{ "model": { "rank": 12986, "code": "thing-q656732", "model_id": "vr.tr.deletion-mutation", "name": "deletion mutation", "purpose": "Let an agent explain deletion mutations and their scales, relay mechanisms, detection and clinical significance from genetics references in general terms, describe named deletion syndromes, and distinguish deletions from insertions, duplications, point mutations and whole chromosome loss, routing people with genetic concerns to clinicians.", "family": "Thing Registry", "category": "Activities and processes", "status": "research-draft", "kind": "thing", "plane": "ACT", "domain": "ACT.PRC", "industry": "", "version": "", "url": "/models/thing/q656732/", "tier": 2, "score": 38, "payload": { "layer": "wikidata", "aliases": [ "partial deletion of chromosome X", "partial autosomal monosomy", "Y chromosome microdeletion" ], "aliasCount": 3, "merged": 3, "knownIn": 38, "facets": null, "markers": [], "lexicalClass": "", "senseRank": null, "alsoRegisteredAs": null, "source": { "dataset": "wikidata", "item": "Q656732", "url": "https://www.wikidata.org/wiki/Q656732", "license": "CC0 1.0" } }, "research": { "vercy": "1.0-draft", "publication": { "status": "research-draft", "adjudicationStatus": "unreviewed", "publishableCanonical": false, "generatedAt": "2026-09-13T13:48:29Z", "providers": [ "Claude" ], "breadth": "written by Claude from model knowledge without web access - no source was read, every claim is a lead to verify", "pass": 2, "wave": 4, "engine": "claude" }, "metaModel": { "id": "THING-Q656732", "registryId": "vr.tr.deletion-mutation", "name": "deletion mutation", "version": "0.2.0-wave.4", "entryKind": "thing", "family": "Thing Registry", "domain": [ "ACT.PRC" ], "status": "research-draft" }, "canonicalUrl": "https://ver.cy/models/thing/q656732/", "model": { "registry_id": "vr.tr.deletion-mutation", "name": "deletion mutation", "purpose": "Let an agent explain deletion mutations and their scales, relay mechanisms, detection and clinical significance from genetics references in general terms, describe named deletion syndromes, and distinguish deletions from insertions, duplications, point mutations and whole chromosome loss, routing people with genetic concerns to clinicians.", "definition": "A mutation in which a segment of DNA is lost, from a single base to large chromosome regions, including partial deletions of the X chromosome, partial autosomal monosomies such as cri du chat syndrome, and Y chromosome microdeletions associated with male infertility; deletions can cause frameshifts, loss of gene function and genetic disorders, and are detected by sequencing and chromosomal microarray.", "what_it_is_for": "Not applicable; a mutation type.", "affordances": [ "explain scales and mechanisms", "relay detection and significance", "describe syndromes", "distinguish related mutations" ], "distinguishing_features": [ "Loss of sequence", "Frameshift potential", "Small to chromosomal", "Detectable by sequencing and arrays" ], "appearance": "Not a visible object; a missing DNA segment.", "visual_identification": [ "Loss of a DNA segment", "Small deletions, partial X deletions, partial autosomal monosomy, Y microdeletions", "Insertions add bases; duplications copy; point mutations substitute; monosomy loses a whole chromosome" ], "physical_properties": [ { "quantity": "scale", "typical_range": "from 1 base to megabases", "unit": "note", "note": "" }, { "quantity": "Y microdeletion regions", "typical_range": "AZFa, AZFb, AZFc", "unit": "list", "note": "" }, { "quantity": "22q11.2 deletion incidence", "typical_range": "about 1 in 4000", "unit": "births", "note": "" } ], "families_and_kinds": [ "small deletions and frameshift deletions", "gene deletions", "microdeletions such as 22q11.2 and Y chromosome microdeletions", "partial chromosome deletions including partial X deletions", "partial autosomal monosomies", "somatic deletions in cancer" ], "related_models": [ { "relation": "is a kind of", "target": "deletion", "why": "in registry terms" }, { "relation": "is a kind of", "target": "single gene mutation", "why": "in registry terms, at small scale" }, { "relation": "is contrasted with", "target": "insertion mutation", "why": "which adds sequence" }, { "relation": "is detected by", "target": "chromosomal microarray", "why": "and sequencing" } ], "identifiers": [], "standards_and_regulation": [ "HGVS nomenclature for describing deletions", "ACMG variant classification guidelines", "Genetic testing and counselling standards" ], "failure_modes_and_hazards": [ "Agents interpreting personal genetic results", "Confusing deletion scales and terms", "Registry aliases naming specific clinical categories" ], "in_scope": [], "out_of_scope": [], "characteristics": [] }, "sources": [], "structure": { "bundles": [ { "id": "understand", "name": "Understand", "description": "What a deletion mutation is.", "rationale": "Science.", "layers": [ { "id": "definition", "name": "Definition", "description": "Definition