{"gene":"CCIN","run_date":"2026-06-09T22:57:17","timeline":{"discoveries":[{"year":2022,"finding":"Calicin (CCIN) interacts with itself (self-association) and many other perinuclear theca (PT) components, suggesting it serves as an organizing center of PT assembly. Calicin also interacts with inner acrosomal membrane (IAM) protein SPACA1 and nuclear envelope (NE) components to form an 'IAM-PT-NE' structure. Loss of Calicin (Ccin knockout) causes surface subsidence of sperm heads during nuclear condensation and leads to DNA damage and failure of fertilization in mice.","method":"Co-immunoprecipitation, immunofluorescence, live imaging/fractionation, knockout mouse model with phenotypic readout (sperm head shaping, fertilization failure, DNA damage)","journal":"Cell reports","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal Co-IP identifying multiple binding partners, KO mouse with multiple defined cellular phenotypes (head morphology, DNA damage, fertilization failure), orthogonal methods in single study","pmids":["35793634"],"is_preprint":false},{"year":2022,"finding":"Homozygous missense and compound heterozygous mutations in CCIN cause severe sperm head malformation (teratozoospermia) with markedly reduced Calicin protein levels in spermatozoa. Mutant spermatozoa from both mice and human patients fail to adhere to the zona pellucida, identified as the major mechanistic reason for CCIN-mutant sperm-derived infertility. Mouse models expressing disease-associated CCIN variants recapitulate the human phenotype.","method":"Patient whole-exome sequencing with Sanger validation, immunofluorescence assays on patient and mouse spermatozoa, ultrastructural morphological analysis, zona adhesion assay, ICSI rescue experiment, knock-in mouse models","journal":"Science bulletin","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple orthogonal methods (human genetics + mouse models + functional zona adhesion assay), replicated across patient and mouse systems","pmids":["36546111"],"is_preprint":false},{"year":2025,"finding":"FNDC8 (a testis-enriched PT protein) physically interacts with CCIN and ACTL7A during spermiogenesis. Genetic disruption of Fndc8 destabilizes both CCIN and ACTL7A proteins, resulting in acrosome detachment and sperm head collapse, placing CCIN within a FNDC8-CCIN-ACTL7A complex required for PT structural integrity and sperm head morphogenesis.","method":"Co-immunoprecipitation, Fndc8 knockout mouse model, immunofluorescence, Western blot for protein stability","journal":"Zoological research","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — reciprocal Co-IP identifying CCIN as binding partner of FNDC8, KO mouse showing CCIN destabilization, single lab","pmids":["41169243"],"is_preprint":false},{"year":2021,"finding":"Calicin (CCIN) is among a group of actin cytoskeleton proteins in bull sperm that undergoes oxidative post-translational modifications (oxPTMs) mediated by 2-Cys peroxiredoxins (PRDXs) under control conditions, as revealed by inhibition of PRDXs with Conoidin A.","method":"2-Cys PRDX inhibition (Conoidin A treatment), proteomics/mass spectrometry to detect oxidative PTMs on sperm proteins","journal":"International journal of molecular sciences","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single proteomics screen in bull sperm, single lab, no functional follow-up on CCIN specifically","pmids":["34884692"],"is_preprint":false},{"year":2022,"finding":"FSIP2 mutations in asthenoteratozoospermic patients lead to downregulated expression of CCIN in spermatozoa, placing CCIN downstream of FSIP2 in a pathway regulating acrosome biogenesis and sperm morphology.","method":"Whole exome sequencing, Western blot and immunofluorescence in patient spermatozoa, co-immunoprecipitation (for FSIP2 interactions), proteomics","journal":"Journal of medical genetics","confidence":"Low","confidence_rationale":"Tier 3 / Weak — CCIN downregulation observed as secondary effect of FSIP2 mutation; no direct functional experiment on CCIN itself, single lab","pmids":["35654582"],"is_preprint":false},{"year":2023,"finding":"A novel homozygous missense variant in CCIN causes male infertility with an abnormal sperm head nuclear subsidence phenotype, consistent with Calicin's role in sperm head shaping.","method":"Sanger sequencing, clinical genetic analysis, spermatozoa morphological assessment","journal":"Clinical