In the Avengers vs X-men preview, the line-up shows Namor as an x-man, and indeed he's in the preview comic! I did some research and it turns out Xavier and Magneto have long (since 1964!) suspected him to be a mutant, and that Emma Frost requested him to join in Dark Reign, but why would he stay? I thought Namor had an undersea kingdom to be arrogant over?
If Wikipedia - X-Men is correct (not usually a good citation), at the end of 2009, within the Nation X story arc, Magneto rejoins X-Men (Uncanny X-Men #516) as leader and Namor joins Magneto & the other X-Men in developing Utopia for both mutants and Atlanteans (Uncanny X-Men #520)
The above arc plot points appear backed, in part, by minor descriptions at marvel.com and other reviews.
If/when forced to pick a side in Avengers vs X-Men, it's very possible that the recent allegiance and co-operation with the X-Men around Utopia within this arc is why he aligns with the X-Men.
Namor is himself a mutant.
In the Fantastic Four story arc "Wolf at the Door," Sue Richards works as a public school teacher. During one scene, she's teaching the class about mutants, and during the lesson, describes Namor as the first mutant.
His flight capabilities, super-strength, and longevity are all results of his mutation.
I think somewhere - I don't know quite where - Marvel has confirmed that Namor is indeed an x-gene mutant. His human father was an x-gene carrier and that's why Namor has wings on his feet and is considerably stronger than normal Atlanteans, who themselves are already superstrong to endure the pressure of the deep. In short, he's an Atlantean-human mutant hybrid.