and scales.", "findings": [ { "id": "definition-finding", "name": "Definition", "description": "Definition.", "questions": [ { "text": "What is a deletion mutation, and how do small, gene-level and chromosomal deletions differ from insertions, duplications and monosomy?", "kind": "definition" }, { "text": "Is the question about genetics in general, a syndrome or a personal genetic result needing a clinician?", "kind": "boundary" } ] } ] }, { "id": "mechanisms", "name": "Mechanisms", "description": "Mechanisms.", "findings": [ { "id": "mechanisms-finding", "name": "Mechanisms", "description": "Mechanisms.", "questions": [ { "text": "How do deletions arise through replication errors, recombination and repair?", "kind": "definition" }, { "text": "Which entry fits DNA repair?", "kind": "action" } ] } ] } ] }, { "id": "effects", "name": "Effects", "description": "Effects.", "rationale": "Science.", "layers": [ { "id": "molecular", "name": "Molecular", "description": "Molecular effects.", "findings": [ { "id": "molecular-finding", "name": "Molecular", "description": "Molecular.", "questions": [ { "text": "How do deletions cause frameshifts and loss of function?", "kind": "provenance" }, { "text": "Which references are standard?", "kind": "provenance" } ] } ] }, { "id": "clinical", "name": "Clinical", "description": "Clinical effects.", "findings": [ { "id": "clinical-finding", "name": "Clinical", "description": "Clinical.", "questions": [ { "text": "What disorders result from partial X deletions, partial autosomal monosomies and Y microdeletions, in general terms?", "kind": "provenance" }, { "text": "Which sources are cited?", "kind": "provenance" } ] } ] } ] }, { "id": "detect", "name": "Detect", "description": "Detection.", "rationale": "Practice.", "layers": [ { "id": "methods", "name": "Methods", "description": "Methods.", "findings": [ { "id": "methods-finding", "name": "Methods", "description": "Methods.", "questions": [ { "text": "How are deletions detected by sequencing, MLPA and chromosomal microarray?", "kind": "measurement" }, { "text": "Which entry fits chromosomal microarray analysis?", "kind": "action" } ] } ] }, { "id": "nomenclature", "name": "Nomenclature", "description": "Nomenclature.", "findings": [ { "id": "nomenclature-finding", "name": "Nomenclature", "description": "Nomenclature.", "questions": [ { "text": "How are deletions named under HGVS and classified under ACMG guidelines?", "kind": "provenance" }, { "text": "Which entry fits HGVS nomenclature?", "kind": "action" } ] } ] } ] }, { "id": "context", "name": "Context", "description": "Counselling and research.", "rationale": "Context.", "layers": [ { "id": "counselling", "name": "Counselling", "description": "Genetic counselling.", "findings": [ { "id": "counselling-finding", "name": "Counselling", "description": "Counselling.", "questions": [ { "text": "What does genetic counselling involve for deletion syndromes, in general terms?", "kind": "provenance" }, { "text": "Is the user seeking personal counselling, which needs a professional?", "kind": "boundary" } ] } ] }, { "id": "research", "name": "Research", "description": "Research and evolution.", "findings": [ { "id": "research-finding", "name": "Research", "description": "Research.", "questions": [ { "text": "What roles do deletions play in evolution and cancer research?", "kind": "provenance" }, { "text": "Which entry fits copy number variation?", "kind": "action" } ] } ] } ] } ] }, "openQuestions": [ "Should Y chromosome microdeletion and partial monosomy be separate primary entries?", "How should genetics references be linked?", "The registry entry has merged aliases naming clinical categories; should they be split off?" ], "statistics": { "bundles": 4, "layers": 8, "findings": 8, "questions": 16 } }, "draft": { "generator": "vr.draft.v3", "status": "draft-generated", "researched": false, "archetype": "abstract concept", "method": "Written from the archetype playbook - what this kind of thing needs beyond identity and provenance - and from the structure that recurred across 6,333 models already researched by two engines. Applied to this entry by rule. No source was read for this thing and no claim here is researched. This entry carries no facets of its own, so they were inferred from its domain - a guess about a whole domain applied to one thing.", "facetsInferred": true, "nextPass": "A researcher replaces this draft with a sourced specification. Treat every sentence below as a proposal to argue with.", "purpose": "Give an agent a durable, checkable way to recognise a deletion mutation, record what state it is in, and decide what may be done with it.", "whatItIs": "Let an agent explain deletion mutations and their scales, relay mechanisms, detection and clinical significance from genetics references in general terms, describe named deletion syndromes, and distinguish deletions from insertions, duplications, point mutations and whole chromosome