In all of my conlangs with noun gender or class, I’ve used stem vowel (or lack thereof) to indicate gender.  I am considering using some other ending not including the stem vowel to indicate noun class.  My latest language, called Shonkasikas (“Mountain Speech”), has various patterns for noun declension patterns based on the ‘full stem’ ending, but gender based on the stem vowel.

For example, nouns ending in –us, –u, and –ur in the nominative singular would have different declension paradigms, but would likely all be masculine.

What I am considering is having –s mark, for example, masculine, –r common, –n neuter and nothing mark feminine.

I am still tweaking this. We shall see.