{"gene":"SPATA46","run_date":"2026-06-10T07:46:39","timeline":{"discoveries":[{"year":2016,"finding":"SPATA46 is a nuclear membrane protein expressed predominantly in condensed spermatids, localizing to the subacrosomal area via a transmembrane region in its N-terminus. Knockout of Spata46 in mice caused abnormal sperm head shape (discontinuous nuclear envelope, cavity in nucleus), failure of sperm-egg fusion, and male subfertility, establishing SPATA46 as essential for sperm head reshaping and sperm-egg fusion.","method":"Knockout mouse model, immunolocalization, in vitro fertilization assay, antibody blocking experiment","journal":"Biology of reproduction","confidence":"High","confidence_rationale":"Tier 2 / Moderate — clean KO mouse with defined cellular and functional phenotypes (nuclear envelope defects, sperm-egg fusion failure), multiple orthogonal methods (IHC, KO, in vitro fertilization, antibody blocking), single lab","pmids":["27488028"],"is_preprint":false},{"year":2022,"finding":"SPATA46 (as a nuclear envelope protein) interacts with ACTRT1 at the subacrosomal region to anchor developing acrosomes to the nucleus. Loss of ACTRT1 weakened interactions between the acrosomal membrane protein SPACA1 and the ACTRT1 complex, implicating SPATA46 as part of the acrosome-nucleus connection machinery.","method":"Co-immunoprecipitation, knockout mouse model, immunolocalization","journal":"Development (Cambridge, England)","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — Co-IP identifying SPATA46 as an ACTRT1 interactor, supported by KO phenotype, but mechanistic role of SPATA46 itself is inferred rather than directly tested","pmids":["35616329"],"is_preprint":false},{"year":2014,"finding":"TEKT2BP2 (SPATA46) was identified as a TEKT2-binding protein by yeast two-hybrid screening from a mouse testis library, indicating a physical interaction between SPATA46 and the flagellar protein TEKT2.","method":"Yeast two-hybrid screen","journal":"The journal of histochemistry and cytochemistry","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single yeast two-hybrid result, no confirmation by orthogonal method (Co-IP or pulldown) in the same paper for TEKT2BP2 specifically","pmids":["24394471"],"is_preprint":false},{"year":2020,"finding":"USP26-mediated deubiquitination of the androgen receptor (AR) upregulates SPATA46 protein expression in Leydig cells, placing SPATA46 downstream of the AR signaling pathway in spermatogenesis-related regulation.","method":"Co-immunoprecipitation, immunofluorescence, western blot, plasmid overexpression/inhibition in TM3 Leydig cells","journal":"Advances in clinical and experimental medicine","confidence":"Low","confidence_rationale":"Tier 3 / Weak — SPATA46 upregulation is a downstream readout; single lab, indirect evidence of pathway placement, no direct experiment on SPATA46 mechanism","pmids":["33064378"],"is_preprint":false}],"current_model":"SPATA46 is a transmembrane nuclear envelope protein expressed in condensed spermatids that localizes to the subacrosomal region, where it is required for maintaining nuclear envelope integrity during sperm head shaping and for sperm-egg fusion; it physically interacts with the flagellar protein TEKT2 and the perinuclear theca protein ACTRT1 to help anchor the acrosome to the sperm nucleus, and its expression is regulated downstream of androgen receptor signaling via USP26-mediated deubiquitination."},"narrative":{"mechanistic_narrative":"SPATA46 is a transmembrane nuclear envelope protein expressed predominantly in condensed spermatids that is essential for sperm head reshaping and sperm-egg fusion [PMID:27488028]. It localizes to the subacrosomal region through an N-terminal transmembrane region, and loss of SPATA46 in mice produces abnormal sperm head morphology with a discontinuous nuclear envelope and intranuclear cavities, failure of sperm-egg fusion, and male subfertility, establishing its role in maintaining nuclear envelope integrity during spermiogenesis [PMID:27488028]. SPATA46 forms part of the acrosome-nucleus connection machinery, interacting with the perinuclear theca protein ACTRT1 at the subacrosomal region to anchor the developing acrosome to the nucleus [PMID:35616329]. Beyond these functions, the molecular activity of SPATA46 itself has not been directly characterized in the available corpus.","teleology":[{"year":2014,"claim":"Before any functional study, a physical partner was sought for SPATA46, and a yeast two-hybrid screen from a mouse testis library identified it as a TEKT2-binding protein, providing the first link to the sperm flagellar/cytoskeletal machinery.","evidence":"Yeast two-hybrid screen of a mouse testis library","pmids":["24394471"],"confidence":"Low","gaps":["Single yeast two-hybrid result not confirmed by Co-IP or pulldown for SPATA46/TEKT2BP2","Functional consequence of the TEKT2 interaction untested","No localization data tying