The World of Command and the World of Creation
I agree with Helen but some elaboration might help.
7:54 ........ Remember! To Him belongs the World of Creation, and to Him belongs the World of Command. Exalted is God, the Sustainer of the Worlds.
"BE" is the Cause and "SO IT IS" is the Effect.
In other words, when God decrees a matter, it starts happening.
KUN (Be) belongs to Allah's World of Command. FAYAKOON (So it is) pertains to His World of Creation.
In the World of Command (AMR), Allah designs laws as He wills. It is only in the World of Creation (KHALQ) that He implements those laws, and then, never changes them. So, He is absolutely Capable of devising any law in His World of Command.
3:47 Mary exclaimed! “O My Sustainer, How shall I have a son when no man has (intimately) touched me?” He said, “Just as God creates everyone according to His laws (3:40). When God decrees a matter, it starts happening.”
3:59 With God, the example of Jesus is that of Adam (other humans) who were initially created from dust and then evolved through different stages of life (22:5, 30:20). He created him (the human) beginning from inorganic matter, then He said to him, “Be! And he is.”
The process of procreation goes on - “IS”.
Kun fayakoon = The moment God decrees a thing, it starts happening.
16:40 Whenever We will anything to be, We say to it Our Word, “Be” and it is. [The moment We pass a decree in the World of Command, it starts happening]
19:35 It does not befit God that He would beget a son. He is Glorious, High above (what they say). When He decrees a thing, it starts happening.