Appendix: Quick Reference
Initial Posting: May 6, 2008; Last Update: January 31, 2019.
Estimated reading time: 1 minute
Naming Conventions
Sequence variants / pathogenic variants: Human Gene Variation Society (
varnomen.hgvs.org)
Standard nomenclature for DNA and protein amino acid sequence.
GeneReviews uses the nomenclature guidelines at varnomen.hgvs.org. If the standard nomenclature for a sequence variant cannot be determined, the variant is designated as an alias and a reference to the earliest reported description of the variant is provided.
Table 1.
Basic structure for DNA and Protein Amino Acid Sequence Nomenclature
View in own window
Prefix | Type of Sequence from which the Number(s) are Derived | Example | Interpretation | Commonly Describes |
---|
c. | coding DNA sequence, where nucleotide #1 is the first nucleotide of the first codon | c.535T>C | The T at nucleotide number 535 of the coding region changed to a C. | Nucleotide changes in genes (exons, splice sites, untranslated regions) |
p. | protein amino acid sequence, where #1 is the first amino acid residue of the protein | p.Cys179Arg | The cysteine amino acid at residue 179 changed to an arginine. | Amino acid changes in a protein |
g. | genomic DNA sequence, where #1 is the first nucleotide in a given reference sequence | g.66781T>C | The T at nucleotide 66781 in the genomic reference sequence changed to a C. | Nucleotide changes in introns, regulatory, and intergenic regions |
m. | mitochondrial DNA sequence, where #1 is the first nucleotide in the sequence of the entire mitochondrion genome | m.8994T>C | The T at nucleotide 8994 of the mitochondrial genome changed to a C. | Coding and non-coding variants of mitochondrial genome |
Reference sequence. For the variant nomenclature to be valid, a reference sequence is required. Reference sequences are found at www.ncbi.nlm.nih.gov. Note:
Abbreviations for amino acids.
GeneReviews standard is use of the 3-letter symbol for amino acids.
Table 2.
View in own window
Name | Symbol |
---|
3-Letter | 1-Letter |
---|
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 |
stop codon | Ter 1 |
- *
2
|
- 1.
Previously designated as X or *
- 2.
Previously designated as X