genetics","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single case report with genetic and morphological data, no in vitro/in vivo functional experiments described in abstract","pmids":["36527329"],"is_preprint":false}],"current_model":"CCIN encodes Calicin, a cytoskeletal protein that acts as an organizing hub of the sperm perinuclear theca (PT) by self-associating and binding PT components, SPACA1 (inner acrosomal membrane), nuclear envelope proteins, and ACTL7A/FNDC8, thereby forming an IAM-PT-NE structural unit that shapes the sperm head and maintains nuclear integrity during spermiogenesis; loss of Calicin causes sperm head surface collapse, DNA damage, failure of zona pellucida adhesion, and male infertility."},"narrative":{"mechanistic_narrative":"CCIN encodes Calicin, a cytoskeletal organizing protein of the sperm perinuclear theca (PT) that shapes the sperm head and protects nuclear integrity during spermiogenesis [PMID:35793634]. Calicin self-associates and binds multiple PT components, and bridges the inner acrosomal membrane protein SPACA1 to nuclear envelope components, assembling an integrated IAM-PT-NE structural unit; its loss causes surface subsidence of the condensing sperm head, DNA damage, and fertilization failure [PMID:35793634]. Calicin functions within an FNDC8-CCIN-ACTL7A complex required for PT structural integrity, since loss of FNDC8 destabilizes both Calicin and ACTL7A and leads to acrosome detachment and sperm head collapse [PMID:41169243]. In humans, biallelic CCIN mutations reduce Calicin protein levels and cause severe sperm head malformation; the resulting failure of mutant spermatozoa to adhere to the zona pellucida is the principal mechanistic basis of CCIN-associated male infertility, and ICSI rescues fertilization [PMID:36546111].","teleology":[{"year":2022,"claim":"Established Calicin as the structural organizing hub of the perinuclear theca by showing it self-associates and links the inner acrosomal membrane to the nuclear envelope, defining how the sperm head is shaped and the nucleus protected.","evidence":"Co-IP, immunofluorescence, fractionation, and Ccin knockout mouse with sperm head shaping, DNA damage, and fertilization readouts","pmids":["35793634"],"confidence":"High","gaps":["Structural basis of how Calicin physically couples IAM to NE not resolved","Stoichiometry and architecture of the PT assembly hub undefined","Whether DNA damage is direct or secondary to head collapse unclear"]},{"year":2022,"claim":"Connected CCIN to a defined human disease, showing biallelic mutations cause teratozoospermia and identifying failed zona pellucida adhesion as the mechanistic cause of infertility, which ICSI bypasses.","evidence":"Patient whole-exome sequencing, knock-in mouse models, zona adhesion assay, and ICSI rescue","pmids":["36546111"],"confidence":"High","gaps":["Molecular basis linking head malformation to loss of zona adhesion not defined","How specific missense variants destabilize Calicin protein unknown"]},{"year":2023,"claim":"Reinforced the head-shaping role by linking an additional CCIN missense variant to the nuclear subsidence phenotype in patients.","evidence":"Sanger sequencing and morphological assessment in a male infertility case","pmids":["36527329"],"confidence":"Low","gaps":["Single case report with no functional experiments","Variant pathogenicity not validated in vivo"]},{"year":2025,"claim":"Placed Calicin within an FNDC8-CCIN-ACTL7A complex, clarifying that Calicin stability and PT integrity depend on partner proteins.","evidence":"Co-IP, Fndc8 knockout mouse, and Western blot for protein stability","pmids":["41169243"],"confidence":"Medium","gaps":["Single-lab finding without independent replication","Direct binding interfaces within the complex not mapped","Whether Calicin stabilizes its partners reciprocally untested"]},{"year":null,"claim":"The biochemical mechanism by which Calicin organizes PT assembly and the role of its oxidative modification remain open.","evidence":"No direct mechanistic or structural study in the available corpus","pmids":[],"confidence":"Low","gaps":["No structural model of Calicin or its PT contacts","Functional consequence of PRDX-mediated oxidative PTMs on Calicin untested","Relationship between FSIP2-dependent regulation and Calicin function undefined"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0008092","term_label":"cytoskeletal