What is an allele?
An allele is a specific version of a gene that differs in DNA sequence
- Every gene can exist in multiple allele forms
- Alleles differ because of mutations (DNA sequence changes)
- Each individual inherits 1 allele from mother and 1 allele from father
What causes different alleles to exist?
Different alleles arise due to DNA sequence mutations such as:
Single nucleotide substitutions
Insertions, Deletions
Translocations
Inversions
Mutations create new alleles (not all alleles are functional)
What is the WT allele
WT allele = historically defined ‘normal’ allele
- WT is arbitrary and defined by convention
- WT = functional allele
- WT produces normal gene product (protein, mRNA, regulatory RNA)
What is a mutant allele
Mutant allele = allele whose DNA sequence differs from wild type
- Can be functional, nonfunctional, GOF, LOF, or neutral
Mutation does not always mean harmful
Why is allele classification important?
Allele classification helps determine
- How mutations affect gene function
- Whether mutations are dominant or recessive
- How mutations cause disease
- How inheritance patterns work
- How protein function is altered
What are the three major allele classification systems
Alleles can be classified based on
- Transmission (inheritance pattern)
- Dominant vs Recessive
- Haplosufficient vs haploinsufficient - Molecular consequence (DNA/Protein level)
- Silent, missense, nonsense, frameshift - Functional Consequence
- LOF, GOF, Dominant Negative, Mis-Expression
What is dominance?
Dominance describes which allele determines phenotype in heterozygote
- WT/Mutant (Phenotype depends on a dominance relationship)
How do you determine dominance?
Look at the heterozygote phenotype
- Wt/Mutant heterozygote - If phenotype looks like WT - WT is dominant, if heterozygote looks intermediate - incomplete dominance
What is Haplosufficiency
Haplosufficient = One copy of WT allele is sufficient to produce normal phenotype
Equivalent to complete dominance
What is Haploinsufficiency
Haploinsufficient = one copy of WT allele is NOT sufficient to produce normal phenotype
WT/Mutant = abnormal phenotype
Incomplete dominance
Why is haplosufficiency a property of the WT allele and NOT the mutant allele?
Because haplosufficiency depends on whether ONE functional allele (WT, not mutant) produces enough protein
- Haploinsufficiency is about whether the WT allele can produce enough functional protein
Example of Haploinsufficiency (PAX6 Gene)
WT/WT - Normal Eyes
WT/Mutant - aniridia (missing iris)
Mutant/Mutant - no eyes, death
One WT copy is insufficient - therefore haploinsufficient gene
How can you distinguish haploinsufficiency from dominant negative mutation
Add extra WT allele and if the phenotype becomes normal, then haploinsufficiency. If the phenotype remains abnormal, the dominant negative mutation
Dominant negative interferes with WT function
What is a synonymous (silent) mutation
DNA mutation that does not change the amino acid
Ex. AAA - AAG but both codons code for lysine, so the protein sequence is unchanged
Why can silent mutations still affect function?
They can affect mRNA stability, translation efficiency, splicing, protein folding efficiency
Silent does not always mean harmless
What is a missense mutation?
Mutation that changes one amino acid
AAA - ACA Which is Lysine to Threonine
- Can be harmless, mild effect, severe effect
What is a nonsense mutation?
Mutation that introduces premature stop codon
AAA - UAA (Lysine to stop codon)
- Results in a truncated protein which usually ends in sever loss of function
What is a frameshift mutation?
Insertion or deletion not divisible by 3 which shifts the reading frame
- Results in completely different amino acid sequence and a nonfunctional protein.
- Very severe mutation
What happens if insertion/deletion is multiple of 3
Adds or removes amino acids but preserves reading frame
- Protein may still function (less severe than frameshift)
How do chromosomal mutations affect alleles?
Translocations and Inversions can cause gene disruption, gene fusion, mis-expression
Major functional consequences
What is a LOF allele?
Mutation that reduces or eliminates protein function
Ex.
Null - No function
Hypomorphic - Partial Function
What is a null allele?
does not produce a functional protein - Complete loss of function
Causes of null alleles:
- Nonsense mutation (premature stop codon)
- Frameshift mutation
- Deletion
What is a hypomorphic allele
Partial loss of function allele
- Produces reduced protein function
- Not completely inactive
What is a conditional allele
Allele that functions normally only under certain conditions
- Ex. Temperature sensitive mutations (Functional at one temp, nonfunctional at another)
