{"gene":"CYLC2","run_date":"2026-04-28T17:28:53","timeline":{"discoveries":[{"year":2023,"finding":"CYLC2 (Cylicin 2) is a testis-specific cytoskeletal protein that localizes to the acrosomal region of round spermatids and then to the calyx within the perinuclear theca at the posterior part of mature sperm nuclei. CRISPR/Cas9-mediated Cylc2 knockout in mice demonstrated that CYLC2 is essential for proper calyx assembly during spermiogenesis; loss of CYLC2 results in decreased epididymal sperm counts, impaired shedding of excess cytoplasm, severe structural sperm malformations, and infertility.","method":"CRISPR/Cas9 gene knockout in mice, phenotypic characterization of sperm morphology and motility, immunolocalization","journal":"eLife","confidence":"High","confidence_rationale":"Tier 2 — clean KO with defined cellular phenotype, multiple orthogonal readouts, replicated across single and compound mutant lines","pmids":["38013430"],"is_preprint":false},{"year":2023,"finding":"CYLC2 contains lysine-rich repeats that confer an overall positive charge, consistent with its role as a structural cytoskeletal component of the calyx/perinuclear theca. Compound Cylc1/Cylc2 double-knockout males showed additive infertility compared to single knockouts, indicating the two Cylicins partially compensate for one another during calyx assembly.","method":"CRISPR/Cas9 compound mutant analysis, genetic epistasis, protein domain analysis","journal":"eLife","confidence":"High","confidence_rationale":"Tier 2 — genetic epistasis via compound KO lines with defined fertility and structural phenotypes","pmids":["38013430"],"is_preprint":false},{"year":2008,"finding":"CYLC2 protein was identified as a constituent of the mouse spermatozoon proteome, confirming its presence as a structural sperm protein.","method":"LC-MS/MS proteomic profiling of mouse spermatozoa after IPG strip prefractionation","journal":"Proteomics","confidence":"Medium","confidence_rationale":"Tier 3 — mass spectrometry identification in a proteome survey, no functional follow-up","pmids":["18340633"],"is_preprint":false}],"current_model":"CYLC2 is a testis-specific, lysine-rich cytoskeletal protein that localizes first to the acrosomal region of round spermatids and then to the calyx of the perinuclear theca in mature sperm; it is required for proper calyx assembly during spermiogenesis, and its loss in mice causes structural sperm malformations, cytoplasm shedding defects, and male infertility, with partial functional redundancy with the paralog CYLC1."},"narrative":{"teleology":[{"year":2008,"claim":"Proteomic detection of CYLC2 in mouse spermatozoa established it as a bona fide sperm protein, but its function and subcellular localization remained unknown.","evidence":"LC-MS/MS proteomic profiling of mouse spermatozoa","pmids":["18340633"],"confidence":"Medium","gaps":["Identification was catalog-level; no functional or localization data provided","No validation by orthogonal methods such as immunofluorescence"]},{"year":2023,"claim":"CRISPR/Cas9 knockout and immunolocalization resolved CYLC2's precise subcellular trajectory during spermiogenesis and demonstrated its requirement for calyx assembly, cytoplasm shedding, sperm structural integrity, and male fertility, while compound mutants with CYLC1 revealed partial paralog compensation.","evidence":"CRISPR/Cas9 single and compound Cylc1/Cylc2 knockout mice with phenotypic characterization of sperm morphology, motility, fertility, and immunolocalization","pmids":["38013430"],"confidence":"High","gaps":["Direct binding partners within the perinuclear theca have not been identified","No structural model for how lysine-rich repeats mediate calyx assembly","Whether CYLC2 loss causes male infertility in humans has not been tested"]},{"year":null,"claim":"The molecular mechanism by which CYLC2 organizes the calyx — including its direct protein–protein interactions, higher-order assembly, and the basis for partial redundancy with CYLC1 — remains unresolved.","evidence":"","pmids":[],"confidence":"Low","gaps":["No interactome or co-immunoprecipitation data for CYLC2","No in vitro reconstitution of calyx-like structures with purified Cylicins","Human genetic evidence linking CYLC2 mutations to infertility is absent"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0005198","term_label":"structural molecule activity","supporting_discovery_ids":[0,1]}],"localization":[{"term_id":"GO:0005856","term_label":"cytoskeleton","supporting_discovery_ids":[0,1]},{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[0]}],"pathway":[{"term_id":"R-HSA-1474165","term_label":"Reproduction","supporting_discovery_ids":[0,1]}],"complexes":[],"partners":["CYLC1"],"other_free_text":[]},"mechanistic_narrative":"CYLC2 is a testis-specific, lysine-rich cytoskeletal protein that localizes to the acrosomal region of round spermatids and subsequently to the calyx of the perinuclear theca in mature spermatozoa [PMID:38013430]. CYLC2 is essential for proper calyx assembly during spermiogenesis; its loss in mice causes decreased epididymal sperm counts, impaired cytoplasm shedding, severe structural sperm malformations, and male infertility, with partial functional redundancy provided by the paralog CYLC1 as demonstrated by additive defects in compound knockouts [PMID:38013430]."