Standards

• nucleotide - DNA
• nucleotide - RNA
• genetic code
• amino acid code
• cytogenetic band > nucleotide position

Nucleotides (DNA / RNA)

At DNA and RNA level HGVS nomenclature follows the Nomenclature for Incompletely Specified Bases in Nucleic Acid Sequences (see IUBMB (NC-IUB)), specifying the description of nucleotides (see list) and the NCBI standards for sequence files and database searches (e.g. BLAST).

DNA

*used in alignment only

RNA

Genetic Code

At the protein level HGVS nomenclature follows the Nomenclature and Symbolism for Amino Acids and Peptides (see IUPAC-IUB), specifying the description of amino acids. In addition HGVS nomenclature uses “Ter” (three-letter amino acid code) and “*” (three- and one-letter amino acid code) to indicate a translation termination (stop) codon. NOTE: in older versions the “X was used instead. In the Table below, to support translation from a DNA sequence, we have used a “T” in the codons although in nature RNA is translated so the codons contain U’s.

Amino Acid Descriptions

At the protein level HGVS nomenclature follows the Nomenclature and Symbolism for Amino Acids and Peptides (see IUPAC-IUB), specifying the description of amino acids. In addition HGVS nomenclature uses “Ter” (three-letter amino acid code) and “*” (three- and one-letter amino acid code) to indicate a translation termination (stop) codon (NOTE: in older versions the “X was used instead). In the Table below, to support translation from a DNA sequence, we have used a “T” in the codons although in nature RNA is translated so the codons contain U’s.

One Letter Code	Three Letter Code	Amino Acid	Possible Codons	Systemic Name	Formula
A	Ala	Alanine	GCA, GCC, GCG, GCT	2-Aminopropanoic acid	CH3-CH(NH2)-COOH
B	Asx	Aspartic acid or Asparagine	AAC, AAT, GAC, GAT
C	Cys	Cysteine	TGC, TGT	2-Amino-3-mercaptopropanoic acid	HS-CH2-CH(NH2)-COOH
D	Asp	Aspartic acid	GAC, GAT	2-Aminobutanedioic acid	HOOC-CH2-CH(NH2)-COOH
E	Glu	Glutamic acid	GAA, GAG	2-Aminopentanedioic acid	HOOC-[CH2]2-CH(NH2)-COOH
F	Phe	Phenylalanine	TTC, TTT	2-Amino-3-phenylpropanoic acid	C6H5-CH2-CH(NH2)-COOH
G	Gly	Glycine	GGA, GGC, GGG, GGT	Aminoethanoic acid	CH2(NH2)-COOH
H	His	Histidine	CAC, CAT	2-Amino-3-(1H-imidazol-4-yl)-propanoic acid
I	Ile	Isoleucine	ATA, ATC, ATT	2-Amino-3-methylpentanoic acid	C2H5-CH(CH3)-CH(NH2)-COOH
K	Lys	Lysine	AAA, AAG	2,6-Diaminohexanoic acid	H2N-[CH2]4-CH(NH2)-COOH
L	Leu	Leucine	CTA, CTC, CTG, CTT, TTA, TTG	2-Amino-4-methylpentanoic acid	(CH3)2CH-CH2-CH(NH2)-COOH
M	Met	Methionine	ATG (translation initiation)	2-Amino-4-(methylthio)butanoic acid	CH3-S-[CH2]2-CH(NH2)-COOH
N	Asn	Asparagine	AAC, AAT	2-Amino-3-carbamoylpropanoic acid	H2N-CO-CH2-CH(NH2)-COOH
P	Pro	Proline	CCA, CCC, CCG, CCT	Pyrrolidine-2-carboxylic acid
Q	Gln	Glutamine	CAA, CAG	2-Amino-4-carbamoylbutanoic acid	H2N-CO-[CH2]2-CH(NH2)-COOH
R	Arg	Arginine	AGA, AGG, CGA, CGC, CGG, CGT	2-Amino-5-guanidinopentanoic acid	H2N-C(=NH)-NH-[CH2]3-CH(NH2)-COOH
S	Ser	Serine	AGC, AGT, TCA, TCC, TCG, TCT	2-Amino-3-hydroxypropanoic acid	HO-CH2-CH(NH2)-COOH
T	Thr	Threonine	ACA, ACC, ACG, ACT	2-Amino-3-hydroxybutanoic acid	CH3-CH(OH)-CH(NH2)-COOH
U	Sec	Selenocysteine	TGA		H2N-CH(COOH)–CH2-SeH
V	Val	Valine	GTA, GTC, GTG, GTT	2-Amino-3-methylbutanoic acid	(CH3)2CH-CH(NH2)-COOH
W	Trp	Tryptophan	TGG	2-Amino-3-(lH-indol-3-yl)-propanoic acid
Xa	Xaa	unknown or ‘other’	NNN
Y	Tyr	Tyrosine	TAC, TAT	2-Amino-3-(4-hydroxyphenyl)-propanoic acid
Z	Glx	Glutamic acid or Glutamine
*	Ter or *	Termination	TAA, TAG, TGA (translation termination)	HGVS addition (V2.0)

^aTo prevent confusion, since ‘X’ has been used to indicate a translation stop codon, use ‘Xaa’ only.

ISCN cytogenetic band to chromosome positions

NOTE: We are in contact with the ISCN to learn whether the translation tables shown is recognised by ISCN as correct.

To facilitate translating variant descriptions based on ISCN recommendations, human chromosomal band descriptions need to be translated to genomic positions (see Complex (HGVS/ISCN)). For this translation the table below can be used. Translations are shown for genome builds hg19/GRCh37 and hg38/GRCh38. Translation is based on the UCSC cytoBand file downloadeds for hg19 and hg38.