Biallelic CACNA2D1 loss-of-function variants cause early-onset developmental epileptic encephalopathy

Voltage-gated calcium (Ca-V) channels form three sub-families (Ca(V)1-3). The Ca(V)1 and Ca(V)2 channels are heteromeric, consisting of an alpha(1) pore-forming subunit, associated with auxiliary Ca-V beta and alpha(2)delta subunits. The alpha(2)delta subunits are encoded in mammals by four genes, CACNA2D1-4. They play important roles in trafficking and function of the Ca-V channel complexes. Here we report biallelic variants in CACNA2D1, encoding the alpha(2)delta-1 protein, in two unrelated individuals showing a developmental and epileptic encephalopathy (DEE). Patient 1 has a homozygous frameshift variant c.818_821dup/p.(Ser275Asnfs*13) resulting in nonsense-mediated mRNA decay of the CACNA2D1 transcripts, and absence of alpha(2)delta-1 protein detected in patient-derived fibroblasts. Patient 2 is compound heterozygous for an early frameshift variant c.13_23dup/p.(Leu9Alafs*5), highly likely representing a null allele, and a missense variant c.626G>A/p.(Gly209Asp). Our functional studies show that this amino-acid change severely impairs the function of alpha(2)delta-1 as a calcium channel subunit, with strongly reduced trafficking of alpha(2)delta-1(G209D) to the cell surface, and a complete inability of alpha(2)delta-1(G209D) to increase the trafficking and function of Ca(V)2 channels. Thus biallelic loss-of-function variants in CACNA2D1 underlie the severe neurodevelopmental disorder in these two patients. Our results demonstrate the critical importance and non-interchangeability of alpha(2)delta-1 and other alpha(2)delta proteins for normal human neuronal development.