Fig. 3
Chol-phenotype landscape and Chol-structure in the absence and presence of SAHA. a NPC1 variants are positioned by their variant sequence position (VarSeqP) (x-axis) normalized to the full-length sequence and the measured TrIdx values of NPC1 variants (y-axis) in the absence (left panel) or presence (right panel) of SAHA. The projected z-axis (color gradient) is defined by the measured Chol of each variant normalized to I1061T. The spatial relationships of pairwise comparisons of variants are illustrated as black lines. b The molecular variogram illustrating the spatial variance of measured Chol for distance values defined by VarSeqP and TrIdx in the absence (black line) or presence (red line) of SAHA (see Methods; Supplementary Fig. 7a). c The VSP predicted Chol-phenotype landscape is shown as a heatmap in the absence (left panel) or presence (right panel) of SAHA. Confidence relationships (see Supplementary Fig. 7b) within the molecular variogram range are plotted as contour lines with the top 25% confidence quartile shown as a bold line in control condition (left panel) and top 5% confidence level shown as bold in SAHA condition (right panel). Color-scale values: severe Chol accumulation (red); WT Chol accumulation (green). I1061T ER-restricted variant is bolded. Dashed ovals 3 and 4 highlight two SCV clusters defined by the top 25% quartile that have good TrIdx but defective Chol. d Mapping the Chol-phenotype landscape on the NPC1 structure25,29. The highest confident prediction of the Chol value and the corresponding TrIdx value is assigned for each residue with ball color representing Chol, ball size representing TrIdx, and transparency representing prediction confidence. SCV clusters 3 and 4 are selectively highlighted as balls in cartoon presentation of the structure. The proposed cholesterol flow path is shown in gray arrow. e Transmembrane region is shown in side view as cylinders (upper panel) or in top view as loops (lower panel) colored by predicted Chol value. Transmembrane helices 1–13 are labeled. The variants in SCV clusters 3 and 4 are labeled and shown in spheres (upper panel) or with C-alpha shown in balls (lower panel)
