Kimura's ''neutral evolution'' only works if the vast majority of the genome has no function. Even if only 5% of it were functional, a mutation rate of 40mpipg would result in two mutations falling into the functional part of it.
Are you under the impression that a mutation in a gene "breaks" it? Renders it useless? Is deleterious 100% of the time?
That is simply not true.
From an interview with Misha Angrist, otherwise known as member four of the Personal Genome Project:
And similarly, we know that common diseases tend to be caused by a combination of many genes and the environment, probably interacting in subtle and complicated ways that make a deterministic scenario extremely unlikely.
When I look at my own genome I see dozens and dozens of broken genes. I see hundreds of mutations that, by all rights, should have put a stop to me when I was a microscopic ball of cells inside my Mom. But here I am, reading Harry Potter to my healthy and amazing kids, both of whom have half of my broken genes and half of their otherwise perfect mother
A Conversation with Misha Angrist, Publisher of His Genome - The Awl