Published
mutation
vr.tr.mutation · thing-q42918
Let an agent handle mutations by type, location, effect and evidence, with standard nomenclature, and avoid giving individual genetic advice.
Thing Registry Activities and processes ACT.PRC
Bundle → Layer → Finding → QuestionsClassifiersWhat it isWhy it existsDistinguishing featuresWhat robots and AI may and may not doMoral aspectsOwnersLinks to other meta-modelsIdentity and identifiersDirect propertiesRecognitionCapabilities and actionsHazards and failure modesStandards and interfacesContext of useSources
Bundle → Layer → Finding → Questions Filled
4 bundles · 8 layers · 8 findings · 16 questions
Description What changed.
Notation
HGVS.
Notation
Variant notation.
- What is the HGVS description, on which reference sequence? provenance
- Which gene is affected? definition
Type
Substitution, indel.
Type
Variant type.
- What type of mutation is it? definition
- Is it germline or somatic? definition
Effect What it does.
Molecular effect
On protein.
Molecular effect
Effect on product.
- What does it do to the gene product? definition
- How is that known? provenance
Clinical significance
Classification.
Classification
Clinical classification.
- How is it classified, by which lab or database? provenance
- Has the classification changed? provenance
Origin How it arose.
Cause
Spontaneous or induced.
Cause
Cause.
- How did it arise? definition
- Is it inherited? boundary
Frequency
Population.
Frequency
Population frequency.
- How common is it in populations, according to gnomAD or similar? measurement
- Which populations? boundary
Handling Advice and privacy.
Counselling
Professional advice.
Referral
When to refer.
- Should the person be referred to genetic counselling? action
- What can the agent say in general terms? boundary
Privacy
Genetic data.
Privacy
Genetic data rules.
- Is genetic data being shared lawfully? boundary
- Who else might be affected, such as relatives? boundary
Classifiers Filled
- Family
- Thing Registry
- Category
- Activities and processes
- Entry kind
- thing
- Plane
- ACT
- Domain
- ACT.PRC
- Other names and narrower kinds
- 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
What it is Filled
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.
Why it exists Filled
Let an agent handle mutations by type, location, effect and evidence, with standard nomenclature, and avoid giving individual genetic advice.
Distinguishing features Filled
- Change in DNA sequence
- Germline or somatic
- Effects range from none to severe
- Interpretation requires evidence and expert review
What robots and AI may and may not do Filled
Must not
- 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.
Only with a human decision
- Telling a person about a significant genetic finding.
May
- Explain mutations in general terms with cited science.
- Report variant data from curated databases, stating clinical significance as classified.
Moral aspects Filled
- Genetic data reveals information about relatives too.
- Genetics has been misused to justify discrimination.
Who is affected
- Patients
- Relatives
- Research participants
Owners Filled
Steward
Nobody owns a mutation; genetic data belongs to the person it describes.
Master systems
- Genetic variant databases
Links to other meta-models Filled
parent
- Q102116514 - registry parent class
- Q115865817 - registry parent class
- Q15304597 - registry parent class
- Q2996394 - registry parent class
related
- DNA and protein - molecules
- evolution - variation
- disease - genetic disease
- sequence variant - variation
What else AI and robots need to interact with it Filled
Identity and identifiers required Filled
- 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
Direct properties not applicable Not applicable
Not applicable
Plane ACT: no invented physical properties.
Recognition optional Filled
- 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 and actions required Filled
- detect it, by sequencing
- name it, with HGVS nomenclature
- interpret its effect, with evidence
- study its evolutionary role
Hazards and failure modes required Filled
- Over-interpreting variants of uncertain significance
- Individual genetic advice without a genetic counsellor
- Genetic discrimination
Standards and interfaces required Filled
- HGVS nomenclature
- ACMG/AMP variant classification guidelines
- Genetic data protection law
Context of use required Filled
- 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 Filled
- Wikidata item Q42918: mutation - identity and sense of the item
- Wikipedia: Mutation - general description of the item
Open questions
- 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?
Machine files
Provenance
thing registry research (pass 2) · unreviewed
Built from: models/things/publications/thing-q42918/spec.json