the interaction to a subcellular compartment"]},{"year":2016,"claim":"Whether SPATA46 has an essential role in spermiogenesis was unknown until a knockout mouse defined it as a subacrosomal nuclear envelope protein required for sperm head reshaping and fertilization.","evidence":"Spata46 knockout mouse with immunolocalization, in vitro fertilization assay, and antibody blocking","pmids":["27488028"],"confidence":"High","gaps":["Molecular activity of SPATA46 not defined","Mechanism by which it maintains nuclear envelope continuity unresolved","How it mediates sperm-egg fusion not established at the molecular level"]},{"year":2020,"claim":"To place SPATA46 in a regulatory pathway, USP26-mediated deubiquitination of the androgen receptor was shown to upregulate SPATA46 protein, positioning it downstream of AR signaling.","evidence":"Co-IP, immunofluorescence, western blot, and overexpression/inhibition in TM3 Leydig cells","pmids":["33064378"],"confidence":"Low","gaps":["SPATA46 measured only as a downstream readout, not mechanistically tested","Single lab, indirect pathway placement","Leydig cell context differs from the spermatid site of SPATA46 function"]},{"year":2022,"claim":"How SPATA46 contributes to acrosome attachment was addressed by identifying it as an ACTRT1 interactor at the subacrosomal region, integrating it into the acrosome-nucleus connection complex.","evidence":"Co-immunoprecipitation, knockout mouse, and immunolocalization","pmids":["35616329"],"confidence":"Medium","gaps":["Mechanistic role of SPATA46 within the complex inferred rather than directly tested","No reciprocal validation of the ACTRT1 interaction reported","Relationship between the ACTRT1 and TEKT2 interactions unresolved"]},{"year":null,"claim":"The biochemical activity of SPATA46 and how its membrane anchoring mechanistically preserves nuclear envelope continuity and enables sperm-egg fusion remain undefined.","evidence":"","pmids":[],"confidence":"Low","gaps":["No defined molecular/enzymatic activity","Structural basis of acrosome-nucleus anchoring unknown","Direct molecular mediator of sperm-egg fusion not identified"]}],"mechanism_profile":{"molecular_activity":[],"localization":[{"term_id":"GO:0005635","term_label":"nuclear envelope","supporting_discovery_ids":[0]}],"pathway":[{"term_id":"R-HSA-1474165","term_label":"Reproduction","supporting_discovery_ids":[0]}],"complexes":[],"partners":["ACTRT1","TEKT2"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q5T0L3","full_name":"Spermatogenesis-associated protein 46","aliases":[],"length_aa":261,"mass_kda":29.1,"function":"Plays a role in spermiogenesis and fertilization","subcellular_location":"Nucleus membrane","url":"https://www.uniprot.org/uniprotkb/Q5T0L3/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/SPATA46","classification":"Not Classified","n_dependent_lines":2,"n_total_lines":1208,"dependency_fraction":0.0016556291390728477},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/SPATA46","total_profiled":1310},"omim":[{"mim_id":"617257","title":"SPERMATOGENESIS-ASSOCIATED PROTEIN 46; SPATA46","url":"https://www.omim.org/entry/617257"},{"mim_id":"300487","title":"ACTIN-RELATED PROTEIN T1; ACTRT1","url":"https://www.omim.org/entry/300487"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"","locations":[],"tissue_specificity":"Tissue enriched","tissue_distribution":"Detected in some","driving_tissues":[{"tissue":"testis","ntpm":29.7}],"url":"https://www.proteinatlas.org/search/SPATA46"},"hgnc":{"alias_symbol":["TEKT2BP2"],"prev_symbol":["C1orf111"]},"alphafold":{"accession":"Q5T0L3","domains":[{"cath_id":"1.10.287","chopping":"183-233","consensus_level":"medium","plddt":88.969,"start":183,"end":233}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q5T0L3","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q5T0L3-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q5T0L3-F1-predicted_aligned_error_v6.png","plddt_mean":55.03},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=SPATA46","jax_strain_url":"https://www.jax.org/strain/search?query=SPATA46"},"sequence":{"accession":"Q5T0L3","fasta_url":"https://rest.uniprot.org/uniprotkb/Q5T0L3.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q5T0L3/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q5T0L3"}},"corpus_meta":[{"pmid":"30701647","id":"PMC_30701647","title":"Nuclear envelope dynamics during mammalian spermatogenesis: new insights on male fertility.","date":"2019","source":"Biological reviews of the Cambridge Philosophical Society","url":"https://pubmed.ncbi.nlm.nih.gov/30701647","citation_count":42,"is_preprint":false},{"pmid":"35616329","id":"PMC_35616329","title":"Loss of perinuclear theca ACTRT1 causes acrosome detachment and severe male subfertility in mice.","date":"2022","source":"Development (Cambridge, England)","url":"https://pubmed.ncbi.nlm.nih.gov/35616329","citation_count":29,"is_preprint":false},{"pmid":"24394471","id":"PMC_24394471","title":"Molecular