If nucleotides are acceptable in prosite format because I thought it was protein motifs, the most accurate would be,
The key point is that,
x(0, 1, 3) means zero/ nucleotides (3 indels) or one/ G or C or A nucleotide, and 2 indels or three/ G or C or A nucleotides.
x is any nucleotide i.e. A or G or T or C - it doesn't mean an indel.
x(0, 1) is the best representation of a single indel (you call them gaps), here meaning any nucleotide may or may not be present at a given site.
Example from Prosite documentation:
This pattern, which must be in the N-terminal
of the sequence ('<'), is translated as:
Ala-any-[Ser or Thr]-[Ser or Thr]-(any or none)-Val