Protein Recommendations

Repeated sequences Variant


Definitions

Repeated sequence
a sequence 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..

Description

Format: “prefix”“amino_acid(s)+position_repeat_unit””["”copy_number””]”, e.g. p.(Arg65_Ser67[12])

  • “prefix” = reference sequence used = p.
  • “amino_acid(s)+position_repeat_unit” = amino acids position (range) first repeat copy = Arg65_Ser67
  • [ = opening symbol for allele = [
  • “copy_number” = number of repeat units = 12
  • ] = closing symbol for allele = ]

Note

  • prefix reference sequence accepted is “p.” (protein).
  • 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 amnio acid repeat, starting at position 18, has an estimated size of between 70 to 80 copiess.
      NOTE: the repeat can encoded by a mix of different coding triplets (“cag”, “caa”).