{"gene":"CYLC1","run_date":"2026-04-28T17:28:53","timeline":{"discoveries":[{"year":2023,"finding":"CYLC1 (Cylicin 1) is a testis-specific cytoskeletal protein that localizes to the acrosomal region of round spermatids and to the calyx within the perinuclear theca at the posterior part of mature sperm nuclei. CRISPR/Cas9-mediated Cylc1 knockout in mice caused male subfertility, impaired calyx assembly during spermiogenesis, decreased epididymal sperm counts, impaired shedding of excess cytoplasm, severe structural sperm malformations, and impaired sperm motility.","method":"CRISPR/Cas9 knockout mouse model, immunofluorescence localization, phenotypic characterization of sperm morphology and motility, whole-exome sequencing of infertile men","journal":"eLife","confidence":"High","confidence_rationale":"Tier 2 — clean KO with defined cellular phenotype, multiple orthogonal methods, confirmed in human patients","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 to form 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 interaction assays, CRISPR/Cas9 knockout mice, immunofluorescence, whole-exome sequencing","journal":"eLife","confidence":"High","confidence_rationale":"Tier 2 — reciprocal protein interaction experiments combined with clean KO phenotype and human genetic validation","pmids":["38573307"],"is_preprint":false},{"year":2025,"finding":"Novel missense variants in CYLC1 (p.K328E and p.K324M) do not affect protein expression levels but alter the subcellular localization of CYLC1 and disrupt acrosome morphology in human sperm. Cylc1 knockout mice show acrosome-nuclear detachment confirmed by electron microscopy. The localization of PLCZ1 is also secondarily altered in sperm from affected men.","method":"Western blotting, immunofluorescence, CRISPR/Cas9 KO mouse model, scanning electron microscopy (SEM), transmission electron microscopy (TEM), Sanger sequencing","journal":"Journal of assisted reproduction and genetics","confidence":"Medium","confidence_rationale":"Tier 2 — multiple orthogonal methods in single study, but not yet independently replicated","pmids":["41075067"],"is_preprint":false},{"year":2016,"finding":"C. elegans homologues of human CYLC1 (cylc-1 and cylc-2), which share sequence homology with stathmins and encode small basic proteins with KKD/E repeats, regulate local tubulin concentration at the cell periphery and are required for microtubule growth deceleration in smooth muscle cells.","method":"RNAi/loss-of-function genetics, live imaging of microtubule dynamics in C. elegans, sequence homology analysis","journal":"Molecular biology of the cell","confidence":"Medium","confidence_rationale":"Tier 2 — genetic epistasis with defined MT dynamic phenotype in a model organism ortholog context, single lab","pmids":["26985017"],"is_preprint":false}],"current_model":"CYLC1 encodes a testis-specific, lysine-rich cytoskeletal protein that localizes to the perinuclear theca (calyx) of mature sperm and interacts with inner acrosomal membrane protein SPACA1, nuclear envelope protein FAM209, and other PT proteins to form a sandwich structure anchoring the acrosome to the nucleus; loss of CYLC1 disrupts calyx assembly, causes acrosome-nuclear detachment and sperm head deformities, and results in male subfertility or infertility in both mice and humans."},"narrative":{"teleology":[{"year":2016,"claim":"Prior to mammalian functional work, C. elegans homologues of CYLC1 were shown to regulate microtubule dynamics, establishing that this family of small basic KKD/E-repeat proteins interacts with the cytoskeleton to control tubulin polymerization at the cell periphery.","evidence":"RNAi/loss-of-function genetics and live imaging of microtubule dynamics in C. elegans smooth muscle cells","pmids":["26985017"],"confidence":"Medium","gaps":["C. elegans homologue function in microtubule regulation has not been shown to be conserved in mammalian CYLC1","Mechanism by which KKD/E repeats modulate tubulin dynamics is undefined at a structural level"]},{"year":2023,"claim":"The first mammalian loss-of-function study demonstrated that CYLC1 is required for perinuclear theca calyx assembly and normal sperm morphogenesis, resolving the long-standing question of whether this testis-specific protein is functionally important for male fertility.","evidence":"CRISPR/Cas9 Cylc1 knockout mouse with phenotypic characterization of sperm morphology, motility, and count; immunofluorescence