Scientific Nomenclature

Nucleotides

Blood generally follows the Human Genome Variation Society’s mutation nomenclature recommendations for nucleotides.

Nucleotides are represented by the letters A, C, G, and T; lowercase letters are allowed (to indicate uncertainty in the base call).

Denote nucleotide substitutions and polymorphisms by putting the nucleotide number first and then using a greater-than symbol between the replaced nucleotide and the new nucleotide; all elements should be closed up.

1691G>A G>A

To indicate that a genomic DNA or complementary DNA sequence is used, include “(gDNA [or cDNA] sequence, first described by _____ ^ref#)”; do not preface nucleotide substitutions with the letter g or c.

Denote nucleotide insertions by putting the 2 surrounding nucleotide numbers in front, separated by a hyphen, followed by "ins" and the inserted nucleotide.

186-187insC

Denote nucleotide deletions by specifying the nucleotide number deleted, followed by "del" and the deleted nucleotide.

1997delT

Denote nucleotide codon changes using the substitution scheme above:

GAG>TAG

See the Human Genome Variation Society website for how to handle other situations (eg, intron mutations and IVS-intervening sequences).

Amino acids

In mutation notation, it is acceptable to use abbreviations without expansion (see Amino acid abbreviations below), but follow abbreviations rules elsewhere.

Amino acids may be abbreviated with 1-letter abbreviations or 3-letter abbreviations. Amino acid abbreviations details both abbreviation schemes. Authors should try to use the same scheme consistently throughout an article, though variation is allowed.

A codon number may be used to describe a mutation.

Arg506 Arg506Gln R506 R506Q

If the codon number is not used, then denote the mutation with a full arrow.

Arg→Gln R→Q

If a stop codon is discussed, note that it is sometimes denoted by an abbreviation for unspecified amino acid (Xaa or X); if so, ensure that this abbreviation is consistent with surrounding amino acid abbreviations. Note that other notation is sometimes used (eg, “Stop”).

Arg506Xaa Arg506Stop R506X R506Stop

Amino acid abbreviations

alanine	Ala	A
arginine	Arg	R
asparagine	Asn	N
aspartic acid	Asp	D
cysteine	Cys	C
glutamic acid	Glu	E
glutamine	Gln	Q
glycine	Gly	G
histidine	His	H
isoleucine	Ile	I
leucine	Leu	L
lysine	Lys	K
methionine	Met	M
phenylalanine	Phe	F
proline	Pro	P
serine	Ser	S
threonine	Thr	T
tryptophan	Trp	W
tyrosine	Tyr	Y
valine	Val	V
unspecified aa	Xaa	X