{"schema":"https://ver.cy/schemas/card/1.0.0","id":"vr.tr.mutation","code":"thing-q42918","url":"https://ver.cy/models/thing/q42918/","name":"mutation","alternateNames":["conserved signature indels","gain of function","random mutation","DNA mutation","Soft selective sweep","spontaneous mutation","beneficial mutation","harmful mutation","gene loss","deleterious mutation","founder mutation","Transversion"],"kind":"thing","status":"published","version":"0.2.0-wave.1","language":"en","classifiers":{"family":"Thing Registry","category":"Activities and processes","entryKind":"thing","plane":"ACT","domain":["ACT.PRC"],"industry":[],"navPath":"","tags":[],"facets":{}},"whatItIs":"A change in the nucleotide sequence of an organism genome, arising spontaneously or from mutagens, ranging from single-base substitutions to insertions, deletions and larger rearrangements.","purpose":"Let an agent handle mutations by type, location, effect and evidence, with standard nomenclature, and avoid giving individual genetic advice.","scope":{"in":[],"out":[],"boundaries":[]},"distinguishingFeatures":["Change in DNA sequence","Germline or somatic","Effects range from none to severe","Interpretation requires evidence and expert review"],"structure":{"bundles":[{"id":"description","name":"Description","description":"What changed.","layers":[{"id":"notation","name":"Notation","description":"HGVS.","findings":[{"id":"notation-finding","name":"Notation","description":"Variant notation.","questions":[{"text":"What is the HGVS description, on which reference sequence?","kind":"provenance"},{"text":"Which gene is affected?","kind":"definition"}]}]},{"id":"type","name":"Type","description":"Substitution, indel.","findings":[{"id":"type-finding","name":"Type","description":"Variant type.","questions":[{"text":"What type of mutation is it?","kind":"definition"},{"text":"Is it germline or somatic?","kind":"definition"}]}]}]},{"id":"effect","name":"Effect","description":"What it does.","layers":[{"id":"molecular","name":"Molecular effect","description":"On protein.","findings":[{"id":"molecular-finding","name":"Molecular effect","description":"Effect on product.","questions":[{"text":"What does it do to the gene product?","kind":"definition"},{"text":"How is that known?","kind":"provenance"}]}]},{"id":"clinical","name":"Clinical significance","description":"Classification.","findings":[{"id":"clinical-finding","name":"Classification","description":"Clinical classification.","questions":[{"text":"How is it classified, by which lab or database?","kind":"provenance"},{"text":"Has the classification changed?","kind":"provenance"}]}]}]},{"id":"origin","name":"Origin","description":"How it arose.","layers":[{"id":"cause","name":"Cause","description":"Spontaneous or induced.","findings":[{"id":"cause-finding","name":"Cause","description":"Cause.","questions":[{"text":"How did it arise?","kind":"definition"},{"text":"Is it inherited?","kind":"boundary"}]}]},{"id":"frequency","name":"Frequency","description":"Population.","findings":[{"id":"frequency-finding","name":"Frequency","description":"Population frequency.","questions":[{"text":"How common is it in populations, according to gnomAD or similar?","kind":"measurement"},{"text":"Which populations?","kind":"boundary"}]}]}]},{"id":"handling","name":"Handling","description":"Advice and privacy.","layers":[{"id":"counselling","name":"Counselling","description":"Professional advice.","findings":[{"id":"counselling-finding","name":"Referral","description":"When to refer.","questions":[{"text":"Should the person be referred to genetic counselling?","kind":"action"},{"text":"What can the agent say in general terms?","kind":"boundary"}]}]},{"id":"privacy","name":"Privacy","description":"Genetic data.","findings":[{"id":"privacy-finding","name":"Privacy","description":"Genetic data rules.","questions":[{"text":"Is genetic data being shared lawfully?","kind":"boundary"},{"text":"Who else might be affected, such as relatives?","kind":"boundary"}]}]}]}]},"agentConduct":{"may":["Explain mutations in general terms with cited science.","Report variant data from curated databases, stating clinical significance as classified."],"mustNot":["Interpret a person's genetic variants as a diagnosis.","Disclose a person's genetic data without consent.","Assist in engineering harmful mutations in pathogens.","Use genetic variation to rank people."],"requiresHuman":["Telling a person about a significant genetic finding."]