Contribution of Genetic Changes to Human Disease

Question 1

Definition of DNA variation/variant

Answer 1

Specific loci within the genome at which 2+ alleles may be present

Question 2

Definition of polymorphism

Answer 2

Common DNA variant

Question 3

Definition of mutation

Answer 3

Pathogenic DNA variant

Question 4

Definition of lariat acceptor

Answer 4

Part of premRNA/hnRNA that is involved in transcriptome folding

Question 5

Definition of polypyramidine tract

Answer 5

Region of premRNA/hnRNA that promotes spliceosome assembly

Question 6

Definition of cryptic splice sites

Answer 6

mRNA sequence that has the potential for interacting with the spliceosome

Question 7

Describe the relationship between the frequency of a mutation in the population and the recency of the mutation

Answer 7

Selection dictates what variation remains in the gene pool

Old mutation events not subject to negative selection is likely to be common in the population

Recent mutation events may be unique to ourselves/somatic

Question 8

What is a single nucleotide substitution

Answer 8

1 base in substituted for another

Question 9

What are the 2 types of single nucleotide substitution
Describe them
What is the frequency of each type of single nucleotide substitution?

Answer 9

Transition

• substitution that conserves base chemistry (pyramidines swap with other pyramidines, purines swap with other purines)
• more common

Transversion
-substitution that changes base chemistry

Question 10

What is a deletion

Answer 10

1+ loss of bases

Question 11

What is a insertion

-what are the 2 types

Answer 11

1+ gain of bases between 2 previously adjacent bases
Normally material has been duplicated from previous material

Tandem duplication
-inserted material is the same as the adjacent sequence

Repeat expansion
-inserted material only repeats the last few bases

Question 12

What is an inversion

Answer 12

Inverted sequence is replaced with reverse compliment

Question 13

What is translocation

Answer 13

DNA exchanged between chromosomes

Question 14

What are the effects of DNA mutations

• how many bases could be involved in a mutation
• what are the effects on genes

Answer 14

Deletions, insertions, tandem duplications, inversions range from 1-1mn bases

Rearrangements are often imperfect so sequences at the ends of the blocks may also be disrupted

Inversions and translocations may be benign if breakpoints do not disrupt genes

Question 15

What is functional variation

Answer 15

Not all variation will have a functional/phenotypic consequences

Functional consequence defined by its effect on the functional region of the genome

Almost all reported disease causing variants directly affect functional parts of genes

Question 16

What are the 3 effects of variants in coding regions

Answer 16

Silent

• will not affect protein directly
• may affect splicing

Missense

• single AA change
• effect may be neutral/harmful

Nonsense

• premature termination of the reading frame
• effect => truncated protein/NMD

Question 17

What are the functions of

• lariat acceptor
• polypyramidine tract (bases associated with region?)
• splice acceptor (bases associated with region?)
• splice donor (bases associated with region?)

Answer 17

Lariat acceptor
-involved in transcriptome folding

Polypyramidine tract

• CT rich
• promotes spliceosome assembly

Splice acceptor

• AG rich
• flank exon

Splice donor

• GT rich
• flank exon

Question 18

What are the effects of variants in the splice sites

What does the severity of the mutation depend on

Answer 18

Variants in splice recognition elements => disrupts splicing process
Result depends on
-relative strengths of elements
-severity of change
-proximity of alternatives

Consequences

• exon skipping
• use of cryptic splice sites in exon or intron
• small intron retention
• combination of all the above

Question 19

What is the effect of large genetic rearrangements

Answer 19

Whole exons in a gene can be affected

Critical determinant of effect is whether the reading frame is affected

Question 20

What is the effect of variants in promotor regions

Answer 20

Rare as promotors relatively insensitive to variation

• result in tissue specific phenotypes
• result in developmental stage specific phenotypes

Question 21

What is the effect of variants in UTRs

Answer 21

Some UTRs are more highly conserved than coding regions or promoters

Functions poorly understood
Very few confirmed pathogenic variants

Question 22

What is the effect of variation in polyadenylation

Answer 22

Few characterised variant => reduced transcript levels

Question 23

What are the 2 morphs that lead to loss of function

Answer 23

Amorph
-complete loss of gene function

Hypomorph
-partial loss of gene function

Question 24

What are the 3 morphs that lead to gain of function

Answer 24

Hypermorph
-increase in gene function

Antimorph
-dominant alleles act in opposition to normal gene function

Neomorph
-new gene function

Question 25

What are the effects when the protein loses its function due to variation (recessive)
-3 outcomes

What can prevent loss of function?

Answer 25

Little/no protein produced

Protein is unstable/inappropriately targeted and is degraded

Residue essential for function is missing/critically altered

Presence of a 2nd normal allele can rescue phenotypes => normal heterozygotes
Therefore, loss of function variation is normally recessive

Question 26

What are the effects when the protein loses its function (dominant)
-3 outcomes

Answer 26

Haploinsufficiency
-50% reduction in quantity => loss in protein function

Dominant negatives

• homomultimeric proteins that form => gain in function
• also disrupts normal functioning counterpart

Somatic second hit

• organism can function with 1 mutated gene but a somatic 2nd mutation => rare clones of null cells that don’t function
• recessive at cellular level but dominantly inherited

Question 27

What are the effects when the protein gains functions (dominant)
-2 outcomes

Answer 27

Loss of regulation

• activity of protein loses spatial/temporal specificity
• due to loss of regulatory region/mislocalisation

Novel function

• new function is not typical
• formation of insoluble aggregates