3.2 | Genetic evaluation in all patients with microcephaly
A molecular diagnosis was established in 19 patients (47.5%) from 39 families. In 12 patients, including one sibling pair (30%), 11 PVs or LPVs were identified by WES (Table 2). The inheritance patterns of these mutations were autosomal dominant (n = 9), autosomal recessive (n = 1), and X-linked recessive (n = 1). Another seven patients (17.5%) showed a pathogenic CNV by CMA or LD-WGS (Table 3). Using WES, PVs or LPVs were detected in nine genes previously associated with microcephaly: GNB1 , GNAO1 , TCF4 , ASXL1 ,SMC1A , KMT2A , VPS13B , ACTG1, EP300 , and KMT2D . Five PVs or LPVs were novel variants, and nine PVs or LPVs were de novo variants. Identified variants except BV and LBV were described in Supplementary Table 2.
3.3 | Clinical phenotypes of the patients with a PV/LPV determined by WES
There was a 9-year-old girl (M-011) with an LPV in the GNB1 gene. She presented with infantile spasms at the age of 4 months and was treated with antiepileptic medications. Her epileptic spasms disappeared during infancy, but, she failed to meet developmental milestones. Gradually, different type of seizures and involuntary movements developed, despite being administered a number of antiepileptic medications. A de novo LPV (c.284T>C;p.Leu95Pro) that was absent from the control databases was identified in theGNB1 gene. This c.284T>C variant was previously associated with de novo severe neurodevelopmental disability, hypotonia, and seizures (Petrovski et al., 2016).
In a 4-year-old boy (M-020) suffering from intractable dystonia with severe growth failure and profound psychomotor retardation, a de novo LPV (c.607G>A;p.Gly203Arg) that was absent from the control databases was identified in the GNAO1 gene. A c.607G>A change in GNAO1 was previously reported many times in de novo in epileptic encephalopathy patients, suggesting that mutation hotspot (Arya, Spaeth, Gilbert, Leach, & Holland, 2017).
In patient M-039, a PV (c.3115C>T;p.Gln1039Ter) of theASXL1 gene was identified. She was admitted on the neonatal intensive care unit for congenital hypotonia. Because her respiration was unstable and weak, she needed a tracheostomy and home ventilator support. She showed severe feeding problems and profound failure to thrive. In addition, the patient suffered from intractable epilepsy and severe dystonia. The c.3115C>T variant in ASXL1 was absent in the control population and occurred de novo . This c.3115C>T variant was previously reported mainly as a somatic variant in patients with myelodysplastic syndrome (Wang et al., 2013), but no germline variant has been reported.
In the SMC1A gene, known as a causative gene of Cornelia de Lange syndrome, an LPV (c.2368C>T;p.Arg790Trp) was identified in a male sibling pair (M-055-P, M-055-S) who were clinically suspected of Cornelia de Lange syndrome. They showed distinctive facial features, namely long eyelashes, synophrys, small nose, wide nasal bridge, low-set ears, and small chin. They could not speak a meaningful word and showed severe growth retardation in not only HC but also height and weight. The c.2368C>T variant in SMC1A was hemizygous. The patients’ mother had this variant, in her case, it was heterozygous. There were two unaffected maternal uncles, who have not married. They displayed normal intelligence and facial feature, and did not been tested for the variant. This variant was previously reported to be associated with Cornelia de Lange syndrome (Ansari et al., 2014).