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Repeated Sequences#

Repeated sequence: a sequence between the translation initiation (start) and termination (stop) codon where, compared to a reference sequence, a segment of one or more amino acids (the repeat unit) is present several times, one after the other.

Syntax#

Syntax sequence_identifier ":p." position sequence "[" total_copy_number "]"
Examples
  • NP_0123456.1:p.Ala2[10]
  • NP_0123456.1:p.Ala2[10];[11]
  • NP_0123456.1:p.Arg65_Ser67[12]
Explanation of Symbols
  • position: a position specified as a simple ordinal sequence position
  • sequence: DNA, RNA, or AA sequence
  • sequence_identifier: an identifier for a sequence from a recognized database
  • total_copy_number: The total number of sequence copies in a repeat
See also explanation of grammar used in HGVS Nomenclature.

Notes#

  • all variants should be described on the DNA level; descriptions on the RNA and/or protein level may be given in addition.
  • repeated sequences include both small (mono-, di-, tri-, etc., amino acid) and larger repeats.

Examples#

  • p.Ala2[10]
    a repeated amino acid sequence, with the first Ala-residue located at position 2, is present in 10 copies.
    NOTE: when the repeat is variable in the population and the reference sequence has 10 units, the description p.Ala2[9] is preferred over p.Ala11del.
    NOTE: when the repeat is variable in the population and the reference sequence has 10 units, the description p.Ala2[12] is preferred over p.Ala10_Ala11dup.

  • p.Ala2[10];[11]
    a repeated amino acid sequence, with the first Ala-residue located at position 2, is present in 10 copies on one allele and 11 copies on the other allele.

  • p.Gln18[23]
    a repeated amino acid sequence, with the first Gln-residue located at position 18 is present in 23 copies (HD Gln-repeat based on the HTT (huntingtin) protein reference sequence (GenBank NP_002102.4)).
    NOTE: the protein reference sequence (GenBank NP_002102.4) contains an allele of 23 Gln copies (encoded by 22 cag and 1 caa codons).

    • p.(Gln18)[(70_80)]
      the predicted Gln amino acid repeat, starting at position 18, has an estimated size of between 70 and 80 copies.
      NOTE: the repeat can be encoded by a mix of different coding triplets (cag, caa).