De novo variants in GABRA4 are associated with a neurological phenotype including developmental delay, behavioral abnormalities and epilepsy

Samin A Sajan ^{# 1}, Ralph Gradisch ^{# 2 3}, Florian D Vogel ⁴, Alison J Coffey ⁵, Daria Salyakina ⁶, Diana Soler ⁶, Parul Jayakar ⁷, Anuj Jayakar ⁸, Simona E Bianconi ⁹, Annina H Cooper ⁹, Shuxi Liu ¹⁰, Nancy William ¹¹, Ira Benkel-Herrenbrück ¹², Robert Maiwald ¹³, Corina Heller ¹⁴, Saskia Biskup ^{14 15}, Steffen Leiz ¹⁶, Dominik S Westphal ^{17 18}, Matias Wagner ¹⁷, Amy Clarke ², Thomas Stockner ², Margot Ernst ⁴, Akanchha Kesari ⁵, Martin Krenn ^{19 20}

Nine out of 19 genes encoding GABA_A receptor subunits have been linked to monogenic syndromes characterized by seizures and developmental disorders. Previously, we reported the de novo variant p.(Thr300Ile) in GABRA4 in a patient with epilepsy and neurodevelopmental abnormalities. However, no new cases have been reported since then. Through an international collaboration, we collected molecular and phenotype data of individuals carrying de novo variants in GABRA4. Patients and their parents were investigated either by exome or genome sequencing, followed by targeted Sanger sequencing in some cases. All variants within the transmembrane domain, including the previously reported p.(Thr300Ile) variant, were characterized in silico and analyzed by molecular dynamics (MD) simulation studies. We identified three novel de novo missense variants in GABRA4 (NM_000809.4): c.797 C > T, p.(Pro266Leu), c.899 C > A, p.(Thr300Asn), and c.634 G > A, p.(Val212Ile). The p.(Thr300Asn) variant impacts the same codon as the previously reported variant p.(Thr300Ile) and likely arose post-zygotically as evidenced by sequencing oral mucosal cells. Overlapping phenotypes among affected individuals included developmental delay (4/4), epileptiform EEG abnormalities (3/4), attention deficits (3/4), seizures (2/4), autistic features (2/4) and structural brain abnormalities (2/4). MD simulations of the three variants within the transmembrane domain of the receptor indicate that sub-microsecond scale dynamics differ between wild-type and mutated subunits. Taken together, our findings further corroborate an association between GABRA4 and a neurological phenotype including variable neurodevelopmental, behavioral and epileptic abnormalities.