Weapons are grouped into Classes and Types and some into Sub-Types. The top level, Class, determines which Mods are available for the weapon.
Prototypes are unique Weapons in the game. They come with standard bonuses, cannot be Modded and use a unique Rarity color. Some Prototypes can be acquired from Pursuits, others drop randomly at Activities based on the Enemy Type, and most are available individualy or as part of the Prototype Cache on offer from the runner at the end of Major Arkfalls and some Sieges. Another unique feature is that once acquired Prototypes become available at the Prototype Replicator.
Primes are unique Weapons that are part of a Mod Fusion Event Weapon collection. Each is always Legendary, Rated 10 Stars and comes with fixed bonuses.