loss, routing people with genetic concerns to clinicians.", "characteristics": { "substance": "activity", "origin": "conceptual", "agency": "inert" }, "whatYouCanDoWithIt": [ "observed and measured" ], "distinguishingFeatures": [ "Names folded into this entry, which a task may need to split apart again: partial deletion of chromosome X, partial autosomal monosomy, Y chromosome microdeletion.", "3 finer distinctions are held as aliases rather than separate entries, because telling them apart needs a task that asks for it.", "Described in 38 Wikipedia languages, which is a measure of how widely the thing is known, not of how important it is." ], "openQuestionsForResearch": [ "Which of the bundles below does a real task actually need, and which are ceremony?", "What does this thing have that the facets do not capture at all?", "Which neighbouring kind is most often confused with a deletion mutation, and on what evidence are they told apart?" ], "whatItIsMadeOf": "something that happens over time", "physicalCharacter": [ "Does nothing on its own; everything it does, something else did to it.", "These come from the domain this entry sits in rather than from the entry itself, so treat them as a first guess about the whole domain applied to one thing." ], "whatCanBeDoneWithIt": [ "observe it, measure it, record its state" ], "howItIsRecognised": [ "Nothing to see. What is recognised is an instance of it, and which instances count is exactly what is argued about." ], "relatedModels": [ { "relation": "covers", "note": "Finer kinds folded into this entry because telling them apart needs a task that asks for it. Each is a model waiting to be split out when one does.", "targets": [ "partial deletion of chromosome X", "partial autosomal monosomy", "Y chromosome microdeletion" ] } ], "standing": "Described in 38 Wikipedia languages, which measures how widely it is written about rather than how important or how common it is. 3 finer distinctions are held inside this entry as names rather than as separate models.", "structure": { "bundles": [ { "id": "identity-and-classification", "name": "Identity, naming and classification", "description": "How an agent tells one deletion mutation from another, and a deletion mutation from things that resemble it.", "rationale": "Recognition comes before every other claim. Without stable identity nothing else in the model can be trusted to be about the same thing twice.", "layers": [ { "id": "naming-and-identifiers", "name": "Names and identifiers", "description": "The names this thing goes by and the identifiers that survive translation and time.", "findings": [ { "id": "preferred-name-and-aliases", "name": "Preferred name, aliases and local names", "description": "Which name to use, which names mean the same thing, and which merely sound similar.", "questions": [ { "id": "preferred-name-and-aliases-q01", "text": "What identifies and describes the name of a deletion mutation, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "preferred-name-and-aliases-q02", "text": "Who or what asserted this about the name of a deletion mutation, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "preferred-name-and-aliases-q03", "text": "What may an agent decide or do once the name of a deletion mutation is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] }, { "id": "stable-identifiers", "name": "Stable identifiers and external keys", "description": "Identifiers that keep pointing at this kind of thing across systems and languages.", "questions": [ { "id": "stable-identifiers-q01", "text": "What identifies and describes an identifier for a deletion mutation, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "stable-identifiers-q02", "text": "Who or what asserted this about an identifier for a deletion mutation, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "stable-identifiers-q03", "text": "What may an agent decide or do once an identifier for a deletion mutation is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] }, { "id": "classification-and-granularity", "name": "Classification and granularity", "description": "Where a deletion mutation sits among kinds, and how finely a task needs to cut it.", "findings": [ { "id": "kind-and-parents", "name": "Kind, parents and neighbouring kinds", "description": "The classes this thing belongs to and the ones it is next to.", "questions": [ { "id": "kind-and-parents-q01", "text": "What identifies and describes the kind of a deletion mutation, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "kind-and-parents-q02", "text": "Who or what asserted this about the kind of a deletion mutation, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "kind-and-parents-q03", "text": "What may an agent decide or do once the kind of a deletion mutation is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] }, { "id": "distinguishing-features", "name": "Distinguishing features", "description": "What separates a deletion mutation from the things