In the previous study, mutations were detected by comparative genomics analysis between the wild-type strain Corynebacterium glutamicum SYPS-062 and the mutation strain SYPS-062-33a. The study on five variant genes reversion or deletion revealed that the point mutation of pyruvate dehydrogenase subunit (aceE) was responsible for the more accumulation of by-products in the mutation strain SYPS-062-33a. Based on that, the effect of remaining seven mutant genes on cell growth and L-serine production was further explored. And the seven genes in the high-yield L-serine-producing ΔSSAAI were respectively deleted. After the gene SD36_RS01255 deletion, OD562 decreased by 25.8%, and the titer of L-serine reduced by 26.4% to 19.25 g/L. Subsequently, the functional prediction analysis revealed that the partial region of the protein encoded by SD36_RS01255 was similar to the protein encoded by the plasmid pRiA4b ORF-3 when compared with the NCBI database protein. The deletion of SD36_RS01255 might affect DNA repair, and thus result in slow cell production and L-serine production decline. However, overexpression of SD36_RS01255 had no significant effect on the growth of ΔSSAAI, the titer of L-serine and the accumulation of by-products.