{"gene":"CYLC1","run_date":"2026-06-09T22:57:19","timeline":{"discoveries":[{"year":2023,"finding":"CYLC1 (Cylicin 1) is a structural component of the sperm calyx within the perinuclear theca. CRISPR/Cas9-mediated Cylc1 knockout in mice caused male subfertility, with phenotypic analysis revealing that loss of Cylicins prevents proper calyx assembly during spermiogenesis, resulting in decreased epididymal sperm counts, impaired shedding of excess cytoplasm, severe structural malformations, and impaired sperm motility.","method":"CRISPR/Cas9 knockout mouse model, phenotypic characterization, immunofluorescence, electron microscopy","journal":"eLife","confidence":"High","confidence_rationale":"Tier 2 / Strong — clean KO with defined cellular phenotype, multiple orthogonal methods (immunofluorescence, electron microscopy, fertility assays), replicated with human variant identification","pmids":["38013430"],"is_preprint":false},{"year":2024,"finding":"Cylicin-1 interacts with itself, several other perinuclear theca (PT) proteins, the inner acrosomal membrane (IAM) protein SPACA1, and the nuclear envelope (NE) protein FAM209, forming an 'IAM-cylicins-NE' sandwich structure that anchors the acrosome to the nucleus. Loss of Cylicin-1 in mice leads to acrosome detachment from the nucleus and malformed sperm heads.","method":"Co-immunoprecipitation (protein-protein interaction), Cylc1 knockout mouse model, immunofluorescence, whole exome sequencing of infertile men","journal":"eLife","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal protein interactions identified, KO mouse with defined structural phenotype, multiple orthogonal methods, validated with human variants","pmids":["38573307"],"is_preprint":false},{"year":2024,"finding":"CYLC1 variants (p.K328E and p.K324M) do not affect protein expression levels but alter the localization of CYLC1 protein and acrosome morphology in human sperm. Cylc1 knockout mice show acrosome-nuclear detachment by ultrastructural analysis (SEM/TEM). The localization of PLCZ1 was also altered in sperm from men carrying CYLC1 variants.","method":"Western blotting, immunofluorescence, CRISPR/Cas9 Cylc1 KO mice, SEM/TEM, Sanger sequencing","journal":"Journal of assisted reproduction and genetics","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple orthogonal methods in single lab, KO mouse with ultrastructural phenotype, but single lab study","pmids":["41075067"],"is_preprint":false},{"year":2016,"finding":"C. elegans homologues of human CYLC1 (named cylc-1 and cylc-2), which share sequence homology with stathmins and encode small, highly basic proteins with KKD/E repeats, regulate local tubulin concentration and microtubule growth deceleration at the cell periphery during smooth muscle cell differentiation. Depletion of these homologues abolished the local decrease in soluble tubulin concentration and microtubule deceleration behavior.","method":"RNAi/genetic depletion in C. elegans, live imaging of microtubule dynamics","journal":"Molecular biology of the cell","confidence":"Low","confidence_rationale":"Tier 3 / Weak — C. elegans ortholog study with live imaging, single lab, the function described (microtubule regulation) may not translate directly to mammalian CYLC1 which localizes to sperm perinuclear theca","pmids":["26985017"],"is_preprint":false}],"current_model":"CYLC1 encodes a testis-specific, lysine-rich cytoskeletal protein that is a major structural component of the sperm calyx/perinuclear theca; it forms an 'IAM-cylicins-NE' sandwich complex by interacting with itself, other PT proteins, the inner acrosomal membrane protein SPACA1, and nuclear envelope protein FAM209 to anchor the acrosome to the sperm nucleus, with loss of function causing acrosome detachment, sperm head deformity, defective calyx assembly, and male sub/infertility in mice and humans."},"narrative":{"mechanistic_narrative":"CYLC1 (Cylicin 1) is a testis-specific structural protein of the sperm calyx within the perinuclear theca, where it is required for proper calyx assembly during spermiogenesis and for normal sperm head morphogenesis [PMID:38013430]. Cylicin-1 self-associates and bridges the inner acrosomal membrane to the nuclear envelope by interacting with the IAM protein SPACA1 and the NE protein FAM209, forming an 'IAM-cylicins-NE' sandwich structure that physically anchors the acrosome to the sperm nucleus [PMID:38573307]. Loss of Cylicin-1 in mice disrupts calyx assembly and detaches the acrosome from the nucleus, producing malformed sperm heads, impaired cytoplasmic shedding, reduced epididymal sperm counts, and defective motility, resulting in male subfertility [PMID:38013430, PMID:38573307]. In humans, CYLC1 missense variants do not alter protein abundance but mislocalize the protein and disrupt acrosome morphology and the distribution of the sperm factor PLCZ1, linking CYLC1 dysfunction to male infertility [PMID:41075067].","teleology":[{"year":2023,"claim":"Established that CYLC1 is a structural component of the sperm calyx whose loss disrupts