localization in spermatids and mature sperm; whole-exome sequencing identifying CYLC1 variants in infertile men","pmids":["38013430"],"confidence":"High","gaps":["Molecular mechanism by which CYLC1 loss impairs cytoplasmic shedding was not defined","Relative contributions of CYLC1 versus paralog CYLC2 to calyx function were not resolved"]},{"year":2024,"claim":"Protein interaction mapping revealed that CYLC1 self-associates and bridges the inner acrosomal membrane (via SPACA1) to the nuclear envelope (via FAM209), establishing the molecular architecture of the IAM–cylicins–NE sandwich that anchors the acrosome to the nucleus.","evidence":"Co-immunoprecipitation/protein interaction assays, CRISPR/Cas9 knockout mice, immunofluorescence, human whole-exome sequencing","pmids":["38573307"],"confidence":"High","gaps":["Stoichiometry and direct binding interfaces between CYLC1, SPACA1, and FAM209 have not been structurally resolved","Whether CYLC1 and CYLC2 form heteromeric complexes within the calyx is not established"]},{"year":2025,"claim":"Human missense variants in CYLC1 that do not affect protein expression but alter its subcellular localization confirmed that correct CYLC1 targeting, not merely its presence, is required for acrosome integrity, and revealed secondary displacement of PLCZ1 as a downstream consequence.","evidence":"Western blotting, immunofluorescence, SEM/TEM, and Sanger sequencing of patient sperm; Cylc1 KO mouse confirmation","pmids":["41075067"],"confidence":"Medium","gaps":["Functional consequence of PLCZ1 mislocalization for fertilization competence is not tested","Findings from a single patient cohort await independent replication","Structural basis for how K328E and K324M disrupt CYLC1 targeting is unknown"]},{"year":null,"claim":"It remains unknown how CYLC1 is initially recruited to the acrosomal region in round spermatids, what post-translational modifications regulate its assembly into the calyx, and whether its microtubule-regulatory activity observed in C. elegans homologues plays any role during mammalian spermiogenesis.","evidence":"","pmids":[],"confidence":"Low","gaps":["No structural model of CYLC1 or the calyx complex exists","Mechanism of initial CYLC1 recruitment to the perinuclear theca is undefined","Relationship between invertebrate microtubule regulation and mammalian calyx function is unresolved"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0008092","term_label":"cytoskeletal protein binding","supporting_discovery_ids":[0,1,3]},{"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":[0,1,3]},{"term_id":"GO:0005635","term_label":"nuclear envelope","supporting_discovery_ids":[1]},{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[0,1]}],"pathway":[{"term_id":"R-HSA-1474165","term_label":"Reproduction","supporting_discovery_ids":[0,1,2]}],"complexes":["Perinuclear theca (calyx)"],"partners":["SPACA1","FAM209","CYLC1","CYLC2"],"other_free_text":[]},"mechanistic_narrative":"CYLC1 encodes a testis-specific, lysine-rich cytoskeletal protein that is essential for perinuclear theca (calyx) assembly and acrosome-nucleus attachment during spermiogenesis. CYLC1 localizes to the acrosomal region in round spermatids and to the calyx of the perinuclear theca in mature sperm, where it self-associates and interacts with inner acrosomal membrane protein SPACA1 and nuclear envelope protein FAM209, forming an IAM–cylicins–NE sandwich structure that mechanically anchors the acrosome to the sperm nucleus [PMID:38573307]. CRISPR/Cas9-mediated Cylc1 knockout in mice causes male subfertility characterized by impaired calyx assembly, acrosome-nuclear detachment, severe sperm head deformities, defective cytoplasmic shedding, and reduced motility, and missense variants in human CYLC1 similarly disrupt acrosome morphology and CYLC1 localization, establishing CYLC1 deficiency as a cause of human male infertility [PMID:38013430, PMID:41075067]."},"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":5,"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":5203,"output_tokens":1141,"usd":0.016362},"stage2":{"model":"claude-opus-4-6","input_tokens":4340,"output_tokens":1691,"usd":0.095963},"total_usd":0.112325,"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\": \"CYLC1 (Cylicin 1) is a testis-specific cytoskeletal protein that localizes to the acrosomal region of round spermatids and to the calyx within the perinuclear theca at the posterior part of mature sperm nuclei. CRISPR/Cas9-mediated Cylc1 knockout in mice caused male subfertility, impaired calyx assembly during spermiogenesis, decreased epididymal sperm counts, impaired shedding of excess cytoplasm, severe structural sperm malformations, and impaired sperm motility.