"function":"Required for correct axoneme development in spermatozoa. Important for normal development of the manchette and sperm head morphology. Essential for male fertility. Plays a role in localization of the intraflagellar transport protein IFT20 to the manchette, suggesting function as an adapter for dynein-mediated protein transport during spermatogenesis (PubMed:31048344, PubMed:31151990, PubMed:31278745). Also plays a role in bone growth where it seems to be required for normal osteoblast differentiation (By similarity)","subcellular_location":"Cell projection, cilium, flagellum; Cytoplasm; Golgi apparatus","url":"https://www.uniprot.org/uniprotkb/Q9C093/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/SPEF2","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/SPEF2","total_profiled":1310},"omim":[{"mim_id":"621121","title":"CILIA- AND FLAGELLA-ASSOCIATED PROTEIN 54; CFAP54","url":"https://www.omim.org/entry/621121"},{"mim_id":"619712","title":"SPERMATOGENIC FAILURE 65; SPGF65","url":"https://www.omim.org/entry/619712"},{"mim_id":"619144","title":"SPERMATOGENIC FAILURE 49; SPGF49","url":"https://www.omim.org/entry/619144"},{"mim_id":"618751","title":"SPERMATOGENIC FAILURE 43; SPGF43","url":"https://www.omim.org/entry/618751"},{"mim_id":"618704","title":"CILIA- AND FLAGELLA-ASSOCIATED PROTEIN 221; CFAP221","url":"https://www.omim.org/entry/618704"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Primary cilium","reliability":"Supported"},{"location":"Flagellar centriole","reliability":"Supported"},{"location":"Nuclear bodies","reliability":"Additional"},{"location":"Cytosol","reliability":"Additional"},{"location":"Mid piece","reliability":"Additional"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in many","driving_tissues":[],"url":"https://www.proteinatlas.org/search/SPEF2"},"hgnc":{"alias_symbol":["KPL2","FLJ23577","CT122"],"prev_symbol":[]},"alphafold":{"accession":"Q9C093","domains":[{"cath_id":"1.10.418.10","chopping":"2-145","consensus_level":"high","plddt":81.091,"start":2,"end":145},{"cath_id":"-","chopping":"517-546_1016-1076_1112-1198_1209-1216_1239-1282_1336-1411","consensus_level":"medium","plddt":84.9504,"start":517,"end":1411},{"cath_id":"-","chopping":"1462-1524","consensus_level":"medium","plddt":81.973,"start":1462,"end":1524}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9C093","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q9C093-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q9C093-F1-predicted_aligned_error_v6.png","plddt_mean":70.5},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=SPEF2","jax_strain_url":"https://www.jax.org/strain/search?query=SPEF2"},"sequence":{"accession":"Q9C093","fasta_url":"https://rest.uniprot.org/uniprotkb/Q9C093.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q9C093/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9C093"}},"corpus_meta":[{"pmid":"21715716","id":"PMC_21715716","title":"Loss of SPEF2 function in mice results in spermatogenesis defects and primary ciliary dyskinesia.","date":"2011","source":"Biology of reproduction","url":"https://pubmed.ncbi.nlm.nih.gov/21715716","citation_count":106,"is_preprint":false},{"pmid":"18713476","id":"PMC_18713476","title":"Partial duplication of the PRLR and SPEF2 genes at the late feathering locus in chicken.","date":"2008","source":"BMC genomics","url":"https://pubmed.ncbi.nlm.nih.gov/18713476","citation_count":80,"is_preprint":false},{"pmid":"16549801","id":"PMC_16549801","title":"An intronic insertion in KPL2 results in aberrant splicing and causes the immotile short-tail sperm defect in the pig.","date":"2006","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/16549801","citation_count":78,"is_preprint":false},{"pmid":"19889948","id":"PMC_19889948","title":"Expression of SPEF2 during mouse spermatogenesis and identification of IFT20 as an interacting protein.","date":"2009","source":"Biology of reproduction","url":"https://pubmed.ncbi.nlm.nih.gov/19889948","citation_count":76,"is_preprint":false},{"pmid":"31151990","id":"PMC_31151990","title":"Loss-of-function mutations in SPEF2 cause multiple morphological abnormalities of the sperm flagella (MMAF).","date":"2019","source":"Journal of medical