PTPN11 mutations in Noonan syndrome: molecular spectrum, genotype-phenotype correlation, and phenotypic heterogeneity

Abstract

Noonan syndrome (NS) is a developmental disorder characterized by facial dysmorphia, short stature, cardiac defects, and skeletal malformations. We recently demonstrated that mutations in PTPN11, the gene encoding the non-receptor-type protein tyrosine phosphatase SHP-2 (src homology region 2-domain phosphatase-2), cause NS, accounting for approximately 50% of cases of this genetically heterogeneous disorder in a small cohort. All mutations were missense changes and clustered at the interacting portions of the amino-terminal src-homology 2 (N-SH2) and protein tyrosine phosphatase (PTP) domains. A gain of function was postulated as a mechanism for the disease. Here, we report the spectrum and distribution of PTPN11 mutations in a large, well-characterized cohort with NS. Mutations were found in 54 of 119 (45%) unrelated individuals with sporadic or familial NS. There was a significantly higher prevalence of mutations among familial cases than among sporadic ones. All defects were missense, and several were recurrent. The vast majority of mutations altered amino acid residues located in or around the interacting surfaces of the N-SH2 and PTP domains, but defects also affected residues in the C-SH2 domain, as well as in the peptide linking the N-SH2 and C-SH2 domains. Genotype-phenotype analysis revealed that pulmonic stenosis was more prevalent among the group of subjects with NS who had PTPN11 mutations than it was in the group without them (70.6% vs. 46.2%; P<.01), whereas hypertrophic cardiomyopathy was less prevalent among those with PTPN11 mutations (5.9% vs. 26.2%; P<.005). The prevalence of other congenital heart malformations, short stature, pectus deformity, cryptorchidism, and developmental delay did not differ between the two groups. A PTPN11 mutation was identified in a family inheriting Noonan-like/multiple giant-cell lesion syndrome, extending the phenotypic range of disease associated with this gene.

Figure 1

Cosegregation of PTPN11 mutations and Noonan phenotype. A, Restriction analysis of PTPN11 PCR product containing exon 8, showing segregation of the 922A→G mutation in the original large family with NS that shows linkage to 12q24 (Jamieson et al. 1994). The family tree is shown above. The mutation introduces an EcoRV restriction site, resulting in 246- and 366-bp products, whereas the wild-type allele remains undigested (612 bp). B, DHPLC elution profiles of PTPN11 exon 8 PCR products, showing segregation of the 923A→G change in a family inheriting Noonan-like/multiple giant-cell lesion syndrome (Bertola et al. 2001). A single peak characterizes the wild-type profile, and a variant profile, characterized by two peaks, is observed in all affected family members. The family tree is shown on the left. The gray-shaded symbol indicates an indeterminate phenotype.

Figure 2

Location of mutated residues in SHP-2 in the inactive conformation: Cα trace of the N-SH2 (thin blue line), C-SH2 (thin magenta line), and PTP (thin orange line) domains; and N-SH2/C-SH2 and C-SH2/PTP linkers (thin gray lines), according to Hof et al. (1998). The views represented in panels A and B are orthogonal to each other. Mutated residues are indicated with their side chains as thick lines (N-SH2 residues located in or close to the N-SH2/PTP interaction surface are shown in white; linker, C-SH2, and N-SH2-phosphopeptide binding residues are shown in green; and PTP residues located in or close to the N-SH2/PTP interaction surface are shown in red).