If your recommender has not yet submitted their recommendation or will not be able to submit your recommendation on time, you should still submit your application prior to the deadline. You do not need to wait for your recommendation to be in before you submit your application.
Your recommender should do their best to submit the recommendation as soon as possible. If your recommender is unable to submit due to technical difficulties, please review this FAQ for the appropriate steps to take: My recommender is having technical problems submitting my recommendation. What should I do?