OBJECTIVETo delineate the nature and origin of chromosomal copy number variants (CNVs) in a boy with mental retardation and multiple congenital malformation.

METHODSThe karyotypes of the patient and his parents were analyzed with routine G-banded chromosomal analysis. Genome DNA was analyzed by next generation sequencing (NGS).

RESULTSThe patient was found to harbor a structural aberration involving chromosome 3p. The karyotype of his father was 46,XY,t(3;7)(p26;q31), while his mother was found to be normal. NGS analysis of the patient revealed a 2.16 Mb microdeletion at 3p26.3-pter and a duplication at 7q31.33-qter.

CONCLUSIONThe structural aberration of 3p carried by the patient has derived from his father whom carried a balanced translocation of t(3;7), and his karyotype was finally determined as 46,XY,der(3) t(3;7)(p26.3;q31.33)pat. The abnormal phenotype of the patient can probably be attributed to the presence of 3p26.3-pter microdeletion and 7q31.33-qter duplication.