Proficiency Bonus

All classes get a Proficiency bonus, which is applied to various attributes and effects. Half of the bonus is applied to Minor Class Skills, racial skills, medium saving throws, and Resilience. The full bonus is applied to Major Class Skills, any skill that is both a racial skill and a Minor Class Skill, high saving throws, and to the following attributes: max Mana Charge, max Stress Limit, max Chi Points, and Willpower defense. 1.5x is applied to any saving throw or class skill labeled as "Prime;" no saving throws can be Prime by default, and typically only skills that are both a Major Class Skill and a racial skill become Prime.
At Level 1, a character's Proficiency bonus is +2. Every 5th Level, it increases by an additional 2 points, up to +42 at Level 100.
In addition to what has already been mentioned, other aspects of a character may apply the Proficiency bonus, depending on the character's class. Attack rolls (melee, ranged, touch, ray, and mind), combat maneuver bonuses & grapple difficulty rating, magic difficulty rating, the armor value and warding bonus from armor, and deflection from shields can all get a bonus from Proficiency if the class grants it.