ClinVar Genomic variation as it relates to human health

Variant summary: The PTPN11 c.844A>G variant affects a conserved nucleotide, resulting in an amino acid change from Ile to Val in functionally important protein tyrosine phosphatase (PTP) domain. 2/4 in-silico tools predict this variant to be damaging, and published functional studies are consistent with the variant being an activating mutation; gain of function is a known molecular mechanism in Noonan Syndrome. This variant was not found in approximately 118834 control chromosomes; however, the variant is a known recurrent pathogenic mutation causing Noonan Syndrome reported in the literature. It has been reported in sporadic as well as familial Noonan cases. Additionally, multiple clinical laboratories have classified this variant as pathogenic. Taken together, this variant has been classified as a Disease Variant/Pathogenic.

PS3, PS4, PM1, PM2, PP2

Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as Pathogenic. Following criteria are met: 0103 - Both loss of function and gain of function are known mechanisms of disease for this gene. Metachondromatosis (MIM#156250) and Noonan syndrome with multiple lentigines have been associated with loss of function variants, whereas Noonan syndrome 1 (MIM#163950) is caused by gain of function variants (PMIDs: 11992261, 24935154, 21533187). (I) 0107 - This gene is associated with autosomal dominant disease. (I) 0115 - Variants in this gene are known to have variable expressivity (GeneReviews). (I) 0200 - Variant is predicted to result in a missense amino acid change from isoleucine to valine. (I) 0251 - This variant is heterozygous. (I) 0302 - Variant is present in gnomAD (v3) <0.001 for a dominant condition (1 heterozygote, 0 homozygotes). (SP) 0502 - Missense variant with conflicting in silico predictions and uninformative conservation. (I) 0600 - Variant is located in the annotated protein-tyrosine phosphatase domain (DECIPHER). (I) 0801 - This variant has strong previous evidence of pathogenicity in unrelated individuals. This variant has been reported many times as pathogenic, and observed in individuals with Noonan syndrome and LEOPARD syndrome (ClinVar). (SP) 1208 - Inheritance information for this variant is not currently available in this individual. (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign

The p.Ile282Val variant in PTPN11 has been reported in >20 individuals with clin ical features of Noonan syndrome or LEOPARD syndrome (Tartaglia 2001, Tartaglia 2002, Mustane 2003, Binder 2005, Tartaglia 2006, Jongmans 2011, LMM unpublished data), and is absent from large population studies. In addition, functional evid ence suggests that this variant increases the activity of the PTPN11 protein, wh ich is consistent with other pathogenic variants in PTPN11 (Fragale 2004, Tartag lia 2006, Martinelli 2008). In summary, this variant meets our criteria to be cl assified as pathogenic for Noonan syndrome and LEOPARD syndrome in an autosomal dominant manner (http://www.partners.org/personalizedmedicine/LMM).

Same nucleotide change resulting in same amino acid change has been previously reported as pathogenic/likely pathogeic with strong evidence and observed in at least four similarly affected unrelated individuals (ClinVar ID: VCV000040525.21, PMID: 24037001, 22488759, and 21784453, 18372317, PS1 and PS4). It is not observed in the gnomAD v2.1.1 dataset (PM2). A different missense change at the same codon (p.Arg78Cys) has been reported as pathogenic/likely pathogenic with strong evidence (ClinVar ID: VCV000158442.1, PM5). Missense changes are a common disease-causing mechanism (PP2). Patient's phenotype is considered compatible with Noonan syndrome (3billion dataset, PP4).Therefore, this variant is classified as pathogenic according to the recommendation of ACMG/AMP guideline.