perinuclear theca assembly, defining its role in spermiogenesis and male fertility.","evidence":"CRISPR/Cas9 Cylc1 knockout mouse with immunofluorescence, electron microscopy, and fertility assays","pmids":["38013430"],"confidence":"High","gaps":["Did not define the molecular binding partners that recruit Cylicin-1 to the calyx","Subfertility rather than complete sterility leaves the requirement incompletely defined"]},{"year":2024,"claim":"Resolved how CYLC1 anchors the acrosome to the nucleus by identifying an IAM-cylicins-NE sandwich built on interactions with SPACA1 and FAM209, explaining the acrosome-detachment phenotype.","evidence":"Co-immunoprecipitation, Cylc1 knockout mouse, immunofluorescence, and whole exome sequencing of infertile men","pmids":["38573307"],"confidence":"High","gaps":["Stoichiometry and structural arrangement of the sandwich complex not determined","Which other PT proteins participate not fully enumerated"]},{"year":2024,"claim":"Showed that human CYLC1 missense variants act by mislocalizing the protein rather than reducing its expression, and that this perturbs acrosome morphology and PLCZ1 distribution, connecting variant biology to functional consequences.","evidence":"Western blotting, immunofluorescence, CRISPR/Cas9 Cylc1 KO mice, SEM/TEM, and Sanger sequencing of variant carriers","pmids":["41075067"],"confidence":"Medium","gaps":["Single-lab study without independent replication","Mechanistic basis for variant-induced mislocalization not established","Causal link between PLCZ1 mislocalization and fertilization outcome not demonstrated"]},{"year":null,"claim":"Whether mammalian CYLC1 retains any microtubule-regulatory or tubulin-sequestering activity analogous to its C. elegans homologues remains unresolved.","evidence":"","pmids":[],"confidence":"Low","gaps":["C. elegans cylc-1/cylc-2 microtubule-regulation function has not been tested in mammalian CYLC1","No biochemical activity assigned to mammalian CYLC1 beyond its structural anchoring role"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0005198","term_label":"structural molecule activity","supporting_discovery_ids":[0,1]},{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[1]}],"localization":[{"term_id":"GO:0005856","term_label":"cytoskeleton","supporting_discovery_ids":[0]},{"term_id":"GO:0005635","term_label":"nuclear envelope","supporting_discovery_ids":[1]}],"pathway":[{"term_id":"R-HSA-1474165","term_label":"Reproduction","supporting_discovery_ids":[0,1]}],"complexes":["IAM-cylicins-NE sandwich complex","sperm calyx / perinuclear theca"],"partners":["SPACA1","FAM209","CYLC1"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"P35663","full_name":"Cylicin-1","aliases":["Cylicin I","Multiple-band polypeptide I"],"length_aa":651,"mass_kda":74.2,"function":"Plays a role in the establishment of normal sperm morphology during spermatogenesis and is required for acrosome attachment to the nuclear envelope","subcellular_location":"Cytoplasm, cytoskeleton, perinuclear theca, calyx; Cytoplasm, cytoskeleton, perinuclear theca","url":"https://www.uniprot.org/uniprotkb/P35663/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/CYLC1","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/CYLC1","total_profiled":1310},"omim":[{"mim_id":"604035","title":"CYLICIN 2; CYLC2","url":"https://www.omim.org/entry/604035"},{"mim_id":"301119","title":"SPERMATOGENIC FAILURE, X-LINKED, 8; SPGFX8","url":"https://www.omim.org/entry/301119"},{"mim_id":"300768","title":"CYLICIN 1; CYLC1","url":"https://www.omim.org/entry/300768"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Calyx","reliability":"Supported"},{"location":"Perinuclear theca","reliability":"Additional"}],"tissue_specificity":"Tissue enriched","tissue_distribution":"Detected in single","driving_tissues":[{"tissue":"testis","ntpm":29.7}],"url":"https://www.proteinatlas.org/search/CYLC1"},"hgnc":{"alias_symbol":[],"prev_symbol":[]},"alphafold":{"accession":"P35663","domains":[],"viewer_url":"https://alphafold.ebi.ac.uk/entry/P35663","model_url":"https://alphafold.ebi.ac.uk/files/AF-P35663-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-P35663-F1-predicted_aligned_error_v6.png","plddt_mean":45.53},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=CYLC1","jax_strain_url":"https://www.jax.org/strain/search?query=CYLC1"},"sequence":{"accession":"P35663","fasta_url":"https://rest.uniprot.org/uniprotkb/P35663.