{"id":"W4407476090","doi":"10.1101/2025.02.11.25322033","title":"The ClinGen Severe Combined Immunodeficiency Disease Variant Curation Expert Panel: Specifications for classification of variants in <i>ADA</i> , <i>DCLRE1C</i> , <i>IL2RG</i> , <i>IL7R</i> , <i>JAK3</i> , <i>RAG1</i> , and <i>RAG2</i>","year":2025,"lang":"en","type":"preprint","venue":"medRxiv","topic":"Immunodeficiency and Autoimmune Disorders","field":"Immunology and Microbiology","cited_by":2,"is_retracted":false,"has_abstract":true,"ca_institutions":"Canadian Institutes of Health Research","funders":"National Institute of Child Health and Human Development; National Institutes of Health; California Institute of Regenerative Medicine","keywords":"Recombination-activating gene; Interleukin-7 receptor; Immunodeficiency; Biology; Computational biology; Medicine; Immunology; Genetics; Gene; Immune system","routes":{"ca_aff":true,"ca_fund":false,"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":["metaepi_narrow","sts"],"consensus_categories":[],"category_scores_codex":[0.002383098,0.001046138,0.001342719,0.0003987591,0.001325543,0.0002008608,0.002002036,0.0009388032,0.00002881929],"category_scores_gemma":[0.0008648302,0.0009067302,0.00055624,0.0008582252,0.001109766,0.0003776237,0.0009267726,0.001464874,0.00002738628],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.0001527952,"about_ca_system_score_gemma":0.001038497,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.0003624567,"about_ca_topic_score_gemma":0.00006516897,"domain_scores_codex":[0.9931999,0.0009017483,0.002674301,0.001738191,0.0002663222,0.001219558],"domain_scores_gemma":[0.9935459,0.001780763,0.001511378,0.002502413,0.0006037121,0.00005587075],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"not_applicable","study_design_scores_codex":[0.01205044,0.01008469,0.01574215,0.004226492,0.002333524,0.0000391744,0.01283103,0.00295875,0.6613416,0.1747576,0.02074433,0.08289023],"study_design_scores_gemma":[0.02127812,0.0008800376,0.1031958,0.003941681,0.001716875,0.0000887315,0.005998144,0.006657252,0.01829059,0.03458965,0.7976135,0.005749665],"study_design_candidate":"not_applicable","study_design_consensus":null,"genre_codex":"review","genre_gemma":"empirical","genre_scores_codex":[0.3617972,0.5312287,0.02376938,0.0201284,0.02070177,0.01887728,0.006865222,0.0009795054,0.01565251],"genre_scores_gemma":[0.9752456,0.01743017,0.0002265983,0.0009668388,0.00004051001,0.001781539,0.002031836,0.0001036454,0.002173277],"genre_candidate":"empirical","genre_consensus":null,"teacher_disagreement_score":0.7768691,"threshold_uncertainty_score":0.9999746,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.04175612171940985,"score_gpt":0.2710224082534768,"score_spread":0.2292662865340669,"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."}}