We describe a case of a 15-month-old boy who presented with pancytopenia, growth retardation, microcephaly, history of vaccine-related rubella, elevated immunoglobulin G level, and decreased T and B lymphocyte levels. Next-generation sequencing revealed LIG4 pathogenic genes and compound heterozygous mutations, namely missense mutation c.833G>T (p.Arg278Leu) and deletion mutation c.1271_1275del (p.Lys424Argfs*20).