{"id":"W4410480527","doi":"10.1002/pro.70155","title":"A quantitative comparison of the deleteriousness of missense and nonsense mutations using the structurally resolved human protein interactome","year":2025,"lang":"en","type":"article","venue":"Protein Science","topic":"Bioinformatics and Genomic Networks","field":"Biochemistry, Genetics and Molecular Biology","cited_by":3,"is_retracted":false,"has_abstract":true,"ca_institutions":"McGill University","funders":"Natural Sciences and Engineering Research Council of Canada; Canada Research Chairs; Canada Foundation for Innovation","keywords":"Missense mutation; Interactome; Nonsense mutation; Genetics; Nonsense; Biology; Phenotype; Mutation; Mendelian inheritance; Computational biology; Gene","routes":{"ca_aff":true,"ca_fund":true,"ca_venue":false,"about_ca":false,"invisible_to_affiliation_only":false},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0003336013,0.00007387805,0.0001080347,0.00003838511,0.0002657664,0.00003286935,0.0003087719,0.0000360732,0.00000109396],"category_scores_gemma":[0.0001342592,0.00004404719,0.00003363812,0.0002684375,0.001033351,0.000007105656,0.0002312836,0.00007780008,6.278707e-8],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.000008695622,"about_ca_system_score_gemma":0.0001344319,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00005388994,"about_ca_topic_score_gemma":0.00006259087,"domain_scores_codex":[0.9993047,0.00005141124,0.000265159,0.0001384758,0.0001191176,0.0001211423],"domain_scores_gemma":[0.999301,0.00001636612,0.0002152692,0.0002782469,0.0001696416,0.00001952442],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"bench_or_experimental","study_design_scores_codex":[0.00002654428,0.00001002401,0.0002488343,0.00003215741,0.000009598011,7.585265e-8,0.0007534728,0.000160208,0.9964171,0.001546386,0.000003481375,0.0007921098],"study_design_scores_gemma":[0.0002194169,0.0001411774,0.00332749,0.000167414,0.00001305966,0.00000406849,0.001382147,0.01670198,0.9764878,0.001404188,0.00006539734,0.00008592294],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9945429,0.0001724571,0.004441515,0.0001353249,0.00003461336,0.0005693103,0.000007431825,0.000001670122,0.00009478731],"genre_scores_gemma":[0.9947746,6.899086e-7,0.005124905,0.00002890881,0.000005626886,0.00001120919,0.000001411386,0.000002792865,0.00004987686],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.01992937,"threshold_uncertainty_score":0.3807424,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.02434416560539688,"score_gpt":0.3422780835628101,"score_spread":0.3179339179574132,"validation_status":"score_only:v0-immature-baseline","note":"Baseline scores from an immature model (maturity gate not passed). Scores rank; they never assert a category."}}