Overview
This lecture covers what causes genetic disease at the DNA level: normal genetic variation versus pathogenic mutation, the classes of mutation from whole-chromosome down to single-base changes, how a mutation’s effect depends on its type and location, and the distinction between somatic and germline mutations for inheritance.
Normal variation vs disease-causing change
- Health/disease risk is influenced by lifestyle (53%), environment (21%), genetics/body makeup (16%) and medical care (10%).
- Two unrelated humans are 99.5% identical at the DNA level; the 0.5% difference underlies normal variation in anatomy, physiology, dietary intolerances, infection susceptibility, drug responses, and to some degree personality, artistic talent and athletic aptitude.
- Essentially every base pair is expected to vary in someone, somewhere, but highly conserved genes (or critical regions such as an enzyme’s active site) show much less variation.
- This normal variation, together with environment and lifestyle, subtly alters disease susceptibility rather than directly causing serious illness.
Polymorphisms vs mutations
- Polymorphisms are common sequence variants in the population, arising through the same mechanisms as mutations.
- A DNA change that deviates from the normal common variants is called a mutation. Mutations can be:
- Neutral: no effect on the functional gene product.
- Advantageous (rare): a new or improved function.
- Disadvantageous (pathogenic): a deleterious effect on the gene product; the cause of genetic disease.
- Mutation rates vary widely by locus, e.g. achondroplasia (FGFR3) 1.4x10^-5, Duchenne muscular dystrophy (DMD) 3.5-10.5x10^-5, and haemophilia B (F9) 2-3x10^-6 mutations per locus per generation [slide does not elaborate further on why rates differ between genes].
What determines a mutation’s effect
A mutation’s effect on its gene product depends on:
- Type of mutation.
- Location within the gene.
- Location within the 3D protein structure (or ncRNA sequence) — e.g. where a change falls within haemoglobin’s four-chain quaternary structure (two alpha, two beta chains, each folded around a heme-Fe2+ group) determines its consequence.
Types of mutation by scale
- Chromosomal: whole chromosomes gained or lost, from missegregation during meiosis. Severe gene-dosage consequences, so usually leads to early natural abortion; the most common non-viable class of human mutation.
- Subchromosomal: a chunk of one or more chromosomes changes. Also severe gene-dosage consequences and early natural abortion. Subtypes:
- Deletion: a segment is lost.
- Duplication: a segment is copied, appearing twice.
- Inversion: a segment reverses orientation in place.
- Insertion: a segment from elsewhere is inserted.
- Translocation: segments are exchanged between two different chromosomes.
- DNA-level: smaller sequence alterations, caused by replication errors or unrepaired DNA damage from mutagens. These are the most common class of viable human mutation.
DNA-level mutation types
- Single nucleotide substitutions (point mutations): only the base changes, not the sugar-phosphate backbone. Outcomes:
- Silent (synonymous): base changes, amino acid sequence unchanged.
- Missense (non-synonymous): one amino acid changes (e.g. Pro to Ser).
- Nonsense: creates a premature stop codon, producing a truncated protein.
- Frameshift (e.g. 1bp deletion): shifts every downstream codon.
- Small insertions or deletions (indels): if the number of bases inserted/deleted is not a multiple of 3, the reading frame shifts from that point onward, changing the amino acid sequence downstream and often producing a premature stop codon (because the new frame introduces a stop codon by chance).
- (Frameshift, covered above as a consequence of indels not in multiples of 3.)
- Dynamic mutations: expansion of a polymorphic DNA repeat (usually 2-4 nucleotides repeated) beyond a copy-number threshold. Leads to abnormal gene products, abnormal regulation of gene expression, or frameshift.
- Example: Huntington’s disease. The HD gene (short arm of chromosome 4) normally has fewer than 36 CAG repeats, each coding for glutamine, producing normal cytoplasmic huntingtin (Htt). More than 36 CAG repeats produces abnormal huntingtin (mHtt) with an expanded glutamine chain, causing Huntington’s disease.
Relative frequency of mutation types in human disease
Nucleotide substitutions: missense 50%, nonsense 10%, RNA-processing mutations (destroying or creating splice/cap/polyadenylation sites) 10%, splice-site mutations causing frameshift and premature stop codons 10%, long-range regulatory mutations rare.
