Novel variants in TUBA1A cause congenital fibrosis of the extraocular muscles with or without malformations of cortical brain development

Abstract

Variants in multiple tubulin genes have been implicated in neurodevelopmental disorders, including malformations of cortical development (MCD) and congenital fibrosis of the extraocular muscles (CFEOM). Distinct missense variants in the beta-tubulin encoding genes TUBB3 and TUBB2B cause MCD, CFEOM, or both, suggesting substitution-specific mechanisms. Variants in the alpha tubulin-encoding gene TUBA1A have been associated with MCD, but not with CFEOM. Using exome sequencing (ES) and genome sequencing (GS), we identified 3 unrelated probands with CFEOM who harbored novel heterozygous TUBA1A missense variants c.1216C>G, p.(His406Asp); c.467G>A, p.(Arg156His); and c.1193T>G, p.(Met398Arg). MRI revealed small oculomotor-innervated muscles and asymmetrical caudate heads and lateral ventricles with or without corpus callosal thinning. Two of the three probands had MCD. Mutated amino acid residues localize either to the longitudinal interface at which α and β tubulins heterodimerize (Met398, His406) or to the lateral interface at which tubulin protofilaments interact (Arg156), and His406 interacts with the motor domain of kinesin-1. This series of individuals supports TUBA1A variants as a cause of CFEOM and expands our knowledge of tubulinopathies.

Conflict of interest statement

The authors declare that they have no conflict of interest.

Figures

Fig. 1. TUBA1A variants are associated with CFEOM.

A–I Five positions of gaze in Individual 1 prior to her first strabismus surgery at 2.5 years of age, demonstrating ophthalmic features consistent with CFEOM. The individual’s eye movements were directed as follows: (A) up; (B) right; (C) forward; (D) left; (E) down. Notable ophthalmic features include: (A) bilateral limitations of upgaze and convergence on attempted upgaze; (C) Bilateral ptosis and primary eye position in downgaze; (B, D): full horizontal eye movements; (E): mild bilateral limitations of downgaze and preferred chin-up head positioning. F Axial T2 weighted MR image (2 mm/0 mm gap thickness) at the level of the interpeduncular and suprasellar cisterns faintly demonstrates the oculomotor nerves (arrows). Although the slice thickness was not optimized for cranial nerve imaging, these nerves appear hypoplastic. G Coronal T1 MPRAGE image (0.9 mm/0 mm gap thickness) through the orbits demonstrates small superior and medial rectus muscles bilaterally (arrows).

Fig. 2. Brain MRI demonstrates features of classic tubulinopathies with or without MCD.

A–F MR images from Individual 1 at 20 months of age. A Midline sagittal T1 FLAIR MR image reveals deficiency of the rostrum of the corpus callosum. B Axial T2 and (C) coronal T1 MPRAGE MR images demonstrate an asymmetrically smaller, foreshortened body of the left caudate nucleus (white arrows) with mild prominence and dysmorphism of the ipsilateral lateral ventricle. D Axial T1 FLAIR MR image (5 mm/2.25 mm gap thickness) demonstrates thickening and irregularity of the posterior perisylvian cortex (white arrows), most pronounced on the right. E, F Coronal T1 MPRAGE MR images (0.9 mm/0 mm gap thickness) confirm bilateral perisylvian polymicrogyria (white arrows). G–I MR images from Individual 2 at 13 months of age. G 1.5T Siemens Symphony midline sagittal T1 MR image (4 mm/0.8 mm gap thickness) reveals mild thinning of the body and splenium (arrow) of the corpus callosum. H Axial (4 mm/0.8 mm gap) and (I) coronal (2 mm/ 0 mm gap) turbo spin echo T2 weighted MR images show asymmetric lateral ventricles and caudate nuclei, with the body of the right caudate nucleus appearing slightly smaller than the left (arrow). J Axial spin echo 1.5 T Siemens Symphony T1 MR image (4 mm/ 0.8 mm gap) demonstrating the perisylvian cortex. The cortical architecture is not well assessed for MCD due to a combination of technical parameters and age-appropriate incompletely myelinated subcortical white matter. K Anterior coronal (2 mm/ 0 mm gap) turbo spin echo T2 weighted MR image shows interdigitating frontal lobes (arrows) attributed to deficiency of the falx cerebri. L–P MR images from Individual 3 at 7 years of age. L Midline reconstructed sagittal T1 MPRAGE MR image (0.8 mm/ 0 mm interslice gap) reveals accentuation of the usual thinning of the posterior body of the corpus callosum (arrow). M Axial T2 (4 mm/1.2 mm gap) and N coronal T1 MPRAGE (1.2 mm/0 mm gap) MR images show asymmetric lateral ventricles and caudate nuclei, with the body of the left caudate nucleus appearing smaller than the right (arrow). O Reformatted axial (0.8 mm thickness) and (P) direct coronal (1.2 mm/ 0 mm gap) T1 3D MPRAGE MR images demonstrate irregular, thickened perisylvian cortex, more pronounced on the right, consistent with polymicrogyria (arrows).

Fig. 3. Structural modeling of tubulinopathy variants.

Structures were obtained from PDB ID: 3JAK (A–C, E) and PDB ID: 4HNA (D). A α and β tubulin monomers within a portion of a microtubule. Representative lateral and longitudinal interfaces are indicated. B α tubulin monomer with TUBA1A tubulinopathy-associated residues colored. C α and β tubulin monomers at the heterodimerization interface. Colored beta tubulin residues are associated with substitutions in TUBB3 and/or TUBB2B. For simplicity, residues associated with isolated MCD or MCD with involvement of cranial nerves other than CN3 are omitted in this view. D α and β tubulin complexed with kinesin-1. Colored beta tubulin residues are associated with substitutions in TUBB3 and/or TUBB2B. For simplicity, residues associated with isolated MCD or MCD with involvement of cranial nerves other than CN3 are omitted in this view. Polar interactions between kinesin and alpha or beta tubulin residues are shown with dashed lines. Distance between kinesin-Lys256 and α-His406 is shown. E Lateral interface between α tubulin residues in adjacent microtubule protofilaments. Key: α tubulin (gold); β tubulin (silver); kinesin-1 (pink); residues associated with CFEOM but not MCD (red); residues associated with CFEOM+MCD (purple); residues associated with MCD in the absence of CFEOM (cyan); residues associated with CFEOM ± MCD (orange); residues associated with CFEOM in the absence of MCD, or associated with MCD in the absence of CFEOM depending on substitution (brown); residues associated with MCD ± CFEOM (yellow); previously reported residues associated with putative CFEOM in the absence of MCD (black; [50]); reported residues associated with MCD and anomalies of cranial nerves other than CN III (green; [25]). *residues reported for the first time in this work (Arg156, Met398, and His406). ●-Previously reported residues associated with putative CN3 phenotypes [50].