genetics","url":"https://pubmed.ncbi.nlm.nih.gov/31151990","citation_count":65,"is_preprint":false},{"pmid":"31048344","id":"PMC_31048344","title":"Homozygous mutations in SPEF2 induce multiple morphological abnormalities of the sperm flagella and male infertility.","date":"2019","source":"Journal of medical genetics","url":"https://pubmed.ncbi.nlm.nih.gov/31048344","citation_count":60,"is_preprint":false},{"pmid":"31545650","id":"PMC_31545650","title":"SPEF2- and HYDIN-Mutant Cilia Lack the Central Pair-associated Protein SPEF2, Aiding Primary Ciliary Dyskinesia Diagnostics.","date":"2020","source":"American journal of respiratory cell and molecular biology","url":"https://pubmed.ncbi.nlm.nih.gov/31545650","citation_count":58,"is_preprint":false},{"pmid":"28619825","id":"PMC_28619825","title":"SPEF2 functions in microtubule-mediated transport in elongating spermatids to ensure proper male germ cell differentiation.","date":"2017","source":"Development (Cambridge, England)","url":"https://pubmed.ncbi.nlm.nih.gov/28619825","citation_count":58,"is_preprint":false},{"pmid":"10100999","id":"PMC_10100999","title":"Cloning and characterization of KPL2, a novel gene induced during ciliogenesis of tracheal epithelial cells.","date":"1999","source":"American journal of respiratory cell and molecular biology","url":"https://pubmed.ncbi.nlm.nih.gov/10100999","citation_count":41,"is_preprint":false},{"pmid":"36873931","id":"PMC_36873931","title":"Pathogenic gene variants in CCDC39, CCDC40, RSPH1, RSPH9, HYDIN, and SPEF2 cause defects of sperm flagella composition and male infertility.","date":"2023","source":"Frontiers in genetics","url":"https://pubmed.ncbi.nlm.nih.gov/36873931","citation_count":25,"is_preprint":false},{"pmid":"29339787","id":"PMC_29339787","title":"Cilia-related protein SPEF2 regulates osteoblast differentiation.","date":"2018","source":"Scientific reports","url":"https://pubmed.ncbi.nlm.nih.gov/29339787","citation_count":24,"is_preprint":false},{"pmid":"22394230","id":"PMC_22394230","title":"L1 insertion within SPEF2 gene is associated with increased litter size in the Finnish Yorkshire population.","date":"2011","source":"Journal of animal breeding and genetics = Zeitschrift fur Tierzuchtung und Zuchtungsbiologie","url":"https://pubmed.ncbi.nlm.nih.gov/22394230","citation_count":21,"is_preprint":false},{"pmid":"34755699","id":"PMC_34755699","title":"Sperm flagellar 2 (SPEF2) is essential for sperm flagellar assembly in humans.","date":"2022","source":"Asian journal of andrology","url":"https://pubmed.ncbi.nlm.nih.gov/34755699","citation_count":19,"is_preprint":false},{"pmid":"17610085","id":"PMC_17610085","title":"Infertile Finnish Yorkshire boars carry a full-length LINE-1 retrotransposon within the KPL2 gene.","date":"2007","source":"Molecular genetics and genomics : MGG","url":"https://pubmed.ncbi.nlm.nih.gov/17610085","citation_count":17,"is_preprint":false},{"pmid":"37801226","id":"PMC_37801226","title":"circ_SPEF2 Regulates the Balance of Treg Cells by Regulating miR-16-5p/BACH2 in Lymphoma and Participates in the Immune Response.","date":"2023","source":"Tissue engineering and regenerative medicine","url":"https://pubmed.ncbi.nlm.nih.gov/37801226","citation_count":10,"is_preprint":false},{"pmid":"36615117","id":"PMC_36615117","title":"Novel SPEF2 Variant in a Japanese Patient with Primary Ciliary Dyskinesia: A Case Report and Literature Review.","date":"2022","source":"Journal of clinical medicine","url":"https://pubmed.ncbi.nlm.nih.gov/36615117","citation_count":6,"is_preprint":false},{"pmid":"24712415","id":"PMC_24712415","title":"A recent L1 insertion within SPEF2 gene is associated with changes in PRLR expression in sow reproductive organs.","date":"2014","source":"Animal genetics","url":"https://pubmed.ncbi.nlm.nih.gov/24712415","citation_count":5,"is_preprint":false},{"pmid":"39753944","id":"PMC_39753944","title":"Novel variants of FSIP2 and SPEF2 cause varying degrees of spermatozoa damage in MMAF patients and favorable ART outcomes.","date":"2025","source":"Journal of assisted reproduction and genetics","url":"https://pubmed.ncbi.nlm.nih.gov/39753944","citation_count":4,"is_preprint":false},{"pmid":"34679903","id":"PMC_34679903","title":"Search for Associations of FSHR, INHA, INHAB, PRL, TNP2 