},"prefetch_data":{"uniprot":{"accession":"Q14093","full_name":"Cylicin-2","aliases":["Cylicin II","Multiple-band polypeptide II"],"length_aa":348,"mass_kda":39.1,"function":"Plays a role in the establishment of normal sperm morphology during spermatogenesis. It is required for acrosome attachment to the nuclear envelope, and proper manchette elongation and disassembly","subcellular_location":"Cytoplasm, cytoskeleton, perinuclear theca, calyx; Cytoplasm, cytoskeleton, perinuclear theca","url":"https://www.uniprot.org/uniprotkb/Q14093/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/CYLC2","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/CYLC2","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":43.6}],"url":"https://www.proteinatlas.org/search/CYLC2"},"hgnc":{"alias_symbol":[],"prev_symbol":[]},"alphafold":{"accession":"Q14093","domains":[],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q14093","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q14093-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q14093-F1-predicted_aligned_error_v6.png","plddt_mean":49.94},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=CYLC2","jax_strain_url":"https://www.jax.org/strain/search?query=CYLC2"},"sequence":{"accession":"Q14093","fasta_url":"https://rest.uniprot.org/uniprotkb/Q14093.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q14093/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q14093"}},"corpus_meta":[{"pmid":"18340633","id":"PMC_18340633","title":"The mouse sperm proteome characterized via IPG strip prefractionation and LC-MS/MS 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development","url":"https://pubmed.ncbi.nlm.nih.gov/31134708","citation_count":29,"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":"30297789","id":"PMC_30297789","title":"Typing tumors using pathways selected by somatic evolution.","date":"2018","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/30297789","citation_count":16,"is_preprint":false},{"pmid":"33285124","id":"PMC_33285124","title":"Comparison of spermatozoal RNA extraction methods in goats.","date":"2020","source":"Analytical biochemistry","url":"https://pubmed.ncbi.nlm.nih.gov/33285124","citation_count":14,"is_preprint":false},{"pmid":"34313325","id":"PMC_34313325","title":"Whole genome sequencing identifies rare germline variants enriched in cancer related genes in first degree relatives of familial pancreatic cancer patients.","date":"2021","source":"Clinical genetics","url":"https://pubmed.ncbi.nlm.nih.gov/34313325","citation_count":10,"is_preprint":false},{"pmid":"35709667","id":"PMC_35709667","title":"Mixed model-based eQTL analysis reveals lncRNAs associated with regulation of genes involved in sex determination and spermatogenesis: The key to understanding human gender imbalance.","date":"2022","source":"Computational biology and chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/35709667","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":6169,"output_tokens":791,"usd":0.015186},"stage2":{"model":"claude-opus-4-6","input_tokens":3972,"output_tokens":922,"usd":0.064365},"total_usd":0.079551,"stage1_batch_id":"msgbatch_011kfMfE81o6CTcyhVUqumuW","stage2_batch_id":"msgbatch_01DTputS6WNkH745x1nVSoBo","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2023,\n      \"finding\": \"CYLC2 (Cylicin 2) is a testis-specific cytoskeletal protein that localizes to the acrosomal region of round spermatids and then to the calyx within the perinuclear theca at the posterior part of mature sperm nuclei. CRISPR/Cas9-mediated Cylc2 knockout in mice demonstrated that CYLC2 is essential for proper calyx assembly during spermiogenesis; loss of CYLC2 results in decreased epididymal sperm counts, impaired shedding of excess cytoplasm, severe structural sperm malformations, and infertility.\",\n      \"method\": \"CRISPR/Cas9 gene knockout in mice, phenotypic characterization of sperm morphology and motility, immunolocalization\",\n      \"journal\": \"eLife\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — clean KO with defined cellular phenotype, multiple orthogonal readouts, replicated across single and compound mutant lines\",\n      \"pmids\": [\"38013430\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"CYLC2 contains lysine-rich repeats that confer an overall positive charge, consistent with its role as a structural cytoskeletal component of the calyx/perinuclear theca. Compound Cylc1/Cylc2 double-knockout males showed additive infertility compared to single knockouts, indicating the two Cylicins partially compensate for one another during calyx assembly.