Many agents ask for the first 3 chapters. Is a prologue a chapter? So send the prologue & chapters One & two?
Your best to confirm with the particular person as there isn't full standardization.
From the submissions guidelines of the publisher Edge Science Fiction and Fantasy, they consider it separate.
What to Submit
- Required Extras (see below)
- Query/Cover Letter (see below)
- Synopsis (see below)
- Title Page (see below)
- Prologue (optional) (see below)
- Chapters One, Two, Three (do not send more chapters) (see below)
The best way is to clarify this question with an agent you work with. According to the majority of editorial guidelines, a prologue is not considered a chapter, so you should send chapters 1-3.
Unfortunately, there is not a general standardization. Publishers usually provide their own submissions guidelines.