and SPEF2 Genes Polymorphisms with Semen Quality in Russian Holstein Bulls (Pilot Study).","date":"2021","source":"Animals : an open access journal from MDPI","url":"https://pubmed.ncbi.nlm.nih.gov/34679903","citation_count":4,"is_preprint":false},{"pmid":"35965828","id":"PMC_35965828","title":"The ciliary protein Spef2 stimulates acinar Ampkα/Sirt1 signaling and ameliorates acute pancreatitis and associated lung injury.","date":"2022","source":"Annals of translational medicine","url":"https://pubmed.ncbi.nlm.nih.gov/35965828","citation_count":3,"is_preprint":false},{"pmid":"38568462","id":"PMC_38568462","title":"Novel SPEF2 variants cause male infertility and likely primary ciliary dyskinesia.","date":"2024","source":"Journal of assisted reproduction and genetics","url":"https://pubmed.ncbi.nlm.nih.gov/38568462","citation_count":2,"is_preprint":false},{"pmid":"40949679","id":"PMC_40949679","title":"Retraction: The ciliary protein Spef2 stimulates acinar Ampkα/Sirt1 signaling and ameliorates acute pancreatitis and associated lung injury.","date":"2024","source":"Annals of translational medicine","url":"https://pubmed.ncbi.nlm.nih.gov/40949679","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":13301,"output_tokens":3000,"usd":0.042452,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":10420,"output_tokens":3819,"usd":0.073788,"stage2_stop_reason":"end_turn"},"total_usd":0.11624,"stage1_batch_id":"msgbatch_013LWZZT6MWaqB9qyTSeQBmU","stage2_batch_id":"msgbatch_0194ZzQaTGNpruoNJBbEMbt3","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 1999,\n      \"finding\": \"KPL2 (SPEF2) is a novel gene upregulated during ciliogenesis of airway epithelial cells; it encodes a protein >200 kDa containing a calponin homology domain, nuclear localization signals, a P-loop, and a proline-rich region, and is expressed in a stage-specific manner in spermatocytes and round spermatids of the testis.\",\n      \"method\": \"Differential display, Northern blot, RACE-based cDNA sequencing, Southern blot, protein domain analysis\",\n      \"journal\": \"American journal of respiratory cell and molecular biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct cloning and sequence characterization with tissue/stage expression data; single lab, multiple complementary methods\",\n      \"pmids\": [\"10100999\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2006,\n      \"finding\": \"A retrotransposon insertion within an intron of KPL2 (SPEF2) causes aberrant splicing (exon skipping or intronic sequence inclusion) specifically of a testis-expressed isoform, leading to premature translation termination and the immotile short-tail sperm defect in pigs, demonstrating that SPEF2 is required for correct axonemal development in sperm flagella.\",\n      \"method\": \"Positional cloning, porcine-human comparative mapping, RT-PCR splice analysis, sequence analysis\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — positional cloning with molecular characterization of aberrant splicing; replicated in follow-up papers\",\n      \"pmids\": [\"16549801\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2007,\n      \"finding\": \"The intronic insertion in KPL2 (SPEF2) is a full-length LINE-1 retrotransposon capable of retrotransposition; the aberrant splicing it causes involves interference with intronic splice signals and activation of a cryptic splice site.\",\n      \"method\": \"Cloning and sequencing of the insertion, junction analysis, characterization of direct target-site repeats\",\n      \"journal\": \"Molecular genetics and genomics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — detailed molecular characterization of the insertion mechanism; single lab, multiple sequence-based methods\",\n      \"pmids\": [\"17610085\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"SPEF2 protein localizes to the Golgi complex, manchette, basal body, and midpiece of the sperm tail in differentiating germ cells, and physically interacts with the intraflagellar transport protein IFT20 in testis, as demonstrated by yeast two-hybrid assay and co-immunoprecipitation.