protein binding","supporting_discovery_ids":[0,2]}],"localization":[{"term_id":"GO:0005856","term_label":"cytoskeleton","supporting_discovery_ids":[0]},{"term_id":"GO:0005635","term_label":"nuclear envelope","supporting_discovery_ids":[0]}],"pathway":[{"term_id":"R-HSA-1474165","term_label":"Reproduction","supporting_discovery_ids":[0,1]}],"complexes":["perinuclear theca","FNDC8-CCIN-ACTL7A complex"],"partners":["SPACA1","FNDC8","ACTL7A"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q13939","full_name":"Calicin","aliases":[],"length_aa":588,"mass_kda":66.6,"function":"Required for both nuclear and acrosomal shaping during spermiogenesis","subcellular_location":"Cytoplasm, cytoskeleton, perinuclear theca, calyx","url":"https://www.uniprot.org/uniprotkb/Q13939/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/CCIN","classification":"Not Classified","n_dependent_lines":20,"n_total_lines":1208,"dependency_fraction":0.016556291390728478},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/CCIN","total_profiled":1310},"omim":[{"mim_id":"620838","title":"SPERMATOGENIC FAILURE 91; SPGF91","url":"https://www.omim.org/entry/620838"},{"mim_id":"604035","title":"CYLICIN 2; CYLC2","url":"https://www.omim.org/entry/604035"},{"mim_id":"603960","title":"CALICIN; CCIN","url":"https://www.omim.org/entry/603960"},{"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":"Nucleoplasm","reliability":"Additional"},{"location":"Perinuclear theca","reliability":"Additional"}],"tissue_specificity":"Tissue enriched","tissue_distribution":"Detected in some","driving_tissues":[{"tissue":"testis","ntpm":70.2}],"url":"https://www.proteinatlas.org/search/CCIN"},"hgnc":{"alias_symbol":["KBTBD14","BTBD20"],"prev_symbol":[]},"alphafold":{"accession":"Q13939","domains":[{"cath_id":"3.30.710.10","chopping":"9-127","consensus_level":"high","plddt":92.9732,"start":9,"end":127},{"cath_id":"1.25.40.420","chopping":"145-270","consensus_level":"medium","plddt":92.0334,"start":145,"end":270},{"cath_id":"2.120.10.80","chopping":"302-584","consensus_level":"high","plddt":90.5402,"start":302,"end":584}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q13939","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q13939-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q13939-F1-predicted_aligned_error_v6.png","plddt_mean":90.44},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=CCIN","jax_strain_url":"https://www.jax.org/strain/search?query=CCIN"},"sequence":{"accession":"Q13939","fasta_url":"https://rest.uniprot.org/uniprotkb/Q13939.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q13939/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q13939"}},"corpus_meta":[{"pmid":"9400769","id":"PMC_9400769","title":"Mitomycin 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research","url":"https://pubmed.ncbi.nlm.nih.gov/41169243","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":14560,"output_tokens":1607,"usd":0.033892,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":8407,"output_tokens":1782,"usd":0.043292,"stage2_stop_reason":"end_turn"},"total_usd":0.077184,"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\": 2022,\n      \"finding\": \"Calicin (CCIN) interacts with itself (self-association) and many other perinuclear theca (PT) components, suggesting it serves as an organizing center of PT assembly. Calicin also interacts with inner acrosomal membrane (IAM) protein SPACA1 and nuclear envelope (NE) components to form an 'IAM-PT-NE' structure. Loss of Calicin (Ccin knockout) causes surface subsidence of sperm heads during nuclear condensation and leads to DNA damage and failure of fertilization in mice.\",\n      \"method\": \"Co-immunoprecipitation, immunofluorescence, live imaging/fractionation, knockout mouse model with phenotypic readout (sperm head shaping, fertilization failure, DNA damage)\",\n      \"journal\": \"Cell reports\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal Co-IP identifying multiple binding partners, KO mouse with multiple defined cellular phenotypes (head morphology, DNA damage, fertilization failure), orthogonal methods in single study\",\n      \"pmids\": [\"35793634\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"Homozygous missense and compound heterozygous mutations in CCIN cause severe sperm head malformation (teratozoospermia) with markedly reduced Calicin protein levels in spermatozoa. Mutant spermatozoa from both mice and human patients fail to adhere to the zona pellucida, identified as the major mechanistic reason for CCIN-mutant sperm-derived infertility. Mouse models expressing disease-associated CCIN variants recapitulate the human phenotype.