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/P35663/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/P35663"}},"corpus_meta":[{"pmid":"19679225","id":"PMC_19679225","title":"X chromosomal variation is associated with slow progression to AIDS in HIV-1-infected women.","date":"2009","source":"American journal of human genetics","url":"https://pubmed.ncbi.nlm.nih.gov/19679225","citation_count":30,"is_preprint":false},{"pmid":"38013430","id":"PMC_38013430","title":"Cylicins are a structural component of the sperm calyx being indispensable for male fertility in mice and human.","date":"2023","source":"eLife","url":"https://pubmed.ncbi.nlm.nih.gov/38013430","citation_count":16,"is_preprint":false},{"pmid":"35737091","id":"PMC_35737091","title":"Whole-exome sequencing of Indian prostate cancer reveals a novel therapeutic target: POLQ.","date":"2022","source":"Journal of cancer research and clinical oncology","url":"https://pubmed.ncbi.nlm.nih.gov/35737091","citation_count":11,"is_preprint":false},{"pmid":"26985017","id":"PMC_26985017","title":"Identification of microtubule growth deceleration and its regulation by conserved and novel proteins.","date":"2016","source":"Molecular biology of the cell","url":"https://pubmed.ncbi.nlm.nih.gov/26985017","citation_count":8,"is_preprint":false},{"pmid":"38573307","id":"PMC_38573307","title":"Disruption in CYLC1 leads to acrosome detachment, sperm head deformity, and male in/subfertility in humans and mice.","date":"2024","source":"eLife","url":"https://pubmed.ncbi.nlm.nih.gov/38573307","citation_count":6,"is_preprint":false},{"pmid":"25786081","id":"PMC_25786081","title":"Differential expression of miR-499 and validation of predicted target genes in the testicular tissue of swine at different developmental stages.","date":"2015","source":"DNA and cell biology","url":"https://pubmed.ncbi.nlm.nih.gov/25786081","citation_count":4,"is_preprint":false},{"pmid":"41075067","id":"PMC_41075067","title":"Novel CYLC1 variants are associated with male infertility due to sperm head deformity.","date":"2025","source":"Journal of assisted reproduction and genetics","url":"https://pubmed.ncbi.nlm.nih.gov/41075067","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":5922,"output_tokens":1208,"usd":0.017943,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":7793,"output_tokens":1679,"usd":0.04047,"stage2_stop_reason":"end_turn"},"total_usd":0.058413,"stage1_batch_id":"msgbatch_01ACAxJQabDsht39JXeWG22d","stage2_batch_id":"msgbatch_01QEU22A9U5sbPTgsMzTmvSf","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2023,\n      \"finding\": \"CYLC1 (Cylicin 1) is a structural component of the sperm calyx within the perinuclear theca. CRISPR/Cas9-mediated Cylc1 knockout in mice caused male subfertility, with phenotypic analysis revealing that loss of Cylicins prevents proper calyx assembly during spermiogenesis, resulting in decreased epididymal sperm counts, impaired shedding of excess cytoplasm, severe structural malformations, and impaired sperm motility.\",\n      \"method\": \"CRISPR/Cas9 knockout mouse model, phenotypic characterization, immunofluorescence, electron microscopy\",\n      \"journal\": \"eLife\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — clean KO with defined cellular phenotype, multiple orthogonal methods (immunofluorescence, electron microscopy, fertility assays), replicated with human variant identification\",\n      \"pmids\": [\"38013430\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"Cylicin-1 interacts with itself, several other perinuclear theca (PT) proteins, the inner acrosomal membrane (IAM) protein SPACA1, and the nuclear envelope (NE) protein FAM209, forming an 'IAM-cylicins-NE' sandwich structure that anchors the acrosome to the nucleus. Loss of Cylicin-1 in mice leads to acrosome detachment from the nucleus and malformed sperm heads.\",\n      \"method\": \"Co-immunoprecipitation (protein-protein interaction), Cylc1 knockout mouse model, immunofluorescence, whole exome sequencing of infertile men\",\n      \"journal\": \"eLife\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal protein interactions identified, KO mouse with defined structural phenotype, multiple orthogonal methods, validated with human variants\",\n      \"pmids\": [\"38573307\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"CYLC1 variants (p.K328E and p.K324M) do not affect protein expression levels but alter the localization of CYLC1 protein and acrosome morphology in human sperm. Cylc1 knockout mice show acrosome-nuclear detachment by ultrastructural analysis (SEM/TEM). The localization of PLCZ1 was also altered in sperm from men carrying CYLC1 variants.\",\n      \"method\": \"Western blotting, immunofluorescence, CRISPR/Cas9 Cylc1 KO mice, SEM/TEM, Sanger sequencing\",\n      \"journal\": \"Journal of assisted reproduction and genetics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple orthogonal methods in single lab, KO mouse with ultrastructural phenotype, but single lab study\",\n      \"pmids\": [\"41075067\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"C. elegans homologues of human CYLC1 (named cylc-1 and cylc-2), which share sequence homology with stathmins and encode small, highly basic proteins with KKD/E repeats, regulate local tubulin concentration and microtubule growth deceleration at the cell periphery during smooth muscle cell differentiation. Depletion of these homologues abolished the local decrease in soluble tubulin concentration and microtubule deceleration behavior.