The affected siblings have similar phenotype, including ID, short stature, and microcephaly. Their mother had a history of seven first-trimester miscarriages and one elective termination because of multiple malformations. This abnormal karyotype was also thought to be responsible for the mother's recurrent miscarriage. WES in combination with CNV-seq analysis is very helpful for identification of the genetic causes of ID without positive karyotype findings.