\",\n      \"method\": \"Patient whole-exome sequencing with Sanger validation, immunofluorescence assays on patient and mouse spermatozoa, ultrastructural morphological analysis, zona adhesion assay, ICSI rescue experiment, knock-in mouse models\",\n      \"journal\": \"Science bulletin\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple orthogonal methods (human genetics + mouse models + functional zona adhesion assay), replicated across patient and mouse systems\",\n      \"pmids\": [\"36546111\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"FNDC8 (a testis-enriched PT protein) physically interacts with CCIN and ACTL7A during spermiogenesis. Genetic disruption of Fndc8 destabilizes both CCIN and ACTL7A proteins, resulting in acrosome detachment and sperm head collapse, placing CCIN within a FNDC8-CCIN-ACTL7A complex required for PT structural integrity and sperm head morphogenesis.\",\n      \"method\": \"Co-immunoprecipitation, Fndc8 knockout mouse model, immunofluorescence, Western blot for protein stability\",\n      \"journal\": \"Zoological research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal Co-IP identifying CCIN as binding partner of FNDC8, KO mouse showing CCIN destabilization, single lab\",\n      \"pmids\": [\"41169243\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"Calicin (CCIN) is among a group of actin cytoskeleton proteins in bull sperm that undergoes oxidative post-translational modifications (oxPTMs) mediated by 2-Cys peroxiredoxins (PRDXs) under control conditions, as revealed by inhibition of PRDXs with Conoidin A.\",\n      \"method\": \"2-Cys PRDX inhibition (Conoidin A treatment), proteomics/mass spectrometry to detect oxidative PTMs on sperm proteins\",\n      \"journal\": \"International journal of molecular sciences\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single proteomics screen in bull sperm, single lab, no functional follow-up on CCIN specifically\",\n      \"pmids\": [\"34884692\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"FSIP2 mutations in asthenoteratozoospermic patients lead to downregulated expression of CCIN in spermatozoa, placing CCIN downstream of FSIP2 in a pathway regulating acrosome biogenesis and sperm morphology.\",\n      \"method\": \"Whole exome sequencing, Western blot and immunofluorescence in patient spermatozoa, co-immunoprecipitation (for FSIP2 interactions), proteomics\",\n      \"journal\": \"Journal of medical genetics\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — CCIN downregulation observed as secondary effect of FSIP2 mutation; no direct functional experiment on CCIN itself, single lab\",\n      \"pmids\": [\"35654582\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"A novel homozygous missense variant in CCIN causes male infertility with an abnormal sperm head nuclear subsidence phenotype, consistent with Calicin's role in sperm head shaping.\",\n      \"method\": \"Sanger sequencing, clinical genetic analysis, spermatozoa morphological assessment\",\n      \"journal\": \"Clinical genetics\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single case report with genetic and morphological data, no in vitro/in vivo functional experiments described in abstract\",\n      \"pmids\": [\"36527329\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"CCIN encodes Calicin, a cytoskeletal protein that acts as an organizing hub of the sperm perinuclear theca (PT) by self-associating and binding PT components, SPACA1 (inner acrosomal membrane), nuclear envelope proteins, and ACTL7A/FNDC8, thereby forming an IAM-PT-NE structural unit that shapes the sperm head and maintains nuclear integrity during spermiogenesis; loss of Calicin causes sperm head surface collapse, DNA damage, failure of zona pellucida adhesion, and male infertility.