Decoding SHP2 mutations by computational saturation mutagenesis

Src-homology-2-containing protein tyrosine phosphatase 2 (SHP2), encoded by the PTPN11 gene, is a master regulator of cell growth, survival, and differentiation. Normally, SHP2 is kept in a self-inhibited state, in which its N-terminal SH2 domain blocks the catalytic site. SHP2 activation is directly tied to the disruption of the self-inhibition. While mutations that disrupt this self-inhibited state can cause developmental disorders and cancer, most SHP2 variants remain functionally uncharacterized. Using computational saturation mutagenesis, we systematically analyzed > 9000 single-amino acid substitutions in the SH2 and PTP domains. Our analysis of binding energy changes identified key residues-especially A72 and G503-whose mutation destabilizes the autoinhibited conformation. Functional assays further demonstrated that mutations within the SH2 and PTP domains significantly enhance enzymatic activity, downstream signaling, and cellular proliferation. By integrating clinical data, we found that pathogenic variants preferentially adopt the destabilizing conformations, directly linking structural changes to disease. This work provides a comprehensive map of SHP2 mutation effects, highlights conformational opening as a key driver of pathogenicity, and establishes a predictive framework for interpreting the functional impact of uncharacterized variants in multi-domain proteins.