A 14-month-old boy was referred to the department of Developmental Behavior Pediatrics at Liuzhou Maternity and Child Healthcare Hospital, Guangxi province, for developmental delay, Achilles tendon contracture, hypertonia, nystagmus, and vision defects. The boy was born at full term following an uneventful pregnancy to non-consanguineous parents of Chinese descent. Neither of the parents nor their related family members had any related symptoms. The boy had normal birth length and weight (52 cm and 3.3 kg) and is now 80 cm and 10.8 kg (update to 17/4/2019). The parents described the boy failing to track light or objects, and nystagmus was noticed since birth. Ophthalmological examination revealed no eye tracking, horizontal tremor of both eyes, exotropia, and corneal transparency. Congenital cataracts were found in the patient. No abnormalities were found in the ophthalmological evaluations for the father of the proband. Developmental milestones were obviously delayed. He could not roll over until 12 months, or get to a sitting position without assistance until 18 months. The boy has had hypertonia and Achilles tendon contracture since birth. The Gesell developmental test was performed and the boy was evaluated a shaving severe developmental delay of adaptability and fine motor skills, moderate developmental delay of large motor skills, and mild developmental delay of language development and personal-social interactions. Magnetic resonance imaging revealed delayed myelination of the brain and formation of the fifth ventricle. Karyotyping showed normal 46, XY. Tandem mass spectrometry was applied to detect possible inherited metabolic diseases for the proband but with negative results.Genetic testing and data analysis. Genomic DNA was extracted from peripheral blood samples of the patient and his parents using the GentraPuregene Blood Kit (Qiagen, Hilden, Germany) according to the manufacturer’s protocol. Proband-only targeted next-generation sequencing using an inherited disease panel (including 2742 disease-causing genes, cat No. 5190–7519, Agilent Technologies, Santa Clara, CA, USA) was performed as described previously []. Original sequencing data were assessed using Fast QC (version 0.11.2) for quality control. The Burrows-Wheeler Alignment tool (version 0.2.10) was employed for aligning sequencing data to the Human Reference Genome (NCBI build 37, hg 19). Single nucleotide variants and small indels were identified by the Genome Analysis Toolkit. All variants were saved in Variant Call Format and uploaded to the Ingenuity Variant Analysis (Ingenuity Systems, Redwood City, CA, USA) and TGex (Translational Genomics Expert) platforms for biological analysis and interpretation. Variants detected by next-generation sequencing were confirmed by Sanger sequencing in the patient and his parents. Copy number variants (CNVs) were identified using CNVkit open source software, a tool kit to infer and visualize copy numbers from targeted DNA sequencing data. Aligned data after the Burrows-Wheeler Alignment process were used as input. Normal reference data used for CNV identification were constructed using sequencing data from 10 normal males and 10 normal females that were previously validated without pathogenic CNVs by a chromosomal microarray platform. Default CNVkit settings were used for CNV identification. CNVs detected through bioinformatics analysis are further validated by chromosomal array analysis using CytoScan 750 k Suite (Thermo Scientific, Waltham, MA, USA). A homozygous variant in OPA1 (NM_015560: c.2189 T > C p.Leu730Ser) was identified in the patient. The variant is absent from all currently available databases including the Genome Aggregation Database. Multiple lines of computational evidence suggest a deleterious effect of this mutation. Sanger sequencing was applied to validate the variant in the pedigree and revealed that the patient’s father carried the same heterozygous variant and his mother was wild-type. CNV analysis, based on read-depth information of the proband, indicated a heterozygous deletion on the short arm of chromosome 3. Chromosomal microarray analysis confirmed this deletion as arr[GRCh37] 3q28q29(191921285_195896838)× 1. Thus, the proband inherited a heterozygous variant in OPA1 gene from his father and developed a de novo 3975 kb microdeletion on chromosome 3 that unmasked the heterozygous variant into a hemizygous form.