The top downregulated genes include Synpo2 and EGR3, which are necessary for synaptic plasticity, long-term potentiation (LTP), learning and memory [47, 48]; Ptpn7, which belongs to a family of protein tyrosine phosphatases also necessary for synaptic plasticity and associated with models of developmental delay [49]; and Gprin3, part of the NMDA receptor complex which regulates the synaptic protein PSD-95 [50] (Fig. 3c, d, Supplemental Data File DEG and Supplemental Fig. 1C). Here, PTPN7 is linked to Global developmental delay.