Abstract Somatic hypermutation (SHM) increases the affinity of antibodies to antigen. While the initial steps of SHM, including development of the lesion, its excision and formation of an abasic site, are well established, the repair and mutation events are still under investigation. Multiple DNA repair pathways have been suggested for the SHM. POLD3, as a part of a scaffold complex, connects error free or error prone DNA polymerases with the processivity factor PCNA and this interaction plays an essential role in mutagenesis and recombination. In this study we tested the role of POLD3 in SHM. We demonstrated elevated expression of POLD3 in activated mice B cells and accumulation of this protein at DNA damaged sites. We created a Burkett’s lymphoma Raji cell clone (Raji 2C9 clone) expressing endogenous mutant POLD3 lacking C-terminus PCNA interaction site, using the CRISPR system. Functional studies shown that the Raji cells expressing mutant variant demonstrated abnormal cell cycle distribution, hyper-sensitivity to genotoxic agents and compromised SHM, compare to the control cells. The frequency of mutations in locus encoding immunoglobulin heavy chain variable region was are five times lower in cells expressing mutant POLD3 compare to control cells. In control cells, mutations accumulated at the RGYW/WRCY “hot spots”, and majority of mutations were C to T or G to A transitions. In cells expressing mutant POLD3 mutations accumulated outside “hot spots” and are represented by transversions. The overall results indicate that POLD3 plays an important role in SHM.