Insertions/deletions: small indels 25%, larger deletions/inversions/fusions/duplications (sometimes mediated by DNA sequence homology) 5%, insertion of a transposon (LINE or Alu element) disrupting transcription or coding sequence rare, dynamic (trinucleotide/tetranucleotide repeat) mutations rare.
Somatic vs germline inheritance
- Somatic mutations: occur in somatic cells during an individual’s life (including the embryo stage). Only cells derived from the originally-mutated cell carry the mutation. Cannot be inherited by offspring.
- Germline mutations: occur in gametes (sperm or oocyte). Every cell in the resulting body carries the mutation, and it is heritable, passed to offspring (in whom, again, all cells are affected).
- The severity of a somatic mutation is most likely influenced by when in development it occurred.
Self-test
- What proportion of the human genome differs between two unrelated individuals, and what categories of variation does this 0.5% underlie?
- Distinguish neutral, advantageous and disadvantageous (pathogenic) mutations.
- List the three factors that determine the effect of a mutation on its gene product.
- Distinguish chromosomal, subchromosomal and DNA-level mutations, including why the first two typically end in early natural abortion.
- List the five types of subchromosomal mutation with a one-line description of each.
- Distinguish silent, missense, nonsense and frameshift single-nucleotide substitutions.
- Explain why an indel only causes a frameshift when the number of bases is not a multiple of three.
- Describe the mechanism of a dynamic mutation and how it causes Huntington’s disease.
- Distinguish somatic from germline mutations in terms of which cells carry them and whether they are heritable.
- A mutation arises in a single skin cell of an adult. Explain whether it can be passed to that person’s children, and why.
Answers
Reveal answers
- 99.5% of DNA sequence is identical between two unrelated individuals; the differing 0.5% underlies variation in anatomy, physiology, dietary intolerances, susceptibility to infections, responses/adverse reactions to medicines, and to some degree personality traits, artistic talent and athletic aptitude.
- Neutral mutations have no effect on the functional gene product; advantageous mutations (rare) confer a new or improved function; disadvantageous (pathogenic) mutations have a deleterious effect on the gene product and cause genetic disease.
- The type of mutation, its location within the gene, and its location within the 3D protein structure (or ncRNA sequence).
- Chromosomal mutations involve a change in the number of whole chromosomes (from meiotic missegregation); subchromosomal mutations involve a change to a chunk of one or more chromosomes (rearrangements or larger indels); both carry severe gene-dosage consequences and so usually cause early natural abortion. DNA-level mutations are smaller sequence alterations from replication errors or unrepaired mutagen damage, and are the most common viable class of human mutation.
- Deletion (a segment is lost); duplication (a segment is copied and appears twice); inversion (a segment reverses orientation in place); insertion (a segment from elsewhere is inserted); translocation (segments are exchanged between two different chromosomes).
- Silent: the base changes but the amino acid sequence is unchanged. Missense: one amino acid changes. Nonsense: a premature stop codon is created, truncating the protein. Frameshift: an indel shifts the reading frame, altering all downstream codons.
- Each codon is 3 bases, so removing or adding bases in a multiple of 3 preserves the reading frame downstream (though it changes the number of amino acids); removing or adding a number of bases not divisible by 3 shifts every subsequent codon out of frame, changing the amino acid sequence from that point on and often creating a premature stop codon.
- A dynamic mutation is the expansion of a polymorphic repeat (usually 2-4 nucleotides) beyond a copy-number threshold. In Huntington’s disease, the HD gene normally has fewer than 36 CAG (glutamine-coding) repeats, producing normal huntingtin; expansion beyond 36 repeats produces abnormal huntingtin with an expanded glutamine chain, causing the disease.
- Somatic mutations occur in somatic cells during life (including embryonic stage); only their cellular descendants carry the mutation, and it cannot be inherited. Germline mutations occur in gametes; every cell of the resulting body carries the mutation, and it is heritable to offspring.
- It cannot be passed to their children, because it is a somatic mutation: it occurred in a somatic (skin) cell, not in a gamete, so only cells derived from that cell carry it and it is not transmitted through the germline.