Quick reference - characters used in the description of sequence changes

Since references to WWW-sites are not yet acknowledged as citations, please mention den Dunnen JT and Antonarakis SE (2000). Hum.Mutat. 15:7-12 when referring to these pages.

Symbols used

Below an overview of all different signs and characters used in the description of sequence variants with their meaning.

• numbering
  • -1 = first nucleotide 5' of the ATG translation initiation codon
  • *1 = the first nucleotide 3' of the translation stop codon
  • N+1 = nucleotide in an intron; the first nucleotide in the intron 3' of the splice donor site at position N of the coding DNA reference sequence
  • N-1 = nucleotide in an intron; the first nucleotide in the intron 5' of the splice acceptor site at position N of the coding DNA reference sequence
  • reference sequences
    • c. = coding DNA reference sequence
    • g. = genomic reference sequence
    • m. = mitochondrial reference sequence
    • r.  = RNA reference sequence
    • p. = protein reference sequence
• specific characters
  • + (plus) = see nucleotide numbering
  • - (minus) = see nucleotide numbering
  • * (asterisk) = see nucleotide numbering
    NOTE: because of existing IUB/IUPAC conventions this character can be expected to be used in future to indicate a stop codon (instead of the currently recommended X)
  • _ (underscore) = see nucleotide numbering, used to indicate a range (e.g. in combination
            with a deletion, insertion or variable sequence)
  • > (greater then) = changes to
    • c.5T>G substitution at DNA level
    • p.Leu30_Cys42>SerfsX3 insertion/deletion on protein level)
  • : (colon) = used to separate indicator (e.g. reference sequence used) and the actual description of a variant
            e.g. M13855.3:c.1A>G 
  • ; (semi-colon) =  separator between different changes in one allele
  • , (comma) =  separator between different nucleotides (mosaic cases), transcripts or 
            proteins generated from one allele (chromosome)
  • () = indicates the range of uncertainty in the description of a change
  • [] = encloses several changes, transcripts or proteins from one allele
    • c.[76A>C]+[83G>C] changes at the two alleles
    • c.[76A>C; 83G>C] two changes in one allele
    • r.[76a>c, 73_88del] two transcripts from one allele
  • {} = encloses a database accession.version number when two indicators are used
            e.g. DMD{NM_004006.1}:c.3G>T
  • ? (question mark) = unknown
  • =  (equals) = indicates 'identical to reference sequence' (no change, wild type sequence)
• nucleotides and amino acids
  • DNA
    • A = adenine
    • C = cytosine
    • G = guanine
    • T = thymidine
  • RNA
    • a = adenine
    • c = cytosine
    • g = guanine
    • u = uracil
  • protein
    • one and three letter amino acid code
    • X = translation stop codon
• others
  • chr = chromosome (e.g. chr19 or chrX)
  • del = deletion
  • dup = duplication
  • ext = extension (e.g. N- or C-terminus of protein)
  • ins = insertion
  • inv = inversion
  • con = (gene) conversion
  • fs = frame shift
  • t = translocation; e.g. t(X;4)(p21.2;q34)

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