Simulation of chemical kinetic processes in combustion engine environments has become ubiquitous towards the understanding of combustion phenomenology, the evaluation of controlling parameters, and the design of configurations and/or control strategies. Such calculations are not free from error however, and the interpretation of simulation results must be considered within the context of uncertainties in the chemical kinetic model. Uncertainties arise due to structural issues (e.g., included/missing reaction pathways), as well as inaccurate descriptions of kinetic rate parameters and thermochemistry. In fundamental apparatuses like rapid compression machines and shock tubes, computed constant-volume ignition delay times for simple, single-component fuels can have variations on the order of factors of 2-4. This work investigates how kinetic rate parameter uncertainties manifest themselves in terms of combustion phasing under variable-volume, homogeneous charge compression ignition combustion. Iso-octane is used under lean fuel loadings (equivalence ratio = 0.35) at naturally aspirated conditions, where a range of combustion phasings is achieved via changes to the initial, bottom dead center (BDC) temperature, covering phasings from near top dead center (TDC) to 18 crank angle degrees (CAD) after TDC (according to the base model). Under this scenario, it is found that the confidence interval is fairly narrow near TDC (±2.6 CAD, interquartile range), but increases substantially with retarded phasing (e.g., ±13.2 CAD at 15° aTDC). This trend is influenced by a shift in the chemical kinetic pathways controlling autoignition timing, where the TDC phasing for this system is controlled not only by H2O2 and HO2 chemistry, but by well-studied, small-molecule reactions in the foundational chemistry sub-mechanism, while retarded phasings, owing to cooler compressed temperatures, are influenced more by fuel-specific reactions, such as isomerization of OOQOOH and formation of carbonylhydroperoxide, which are less well-known and thus have greater extents of uncertainty.