Translation:Do you have a pencil?
I was given "have" as the verb which seems completely off. I'm pretty positive that someone owning or having an object is shown through ある.
Do you have a pencil? I put the topic because it distinguishes the sentence from "Is there a pencil?"
Meanwhile もつ is used for carrying an object, like a synonym in a sense. えんぴつをもちますか？ Do you carry a pencil? えんぴつをもっていますか？ Are you carrying a pencil?