{"gene":"CCDC97","run_date":"2026-06-09T22:57:17","timeline":{"discoveries":[{"year":2026,"finding":"CCDC97 protein binds to the splicing factor SF3B complex to participate in pre-mRNA splicing.","method":"Reported as an established interaction in the context of a pan-cancer analysis paper; no primary experimental method described in the abstract beyond database/literature reference.","journal":"Analytical cellular pathology (Amsterdam)","confidence":"Low","confidence_rationale":"Tier 4 / Weak — stated as background fact in a bioinformatics paper with no primary experimental validation described in the abstract","pmids":["41810918"],"is_preprint":false},{"year":2025,"finding":"Knockdown of CCDC97 in HCC cells suppressed cell migration, invasion, and proliferation in vitro, indicating CCDC97 is required for these malignant behaviors.","method":"siRNA/shRNA knockdown in HCC cell lines with migration, invasion, and proliferation assays","journal":"Xi bao yu fen zi mian yi xue za zhi = Chinese journal of cellular and molecular immunology","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single lab, single set of in vitro loss-of-function assays with phenotypic readouts but no pathway placement or molecular mechanism identified","pmids":["39799421"],"is_preprint":false}],"current_model":"CCDC97 is reported to interact with the SF3B splicing factor complex to participate in pre-mRNA splicing, and its loss-of-function in hepatocellular carcinoma cells suppresses migration, invasion, and proliferation, but the detailed molecular mechanism linking its splicing role to these cellular phenotypes remains uncharacterized."},"narrative":{"mechanistic_narrative":"CCDC97 is a poorly characterized protein implicated in pre-mRNA splicing through reported association with the SF3B splicing factor complex [PMID:41810918]. Loss-of-function studies in hepatocellular carcinoma cells show that CCDC97 knockdown suppresses migration, invasion, and proliferation, indicating it is required for these malignant behaviors [PMID:39799421]. Beyond these observations, no mechanistic detail linking the splicing association to the cellular phenotypes has been characterized in the available corpus.","teleology":[{"year":2025,"claim":"To establish whether CCDC97 has any functional role in cancer cells, loss-of-function assays tested its requirement for malignant behaviors, showing it is needed for migration, invasion, and proliferation in HCC.","evidence":"siRNA/shRNA knockdown in HCC cell lines with migration, invasion, and proliferation assays","pmids":["39799421"],"confidence":"Low","gaps":["Single-lab in vitro phenotypic readouts without molecular mechanism or pathway placement","No in vivo validation of the tumor phenotype","No rescue experiment to confirm specificity"]},{"year":2026,"claim":"To place CCDC97 in a molecular pathway, it was reported to bind the SF3B splicing factor complex, implicating it in pre-mRNA splicing.","evidence":"Stated as a background interaction in a pan-cancer bioinformatics analysis with no primary experimental validation described","pmids":["41810918"],"confidence":"Low","gaps":["Interaction asserted as background fact without primary experimental validation in the source","No direct biochemical demonstration of SF3B binding","No link established between the splicing role and the HCC phenotype"]},{"year":null,"claim":"The molecular mechanism connecting CCDC97's reported splicing function to its requirement for cancer cell migration, invasion, and proliferation is unresolved.","evidence":"","pmids":[],"confidence":"Low","gaps":["No splicing substrates or affected transcripts identified","No structural or biochemical characterization of CCDC97","No subcellular localization established in the corpus"]}],"mechanism_profile":{"molecular_activity":[],"localization":[],"pathway":[],"complexes":[],"partners":[],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q96F63","full_name":"Coiled-coil domain-containing protein 97","aliases":[],"length_aa":343,"mass_kda":38.9,"function":"May play a role pre-mRNA splicing through the association with the splicing factor SF3B complex which is involved in branch-site recognition","subcellular_location":"Nucleus","url":"https://www.uniprot.org/uniprotkb/Q96F63/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/CCDC97","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":[{"gene":"COMMD2","stoichiometry":10.0},{"gene":"RSL1D1","stoichiometry":10.0},{"gene":"SF3B1","stoichiometry":10.0},{"gene":"SF3B5","stoichiometry":10.0},{"gene":"SF3B6","stoichiometry":10.0},{"gene":"COMMD6","stoichiometry":4.0},{"gene":"COMMD4","stoichiometry":0.2},{"gene":"SF3A1","stoichiometry":0.2},{"gene":"SF3B3","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/search/CCDC97","total_profiled":1310},"omim":[],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Nucleoplasm","reliability":"Supported"},{"location":"Plasma membrane","reliability":"Additional"},{"location":"Cytosol","reliability":"Additional"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/CCDC97"},"hgnc":{"alias_symbol":["FLJ40267","MGC20255"],"prev_symbol":[]},"alphafold":{"accession":"Q96F63","domains":[{"cath_id":"-","chopping":"59-145","consensus_level":"high","plddt":86.2982,"start":59,"end":145},{"cath_id":"-","chopping":"149-201_222-252_274-330","consensus_level":"medium","plddt":91.1082,"start":149,"end":330}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q96F63","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q96F63-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q96F63-F1-predicted_aligned_error_v6.png","plddt_mean":77.0},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=CCDC97","jax_strain_url":"https://www.jax.org/strain/search?query=CCDC97"},"sequence":{"accession":"Q96F63","fasta_url":"https://rest.uniprot.org/uniprotkb/Q96F63.