\",\n      \"method\": \"Immunofluorescence localization, yeast two-hybrid assay, co-immunoprecipitation\",\n      \"journal\": \"Biology of reproduction\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal interaction confirmed by two orthogonal methods (Y2H + Co-IP); single lab\",\n      \"pmids\": [\"19889948\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"Loss of SPEF2 function in mice (bgh mutation, nonsense variant) causes shortened sperm flagella with disorganized axonemal and accessory structures, reduced numbers of elongating spermatids, and reduced cilia beat frequency in respiratory epithelium (with ultrastructurally normal cilia), establishing SPEF2 as required for cilia motility and sperm tail assembly.\",\n      \"method\": \"Positional cloning, Western blot (protein loss validation), histopathology, immunofluorescence, electron microscopy, video microscopy of cilia beat frequency\",\n      \"journal\": \"Biology of reproduction\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — positional cloning of causative mutation validated by Western blot, multiple structural/functional readouts; replicated across species\",\n      \"pmids\": [\"21715716\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"SPEF2 functions in microtubule-mediated protein transport during spermatid differentiation: it interacts with cytoplasmic dynein 1 and GOLGA3 (novel interaction partners), co-localizes with dynein 1 in the manchette, and is required for dynein 1-dependent transport of IFT20 from the Golgi to the manchette; loss of SPEF2 also causes basal body duplication and failure of manchette migration, resulting in abnormal sperm head shape.\",\n      \"method\": \"Male germ cell-specific Spef2 knockout mouse, co-immunoprecipitation, immunofluorescence co-localization, dynein inhibition assay\",\n      \"journal\": \"Development (Cambridge, England)\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — cell-type-specific KO with defined phenotype, novel interactions confirmed by Co-IP, functional epistasis via dynein inhibition; multiple orthogonal methods in one study\",\n      \"pmids\": [\"28619825\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"SPEF2 is expressed in osteoblasts and cartilage; Spef2 knockout mice exhibit growth retardation, shorter long bones, reduced bone mineral content, and compromised in vitro osteoblast differentiation, revealing a role for SPEF2 in bone formation and osteoblast differentiation.\",\n      \"method\": \"Spef2 knockout mouse model, X-ray analysis, bone histology, in vitro osteoblast differentiation assay\",\n      \"journal\": \"Scientific reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — KO mouse with defined skeletal phenotype and in vitro differentiation assay; single lab\",\n      \"pmids\": [\"29339787\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"Loss-of-function mutations in SPEF2 (affecting long testis-specific isoforms encoding the IFT20-binding domain) cause multiple morphological abnormalities of the sperm flagella (MMAF) in humans, with disrupted axonemal structure, mitochondrial sheath defects, and reduced SPEF2 protein in spermatozoa.\",\n      \"method\": \"Whole exome sequencing, transmission electron microscopy, Western blot, immunofluorescence on patient spermatozoa\",\n      \"journal\": \"Journal of medical genetics\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — independently identified in two separate cohorts (Chinese and Iranian) with multiple orthogonal functional validation methods\",\n      \"pmids\": [\"31151990\", \"31048344\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"SPEF2 deficiency in MMAF patients alters the localization of the axonemal protein CFAP69, indicating that SPEF2 is required for proper targeting of other axonemal proteins in the sperm flagellum.\",\n      \"method\": \"Immunofluorescence assay on patient spermatozoa\",\n      \"journal\": \"Journal of medical genetics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — immunofluorescence in patient cells; replicated across two separate cohorts\",\n      \"pmids\": [\"31048344\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"SPEF2 is a central pair (CP)-associated protein in respiratory cilia; in HYDIN-mutant cells, SPEF2 is absent from cilia, demonstrating that SPEF2 localization to the CP apparatus depends on functional HYDIN.