Understanding Molecular Basis of PTPN11-Related Diseases

TL;DR

This study investigates how different missense variants in the PTPN11 gene affect protein function and contribute to diseases like Noonan syndrome, using computational tools to predict structural and functional impacts.

Contribution

It introduces a combined computational approach using MutPred2 and AlphaFold2 to analyze the molecular effects of PTPN11 variants and distinguish pathogenic from benign mutations.

Findings

LOF and GOF variants have distinct mechanisms affecting binding functions

NS-associated variants are more likely to be pathogenic

Structural predictions correlate with disease severity

Abstract

The PTPN11 gene encodes the Src homology 2 domain-containing protein tyrosine phosphatase (SHP2), a key regulator of cell growth, differentiation, and apoptosis through its modulation of various signaling pathways, including the RAS/MAPK signaling pathway. Missense variants in PTPN11 disrupt SHP2's proper catalytic activity and the regulation of signaling pathways, leading to disorders such as Noonan syndrome (NS), LEOPARD syndrome (LS), or juvenile myelomonocytic leukemia (JMML). These missense variants have molecular disruptions resulting in gains and losses of function at both the molecular and phenotypic levels. Depending on their location within SHP2, missense substitutions disrupt inter-domain regulation or impair phosphatase function, resulting in altered phosphatase activity. In this study, we investigate the molecular basis underlying the differential pathogenicity of PTPN11 missense variants and predict the structural consequences of these variants using MutPred2 and AlphaFold2. We find that LOF and GOF variants display distinct functional mechanisms in sodium and DNA binding, and that NS-associated missense variants identified in fetuses with ultrasound-detected anomalies and familiar cases are more likely to be pathogenic.