Quick reference - definitions and characters used

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.

Definitions

for the description of sequence variants the following definitions are used

• substitution   =   a sequence change where one nucleotide is replaced by one other nucleotide
          NOTE:  a sequence change where one nucleotide is replaced by more then one other nucleotides is an delins (deletion-insertion)
          NOTE:  a sequence change where more then one nucleotides are replaced by one or more other nucleotides is an delins (deletion-insertion)
• deletion   =   a sequence change where one or more nucleotides are removed (deleted)
• duplication   =   a sequence change where a copy of one or more nucleotides are inserted directly 3'-flanking of the original copy
          NOTE:  when the copied sequence is not inserted directly 3'-flanking of the original copy the change is called an insertion
• insertion   =   a sequence change where one or more nucleotides are inserted between two original nucleotides but where the insertion is not a copy of a sequence immediately 5'-flanking (see duplication)
• inversion   =   a sequence change where more then one nucleotides replacing the original sequence are the reverse complement of the original sequence
• conversion   =   a sequence change where a range of nucleotides replacing the original sequence are a copy of a sequence elsewhere in the genome

Characters used

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

• numbering
  • reference sequences
    • c. = coding DNA reference sequence
    • g. = genomic reference sequence
    • m. = mitochondrial reference sequence
    • r.  = RNA reference sequence
    • p. = protein reference sequence
  • genomic reference sequence
    • N = nucleotide N in reference sequence (e.g. 311A>G)
  • coding DNA reference sequence
    • N = nucleotide N in protein coding sequence (e.g. 11A>G)
    • -N = nucleotide N 5' of the ATG translation initiation codon (e.g. -4A>G)
      NOTE: so located in the 5'UTR or 5' of the transcritption initiation site (upstream of the gene, incl. promoter)
    • *N = nucleotide N 3' of the translation stop codon (e.g. *6A>G)
      NOTE: so located in the 3'UTR or 3' of the polyA-addition site (incl.downstream of the gene)
    • N+M = nucleotide M in the intron after (3' of) position N in the coding DNA reference sequence (e.g. 30+4A>G)
    • N-M = nucleotide M in the intron before (5' of) position N in the coding DNA reference sequence (e.g. 301-2A>G)
    • -N+M / -N-M = nucleotide in an intron in the 5'UTR (e.g. -45+4A>G)
    • *N+M / *N-M = nucleotide in an intron in the 3'UTR (e.g. *212-2A>G)
• 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) = 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
    • c.[76A>C];[83G>C] changes in the two alleles (chromosomes)
    • c.[76A>C;83G>C] two changes in one allele (chromosome)
    • c.[76A>C (;) 83G>C] two changes where it is unknown whether they are in the same or different alleles (chromosomes)
  • , (comma) =  separator between different nucleotides (mosaic cases), transcripts or 
            proteins generated from one allele (chromosome)
  • [] = encloses several changes, transcripts or proteins from one allele
    • c.[76A>C];[83G>C] changes in the two alleles (chromosomes)
    • c.[76A>C; 83G>C] two changes in one allele (chromosome)
    • c.[76A>C (;) 83G>C] two changes where it is unknown whether they are in the same or different alleles (chromosomes)
    • c.[=, 83G>C] two variants in one allele (chromosome), i.e. in cases with somatic or germline mosaicism
    • r.[76a>c, 73_88del] two transcripts produced from one allele
  • () = indicates uncertainty in the description of a change
    • ...
    • c.[76A>C (;) 83G>C] two changes where it is unknown whether they are in the same or different alleles (chromosomes)
  • {} = 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)
  • 0 (zero) = indicates no product / nothing
    • c.0 = no DNA from allele detected, e.g. c.[76A>C];[0] for a variant in a X-linked gene in a male
    • r.0 = no RNA from allele detected, e.g. from a promoter variant or deletion
    • p.0 = no protein from allele detected, e.g. from a variant in the translation initiation codon
• nucleotides, codons & amino acids (V2.0)
  • DNA
  • RNA
  • protein
    • one and three letter amino acid code
    • * = translation termination codon  (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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