We describe a case of a Japanese boy with syndromic congenital sideroblastic anemia who presented with various non-hematological symptoms. Genetic analysis showed a heterozygous frameshift mutation (c.1639delA) and T/T genotype of the common coding single nucleotide polymorphism rs10117 (c.1933C>T) in HSPA9. Parental analysis revealed that the father carried the same frameshift mutation as well as rs10117 (T/T) but was not anemic. While the rs10117T allele is associated with lower HSPA9 expression, the expression levels are variable. We speculate that the possible differences in the HSPA9 mRNA expression levels between the child and his father may have caused the phenotypic difference.