most often confused with it.", "questions": [ { "id": "distinguishing-features-q01", "text": "What identifies and describes what distinguishes a deletion mutation, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "distinguishing-features-q02", "text": "Who or what asserted this about what distinguishes a deletion mutation, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "distinguishing-features-q03", "text": "What may an agent decide or do once what distinguishes a deletion mutation is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] } ] }, { "id": "state-and-lifecycle", "name": "State and lifecycle", "description": "The states a deletion mutation passes through and the events that move it between them.", "rationale": "Most decisions about a thing depend on what state it is in now, which is a claim with a time on it, not a property.", "layers": [ { "id": "lifecycle-stages", "name": "Lifecycle stages", "description": "From coming into existence to ceasing to be one of these.", "findings": [ { "id": "stages-and-transitions", "name": "Stages and transitions", "description": "The stages worth naming and what moves a deletion mutation between them.", "questions": [ { "id": "stages-and-transitions-q01", "text": "What identifies and describes the lifecycle of a deletion mutation, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "stages-and-transitions-q02", "text": "Who or what asserted this about the lifecycle of a deletion mutation, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "stages-and-transitions-q03", "text": "What may an agent decide or do once the lifecycle of a deletion mutation is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] }, { "id": "observations-and-status", "name": "Observations and current status", "description": "What is observed about a deletion mutation, how often and by whom.", "findings": [ { "id": "observation-record", "name": "Observation record", "description": "How an observation of a deletion mutation is recorded so that it can be superseded rather than overwritten.", "questions": [ { "id": "observation-record-q01", "text": "What identifies and describes an observation of a deletion mutation, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "observation-record-q02", "text": "Who or what asserted this about an observation of a deletion mutation, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "observation-record-q03", "text": "What may an agent decide or do once an observation of a deletion mutation is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] } ] }, { "id": "process-and-outcome", "name": "Process, inputs and outcome", "description": "How a deletion mutation proceeds, what it needs and what it leaves behind.", "rationale": "An activity is known by its steps and its results, and both have to be recordable while it is still running.", "layers": [ { "id": "steps-and-sequence", "name": "Steps and sequence", "description": "The steps of a deletion mutation, their order and what may run in parallel.", "findings": [ { "id": "steps-and-preconditions", "name": "Steps, preconditions and completion", "description": "What has to be true before each step of a deletion mutation and what marks it done.", "questions": [ { "id": "steps-and-preconditions-q01", "text": "What identifies and describes a step of a deletion mutation, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "steps-and-preconditions-q02", "text": "Who or what asserted this about a step of a deletion mutation, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "steps-and-preconditions-q03", "text": "What may an agent decide or do once a step of a deletion mutation is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] }, { "id": "inputs-and-results", "name": "Inputs, resources and results", "description": "What a deletion mutation consumes and what it produces.", "findings": [ { "id": "inputs-and-outputs", "name": "Inputs, outputs and side effects", "description": "The resources a deletion mutation takes and the results it leaves, wanted or not.", "questions": [ { "id": "inputs-and-outputs-q01", "text": "What identifies and describes the inputs and results of a deletion mutation, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "inputs-and-outputs-q02", "text": "Who or what asserted this about the inputs and results of a deletion mutation, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "inputs-and-outputs-q03", "text": "What may an agent decide or do once the inputs and results of a deletion mutation is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] } ] }, { "id": "definitions-in-contest", "name": "Definitions and who holds them", "description": "What deletion mutation is taken to mean, and by whom.", "rationale": "When a field disagrees about a concept, the disagreement is the content. A model that picks one definition silently destroys the information.", "layers": [ { "id": "competing-definitions", "name": "Competing definitions", "description": "The main