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q96F63/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q96F63"}},"corpus_meta":[{"pmid":"27386823","id":"PMC_27386823","title":"Integrative functional genomics identifies regulatory mechanisms at coronary artery disease loci.","date":"2016","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/27386823","citation_count":113,"is_preprint":false},{"pmid":"34830933","id":"PMC_34830933","title":"Kinome-Wide siRNA Screening Identifies DYRK1B as a Potential Therapeutic Target for Triple-Negative Breast Cancer Cells.","date":"2021","source":"Cancers","url":"https://pubmed.ncbi.nlm.nih.gov/34830933","citation_count":14,"is_preprint":false},{"pmid":"34384032","id":"PMC_34384032","title":"Early-pregnancy maternal body mass index is associated with common DNA methylation markers in cord blood and placenta: a paired-tissue epigenome-wide association study.","date":"2021","source":"Epigenetics","url":"https://pubmed.ncbi.nlm.nih.gov/34384032","citation_count":8,"is_preprint":false},{"pmid":"39799421","id":"PMC_39799421","title":"[CCDC97 influences the immune microenvironment and biological functions in HCC].","date":"2025","source":"Xi bao yu fen zi mian yi xue za zhi = Chinese journal of cellular and molecular immunology","url":"https://pubmed.ncbi.nlm.nih.gov/39799421","citation_count":0,"is_preprint":false},{"pmid":"41810918","id":"PMC_41810918","title":"CCDC97 is a Promising Predictor in Cancer Diagnosis: A Pan Cancer Analysis.","date":"2026","source":"Analytical cellular pathology (Amsterdam)","url":"https://pubmed.ncbi.nlm.nih.gov/41810918","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":4558,"output_tokens":469,"usd":0.010355,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":6785,"output_tokens":930,"usd":0.028587,"stage2_stop_reason":"end_turn"},"total_usd":0.038942,"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\": 2026,\n      \"finding\": \"CCDC97 protein binds to the splicing factor SF3B complex to participate in pre-mRNA splicing.\",\n      \"method\": \"Reported as an established interaction in the context of a pan-cancer analysis paper; no primary experimental method described in the abstract beyond database/literature reference.\",\n      \"journal\": \"Analytical cellular pathology (Amsterdam)\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 4 / Weak — stated as background fact in a bioinformatics paper with no primary experimental validation described in the abstract\",\n      \"pmids\": [\"41810918\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"Knockdown of CCDC97 in HCC cells suppressed cell migration, invasion, and proliferation in vitro, indicating CCDC97 is required for these malignant behaviors.\",\n      \"method\": \"siRNA/shRNA knockdown in HCC cell lines with migration, invasion, and proliferation assays\",\n      \"journal\": \"Xi bao yu fen zi mian yi xue za zhi = Chinese journal of cellular and molecular immunology\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single lab, single set of in vitro loss-of-function assays with phenotypic readouts but no pathway placement or molecular mechanism identified\",\n      \"pmids\": [\"39799421\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"CCDC97 is reported to interact with the SF3B splicing factor complex to participate in pre-mRNA splicing, and its loss-of-function in hepatocellular carcinoma cells suppresses migration, invasion, and proliferation, but the detailed molecular mechanism linking its splicing role to these cellular phenotypes remains uncharacterized.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"CCDC97 is a poorly characterized protein implicated in pre-mRNA splicing through reported association with the SF3B splicing factor complex [#0]. Loss-of-function studies in hepatocellular carcinoma cells show that CCDC97 knockdown suppresses migration, invasion, and proliferation, indicating it is required for these malignant behaviors [#1]. Beyond these observations, no mechanistic detail linking the splicing association to the cellular phenotypes has been characterized in the available corpus.\",\n  \"teleology\": [\n    {\n      \"year\": 2025,\n      \"claim\": \"To establish whether CCDC97 has any functional role in cancer cells, loss-of-function assays tested its requirement for malignant behaviors, showing it is needed for migration, invasion, and proliferation in HCC.\",\n      \"evidence\": \"siRNA/shRNA knockdown in HCC cell lines with migration, invasion, and proliferation assays\",\n      \"pmids\": [\n        \"39799421\"\n      ],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"Single-lab in vitro phenotypic readouts without molecular mechanism or pathway placement\",\n        \"No in vivo validation of the tumor phenotype\",\n        \"No rescue experiment to confirm specificity\"\n      ]\n    },\n    {\n      \"year\": 2026,\n      \"claim\": \"To place CCDC97 in a molecular pathway, it was reported to bind the SF3B splicing factor complex, implicating it in pre-mRNA splicing.\",\n      \"evidence\": \"Stated as a background interaction in a pan-cancer bioinformatics analysis with no primary experimental validation described\",\n      \"pmids\": [\n        \"41810918\"\n      ],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"Interaction asserted as background fact without primary experimental validation in the source\",\n        \"No direct biochemical demonstration of SF3B binding\",\n        \"No link established between the splicing role and the HCC phenotype\"\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"The molecular mechanism connecting CCDC97's reported splicing function to its requirement for cancer cell migration, invasion, and proliferation is unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"No splicing substrates or affected transcripts identified\",\n        \"No structural or biochemical characterization of CCDC97\",\n        \"No subcellular localization established in the corpus\"\n      ]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [],\n    \"localization\": [],\n    \"pathway\": [],\n    \"complexes\": [],\n    \"partners\": [],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":2,"faith_total":2,"faith_pct":100.0}}