\",\n      \"method\": \"Immunofluorescence microscopy on respiratory epithelial cells from PCD patients with HYDIN and SPEF2 mutations\",\n      \"journal\": \"American journal of respiratory cell and molecular biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — large patient cohort (189 individuals) with IF-based protein localization; single lab but broad sample size\",\n      \"pmids\": [\"31545650\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"SPEF2 interacts with RSPH9 (radial spoke head component) and IFT20 in vitro; proteomic analysis of SPEF2-mutant patient spermatozoa reveals downregulation of multiple flagellar assembly proteins including SPAG6, DYNLT1, RSPH1, TOM20, EFHC1, MNS1, and IFT20.\",\n      \"method\": \"Co-immunoprecipitation (in vitro), proteomic analysis (mass spectrometry), Western blot validation\",\n      \"journal\": \"Asian journal of andrology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP for protein interactions combined with proteomics; single lab\",\n      \"pmids\": [\"34755699\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"Pathogenic variants in SPEF2 cause absence or severe reduction of SPEF2 protein in sperm flagella and co-occur with loss of HYDIN in flagella of HYDIN-mutant individuals, providing further evidence for an interaction between HYDIN and SPEF2 in sperm flagella.\",\n      \"method\": \"Immunofluorescence microscopy on sperm flagella, transmission electron microscopy, high-speed video microscopy, genetic testing\",\n      \"journal\": \"Frontiers in genetics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multi-method diagnostic workup across multiple patients; single consortium but cross-validated\",\n      \"pmids\": [\"36873931\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"SPEF2 variants cause absence of the central pair complex in sperm flagella, as demonstrated by ultrastructural analysis, and abolish SPEF2 protein in both spermatozoa and respiratory cilia, linking SPEF2 to central pair apparatus integrity.\",\n      \"method\": \"Whole-exome sequencing, transmission electron microscopy of sperm, immunofluorescence of spermatozoa and nasal cilia, in vitro variant analysis\",\n      \"journal\": \"Journal of assisted reproduction and genetics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple orthogonal methods in patient cells; single study\",\n      \"pmids\": [\"38568462\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"SPEF2 is a large ciliary/flagellar protein that localizes to the manchette, basal body, Golgi complex, and sperm tail midpiece during spermatogenesis, where it acts as a linker for cytoplasmic dynein 1-mediated cargo transport (including IFT20) along microtubules; it physically interacts with IFT20, RSPH9, cytoplasmic dynein 1, and GOLGA3, is required for correct axonemal and accessory structure assembly in sperm flagella and for central pair apparatus integrity in motile cilia, and its loss-of-function causes MMAF and primary ciliary dyskinesia in humans and mice, as well as defects in osteoblast differentiation.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"SPEF2 is a large (>200 kDa) microtubule-associated protein required for the assembly of motile cilia and sperm flagella, originally identified as a gene upregulated during airway ciliogenesis and expressed stage-specifically in spermatocytes and round spermatids [#0]. During spermatid differentiation it localizes to the Golgi complex, manchette, basal body, and sperm tail midpiece and serves as a linker for cytoplasmic dynein 1-mediated cargo transport: it binds cytoplasmic dynein 1 and GOLGA3, co-localizes with dynein in the manchette, and is required for dynein 1-dependent transport of the intraflagellar transport protein IFT20 from the Golgi to the manchette, with its loss causing basal body duplication, failed manchette migration, and abnormal sperm head shape [#3, #5]. Loss of SPEF2 function disrupts axonemal and accessory-structure assembly, shortens sperm flagella, and reduces ciliary beat frequency in respiratory epithelium [#4], and it is needed for correct targeting of other flagellar proteins such as CFAP69 [#8]. In motile cilia and sperm flagella SPEF2 is a central pair (CP) apparatus-associated protein whose ciliary localization depends on functional HYDIN, and its loss results in absence of the central pair complex [#9, #12]. Loss-of-function mutations affecting the long testis-specific, IFT20-binding isoforms cause multiple morphological abnormalities of the sperm flagella (MMAF) in humans, and SPEF2 deficiency is associated with primary ciliary dyskinesia [#7, #11]. Beyond its ciliary roles, SPEF2 also supports osteoblast differentiation and bone formation [#6].