Figure 6. PTEN variant morphological profiles predict clinical phenotypes and reveal disease-specific variant effects.

(A) Venn diagram of clinical phenotypes associated with curated variants (see Methods and Table S5). Each clinical phenotype was associated with a variant if it occurred in at least one proband with that variant.

(B) Receiver operating characteristic (ROC) curves for univariate zero-shot models predicting ClinVar pathogenicity or each clinical phenotype (ASD = autism spectrum disorder, DD = developmental delay, PHTS = PTEN hamartoma tumor syndrome; see Methods for curation criteria) from iPS cell and NGN2-induced neuron-like cell distinguishability scores (this publication, solid lines), yeast fitness scores⁸⁴ (dashed line), VAMPseq scores⁵ (dashed line), or AlphaMissense⁹¹ or EVE⁹² scores(dot-dashed lines). Area under the curve (AUC) scores are shown for each model.

(C) Morphological impact scores for PTEN variants in iPS cells plotted by association with clinical phenotypes. gnomAD v4.1 (blue) and synonymous (green) variants are plotted for comparison. *** indicates Mann-Whitney U p<0.001 and ** indicates p<0.01.

(D) UMAPs of iPS cell (left) and NGN2-induced neurons (right) PTEN variant profiles highlighting curated variants from (B). Triangles indicate association with clinical phenotypes (colors match (D)). gnomAD v4.1 (blue) variants are also plotted. Circles represent other variants, colored green (synonymous) or grey (non-synonymous).

(E) Mislocalization scores (see Methods) for PTEN variants in iPS cells plotted by association with clinical phenotypes. gnomAD v4.1 (blue) and synonymous (green) variants are plotted for comparison. *** indicates Mann-Whitney U p<0.001 and ** indicates p<0.01.

(F) Volcano plots of median PTEN variant effects on iPS cell feature median z-scores (x-axis) against geometric-mean KS-test p-values (y-axis, tested against WT feature distributions) for variants associated with different clinical phenotypes (see (B)). Points are features with area proportional to the number of variants that pass thresholds and colored by imaging channel (see right for legend). iPS cell landmark features are highlighted. Red dashed lines show the Bonferroni-corrected p<0.01 threshold and median effect thresholds.

(G) Macro-averaged multiclass ROC curve for PHTS-associated, ASD/DD-associated, and gnomAD or ClinVar LB/B variants. Curves show one-vs-rest performance for univariant zero-shot models from (B) as well as multivariate support vector classifier models trained on landmark features measured in iPS cells or NGN2-induced neurons (this publication, dotted line). Corresponding macro-averaged AUC are shown.