\",\n      \"method\": \"CRISPR/Cas9 knockout mouse model, immunofluorescence localization, phenotypic characterization of sperm morphology and motility, whole-exome sequencing of infertile men\",\n      \"journal\": \"eLife\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — clean KO with defined cellular phenotype, multiple orthogonal methods, confirmed in human patients\",\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 to form 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 interaction assays, CRISPR/Cas9 knockout mice, immunofluorescence, whole-exome sequencing\",\n      \"journal\": \"eLife\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — reciprocal protein interaction experiments combined with clean KO phenotype and human genetic validation\",\n      \"pmids\": [\"38573307\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"Novel missense variants in CYLC1 (p.K328E and p.K324M) do not affect protein expression levels but alter the subcellular localization of CYLC1 and disrupt acrosome morphology in human sperm. Cylc1 knockout mice show acrosome-nuclear detachment confirmed by electron microscopy. The localization of PLCZ1 is also secondarily altered in sperm from affected men.\",\n      \"method\": \"Western blotting, immunofluorescence, CRISPR/Cas9 KO mouse model, scanning electron microscopy (SEM), transmission electron microscopy (TEM), Sanger sequencing\",\n      \"journal\": \"Journal of assisted reproduction and genetics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — multiple orthogonal methods in single study, but not yet independently replicated\",\n      \"pmids\": [\"41075067\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"C. elegans homologues of human CYLC1 (cylc-1 and cylc-2), which share sequence homology with stathmins and encode small basic proteins with KKD/E repeats, regulate local tubulin concentration at the cell periphery and are required for microtubule growth deceleration in smooth muscle cells.\",\n      \"method\": \"RNAi/loss-of-function genetics, live imaging of microtubule dynamics in C. elegans, sequence homology analysis\",\n      \"journal\": \"Molecular biology of the cell\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — genetic epistasis with defined MT dynamic phenotype in a model organism ortholog context, single lab\",\n      \"pmids\": [\"26985017\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"CYLC1 encodes a testis-specific, lysine-rich cytoskeletal protein that localizes to the perinuclear theca (calyx) of mature sperm and interacts with inner acrosomal membrane protein SPACA1, nuclear envelope protein FAM209, and other PT proteins to form a sandwich structure anchoring the acrosome to the nucleus; loss of CYLC1 disrupts calyx assembly, causes acrosome-nuclear detachment and sperm head deformities, and results in male subfertility or infertility in both mice and humans.\"\n}\n```","stage2_raw":"```json\n{\n  \"mechanistic_narrative\": \"CYLC1 encodes a testis-specific, lysine-rich cytoskeletal protein that is essential for perinuclear theca (calyx) assembly and acrosome-nucleus attachment during spermiogenesis. CYLC1 localizes to the acrosomal region in round spermatids and to the calyx of the perinuclear theca in mature sperm, where it self-associates and interacts with inner acrosomal membrane protein SPACA1 and nuclear envelope protein FAM209, forming an IAM–cylicins–NE sandwich structure that mechanically anchors the acrosome to the sperm nucleus [PMID:38573307]. CRISPR/Cas9-mediated Cylc1 knockout in mice causes male subfertility characterized by impaired calyx assembly, acrosome-nuclear detachment, severe sperm head deformities, defective cytoplasmic shedding, and reduced motility, and missense variants in human CYLC1 similarly disrupt acrosome morphology and CYLC1 localization, establishing CYLC1 deficiency as a cause of human male infertility [PMID:38013430, PMID:41075067].\",\n  \"teleology\": [\n    {\n      \"year\": 2016,\n      \"claim\": \"Prior to mammalian functional work, C. elegans homologues of CYLC1 were shown to regulate microtubule dynamics, establishing that this family of small basic KKD/E-repeat proteins interacts with the cytoskeleton to control tubulin polymerization at the cell periphery.