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

Voltage-gated calcium (Ca(V)) channels form three subfamilies (Ca(V)1–3). The Ca(V)1 and Ca(V)2 channels are heteromeric, consisting of an α(1) pore-forming subunit, associated with auxiliary Ca(V)β and α(2)δ subunits. The α(2)δ 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 α(2)δ-1 protein, in two unrelated individuals showing a developmental and epileptic encephalopathy. 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 α(2)δ-1 protein detected in patient-derived fibroblasts. Patient 2 is compound heterozygous for an early frameshift variant c.13_23dup/p.(Leu9Alafs*5), highly probably 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 α(2)δ-1 as a calcium channel subunit, with strongly reduced trafficking of α(2)δ-1(G209D) to the cell surface and a complete inability of α(2)δ-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 α(2)δ-1 and other α(2)δ proteins for normal human neuronal development.