cloning and subcellular localization of Tektin2-binding protein 1 (Ccdc 172) in rat spermatozoa.","date":"2014","source":"The journal of histochemistry and cytochemistry : official journal of the Histochemistry Society","url":"https://pubmed.ncbi.nlm.nih.gov/24394471","citation_count":21,"is_preprint":false},{"pmid":"27488028","id":"PMC_27488028","title":"Deficiency of SPATA46, a Novel Nuclear Membrane Protein, Causes Subfertility in Male Mice.","date":"2016","source":"Biology of reproduction","url":"https://pubmed.ncbi.nlm.nih.gov/27488028","citation_count":18,"is_preprint":false},{"pmid":"37833923","id":"PMC_37833923","title":"Comprehensive Analysis of the Transcriptome-Wide m6A Methylome in Shaziling Pig Testicular Development.","date":"2023","source":"International journal of molecular sciences","url":"https://pubmed.ncbi.nlm.nih.gov/37833923","citation_count":10,"is_preprint":false},{"pmid":"33064378","id":"PMC_33064378","title":"USP26 deubiquitinates androgen receptor (AR) in the maintenance of sperm maturation and spermatogenesis through the androgen receptor signaling pathway.","date":"2020","source":"Advances in clinical and experimental medicine : official organ Wroclaw Medical University","url":"https://pubmed.ncbi.nlm.nih.gov/33064378","citation_count":10,"is_preprint":false},{"pmid":"32405957","id":"PMC_32405957","title":"Transcriptomic profiling of long non-coding RNAs in non-virus associated hepatocellular carcinoma.","date":"2020","source":"Cell biochemistry and biophysics","url":"https://pubmed.ncbi.nlm.nih.gov/32405957","citation_count":3,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":5572,"output_tokens":1060,"usd":0.016308,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":7641,"output_tokens":1672,"usd":0.040003,"stage2_stop_reason":"end_turn"},"total_usd":0.056311,"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\": 2016,\n      \"finding\": \"SPATA46 is a nuclear membrane protein expressed predominantly in condensed spermatids, localizing to the subacrosomal area via a transmembrane region in its N-terminus. Knockout of Spata46 in mice caused abnormal sperm head shape (discontinuous nuclear envelope, cavity in nucleus), failure of sperm-egg fusion, and male subfertility, establishing SPATA46 as essential for sperm head reshaping and sperm-egg fusion.\",\n      \"method\": \"Knockout mouse model, immunolocalization, in vitro fertilization assay, antibody blocking experiment\",\n      \"journal\": \"Biology of reproduction\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — clean KO mouse with defined cellular and functional phenotypes (nuclear envelope defects, sperm-egg fusion failure), multiple orthogonal methods (IHC, KO, in vitro fertilization, antibody blocking), single lab\",\n      \"pmids\": [\"27488028\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"SPATA46 (as a nuclear envelope protein) interacts with ACTRT1 at the subacrosomal region to anchor developing acrosomes to the nucleus. Loss of ACTRT1 weakened interactions between the acrosomal membrane protein SPACA1 and the ACTRT1 complex, implicating SPATA46 as part of the acrosome-nucleus connection machinery.\",\n      \"method\": \"Co-immunoprecipitation, knockout mouse model, immunolocalization\",\n      \"journal\": \"Development (Cambridge, England)\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — Co-IP identifying SPATA46 as an ACTRT1 interactor, supported by KO phenotype, but mechanistic role of SPATA46 itself is inferred rather than directly tested\",\n      \"pmids\": [\"35616329\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"TEKT2BP2 (SPATA46) was identified as a TEKT2-binding protein by yeast two-hybrid screening from a mouse testis library, indicating a physical interaction between SPATA46 and the flagellar protein TEKT2.\",\n      \"method\": \"Yeast two-hybrid screen\",\n      \"journal\": \"The journal of histochemistry and cytochemistry\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single yeast two-hybrid result, no confirmation by orthogonal method (Co-IP or pulldown) in the same paper for TEKT2BP2 specifically\",\n      \"pmids\": [\"24394471\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"USP26-mediated deubiquitination of the androgen receptor (AR) upregulates SPATA46 protein expression in Leydig cells, placing SPATA46 downstream of the AR signaling pathway in spermatogenesis-related regulation.