This is the intended behavior. In 1.3+ an empty gene name isn't allowed at all, the browser prevents saving the document, and in the backend such genes are removed automatically from requests that do get through (from JSON imports, for example).
Perhaps you would be interested in a generic "comments" field for the genetic area?
We have a large number of patient data already entered, and not being able to retrieve the comment data through the API is somewhat problematic for us.
Would it be possible to have the API return these records as long as users are allowed specify a comment while leaving the gene empty?