In some contexts you can, normally with the use of the word "that". And, generally there is something (comment, information etc) that comes before that, or afterwards.
Are you absolutely certain (that) you gave them the right number?
(Source - Cambridge Dict.)
Are you certain [=sure] you want to leave today?
[here you can omit the "that", or use it, if you wish.]
"Are you certain?"
said in one breath (I mean, the three isolated words "are you certain"?), is said to ask about a statement just made.
John: "I can make it to your party on Saturday."
Joe: "Are you sure?"
John: "How many states does the Colorado river run through?"
John: "Are you certain? This question is for one million dollars!"
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