\",\n  \"teleology\": [\n    {\n      \"year\": 1999,\n      \"claim\": \"Established SPEF2 (KPL2) as a ciliogenesis-associated gene, raising the question of what role its large multidomain protein plays in ciliated and germ cells.\",\n      \"evidence\": \"Differential display and cDNA cloning with stage-specific expression analysis in airway epithelium and testis\",\n      \"pmids\": [\"10100999\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No functional assay linking expression to a ciliary mechanism\", \"Domain functions (CH domain, P-loop) not tested\"]\n    },\n    {\n      \"year\": 2006,\n      \"claim\": \"Showed SPEF2 is genetically required for sperm flagellar axoneme development by linking a disruptive intronic insertion to the porcine immotile short-tail sperm defect.\",\n      \"evidence\": \"Positional cloning and RT-PCR splice analysis in pigs, with comparative mapping\",\n      \"pmids\": [\"16549801\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Molecular mechanism of SPEF2 in axoneme assembly not defined\", \"Protein-level consequences not characterized\"]\n    },\n    {\n      \"year\": 2007,\n      \"claim\": \"Defined the causal lesion as a full-length LINE-1 retrotransposon disrupting splice signals, clarifying how an isoform-specific defect arises.\",\n      \"evidence\": \"Cloning, junction analysis, and target-site repeat characterization of the insertion\",\n      \"pmids\": [\"17610085\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Does not address SPEF2 protein function\", \"Isoform-specific requirement not mapped to a functional domain\"]\n    },\n    {\n      \"year\": 2009,\n      \"claim\": \"Connected SPEF2 to intraflagellar transport by demonstrating it localizes to Golgi, manchette, basal body, and midpiece and binds IFT20.\",\n      \"evidence\": \"Immunofluorescence, yeast two-hybrid, and co-immunoprecipitation in testis\",\n      \"pmids\": [\"19889948\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Directionality/role of the IFT20 interaction not resolved\", \"No motor or transport mechanism yet identified\"]\n    },\n    {\n      \"year\": 2011,\n      \"claim\": \"Established SPEF2 as required for both sperm tail assembly and cilia motility using a loss-of-function mouse with shortened flagella and reduced ciliary beat frequency.\",\n      \"evidence\": \"Positional cloning of bgh nonsense mutation with histology, EM, and video microscopy\",\n      \"pmids\": [\"21715716\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Reduced beat frequency despite normal cilia ultrastructure not mechanistically explained\", \"Molecular cargo/transport role still unconfirmed\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Defined the molecular mechanism: SPEF2 links cytoplasmic dynein 1 and GOLGA3 to drive dynein-dependent IFT20 transport from Golgi to manchette during spermatid differentiation.\",\n      \"evidence\": \"Germ-cell-specific Spef2 knockout, Co-IP, co-localization, and dynein inhibition assay\",\n      \"pmids\": [\"28619825\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether SPEF2 transports cargoes beyond IFT20 not established\", \"Structural basis of dynein/GOLGA3 binding unknown\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Revealed a non-ciliary role for SPEF2 in osteoblast differentiation and bone formation.\",\n      \"evidence\": \"Spef2 knockout mouse with X-ray, bone histology, and in vitro osteoblast differentiation assays\",\n      \"pmids\": [\"29339787\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Molecular pathway linking SPEF2 to osteoblast differentiation unknown\", \"Whether the bone phenotype is cilia-dependent not determined\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Established SPEF2 as a human MMAF gene and showed it is needed for correct targeting of other axonemal proteins.