This is an intronic variant of the NCAPD3 gene (non-SMC condensin II complex subunit D3) and was found in compound heterozygous state in combination with the frameshift mutation NC_000011.9:g.134063952del in a patient with autosomal recessive primary microcephaly-22 (MCPH22 [45]). Here, NCAPD3 is linked to autosomal recessive primary microcephaly.