Complementing the phenotypical spectrum of TUBA1A tubulinopathy and its role in early-onset epilepsies

Abstract

TUBA1A tubulinopathy is a rare neurodevelopmental disorder associated with brain malformations as well as early-onset and intractable epilepsy. As pathomechanisms and genotype-phenotype correlations are not completely understood, we aimed to provide further insights into the phenotypic and genetic spectrum. We here present a multicenter case series of ten unrelated individuals from four European countries using systematic MRI re-evaluation, protein structure analysis, and prediction score modeling. In two cases, pregnancy was terminated due to brain malformations. Amongst the eight living individuals, the phenotypic range showed various severity. Global developmental delay and severe motor impairment with tetraparesis was present in 63% and 50% of the subjects, respectively. Epilepsy was observed in 75% of the cases, which showed infantile onset in 83% and a refractory course in 50%. One individual presented a novel TUBA1A-associated electroclinical phenotype with evolvement from early myoclonic encephalopathy to continuous spike-and-wave during sleep. Neuroradiological features comprised a heterogeneous spectrum of cortical and extracortical malformations including rare findings such as cobblestone lissencephaly and subcortical band heterotopia. Two individuals developed hydrocephalus with subsequent posterior infarction. We report four novel and five previously published TUBA1A missense variants whose resulting amino acid substitutions likely affect longitudinal, lateral, and motor protein interactions as well as GTP binding. Assessment of pathogenic and benign variant distributions in synopsis with prediction scores revealed sections of variant enrichment and intolerance to missense variation. We here extend the clinical, neuroradiological, and genetic spectrum of TUBA1A tubulinopathy and provide insights into residue-specific pathomechanisms and genotype-phenotype correlations.

Fig. 1. Brain imaging of individuals with TUBA1A variants.

Individuals i03 (A), i05 (B), and i06 (C) have common findings of (I) small thalami, (II) dysplastic, namely rounded, rotated basal ganglia without discernible ALIC and altered shape of frontal horns, (III) abnormal brainstem, (IV) a small, rotated vermis, as well as (V) malformations of cortical development. A i03 at 5 months: Simplified gyral pattern and thick cortex with irregular surface and cortex-white matter junction in the perisylvian area, suggestive of polymicrogyria (A_1,2,5). Small thalami, rounded basal ganglia without discernible ALIC (A₂). CC and brainstem are thin, whereas mesencephalon and medulla oblongata are disproportionately thick and long, respectively (A₄). Cerebellar foliation is irregular, with a polymicrogyria-like aspect (A_3,5). The hippocampus is hypoplastic with incomplete enfolding and near vertical orientation (A₆). The left olfactory bulb is missing (A₇; arrows). B i05 at 9 years: Shunted hydrocephalus due to aqueduct stenosis (shunt not depicted) with thick skull and T2-hyperintense residua of bilateral posterior cerebral artery infarction (B_1–3). Gyral pattern is simplified, the cortex is thick with slightly irregular inner surface and faint radial stripes suggestive of cobblestone lissencephaly (B₇). Small thalami and rounded, rotated basal ganglia without discernible ALIC (B₂). Thin, distended CC, presumably a combination of hypoplasia and hydrocephalus (B₄). Abnormal brainstem with short pons as well as disproportionately thick mesencephalon and long medulla oblongata (B₄); asymmetry is best appreciated on axial image (B₃). Cerebellar folia are irregular (B_3,5). The hippocampus is hypoplastic with incomplete enfolding and near vertical orientation (B₆). Both olfactory bulbs are visible (B₈; arrow). C i06 at 2.8 months before shunting of hydrocephalus (motion artefacts on follow-up): Decreased sulci with thick, smooth cortex of the parieto-occipital lobes (C_1,2; arrows) suggestive of pachygyria and irregular internal and external cortical surface in right temporal lobe and bilateral perisylvian areas suggestive of polymicrogyria (C_2,8; arrows). Agenesis of the CC (C_4,6). Abnormal brainstem with disproportionately thick mesencephalon, short pons, long medulla oblongata (C₄), and asymmetry (C₃). Hypoplastic hippocampus and parahippocampal gyrus (C₆) and hypoplastic left olfactory bulb (C_7,8; arrow). ALIC = anterior limb of the internal capsule, CC = corpus callosum.

Fig. 2. Distribution patterns of pathogenic and benign TUBA1A variants.

A Density of pathogenic variants reported in Pubmed (red) and ClinVar (violet). B Linearized TUBA1A protein model including domain annotation and description of herein reported variants (black). C Heatmap visualization of mean REVEL score values for all biologically possible TUBA1A missense variants according to their position in the primary structure. D Density of benign variants reported in gnomAD (light green). Pathogenic variant enrichment can be found in the C-terminal domain and, in particular, at residues Arg2, Arg214, Arg264, Arg402, and Arg422 (N > 10). Distribution of pathogenic compared to benign variants is mainly reciprocal. Variant densities are plotted with respect to their allele count.

Fig. 3. Localization of missense variants in a TUBA1A protein model.

Ribbon diagram of the TUBA1A monomer (highlighted in light blue) surrounded by α- and β-tubulin monomers assembling the microtubule filament (transparent gray; based on PDB: 5JCO). The kinesin KIF1A motor protein is aligned to this structure and shown as ribbon with transparent surface (green; PDB: 2HXF). Amino acid residues affected by missense variants are shown as spheres in (A) for variants previously reported in the literature (magenta) and (B) for novel variants reported here (red). C View from A/B rotated by −90° x-axis and −45° y-axis with the amino acid positions A174 and P173 as spheres and the GTP molecule in stick representation. Both residues are proximal to the GTP binding site and affect the same T5 turn between two α-helix folds. The amino acid changes at these positions likely disrupt binding to the GTP ribose group. D View from A/B rotated by −90° x-axis showing the central TUBA1A monomer (with transparent surface) from luminal with the two amino acid positions D218 and I219 predicted to disrupt the longitudinal interactions at the surface close to the neighboring monomer.