PGx Lecture 3

Question 1

What is an allele

Answer 1

variant/wild type form of a gene at a particular location on a chromosome

Question 2

genotype

Answer 2

combination of alleles; genetic information responsible for a trait.
NOT observable

Question 3

phenotype

Answer 3

physical features that are determined by the genotype and environment. OBSERVABLE

Question 4

Allele nomenclature

VKORC1 1173 T

Answer 4

VKORC1 = gene
1173 = location of nucleotide on the gene
T = nucleotide

Question 5

SNP nomenclature

VKORC1 1173 C > T OR VKORC1 C1173T

Answer 5

VKORC1 = gene
1173 = nucleotide on the gene
C/First letter = original/wild type nucleotide
T/Second letter = nucleotide that has changed

Question 6

*1

Answer 6

Wild type - Always

Question 7

*# designates what

Answer 7

allele (star and number after the gene)

Question 8

CYP2C19

• 1 allele
• 2 allele
• 3 allele

Answer 8

• 1 = wild type activity
• 2 = no enzyme activity
• 3 = no enzyme activity

Question 9

CYP2C9

• 1 allele
• 2 allele
• 3 allele

Answer 9

• 1 = wild type activity
• 2 = decreased enzyme activity
• 3 = decreased enzyme activity

Question 10

Gene nomenclature is in italics (T/F)

Answer 10

True

Question 11

Designations for CYP2C9*3

Answer 11

2 = family
C = subfamily
9 = specific isoform
* = designation for allele
3 = allele number

Question 12

rs naming system used in

Answer 12

SNP database (dbSNP)

Question 13

Genotype nomenclature

Answer 13

allele of interest *2 for CYP2C19

Genotype: CYP2C19 2/2

Question 14

The protein name is italicized (T/F)

Answer 14

False - protein is not italicized

Question 15

CYP2D6 *1

Answer 15

wild-type
Normal
Activity score: 1

Question 16

CYP2D6 *1XN

Answer 16

Gene dupli/ampli
Increased
Activity score: >/= 2

Question 17

CYP2D6 *2

Answer 17

R296C
S486T
SNP
Normal
Activity score: 1

Question 18

CYP2D6 *2XN

Answer 18

Gene dupli/ampli
Increased
Activity score: >/= 2

Question 19

CYP2D6 *3

Answer 19

Frameshift
Non-functional
Activity score: 0

Question 20

CYP2D6 *4

Answer 20

Defective splicing (1846G > A) that results in a truncated nonfunctional protein
Non-functional
Activity score: 0

Question 21

CYP2D6 *5

Answer 21

gene deletion
Non-functional
Activity score: 0

Question 22

CYP2D6 *6

Answer 22

Frameshift
Non-functional
Activity score: 0

Question 23

CYP2D6 *10

Answer 23

P34S
S486T
SNP
Decreased
Activity score: 0.5

Question 24

Exercise:

TPMT*3C is 719A > G or Tyr240Cys

Answer 24

What does TMPT mean: Gene
719: position of nucleotide
240: position of amino acid
Wild type: A or Tyr
Mutation: G or Tyr
SNP mutation: missense b/c amino acid has changed
*3: frameshift/nonfunctional
A > G alphabetic nomenclature

Question 25

Exercise: The allele of CYP2C19*3 is a mutation of 636G > A, which introduces a premature stop codon

Answer 25

What type of mutation is this: nonsense
Allele or genotype: Allele
Is it a SNP? Yes b/c substitution of one nucleotide for another

Question 26

Exercise: The genetic tests show that a person carries TPMT1/3A

Answer 26

Is TPMT1/3A genotype or phenotype, or allele? Genotype
Is the person homozygous or heterozygous for the locus? Heterozygous
TMPT1/3A is based on what nomenclature?
Numeric or alphabetic