The p.Asn308Thr variant has been reported in 7 individuals with clinical feature s of Noonan syndrome (Tartaglia 2006, Pierpont 2009, LMM data) and was absent fr om large population studies. Computational prediction tools and conservation ana lysis suggest that this variant may impact the protein, though this information is not predictive enough to determine pathogenicity. In addition, two amino aci d changes at this position (p.Asn308Ser, p.Asn308Asp) are well established patho genic variants for Noonan syndrome further suggesting that a change at this posi tion may not be tolerated. In summary, this variant meets our criteria to be cla ssified as pathogenic for Noonan syndrome in an autosomal dominant manner based upon frequency in probands and absence from controls.

The p.N308T pathogenic mutation (also known as c.923A>C), located in coding exon 8 of the PTPN11 gene, results from an A to C substitution at nucleotide position 923. The asparagine at codon 308 is replaced by threonine, an amino acid with similar properties. In one study, this mutation was detected in an individual with a clinical diagnosis of Noonan syndrome (Pierpont EI, et al. Genes Brain Behav. 2009;8(3):275-82). This mutation was also described in two individuals who likely had clinical diagnoses of either Noonan syndrome or Leigus syndrome; however, clinical diagnoses were not confirmed (Tartaglia M et al. Am J Hum Genet. 2006; 78(2):279-290). The Asn308 residue has been presented as a mutational hot spot, and two different mutations located in this same residue, p.N308S and p.N308D, have been described in multiple individuals with Noonan syndrome (Qiu W, et al. BMC Struct. Biol. 2014;14():10); Tartaglia M, et al. Nat. Genet. 2001;29(4):465-8; Zenker M, et al. J. Pediatr. 2004;144(3):368-74). Based on the supporting evidence, p.N308T is interpreted as a disease-causing mutation.

ACMG categories: PS1,PM2,PM7,PP3,PP5

Absent from controls (or at extremely low frequency if recessive) in Genome Aggregation Database, Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium.;The prevalence of the variant in affected individuals is significantly increased compared to the prevalence in controls.;Multiple lines of computational evidence support a deleterious effect on the gene or gene product (conservation, evolutionary, splicing impact, etc).;Novel missense change at an amino acid residue where a different missense change determined to be pathogenic has been seen before.;Missense variant in a gene that has a low rate of benign missense variation and where missense variants are a common mechanism of disease.

The PTPN11 c.923A>C; p.Asn308Thr variant (rs121918455, ClinVar Variation ID: 40535), is reported in the literature in several individuals with a clinical diagnosis of Noonan syndrome (Boleti 2023, Daoud 2019, Liu 2022, McCallen 2019, Ndiaye 2014, Pierpont 2009, Shoji 2019, Tartaglia 2006, Weaver 2022, Zenker 2004). This variant is absent from the Genome Aggregation Database (v2.1.1), indicating it is not a common polymorphism. Computational analyses predict that this variant is deleterious (REVEL: 0.941). Additionally, other variants at this codon (c.922A>G, p.Asn308Asp; c.923A>G, p.Asn308Ser) have been reported in individuals with Noonan syndrome and are considered pathogenic (Tartaglia 2001, Tartaglia 2002). Based on available information, this variant is considered to be pathogenic. References: Boleti OD et al. Sudden cardiac death in childhood RASopathy-associated hypertrophic cardiomyopathy: Validation of the HCM risk-kids model and predictors of events. Int J Cardiol. 2023 Dec 15;393:131405. PMID: 37777071. Daoud E, Zwick D. Noonan Syndrome Case Report: PTPN11 and Other Potential Genetic Factors Contributing to Lethal Hypertrophic Right Ventricular Cardiomyopathy. Pediatr Dev Pathol. 2019 Jul-Aug;22(4):386-390. PMID: 30665336. Liu M et al. Genetics etiologies and genotype phenotype correlations in a cohort of individuals with central conducting lymphatic anomaly. Eur J Hum Genet. 2022 Sep;30(9):1022-1028. PMID: 35606495. McCallen LM et al. Cardiac transplantation in children with Noonan syndrome. Pediatr Transplant. 2019 Sep;23(6):e13535. PMID: 31259454. Ndiaye R et al. Mutation N308T of protein tyrosine phosphatase SHP-2in two Senegalese patients with Noonan syndrome. J Med Genet Gen. 2014 6(1): 6-10. Pierpont EI et al. Genotype differences in cognitive functioning in Noonan syndrome. Genes Brain Behav. 2009 Apr;8(3):275-82. PMID: 19077116. Shoji Y et al. Genotype-phenotype correlation analysis in Japanese patients with Noonan syndrome. Endocr J. 2019 Nov 28;66(11):983-994. PMID: 31292302. Tartaglia M et al. Diversity and functional consequences of germline and somatic PTPN11 mutations in human disease. Am J Hum Genet. 2006 Feb;78(2):279-90. PMID: 16358218. Tartaglia M et al. Mutations in PTPN11, encoding the protein tyrosine phosphatase SHP-2, cause Noonan syndrome. Nat Genet. 2001 Dec;29(4):465-8. PMID: 11704759. Tartaglia M et al. PTPN11 mutations in Noonan syndrome: molecular spectrum, genotype-phenotype correlation, and phenotypic heterogeneity. Am J Hum Genet. 2002 Jun;70(6):1555-63. PMID: 11992261. Weaver KN et al. Prevalence of Genetic Diagnoses in a Cohort With Valvar Pulmonary Stenosis. Circ Genom Precis Med. 2022 Aug;15(4):e003635. PMID: 35666834. Zenker M et al. Genotype-phenotype correlations in Noonan syndrome. J Pediatr. 2004 Mar;144(3):368-74. PMID: 15001945.