\",\n      \"evidence\": \"Whole-exome sequencing in two cohorts, TEM, Western blot, and CFAP69 immunofluorescence on patient sperm\",\n      \"pmids\": [\"31151990\", \"31048344\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Mechanism by which SPEF2 directs CFAP69 localization unknown\", \"Genotype-phenotype relationship across isoforms incompletely mapped\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Placed SPEF2 within the central pair apparatus of respiratory cilia and showed its ciliary localization depends on HYDIN.\",\n      \"evidence\": \"Immunofluorescence on respiratory epithelium from HYDIN- and SPEF2-mutant PCD patients\",\n      \"pmids\": [\"31545650\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct HYDIN-SPEF2 physical interaction not demonstrated here\", \"Hierarchy of central pair assembly not fully resolved\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Broadened the interaction network to RSPH9 and confirmed IFT20 binding, while proteomics revealed downstream flagellar assembly proteins depleted upon SPEF2 loss.\",\n      \"evidence\": \"In vitro Co-IP plus mass spectrometry and Western blot on SPEF2-mutant sperm\",\n      \"pmids\": [\"34755699\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct versus indirect nature of proteomic changes not separated\", \"RSPH9 interaction not validated in vivo\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Reinforced a SPEF2-HYDIN relationship in sperm flagella by showing co-loss of the two proteins in mutant flagella.\",\n      \"evidence\": \"Immunofluorescence, TEM, and high-speed video microscopy across multiple patients\",\n      \"pmids\": [\"36873931\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Does not establish direct physical interaction\", \"Whether co-loss reflects shared assembly pathway or mutual stabilization unclear\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Linked SPEF2 directly to central pair complex integrity by showing variants abolish the central pair in sperm flagella and deplete SPEF2 in both sperm and respiratory cilia.\",\n      \"evidence\": \"Whole-exome sequencing, sperm TEM, immunofluorescence of spermatozoa and nasal cilia, in vitro variant analysis\",\n      \"pmids\": [\"38568462\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether SPEF2 is structural to or assembles the central pair not distinguished\", \"Mechanistic link between central pair loss and motility defect not detailed\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How SPEF2 mechanistically connects its dynein/IFT20 cargo-transport role in the manchette to its central pair apparatus role within the assembled axoneme remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No structural model of SPEF2 or its binding interfaces\", \"Whether central pair and transport functions are separable across isoforms unknown\", \"Molecular basis of the osteoblast phenotype uncharacterized\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [3, 5]},\n      {\"term_id\": \"GO:0008092\", \"supporting_discovery_ids\": [5]},\n      {\"term_id\": \"GO:0005198\", \"supporting_discovery_ids\": [9, 12]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005929\", \"supporting_discovery_ids\": [4, 9, 12]},\n      {\"term_id\": \"GO:0005794\", \"supporting_discovery_ids\": [3, 5]},\n      {\"term_id\": \"GO:0005815\", \"supporting_discovery_ids\": [3, 5]},\n      {\"term_id\": \"GO:0005856\", \"supporting_discovery_ids\": [3, 5]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-1852241\", \"supporting_discovery_ids\": [4, 9, 12]},\n      {\"term_id\": \"R-HSA-9609507\", \"supporting_discovery_ids\": [5]},\n      {\"term_id\": \"R-HSA-1474165\", \"supporting_discovery_ids\": [7]},\n      {\"term_id\": \"R-HSA-1643685\", \"supporting_discovery_ids\": [7, 11]}\n    ],\n    \"complexes\": [\n      \"central pair apparatus\",\n      \"manchette\"\n    ],\n    \"partners\": [\n      \"IFT20\",\n      \"DYNC1H1\",\n      \"GOLGA3\",\n      \"RSPH9\",\n      \"HYDIN\",\n      \"CFAP69\"\n    ],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":6,"faith_total":6,"faith_pct":100.0}}