A Novel SPAST Variant Associated with Isolated Spastic Paraplegia

Figure 2

Sequencing data, conservation, and in silico modelling. (a) Sequencing data shown in integrative genomics viewer (Broad Institute) for the proband (upper panel) and a control (lower panel). The nucleotide substitution from adenine (A) to guanine (G) is shown in orange. (b) Evolutionary conservation of the amino acid affected by the spastin p.(Asp584Gly) variant across different species. The affected amino acid is shown in red. Blue indicates amino acids that are similar to the human sequence. Data from Alamut Visual Software (Sophia Genetics) and protein BLAST (https://blast.ncbi.nlm.nih.gov/Blast.cgi). (c) Spastin domain structure and paralog conservation of amino acids 571–597 among 14 related orthologues identified from the protein data bank (PDB). Alignment was created by VarSite (EMBL-EBI). The amino acids in the paralogue alignment are coloured by residue type. Shown below the alignment is the number of disease-causing variants at each position based on the p.(Asp584Gly) substitution reported in our case and reports in the human gene mutation database (HGMD) professional version 2022.2 (QiaGen). N-term = N-terminal sequence, MIT = microtubule interacting and trafficking domain, MTBD = microtubule-binding domain, and AAA = ATPase associated with various cellular activities. The asparagine (D) residue at position 584 is marked with a box. (d) Cartoon modelling of the human spastin hexamonomer. There is one colour for each monomer. The Asp584 residue is shown in red in each of the six monomers. (e) Localization of the p.Asp584 residue (dark red) and its interacting amino acids (orange). Hydrogen bonds (light blue) predicted with p.Arg578, p.Arg581, and p.Ser588. (f) Localization of the p.(Asp584Gly) substitution (dark red) and interacting amino acids (orange). Hydrogen bonds (light blue) are predicted to be formed with p.Ser588, but not with p.Arg578 and p.Arg581. The position of the new amino acid change within the structure was estimated using the Rotamers tool with standard parameters. The modelling in (d), (e), and (f) was performed using ChimeraX-1.5 on the spastin (PDB ID: 6PEN) crystal structure.

(a)

(b)

(c)

(d)

(e)

(f)