Identification of Multiple Candidate Variants in a Family with Autism Spectrum Disorder through Whole Genome Sequencing Analysis

Background: Whole genome sequencing (WGS) has been more widely used as a tool in the clinical diagnosis and it helps increase the diagnosis rate up to 20% in autism spectrum disorders (ASDs). Thus far, more than 100 genes and CNV loci have been reported to be associated with ASD suscpeptibility. However, none are found in >1% of cases with ASDs, suggesting a diverse genetic heterogeneity of the disorders.

Objectives: To identify a putative genetic cause of an individual's ASD.

Methods: WGS in a trio ASD family in combination with internal bioinformatics pipelines and a commercial software VarSeq.

Results: We identified 4 inherited rare damaging missense single nucleotide variants (SNVs) in 4 genes (DNMT3A, PHF2, NRXN2, and SNRPN), and one rare copy number variant (CNV). The CNV is a paternally inherited 14 Kb microdeletion in ZNF517, which is also confirmed by DNA microarray.The variants in DNMT3A and SNRPN were also confirmed by Sanger sequencing. Clinically, the male proband has ASD, moderate intellectual disability, developmental delay, verbal apraxia, post-natal macrocephaly, large stature, adult-onset epilepsy (age 22 years), and mild facial dysmorphism (round facies, bitemporal narrowing, narrow palpebral fissures, low-set and protuberant ears, hypotonia, high arched palate). Neither parent has intellectual disability or ASD, though the father has macrocephaly and over-growth. All of the genes involved in these rare variants and CNV are reported to be ASD-related and involved in brain/neuron development. De novo mutations in the above SNV genes and a recurrent deletion in ZNF517 gene have been identified in cases with ASDs. In our proband, mutations in DNMT3A, PHF2, and SNRPN are paternally inherited while NRXN2 is maternal. DNMT3A is a newly identified ASD candidate gene and its mutation is associated with Tatton-Brown-Rahman Syndrome. Some of the phenotypes are shared in our proband. Functional analysis is in progress including whole transcriptome analyses.

Conclusions: DNMT3A is likely the most relevant gene accounting for both ASD and features concordant with Tattan-Brown-Rahman syndrome. Alternatively, our subject's ASD phenotype reflects a collection of quantitative phenotypic traits associated with each of the multiple ASD risk genes identified and its complex genetic origins.