Through reviewing the results of our NDR reflective tests in the 511 patients with NDDs, we found that the diagnostic yield of NDR was 5.87% in our patient cohort, and the most often causes of NDDs were 15q13.3 microdeletion syndrome, 22q11.2 deletion syndrome, 16p11.2 duplication syndrome, as well as pathogenic variants, including CNVs, in MECP2. This evidence concerns the gene MECP2 and syndrome caused by partial chromosomal deletion.