\",\n      \"method\": \"CRISPR/Cas9 compound mutant analysis, genetic epistasis, protein domain analysis\",\n      \"journal\": \"eLife\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — genetic epistasis via compound KO lines with defined fertility and structural phenotypes\",\n      \"pmids\": [\"38013430\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"CYLC2 protein was identified as a constituent of the mouse spermatozoon proteome, confirming its presence as a structural sperm protein.\",\n      \"method\": \"LC-MS/MS proteomic profiling of mouse spermatozoa after IPG strip prefractionation\",\n      \"journal\": \"Proteomics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 — mass spectrometry identification in a proteome survey, no functional follow-up\",\n      \"pmids\": [\"18340633\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"CYLC2 is a testis-specific, lysine-rich cytoskeletal protein that localizes first to the acrosomal region of round spermatids and then to the calyx of the perinuclear theca in mature sperm; it is required for proper calyx assembly during spermiogenesis, and its loss in mice causes structural sperm malformations, cytoplasm shedding defects, and male infertility, with partial functional redundancy with the paralog CYLC1.\"\n}\n```","stage2_raw":"```json\n{\n  \"mechanistic_narrative\": \"CYLC2 is a testis-specific, lysine-rich cytoskeletal protein that localizes to the acrosomal region of round spermatids and subsequently to the calyx of the perinuclear theca in mature spermatozoa [PMID:38013430]. CYLC2 is essential for proper calyx assembly during spermiogenesis; its loss in mice causes decreased epididymal sperm counts, impaired cytoplasm shedding, severe structural sperm malformations, and male infertility, with partial functional redundancy provided by the paralog CYLC1 as demonstrated by additive defects in compound knockouts [PMID:38013430].\",\n  \"teleology\": [\n    {\n      \"year\": 2008,\n      \"claim\": \"Proteomic detection of CYLC2 in mouse spermatozoa established it as a bona fide sperm protein, but its function and subcellular localization remained unknown.\",\n      \"evidence\": \"LC-MS/MS proteomic profiling of mouse spermatozoa\",\n      \"pmids\": [\"18340633\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Identification was catalog-level; no functional or localization data provided\",\n        \"No validation by orthogonal methods such as immunofluorescence\"\n      ]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"CRISPR/Cas9 knockout and immunolocalization resolved CYLC2's precise subcellular trajectory during spermiogenesis and demonstrated its requirement for calyx assembly, cytoplasm shedding, sperm structural integrity, and male fertility, while compound mutants with CYLC1 revealed partial paralog compensation.\",\n      \"evidence\": \"CRISPR/Cas9 single and compound Cylc1/Cylc2 knockout mice with phenotypic characterization of sperm morphology, motility, fertility, and immunolocalization\",\n      \"pmids\": [\"38013430\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Direct binding partners within the perinuclear theca have not been identified\",\n        \"No structural model for how lysine-rich repeats mediate calyx assembly\",\n        \"Whether CYLC2 loss causes male infertility in humans has not been tested\"\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"The molecular mechanism by which CYLC2 organizes the calyx — including its direct protein–protein interactions, higher-order assembly, and the basis for partial redundancy with CYLC1 — remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"No interactome or co-immunoprecipitation data for CYLC2\",\n        \"No in vitro reconstitution of calyx-like structures with purified Cylicins\",\n        \"Human genetic evidence linking CYLC2 mutations to infertility is absent\"\n      ]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0005198\", \"supporting_discovery_ids\": [0, 1]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005856\", \"supporting_discovery_ids\": [0, 1]},\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [0]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-1474165\", \"supporting_discovery_ids\": [0, 1]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\n      \"CYLC1\"\n    ],\n    \"other_free_text\": []\n  }\n}\n```"}