Direct numerical simulations (DNS) of low and high Karlovitz number (Ka) flames are analysed to investigate the behaviour of the reactive scalar sub-grid scale (SGS) variance in premixed combustion under a wide range of combustion conditions (regimes). An order of magnitude analysis is performed to assess the importance of various terms in the variance evolution equation and the analysis is validated using the DNS results. This analysis sheds light on the relative behaviour among turbulent transport and production, scalar dissipation and chemical processes involved in the evolution of the SGS variance at different Ka. The common expectation is that the variance equation shifts from a reaction-dissipation balance at low Ka to a production–dissipation balance at high Ka with diminishing reaction contribution. However, in large eddy simulation (LES), a high Ka alone does not make the reaction term negligible, as the relative importance of the reaction term has a concurrent increase with filter size. The filter size can be relatively large compared with the Kolmogorov length scale in practical LES of high Ka flames, and as a consequence a reaction–production–dissipation balance may prevail in the variance equation even in a high Ka configuration, and this possibility is quantified using the DNS analysis in this work. This has implications from modelling perspectives, and therefore two commonly used closures in LES for the SGS scalar dissipation rate are investigated a priori to estimate the importance of the above balance in LES modelling. The results are explained to highlight the interplay among turbulence, chemistry and dissipation processes as a function of Ka.