\",\n      \"evidence\": \"RNAi/loss-of-function genetics and live imaging of microtubule dynamics in C. elegans smooth muscle cells\",\n      \"pmids\": [\"26985017\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"C. elegans homologue function in microtubule regulation has not been shown to be conserved in mammalian CYLC1\",\n        \"Mechanism by which KKD/E repeats modulate tubulin dynamics is undefined at a structural level\"\n      ]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"The first mammalian loss-of-function study demonstrated that CYLC1 is required for perinuclear theca calyx assembly and normal sperm morphogenesis, resolving the long-standing question of whether this testis-specific protein is functionally important for male fertility.\",\n      \"evidence\": \"CRISPR/Cas9 Cylc1 knockout mouse with phenotypic characterization of sperm morphology, motility, and count; immunofluorescence localization in spermatids and mature sperm; whole-exome sequencing identifying CYLC1 variants in infertile men\",\n      \"pmids\": [\"38013430\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Molecular mechanism by which CYLC1 loss impairs cytoplasmic shedding was not defined\",\n        \"Relative contributions of CYLC1 versus paralog CYLC2 to calyx function were not resolved\"\n      ]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Protein interaction mapping revealed that CYLC1 self-associates and bridges the inner acrosomal membrane (via SPACA1) to the nuclear envelope (via FAM209), establishing the molecular architecture of the IAM–cylicins–NE sandwich that anchors the acrosome to the nucleus.\",\n      \"evidence\": \"Co-immunoprecipitation/protein interaction assays, CRISPR/Cas9 knockout mice, immunofluorescence, human whole-exome sequencing\",\n      \"pmids\": [\"38573307\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Stoichiometry and direct binding interfaces between CYLC1, SPACA1, and FAM209 have not been structurally resolved\",\n        \"Whether CYLC1 and CYLC2 form heteromeric complexes within the calyx is not established\"\n      ]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Human missense variants in CYLC1 that do not affect protein expression but alter its subcellular localization confirmed that correct CYLC1 targeting, not merely its presence, is required for acrosome integrity, and revealed secondary displacement of PLCZ1 as a downstream consequence.\",\n      \"evidence\": \"Western blotting, immunofluorescence, SEM/TEM, and Sanger sequencing of patient sperm; Cylc1 KO mouse confirmation\",\n      \"pmids\": [\"41075067\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Functional consequence of PLCZ1 mislocalization for fertilization competence is not tested\",\n        \"Findings from a single patient cohort await independent replication\",\n        \"Structural basis for how K328E and K324M disrupt CYLC1 targeting is unknown\"\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"It remains unknown how CYLC1 is initially recruited to the acrosomal region in round spermatids, what post-translational modifications regulate its assembly into the calyx, and whether its microtubule-regulatory activity observed in C. elegans homologues plays any role during mammalian spermiogenesis.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"No structural model of CYLC1 or the calyx complex exists\",\n        \"Mechanism of initial CYLC1 recruitment to the perinuclear theca is undefined\",\n        \"Relationship between invertebrate microtubule regulation and mammalian calyx function is unresolved\"\n      ]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0008092\", \"supporting_discovery_ids\": [0, 1, 3]},\n      {\"term_id\": \"GO:0005198\", \"supporting_discovery_ids\": [0, 1]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005856\", \"supporting_discovery_ids\": [0, 1, 3]},\n      {\"term_id\": \"GO:0005635\", \"supporting_discovery_ids\": [1]},\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [0, 1]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-1474165\", \"supporting_discovery_ids\": [0, 1, 2]}\n    ],\n    \"complexes\": [\n      \"Perinuclear theca (calyx)\"\n    ],\n    \"partners\": [\n      \"SPACA1\",\n      \"FAM209\",\n      \"CYLC1\",\n      \"CYLC2\"\n    ],\n    \"other_free_text\": []\n  }\n}\n```"}