For these reasons, this variant has been classified as Pathogenic. This variant disrupts the p.Asn308 amino acid residue in PTPN11. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 11992261, 19077116, 21340158; s16358218). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt PTPN11 protein function. ClinVar contains an entry for this variant (Variation ID: 40535). This missense change has been observed in individual(s) with clinical features of Noonan syndrome (PMID: 28921562, 28991257). In at least one individual the variant was observed to be de novo. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces asparagine, which is neutral and polar, with threonine, which is neutral and polar, at codon 308 of the PTPN11 protein (p.Asn308Thr).

PTPN11: PS2, PM2, PM5, PP3, PS4:Supporting

Variant summary: PTPN11 c.923A>C (p.Asn308Thr) results in a non-conservative amino acid change located in the PTP type protein phosphatase (IPR000242) of the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant was absent in 251440 control chromosomes (gnomAD). c.923A>C has been reported in the literature in multiple individuals affected with Noonan Syndrome and Related Conditions (e.g. Tartaglia_2006, Lee_2008, Pierpont_2009, Wilbe_2017). These data indicate that the variant is very likely to be associated with disease. In addition, other variants at the same codon have been reported to be associated with Noonan Syndrome, indicating it as a hotspot. Two clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 and cited the variant as pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic.

Identified in patients with cystic hygroma and other abnormal ultrasound findings in published literature (Wilbe et al., 2017; Lee et al., 2009); Not observed in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Missense variants in this gene are often considered pathogenic (HGMD); This variant is associated with the following publications: (PMID: 18759865, 29057136, 15001945, 24803665, 28921562, 28991257, 19077116, 33318624, 32978145, 32368696, 11992261, 9491886, 16053901, 29493581)

PP2, PP3, PM1, PM2_supporting, PS2, PS4

The PTPN11 c.923A>C variant is predicted to result in the amino acid substitution p.Asn308Thr. This variant has been reported in at least four individuals with Noonan syndrome (Tartaglia et al. 2005. PubMed ID: 16358218; Pierpont et al. 2008. PubMed ID: 19077116; Table S9 - Jin et al. 2017. PubMed ID: 28991257). Additionally, this variant has been reported in three affected fetuses with features consistent with Noonan syndrome (Lee et al. 2008. PubMed ID: 18759865; Wilbe et al. 2017. PubMed ID: 28921562). Both de novo inheritance and gonadal mosaicism have been documented (Wilbe et al. 2017. PubMed ID: 28921562; Table S9 - Jin et al. 2017. PubMed ID: 28991257). This variant has not been reported in a large population database, indicating this variant is rare. Different amino acid substitutions (p.Asn308Asp and p.Asn308Ser) affecting the same amino acid have been reported as pathogenic (Human Gene Mutation Database). This variant is interpreted as pathogenic.