As far as I know, there are 3 components included as part of uncertainty.
Uncertainity = Base uncertainity + Clock jitter + Skew
base uncertainity : This comes in from the technology/fab. When the cells are characterized, they are not 100% sure if the values characterized are exact, so for any change/variation which can be there has to be accounted so a number is considered.
Clock jitter : The clock generating unit is supposed to give a perfect clock, but in reality there could be some shift in the edges, this has to be accounted during timing, so the number usually from the clock generating unit spec is considered here.
Skew : In Synthesis the clock is ideal, but when it goes to layout and comes with the CTS, then we have skew coming into picture, so to account for the skew a number usually (expected skew limit) is considered here.
Please correct/add information appropriately.