},"ethics":{"considerations":["Genetic data reveals information about relatives too.","Genetics has been misused to justify discrimination."],"affectedParties":["Patients","Relatives","Research participants"]},"owners":{"steward":"Nobody owns a mutation; genetic data belongs to the person it describes.","roles":[],"masterSystems":["Genetic variant databases"]},"relations":[{"target":"Q102116514","type":"parent","note":"registry parent class"},{"target":"Q115865817","type":"parent","note":"registry parent class"},{"target":"Q15304597","type":"parent","note":"registry parent class"},{"target":"Q2996394","type":"parent","note":"registry parent class"},{"target":"DNA and protein","type":"related","note":"molecules"},{"target":"evolution","type":"related","note":"variation"},{"target":"disease","type":"related","note":"genetic disease"},{"target":"sequence variant","type":"related","note":"variation"}],"interaction":{"identity":{"applicability":"required","items":["Vercy registry: vr.tr.mutation","Wikidata: Q42918 (https://www.wikidata.org/wiki/Q42918)","HGVS notation: for example NM_000492.4:c.1521_1523del standard variant description","ClinVar id: numeric clinical interpretations","dbSNP rs id: rs plus digits variants"]},"properties":{"applicability":"not-applicable","items":[]},"recognition":{"applicability":"optional","items":["Variant notation such as c.1521_1523del","Sequence alignments showing differences","Classifications such as pathogenic or benign","Not visible directly; seen as differences in sequence data or as traits."]},"capabilities":{"applicability":"required","items":["detect it, by sequencing","name it, with HGVS nomenclature","interpret its effect, with evidence","study its evolutionary role"]},"hazards":{"applicability":"required","items":["Over-interpreting variants of uncertain significance","Individual genetic advice without a genetic counsellor","Genetic discrimination"]},"interfaces":{"applicability":"required","items":["HGVS nomenclature","ACMG/AMP variant classification guidelines","Genetic data protection law"]},"context":{"applicability":"required","items":["Mutations drive evolution and cause or influence many diseases; they are studied in genetics and medicine.","point mutations","insertions and deletions (indels)","copy number variants","structural rearrangements","gain-of-function and loss-of-function mutations"]}},"sources":[{"title":"Wikidata item Q42918: mutation","url":"https://www.wikidata.org/wiki/Q42918","note":"identity and sense of the item"},{"title":"Wikipedia: Mutation","url":"https://en.wikipedia.org/wiki/Mutation","note":"general description of the item"}],"openQuestions":["Should variants be instances with HGVS and ClinVar ids?","How should classification changes over time be recorded?","How should agents direct people to genetic counselling?"],"resources":{"spec":"/models/things/publications/thing-q42918/spec.json"},"provenance":{"origin":"thing registry research (pass 2)","builtFrom":["models/things/publications/thing-q42918/spec.json"],"providers":["Claude"],"researchStatus":"unreviewed","generatedAt":"2026-09-11T05:41:45Z","builder":"tools/build_cards.py@1.0.0"},"completeness":{"sections":{"classifiers":"filled","whatItIs":"filled","purpose":"filled","distinguishingFeatures":"filled","structure":"filled","agentConduct":"filled","ethics":"filled","owners":"filled","relations":"filled","interaction.identity":"filled","interaction.properties":"not-applicable","interaction.recognition":"filled","interaction.capabilities":"filled","interaction.hazards":"filled","interaction.interfaces":"filled","interaction.context":"filled","sources":"filled"},"notes":{"_gate":"Published through the thing publication gate 1.0 on 2026-10-06T19:52:00+00:00: completeness 1.00; sense: Wikidata description; 2 live sources; review by codex: pass","interaction.properties":"Plane ACT: no invented physical properties."},"score":1.0}}