How is gender variance classified in the cognitive sciences?
So far, I've found that the American Psychiatric Association's DSM 5 has made it abundantly clear they no longer consider gender variance itself a disorder, to the point of a 2012 position statement on access to care, a 2012 "Position Statement on Discrimination Against Transgender and Gender Variant Individuals", and updated language in the DSM.

It also looks like ICD-11's beta now uses "Gender Incongruence", versus the various "gender identity disorders" under the F64 code in ICD-10.  Link when I have the reputation to post it.