The point is [missing / blunt / worn away]
It doesn't have a point [anymore]
"The point is out" doesn't work for a pencil. It would work for a pen, however. "The pen is out", actually means the ink in it has run out, is empty. Usually, "run" in this usage is only applicable to a liquid, or something considered fluid or flowing in a linear fashion; like time, or toner in a laser printer, or gumballs in a dispenser, or sand in an hourglass.
Student or Learner