Transcript 21 Single Gene Mutations I

Single Gene Mutations and
Inheritance I
April 3, 2008
Lisa Schimmenti, M.D.
Objectives
• Understand the basic types of single gene
mutations
• Understand how mutations lead to abnormal
protein expression
• Understand how a dominant mutation is
passed from parent to child (inherited)
• Know retinoblastoma genetics: dominant
inheritance, but recessive on the cellular
level.
Mutations are a change
in DNA sequence that
leads to a change in
protein expression
The genetic code
A codon is made of 3 base pairs
64 codons total
1 codon (AUG) encodes
methionine and starts
translation of all proteins
60 codons encode 20
amino acids
(redundant code)
A U G
G C A
Met
Ala
ASCO
3 codons stop
protein translation
U A A
Genetics Vocabulary
• Allele: refers to different forms of the
same gene
• Example:
– wildtype allele
– mutant allele
– null allele
More new words
• Phenotype: the physical appearance of
a trait
• Genotype: the allele associated with a
trait
Disease-Associated Mutations
A mutation is a change in the normal base pair
sequence that has been proven to associate with a
disease state
Commonly used to define DNA sequence
changes that alter protein function
ASCO
Disease-Associated
Mutations Alter Protein
Function
Functional protein
ASCO
Nonfunctional or
missing protein
Classes of Mutations
Type of mutations
• Missense: nucleotide change leads to
amino acid change
• Nonsense: change leads to stop codon
• Insertion: addition of nucleotides that
lead to frameshift
• Deletions: deletion of nucleotides
• Splice site: changes RNA splicing
• Expansion of repeat units
Nucleotide substitutions
can occur anywhere in the
genome
A
C
Transitions
G
Transversions
T
Pyr -> Pur
Pur -> Pyr
Pyr -> Pyr
Pur -> Pur
Missense mutation in coding
sequence
Normal sequence
Mutant Sequence
ATG CCG TTT
Met Pro Phe
ATG CTG TTT
Met Leu Phe
Nucleotide changes favor
certain spots
• CpG dinucleotide
– C frequently methylated
– Spontaneous deamidation to T
• 8.5 x more likely to change than any
other dinucleotide pair
Insertions/Deletions
• Insertions (1 bp or >1 bp)
• Deletions (1 bp or >1 bp)
≤ 3 bp change (coding)
• ins or del
– 3 bp - ins or del one AA (most common mutation in CF delF508)
– 2 bp ins or del - frame shift
– 1 bp ins or del - frame shift
• 1 bp substitution
– Silent - “wobble”
– Nonsense - AA to “stop”
– Missense
• Conservative - changes AA to same or similar AA
• Non-conservative - changes AA by function or charge
• May not change a basepair but may change the RNA splice recognition
site
Changes in > 3 bp
• Whole gene deletions or duplications
– Often due to repeated sequences and
mispairing in replications
• Portion of gene deleted or fragment
inserted
– Often due to aberrant splicing
What does it look like?
Normal
THE BIG RED DOG RAN OUT.
Missense
THE BIG RAD DOG RAN OUT.
Nonsense
THE BIG RED.
Frameshift (1 bp deletion)
Frameshift (1 bp insertion)
Frameshift (3bp deletion)
Triplet repeat expansion
Modifed from ASCO
THE BGR EDD OGR ANO….
THE BIG RED DOO GRA NOU
THE BIG DOG RAN OUT.
THE BIG BIG BIG BIG BIG RED DOG
RAN OUT.
Non-coding mutations that
affect gene function
• Promoter/enhancer element
Trinucleotide repeats in 5 and 3’UTRs
• Splice sites
Factors that influence how
mutations alter gene function
• Increase or decrease expression of gene
product
• Is one altered allele sufficient to cause
disease?
• Modifiers
• Proportion of cells affected
• Parent of origin
Effects of mutation on gene product
• Null allele (loss of function) - no gene product
• Hypomorph - decreased amt/activity
• Gain of function - increased amt/activity
• Dominant negative - antagonizes normal product
• Neomorph - novel activity of product
Predicting that a gene product
won’t do the job
• Deletion, nonsense, frameshift of
sequence is deleterious
• Mutation in splice site usually bad
• Missense mutations
– Depends on location in protein
– Is it non-conservative?
• Is the AA conserved in evolution?
Which ones will cause
disease?
• All but silent or conservative missense
sequence changes are likely to
significantly alter product function
• Among frameshifts, location of mutation
alters likelihood of severity
• Mutations in coding sequence are
identified most frequently…but this may
change
You only see the ones that
hurt...
• Sequence changes or variants can be
– Silent (no change in product): Polymorphism
• We have thousands of these
– Manifesting (changing RNA or protein product):
Mutation
We all carry 7-10 gene mutations
AHHHH!
Polymorphism
• A change in DNA sequence that is not
disease causing
• Occurs usually in greater than 1% of
population
• Usually does not change an amino acid
sequence or produces a significant change
(ie: valine for isoleucine)
Autosomal Dominant
Autosomal Dominant
Inheritance
• males and females equally affected
• 1 in 2 chance of affected offspring
from an affected parent
• male to male transmission
• structural genes, transcription
factors
• only one abnormal copy of the
gene (allele) to have the phenotype
Mechanisms yielding
dominant alleles
• Haploinsufficiency: if one copy isn’t
enough for function
• Dominant negative: when a mutant
product dimerizes or oligomerizes
• Gain of Function: FGFR mutations
causing activation of the receptor
without a ligand present
Autosomal Dominant
probabilities
Mother
D
d
d
Dd
Dd
d
dd
Daughters
50% normal
50% affected
dd
Sons
50% normal
50% affected
Variations in the AD “rules”
• Co-dominant expression
• New mutation
• Homozygosity for an AD trait
– May be a more severe phenotype
•
•
•
•
Variable expression
Penetrance
Sex limited
Variation in age of onset
Variations:
Co-dominant expression
Definition: alleles that are both
expressed when they occur in the
heterozygous state.
