repeated sequences¶
Definition¶
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 = ]
Notes¶
- all variants should be described at the DNA level, descriptions at the RNA and/or protein level may be given in addition
- 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").