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Background  Intellectual disability/developmental delay is a complex condition with extraordinary heterogeneity. A large proportion of patients lacks a specific diagnosis. Next generation sequencing, enabling identification of genetic variations in multiple genes, has become an efficient strategy for genetic analysis in intellectual disability/developmental delay.    Methods  Clinical data of 112 Chinese families with unexplained intellectual disability/developmental delay was collected. Targeted next generation sequencing of 454 genes related to intellectual disability/developmental delay was performed for all 112 index patients. Patients with promising variants and their other family members underwent Sanger sequencing to validate the authenticity and segregation of the variants.    Results  Fourteen promising variants in genes  EFNB1, MECP2, ATRX, NAA10, ANKRD11, DHCR7, LAMA1, NFIX, UBE3A, ARID1B  and  PTPRD  were identified in 11 of 112 patients (11/112, 9.82%). Of 14 variants, eight arose de novo ,  and 13 are novel. Nine patients (9/112, 8.03%) got definite molecular diagnoses. It is the first time to report variants in  EFNB1, NAA10, DHCR7, LAMA1  and  NFIX  in Chinese intellectual disability/developmental delay patients and first report about variants in  NAA10  and  LAMA1  in affected individuals of Asian ancestry.    Conclusions  Targeted next generation sequencing of 454 genes is an effective test strategy for patients with unexplained intellectual disability/developmental delay. Genetic heterogenicity is significant in this Chinese cohort and de novo variants play an important role in the diagnosis. Findings of this study further delineate the corresponding phenotypes, expand the mutation spectrum and support the involvement of  PTPRD  in the disease.    Electronic supplementary material  The online version of this article (10.1186/s12881-019-0794-y) contains supplementary material, which is available to authorized users.

Targeted next generation sequencing in 112 Chinese patients with intellectual disability/developmental delay: novel mutations and candidate gene