nomenclature

Question 1

In a coding DNA reference sequence nucleotide “1” is what

Answer 1

A of the ATG start codon

Question 2

do we number the intron

Answer 2

no

Question 3

how can we check that our nt and aa numbering is correct

Answer 3

if the nt number is not the correct multiple of 3 of the amino acid number then it must be wrong

Question 4

what do we put predictions in

Answer 4

curved brackets

Question 5

how do we denote a stop codon

Answer 5

*

Question 6

what does the nomenclature c.145C>T p(Arg49*) mean

Answer 6

substitution at position nt145 C for T
causes Arg to become stop codon
nonsense mutation

Question 7

what does the nomenclature c.135T>A p.(Phe45Leu) mean

Answer 7

substitution at nt135 T for A
causes Phe to become Leu
missense mutation

Question 8

what does the nomenclature c.51-1G>A p.(?) mean

Answer 8

substitution G for A in intron one nucleotide back from nt 51
cannot predict outcome could destroy splice site - cant be sure

Question 9

what does the nomenclature c.104_105delTG p.(Cys34Tyrfs*12) mean

Answer 9

deletion of TG at nt104 and nt105
disrupts ORF
get stop codon 12aa from and including Tyr
frame shift

Question 10

what does the nomenclature c.104insA mean

Answer 10

insertion of A at nt 104

Question 11

what does nomeclature c.104dupT mean

Answer 11

duplication of T at nt104

Question 12

what does the nomenclature c.51-?_141+?(del exon 2) mean

Answer 12

deletion of exon 2 but you dont know where the breakpoint is

Question 13

what does c.133_135delTTT p.(Phe45del) mean

Answer 13

deletion of whole amino acid Phe

Question 14

what do square brackets give

Answer 14

genotype

Question 15

how do you denote mutations in 2 different alleles (in trans)

Answer 15

place ; between 2 sets of square brackets

eg p.[(Phe45Leu)];[(Arg49*)]

Question 16

how do you denote mutations on the same allele (in cis)

Answer 16

put ; within one set of square brackets

eg, [(Phe45Leu);(Arg49*)]

Question 17

how do you denote the genotype when you dont know whether 2 mutations have occured in cis or in trans

Answer 17

use one set of square brackets and put ; in curved brackets

eg. [(Phe45Leu)(;)(Arg49*)]

Question 18

how do you denote heterozygous changes in limited screen

Answer 18

note where youve screened and mutation in one set of square brackets
in next note where was screened and then put = for WT. seperate with ;
eg [94_97del4];[94_97=]

Question 19

how do you denote heterozygous changes when youve screened the full gene

Answer 19

same as limited screen but in WT square brackets dont need the area screened
eg. [94_97del4];[=]

Question 20

how do you denote hemizygous changes

Answer 20

put mutation in one set of square brackets then put [0] as there is no other allele
eg. [135C>A];[0]

Question 21

how do you denote somatic changes where there is a mixed cell population of some WT and some with splice site mutation

Answer 21

c.[51-1G>T/=]