\",\n      \"method\": \"RNAi/genetic depletion in C. elegans, live imaging of microtubule dynamics\",\n      \"journal\": \"Molecular biology of the cell\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — C. elegans ortholog study with live imaging, single lab, the function described (microtubule regulation) may not translate directly to mammalian CYLC1 which localizes to sperm perinuclear theca\",\n      \"pmids\": [\"26985017\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"CYLC1 encodes a testis-specific, lysine-rich cytoskeletal protein that is a major structural component of the sperm calyx/perinuclear theca; it forms an 'IAM-cylicins-NE' sandwich complex by interacting with itself, other PT proteins, the inner acrosomal membrane protein SPACA1, and nuclear envelope protein FAM209 to anchor the acrosome to the sperm nucleus, with loss of function causing acrosome detachment, sperm head deformity, defective calyx assembly, and male sub/infertility in mice and humans.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"CYLC1 (Cylicin 1) is a testis-specific structural protein of the sperm calyx within the perinuclear theca, where it is required for proper calyx assembly during spermiogenesis and for normal sperm head morphogenesis [#0]. Cylicin-1 self-associates and bridges the inner acrosomal membrane to the nuclear envelope by interacting with the IAM protein SPACA1 and the NE protein FAM209, forming an 'IAM-cylicins-NE' sandwich structure that physically anchors the acrosome to the sperm nucleus [#1]. Loss of Cylicin-1 in mice disrupts calyx assembly and detaches the acrosome from the nucleus, producing malformed sperm heads, impaired cytoplasmic shedding, reduced epididymal sperm counts, and defective motility, resulting in male subfertility [#0, #1]. In humans, CYLC1 missense variants do not alter protein abundance but mislocalize the protein and disrupt acrosome morphology and the distribution of the sperm factor PLCZ1, linking CYLC1 dysfunction to male infertility [#2].\",\n  \"teleology\": [\n    {\n      \"year\": 2023,\n      \"claim\": \"Established that CYLC1 is a structural component of the sperm calyx whose loss disrupts perinuclear theca assembly, defining its role in spermiogenesis and male fertility.\",\n      \"evidence\": \"CRISPR/Cas9 Cylc1 knockout mouse with immunofluorescence, electron microscopy, and fertility assays\",\n      \"pmids\": [\"38013430\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Did not define the molecular binding partners that recruit Cylicin-1 to the calyx\",\n        \"Subfertility rather than complete sterility leaves the requirement incompletely defined\"\n      ]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Resolved how CYLC1 anchors the acrosome to the nucleus by identifying an IAM-cylicins-NE sandwich built on interactions with SPACA1 and FAM209, explaining the acrosome-detachment phenotype.\",\n      \"evidence\": \"Co-immunoprecipitation, Cylc1 knockout mouse, immunofluorescence, and whole exome sequencing of infertile men\",\n      \"pmids\": [\"38573307\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Stoichiometry and structural arrangement of the sandwich complex not determined\",\n        \"Which other PT proteins participate not fully enumerated\"\n      ]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Showed that human CYLC1 missense variants act by mislocalizing the protein rather than reducing its expression, and that this perturbs acrosome morphology and PLCZ1 distribution, connecting variant biology to functional consequences.\",\n      \"evidence\": \"Western blotting, immunofluorescence, CRISPR/Cas9 Cylc1 KO mice, SEM/TEM, and Sanger sequencing of variant carriers\",\n      \"pmids\": [\"41075067\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Single-lab study without independent replication\",\n        \"Mechanistic basis for variant-induced mislocalization not established\",\n        \"Causal link between PLCZ1 mislocalization and fertilization outcome not demonstrated\"\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"Whether mammalian CYLC1 retains any microtubule-regulatory or tubulin-sequestering activity analogous to its C. elegans homologues remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"C. elegans cylc-1/cylc-2 microtubule-regulation function has not been tested in mammalian CYLC1\",\n        \"No biochemical activity assigned to mammalian CYLC1 beyond its structural anchoring role\"\n      ]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0005198\", \"supporting_discovery_ids\": [0, 1]},\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [1]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005856\", \"supporting_discovery_ids\": [0]},\n      {\"term_id\": \"GO:0005635\", \"supporting_discovery_ids\": [1]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-1474165\", \"supporting_discovery_ids\": [0, 1]}\n    ],\n    \"complexes\": [\"IAM-cylicins-NE sandwich complex\", \"sperm calyx / perinuclear theca\"],\n    \"partners\": [\"SPACA1\", \"FAM209\", \"CYLC1\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":4,"faith_total":4,"faith_pct":100.0}}