nomenclature Flashcards
In a coding DNA reference sequence nucleotide “1” is what
A of the ATG start codon
do we number the intron
no
how can we check that our nt and aa numbering is correct
if the nt number is not the correct multiple of 3 of the amino acid number then it must be wrong
what do we put predictions in
curved brackets
how do we denote a stop codon
*
what does the nomenclature c.145C>T p(Arg49*) mean
substitution at position nt145 C for T
causes Arg to become stop codon
nonsense mutation
what does the nomenclature c.135T>A p.(Phe45Leu) mean
substitution at nt135 T for A
causes Phe to become Leu
missense mutation
what does the nomenclature c.51-1G>A p.(?) mean
substitution G for A in intron one nucleotide back from nt 51
cannot predict outcome could destroy splice site - cant be sure
what does the nomenclature c.104_105delTG p.(Cys34Tyrfs*12) mean
deletion of TG at nt104 and nt105
disrupts ORF
get stop codon 12aa from and including Tyr
frame shift
what does the nomenclature c.104insA mean
insertion of A at nt 104
what does nomeclature c.104dupT mean
duplication of T at nt104
what does the nomenclature c.51-?_141+?(del exon 2) mean
deletion of exon 2 but you dont know where the breakpoint is
what does c.133_135delTTT p.(Phe45del) mean
deletion of whole amino acid Phe
what do square brackets give
genotype
how do you denote mutations in 2 different alleles (in trans)
place ; between 2 sets of square brackets
eg p.[(Phe45Leu)];[(Arg49*)]
how do you denote mutations on the same allele (in cis)
put ; within one set of square brackets
eg, [(Phe45Leu);(Arg49*)]
how do you denote the genotype when you dont know whether 2 mutations have occured in cis or in trans
use one set of square brackets and put ; in curved brackets
eg. [(Phe45Leu)(;)(Arg49*)]
how do you denote heterozygous changes in limited screen
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=]
how do you denote heterozygous changes when youve screened the full gene
same as limited screen but in WT square brackets dont need the area screened
eg. [94_97del4];[=]
how do you denote hemizygous changes
put mutation in one set of square brackets then put [0] as there is no other allele
eg. [135C>A];[0]
how do you denote somatic changes where there is a mixed cell population of some WT and some with splice site mutation
c.[51-1G>T/=]