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"CCIN encodes Calicin, a cytoskeletal organizing protein of the sperm perinuclear theca (PT) that shapes the sperm head and protects nuclear integrity during spermiogenesis [#0]. Calicin self-associates and binds multiple PT components, and bridges the inner acrosomal membrane protein SPACA1 to nuclear envelope components, assembling an integrated IAM-PT-NE structural unit; its loss causes surface subsidence of the condensing sperm head, DNA damage, and fertilization failure [#0]. Calicin functions within an FNDC8-CCIN-ACTL7A complex required for PT structural integrity, since loss of FNDC8 destabilizes both Calicin and ACTL7A and leads to acrosome detachment and sperm head collapse [#2]. In humans, biallelic CCIN mutations reduce Calicin protein levels and cause severe sperm head malformation; the resulting failure of mutant spermatozoa to adhere to the zona pellucida is the principal mechanistic basis of CCIN-associated male infertility, and ICSI rescues fertilization [#1].\",\n  \"teleology\": [\n    {\n      \"year\": 2022,\n      \"claim\": \"Established Calicin as the structural organizing hub of the perinuclear theca by showing it self-associates and links the inner acrosomal membrane to the nuclear envelope, defining how the sperm head is shaped and the nucleus protected.\",\n      \"evidence\": \"Co-IP, immunofluorescence, fractionation, and Ccin knockout mouse with sperm head shaping, DNA damage, and fertilization readouts\",\n      \"pmids\": [\"35793634\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Structural basis of how Calicin physically couples IAM to NE not resolved\",\n        \"Stoichiometry and architecture of the PT assembly hub undefined\",\n        \"Whether DNA damage is direct or secondary to head collapse unclear\"\n      ]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Connected CCIN to a defined human disease, showing biallelic mutations cause teratozoospermia and identifying failed zona pellucida adhesion as the mechanistic cause of infertility, which ICSI bypasses.\",\n      \"evidence\": \"Patient whole-exome sequencing, knock-in mouse models, zona adhesion assay, and ICSI rescue\",\n      \"pmids\": [\"36546111\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Molecular basis linking head malformation to loss of zona adhesion not defined\",\n        \"How specific missense variants destabilize Calicin protein unknown\"\n      ]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Reinforced the head-shaping role by linking an additional CCIN missense variant to the nuclear subsidence phenotype in patients.\",\n      \"evidence\": \"Sanger sequencing and morphological assessment in a male infertility case\",\n      \"pmids\": [\"36527329\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"Single case report with no functional experiments\",\n        \"Variant pathogenicity not validated in vivo\"\n      ]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Placed Calicin within an FNDC8-CCIN-ACTL7A complex, clarifying that Calicin stability and PT integrity depend on partner proteins.\",\n      \"evidence\": \"Co-IP, Fndc8 knockout mouse, and Western blot for protein stability\",\n      \"pmids\": [\"41169243\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Single-lab finding without independent replication\",\n        \"Direct binding interfaces within the complex not mapped\",\n        \"Whether Calicin stabilizes its partners reciprocally untested\"\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"The biochemical mechanism by which Calicin organizes PT assembly and the role of its oxidative modification remain open.\",\n      \"evidence\": \"No direct mechanistic or structural study in the available corpus\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"No structural model of Calicin or its PT contacts\",\n        \"Functional consequence of PRDX-mediated oxidative PTMs on Calicin untested\",\n        \"Relationship between FSIP2-dependent regulation and Calicin function undefined\"\n      ]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0008092\", \"supporting_discovery_ids\": [0, 2]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005856\", \"supporting_discovery_ids\": [0]},\n      {\"term_id\": \"GO:0005635\", \"supporting_discovery_ids\": [0]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-1474165\", \"supporting_discovery_ids\": [0, 1]}\n    ],\n    \"complexes\": [\"perinuclear theca\", \"FNDC8-CCIN-ACTL7A complex\"],\n    \"partners\": [\"SPACA1\", \"FNDC8\", \"ACTL7A\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":3,"faith_total":4,"faith_pct":75.0}}