Example: ABO blood group antigens
ABO Blood Groups
Defined by the presence or absence of
two antigens on the surface of the red
cell
A and B
•
•
•
•
•
if you have A, you have anti-B antibodies
if you have B you have anti-A antibodies
if you have neither (O) you have both anti- A and -B
Absence of A or B = O
Three allele states: Ia Ib Inull
ABO blood typing:
co-dominant alleles
A/-
-/-
B/-
A/-
AB
AB
A/-
B/-
BB
B/-
BB
BB
Variations: New Mutations
• Occur at a rate of 10-4 to 10-7 per locus
per cell division
• “Hot spots” occur: CG pairs (8.5 x
higher rate)
• More easily seen in a very large gene
• Paternal age effects
Autosomal dominant:
new mutation
dd
dd
dd
dd
dd
dd
Dd
dd
dd
dd
dd
dd
Achondroplasia
•
•
•
•
•
Autosomal dominant
100% penetrance
1/26000: most common genetic dwarfism
80% new mutations
Features
– rhizomelic dwarfism (upper arms and thighs are
short)
– lumbar lordosis (lower spine curves out)
– large head
– small foramen magnum
– intact intellect
– Mutation in FGFR3: activating mutation
Fibroblast Growth Factor
Receptors
• Receptor tyrosine kinases
• Four distinct genes: 1 through 4
• Critical in coordination of proportionate
•
bone growth and development
Signaling regulates cellular processes
Achondroplasia and FGFR
• Mutations in FGFR3 cause
achondroplasia
• Despite frequent new mutations almost
all are caused by the same mutation
(G -> A at nt 1138, causes gly 380 arg)
Effects of homozygosity
dd
dd
dd
Dd
dd
DD
dd
dd
Dd
dd
Dd
Homozygosity for some
dominant traits is lethal
http://www.echt.chm.msu.edu/courseware/blockII/Pathology/382131.jpeg
Homozygosity for
achondroplasia causes very
severe phenotype
AD and variable expression
• Pleiotropy: one gene, many effects
•
•
on different systems
Random chance
Modifier genes
Marfan Syndrome: variable
expression
• Skeletal findings-
•
•
•
disproportionate
long bone growth
Tall Stature
Eyes- dislocated
lenses
Heart-dilation of
aortic arch
http://medgen.genetics.utah.edu
/
AD traits are often variable
in expression
Dd
dd
dd
dd
Tall
Dislocated lenses
Dilated Ao
dd
Dd
dd
Dd
dd
Tall
Dilated Ao
Dislocated lenses
Dilated Ao
Normal
dd
Dd
Dd
Variations:
reduced penetrance
• An individual may carry an altered
•
allele and never manifest
phenotypic evidence of this.
Penetrance: an “all or nothing”
phenomenon in expression of a
trait in a population
–phenotype, NOT genotype
Tumor Suppressor Genes
Clinical Effects of Mutations
• Cancers due to mutations are early in onset
• Cancers due to mutations are often bilateral
• Phenotype is inherited as a dominant trait BUT at the
•
•
cellular level these are manifest as recessive: two
abnormal alleles are required for manifestation
Genotype is that of one germline abnormal allele:
malignancy occurs with environmental damage of
second normal allele (Knudsen two hit hypothesis)
Penetrance reduced: no 2nd hit, no malignancy
occurs
Variation: reduced
penetrance
dd
Dd
dd
Dd
dd
dd
dd
dd
dd
dd
Dd
Familial Retinoblastoma: a
recessive state in the cell
inherited as AD trait
http://www.people.virginia.edu/~rjh9u/retblst.html
http://www.retinoblastoma.com/Images/CT%20Scan.jpg
Familial Retinoblastoma
Case history:
6 month old child found to have leucocoria (white pupil) On exam
there is a large mass in the eye. The other eye has a small
lesion
Father gives the history that his mother had only one eye because
the other was removed when she was a baby. He and his 2 sibs
were healthy and have both eyes
Explanation:
REDUCED PENETRANCE of this trait
Autosomal Dominant: sex
limited trait
Dd
Dd
dd
dd
Dd
dd
Dd
dd
Dd
dd
dd
dd
dd
dd
A sex-limited AD trait
• Familial male precocious puberty
• Pubertal onset in males by age 4.
• Due to gain of function mutation
that keeps the leutinizing hormone
(LH) receptor in an “on” state
Autosomal Dominant:
variation in age of
onset
Dd
Dd
dd
dd
dd
dd
Dd
Dd
Dd
dd
Dd
dd
dd
dd
dd
dd
Variation:
Altered age of onset
•
Huntington’s Chorea
– Progressive dementia
– Choreiform movements
•
•
•
Autosomal Dominant pattern
Age of onset usually after 30
Triplet repeat expansion in the Huntington
gene that can expand
What to expect for the next
lecture:
• Recessive inheritance
• X-linked inheritance
– Dominant
– Recessive
•Population genetics for docs
Example Question
• Find the one true statement about dominant
inheritance :
– A. Male are more commonly affected than
females.
– B. Two copies of the gene carry mutations to have
the phenotype
– C. Only gain of function mutations are dominant.
– D. Haploinsufficiency mutations can only cause
dominant disorders.
– E. Mutations can be passed from fathers to sons.