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
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| 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:
Reference sequences beginning with "NM" refer to coding nucleotide sequences and those beginning with "NP" refer to protein sequences.
Genes may have multiple reference sequences. The reference sequence shown in the GeneReview matches the exon structure and reference used by the majority of citations.
Abbreviations for amino acids.
GeneReviews standard is use of the 3-letter symbol for amino acids.
Table 2.
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| 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
