Figure 3.

FCD and details of DEPDC5 variant. (A) Brain MRI showing FCD. Coronal T₁-weighted brain MRI from Case 1-102398, with DEPDC5 variant NM_001242896.3:c.G4183A:p.A1395T, showing left temporal lobe FCD (right of patient is on the left of the image, following radiological convention), with blurred grey–white interface and cortical thickening apparent in the left temporal lobe across several consecutive slices. (B) MetaDome map of regional constraint in DEPDC5. Grey bar below the graph represents the protein, pink bars showing Pfam domains: PF12257, Vacuolar membrane-associated protein Iml1 domain; PF00610, Domain found in Dishevelled, Egl-10, and Pleckstrin (DEP); A1395 is marked by a vertical green line, with a reported tolerance score of 0.28 (‘intolerant’). (C) VarSite sequence logo for DEPDC5 residues 1375–1414, based on alignment of structural homologues; below the logo is the sequence of DEPDC5 itself, with A1395 boxed; sequence conservation score for this residue was 0.92 [range 0 (low)–1 (high)]; alanine was observed at this position in 31/33 aligned sequences. (D) Structure of the GATOR1-Rag GTPases complex and context of DEPDC5 Ala1395. PDB 6ces, the structure of the heterotrimeric GATOR1 complex (DEPDC5:NPRL2:NPRL3) bound to RagA and RagC GTPases; protein surfaces shown by colour as indicated (except DEPDC5, shown as a ribbon and coloured by structural domains as annotated by Shen et al.³⁹: bright green = N-terminal domain (NTD) (residues 38–165); cyan = SABA domain (166–425); orange = steric hindrance for enhancement of nucleotidase activity (SHEN) domain (721–1010); dark green = DEP domain (1175–1270); violet = C-terminal domain (CTD) (1271–1600); Ala1395 is pink with sidechain atoms shown as spheres. (E and F) Ala1395 lies at an inter-domain interface in DEPDC5. The figure shows selected residues of DEPDC5 from PDB 6ces (chain D); residues of the NTD, SABA domain and CTD are shown as separate surfaces; residues of the SHEN domain and DEP domain are shown as ribbons. F shows the same structure as E with SHEN and DEP domains removed; residues Tyr108 (bright green), Phe326 (blue) and Ala1395 (rose pink) lie in close proximity at a three-way interface between the NTD, SABA and CTD. (G) Enlarged image of the DEPDC5 structure (PDB 6ces, chain D) as in E and F, zoomed to show detail around the three-way interface between the NTD, SABA and CTD; (H) The Ala1395Thr substitution results in reduced space at the inter-domain interface in 6cesD. This figure shows the same structure as G after introduction of the Ala1395Thr variant by in silico mutagenesis. Quantitative results are given in Supplementary material 18. Analysis of DEPDC5 from PDB 6cet is shown in Supplementary Fig. 1