readings and the traditions behind them.", "findings": [ { "id": "definition-map", "name": "Definitions and their holders", "description": "Each definition with the school or body that holds it.", "questions": [ { "id": "definition-map-q01", "text": "Which definitions of deletion mutation are in use, and which tradition or body holds each?", "kind": "definition" }, { "id": "definition-map-q02", "text": "What turns on the difference between them in practice?", "kind": "boundary" } ] } ] }, { "id": "operationalisation", "name": "Operationalisation", "description": "How it is measured or applied when it has to be.", "findings": [ { "id": "operational-record", "name": "Measures and proxies", "description": "Instruments and indicators used to stand in for it.", "questions": [ { "id": "operational-record-q01", "text": "How is deletion mutation operationalised or measured in practice, and by what instrument?", "kind": "measurement" }, { "id": "operational-record-q02", "text": "What does that operationalisation leave out, and when does that matter?", "kind": "boundary" } ] } ] } ] }, { "id": "instances-and-use", "name": "Instances, use and consequence", "description": "What counts as an instance of deletion mutation and what follows from calling something that.", "rationale": "Applying a concept is an act with consequences, so a model must say what the label licenses and what it does not.", "layers": [ { "id": "instances", "name": "What counts as an instance", "description": "Clear cases, borderline cases and non-cases.", "findings": [ { "id": "instance-tests", "name": "Tests for an instance", "description": "What would settle whether something falls under it.", "questions": [ { "id": "instance-tests-q01", "text": "What would settle whether something is an instance of deletion mutation?", "kind": "boundary" }, { "id": "instance-tests-q02", "text": "Which borderline cases are argued about, and on what grounds?", "kind": "definition" } ] } ] }, { "id": "consequence", "name": "Consequence of application", "description": "Rights, duties or decisions that follow from the label.", "findings": [ { "id": "consequence-record", "name": "What the label licenses", "description": "What an agent may do once something is classified this way.", "questions": [ { "id": "consequence-record-q01", "text": "What follows practically once something is treated as deletion mutation?", "kind": "action" }, { "id": "consequence-record-q02", "text": "What must an agent not infer from the label alone?", "kind": "action" } ] } ] } ] }, { "id": "provenance-and-evidence", "name": "Provenance, evidence and time", "description": "Where every claim about a deletion mutation came from and when it held.", "rationale": "A claim without a source and a time cannot be superseded, only overwritten, and an agent that overwrites loses the ability to explain itself.", "layers": [ { "id": "source-and-authority", "name": "Source and authority", "description": "Who said it, on what evidence, and how strongly.", "findings": [ { "id": "claim-provenance", "name": "Claim provenance and confidence", "description": "The authority behind each claim about a deletion mutation and how confident it is.", "questions": [ { "id": "claim-provenance-q01", "text": "What identifies and describes a claim about a deletion mutation, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "claim-provenance-q02", "text": "Who or what asserted this about a claim about a deletion mutation, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "claim-provenance-q03", "text": "What may an agent decide or do once a claim about a deletion mutation is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] }, { "id": "time-and-versions", "name": "Time, versions and supersession", "description": "When a claim was true, when it was learnt, and what replaced it.", "findings": [ { "id": "validity-and-supersession", "name": "Validity period and supersession", "description": "How an old claim about a deletion mutation is retired without being erased.", "questions": [ { "id": "validity-and-supersession-q01", "text": "What identifies and describes the validity of a claim about a deletion mutation, and in what units or vocabulary?", "kind": "definition", "answer_data": [ "identifiers", "types and classes", "values with units", "explicit unknowns" ] }, { "id": "validity-and-supersession-q02", "text": "Who or what asserted this about the validity of a claim about a deletion mutation, by which method, and when was it true?", "kind": "provenance", "answer_data": [ "authority", "method", "evidence", "event time", "knowledge time" ] }, { "id": "validity-and-supersession-q03", "text": "What may an agent decide or do once the validity of a claim about a deletion mutation is known, and what must it refuse?", "kind": "action", "answer_data": [ "permitted actions", "preconditions", "refusals", "escalation" ] } ] } ] } ] } ] }, "statistics": { "bundles": 6, "layers": 12, "findings": 14, "questions": 38 } } } }