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Research draft

mutation

vr.tr.mutation · ACT.PRC

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

Research draft, second pass

A second pass drafted this model: the structure a model of this thing needs, and what is known about it in the world. The line under this one says how the second half was obtained - researched against sources, or recalled without web access, in which case nothing here was read anywhere and every claim is a lead to verify. Unreviewed either way.

written by Claude from model knowledge without web access - no source was read, every claim is a lead to verify

Researched by: Claude

Purpose and description

Let an agent handle mutations by type, location, effect and evidence, with standard nomenclature, and avoid giving individual genetic advice.

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.

What it is for: Mutations drive evolution and cause or influence many diseases; they are studied in genetics and medicine.

It can be detect it, by sequencing; name it, with HGVS nomenclature; interpret its effect, with evidence; study its evolutionary role.

Distinguishing features

Change in DNA sequence

Germline or somatic

Effects range from none to severe

Interpretation requires evidence and expert review

What it looks like

Not visible directly; seen as differences in sequence data or as traits.

How it is recognised

Variant notation such as c.1521_1523del

Sequence alignments showing differences

Classifications such as pathogenic or benign

Related models

changes - molecules

DNA and protein

drives - variation

evolution

can cause - genetic disease

disease

is a kind of - variation

sequence variant

In practice

Families and kinds

point mutations

insertions and deletions (indels)

copy number variants

structural rearrangements

gain-of-function and loss-of-function mutations

Identifiers

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

Standards and regulation

HGVS nomenclature

ACMG/AMP variant classification guidelines

Genetic data protection law

Failure modes and hazards

Over-interpreting variants of uncertain significance

Individual genetic advice without a genetic counsellor

Genetic discrimination

Also called

conserved signature indelsgain of functionrandom mutationDNA mutationSoft selective sweepspontaneous mutationbeneficial mutationharmful mutationgene lossdeleterious mutationfounder mutationTransversionparthenocarpypoint mutationframeshift mutationcopy-number variationsingle gene mutationindelloss of function mutationinsertion mutationdriver mutationparamutationRevertantsomatic mutationtruncating mutationde novo mutationchromosomal rearrangementInduced mutationneutral mutationadaptive mutationgermline mutationallelic imbalancetrinucleotide repeat expansionsequence inversionsequence deletionbase pair mismatchgenetic suppressionpetite mutationgene duplicationSynonymous substitution

+98

Where this came from

wikidata · CC0 1.0

Source repository Registry entry point

Drafted structure

Bundle to layer to finding to question, as the second pass will find it: 4 bundles · 8 layers · 8 findings · 16 questions.

Description What changed.

Standard notation avoids ambiguity.

Notation

HGVS.

Notation

Variant notation.

  1. What is the HGVS description, on which reference sequence? provenance
  2. Which gene is affected? definition

Type

Substitution, indel.

Type

Variant type.

  1. What type of mutation is it? definition
  2. Is it germline or somatic? definition
Effect What it does.

Effect needs evidence.

Molecular effect

On protein.

Molecular effect

Effect on product.

  1. What does it do to the gene product? definition
  2. How is that known? provenance

Clinical significance

Classification.

Classification

Clinical classification.

  1. How is it classified, by which lab or database? provenance
  2. Has the classification changed? provenance
Origin How it arose.

Origin informs inheritance.

Cause

Spontaneous or induced.

Cause

Cause.

  1. How did it arise? definition
  2. Is it inherited? boundary

Frequency

Population.

Frequency

Population frequency.

  1. How common is it in populations, according to gnomAD or similar? measurement
  2. Which populations? boundary
Handling Advice and privacy.

Genetic information is sensitive.

Counselling

Professional advice.

Referral

When to refer.

  1. Should the person be referred to genetic counselling? action
  2. What can the agent say in general terms? boundary

Privacy

Genetic data.

Privacy

Genetic data rules.

  1. Is genetic data being shared lawfully? boundary
  2. Who else might be affected, such as relatives? boundary

What the second pass must settle

  • 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?
Draft as JSON