\",\n      \"method\": \"Co-immunoprecipitation, immunofluorescence, western blot, plasmid overexpression/inhibition in TM3 Leydig cells\",\n      \"journal\": \"Advances in clinical and experimental medicine\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — SPATA46 upregulation is a downstream readout; single lab, indirect evidence of pathway placement, no direct experiment on SPATA46 mechanism\",\n      \"pmids\": [\"33064378\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"SPATA46 is a transmembrane nuclear envelope protein expressed in condensed spermatids that localizes to the subacrosomal region, where it is required for maintaining nuclear envelope integrity during sperm head shaping and for sperm-egg fusion; it physically interacts with the flagellar protein TEKT2 and the perinuclear theca protein ACTRT1 to help anchor the acrosome to the sperm nucleus, and its expression is regulated downstream of androgen receptor signaling via USP26-mediated deubiquitination.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"SPATA46 is a transmembrane nuclear envelope protein expressed predominantly in condensed spermatids that is essential for sperm head reshaping and sperm-egg fusion [#0]. It localizes to the subacrosomal region through an N-terminal transmembrane region, and loss of SPATA46 in mice produces abnormal sperm head morphology with a discontinuous nuclear envelope and intranuclear cavities, failure of sperm-egg fusion, and male subfertility, establishing its role in maintaining nuclear envelope integrity during spermiogenesis [#0]. SPATA46 forms part of the acrosome-nucleus connection machinery, interacting with the perinuclear theca protein ACTRT1 at the subacrosomal region to anchor the developing acrosome to the nucleus [#1]. Beyond these functions, the molecular activity of SPATA46 itself has not been directly characterized in the available corpus.\",\n  \"teleology\": [\n    {\n      \"year\": 2014,\n      \"claim\": \"Before any functional study, a physical partner was sought for SPATA46, and a yeast two-hybrid screen from a mouse testis library identified it as a TEKT2-binding protein, providing the first link to the sperm flagellar/cytoskeletal machinery.\",\n      \"evidence\": \"Yeast two-hybrid screen of a mouse testis library\",\n      \"pmids\": [\"24394471\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"Single yeast two-hybrid result not confirmed by Co-IP or pulldown for SPATA46/TEKT2BP2\", \"Functional consequence of the TEKT2 interaction untested\", \"No localization data tying the interaction to a subcellular compartment\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"Whether SPATA46 has an essential role in spermiogenesis was unknown until a knockout mouse defined it as a subacrosomal nuclear envelope protein required for sperm head reshaping and fertilization.\",\n      \"evidence\": \"Spata46 knockout mouse with immunolocalization, in vitro fertilization assay, and antibody blocking\",\n      \"pmids\": [\"27488028\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Molecular activity of SPATA46 not defined\", \"Mechanism by which it maintains nuclear envelope continuity unresolved\", \"How it mediates sperm-egg fusion not established at the molecular level\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"To place SPATA46 in a regulatory pathway, USP26-mediated deubiquitination of the androgen receptor was shown to upregulate SPATA46 protein, positioning it downstream of AR signaling.\",\n      \"evidence\": \"Co-IP, immunofluorescence, western blot, and overexpression/inhibition in TM3 Leydig cells\",\n      \"pmids\": [\"33064378\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"SPATA46 measured only as a downstream readout, not mechanistically tested\", \"Single lab, indirect pathway placement\", \"Leydig cell context differs from the spermatid site of SPATA46 function\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"How SPATA46 contributes to acrosome attachment was addressed by identifying it as an ACTRT1 interactor at the subacrosomal region, integrating it into the acrosome-nucleus connection complex.\",\n      \"evidence\": \"Co-immunoprecipitation, knockout mouse, and immunolocalization\",\n      \"pmids\": [\"35616329\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanistic role of SPATA46 within the complex inferred rather than directly tested\", \"No reciprocal validation of the ACTRT1 interaction reported\", \"Relationship between the ACTRT1 and TEKT2 interactions unresolved\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"The biochemical activity of SPATA46 and how its membrane anchoring mechanistically preserves nuclear envelope continuity and enables sperm-egg fusion remain undefined.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No defined molecular/enzymatic activity\", \"Structural basis of acrosome-nucleus anchoring unknown\", \"Direct molecular mediator of sperm-egg fusion not identified\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [],\n    \"localization\": [\n      {\"term_id\": \"GO:0005635\", \"supporting_discovery_ids\": [0]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-1474165\", \"supporting_discovery_ids\": [0]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\"ACTRT1\", \"TEKT2\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"faith_supported":3,"faith_total":3,"faith_pct":100.0}}