PS3, PS4, PM2, PP2

The PTPN11 c.844A>G; p.Ile282Val variant (rs397507529) is reported in the literature in several individuals affected with noonan syndrome including multiple de novo occurrences (Binder 2005, Inoue 2020, Jongmans 2011, Pierpont 2009, Tartaglia 2001, Tartaglia 2003, Yang 2018). This variant occurs within the highly conserved phosphotyrosine phosphatase (PTP) domain and in vitro/in vivo functional analyses demonstrate a significant increase in basal level phosphatase activity consistent with the gain-of-function disease mechanisms of noonan syndrome (Fragale 2004, Martinelli 2008, Tartaglia 2006). This variant is also reported in ClinVar (Variation ID: 40525). This variant is absent from the Genome Aggregation Database, indicating it is not a common polymorphism. The isoleucine at codon 282 is highly conserved, but computational analyses are uncertain whether this variant is neutral or deleterious (REVEL: 0.525). Based on available information, this variant is considered to be pathogenic. References: Binder G et al. PTPN11 mutations are associated with mild growth hormone resistance in individuals with Noonan syndrome. J Clin Endocrinol Metab. 2005 Sep;90(9):5377-81. PMID: 15985475. Fragale A et al. Noonan syndrome-associated SHP2/PTPN11 mutants cause EGF-dependent prolonged GAB1 binding and sustained ERK2/MAPK1 activation. Hum Mutat. 2004 Mar;23(3):267-77. PMID: 14974085. Inoue T et al. Contribution of gene mutations to Silver-Russell syndrome phenotype: multigene sequencing analysis in 92 etiology-unknown patients. Clin Epigenetics. 2020 Jun 16;12(1):86. PMID: 32546215. Jongmans MC et al. Cancer risk in patients with Noonan syndrome carrying a PTPN11 mutation. Eur J Hum Genet. 2011 Aug;19(8):870-4. PMID: 21407260. Martinelli S et al. Diverse driving forces underlie the invariant occurrence of the T42A, E139D, I282V and T468M SHP2 amino acid substitutions causing Noonan and LEOPARD syndromes. Hum Mol Genet. 2008 Jul 1;17(13):2018-29. PMID: 18372317. Pierpont EI et al. Genotype differences in cognitive functioning in Noonan syndrome. Genes Brain Behav. 2009 Apr;8(3):275-82. PMID: 19077116. 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. Somatic mutations in PTPN11 in juvenile myelomonocytic leukemia, myelodysplastic syndromes and acute myeloid leukemia. Nat Genet. 2003 Jun;34(2):148-50. PMID: 12717436. Yang L et al. Pathogenic gene screening in 91 Chinese patients with short stature of unknown etiology with a targeted next-generation sequencing panel. BMC Med Genet. 2018 Dec 12;19(1):212. PMID: 30541462.

The c.844A>G (p.I282V) alteration is located in coding exon 7 of the PTPN11 gene. This alteration results from a A to G substitution at nucleotide position 844, causing the isoleucine (I) at amino acid position 282 to be replaced by a valine (V). This variant is unlikely to be causative of Metachondromatosis; however, it would be expected to be causative of PTPN11-related RASopathy based on mechanism of disease. Based on data from gnomAD, the G allele has an overall frequency of 0.0006571% (1/152190) total alleles studied. The highest observed frequency was 0.006548% (1/15272) of Latino/Admixed American alleles. This alteration has been reported in multiple patients in the literature with Noonan syndrome (Tartaglia, 2001; Musante, 2003; Tartaglia, 2006) and as de novo in multiple individuals with clinical features consistent with PTPN11-related RASopathy (Swarts, 2022; DECIPHER v.9.32). Another alteration at the same codon, c.846C>G (p.I282M), has been detected in individuals who have a phenotype consistent with Noonan syndrome (Atik, 2016; Kruszka, 2017; Chinton, 2019; Castellanos, 2020). This amino acid position is highly conserved in available vertebrate species. The p.I282 amino acid is located in the PTP (catalytic) domain of the SHP-2 protein. It contributes to the hydrophobic region binding the pY-phenyl ring and interacts with N-SH2 domain residues (Tartaglia, 2006). The SHP-2 protein switches between inactive and active conformations, depending on its binding to phosphotyrosyl (pY)&ndash;containing signaling partners. In the unliganded inactive conformation, the N-SH2 domain interacts extensively with the PTP domain, blocking the active site. Functional analysis demonstrated that the p.I282V alteration perturbs the stability of the N-SH2/PTP interaction required to maintain SHP2 in its catalytically inactive conformation. This in combination with an increased intrinsic catalytic activity results in a 3-fold upregulation of SHP-2 activity (Martinelli, 2008). The in silico prediction for this alteration is inconclusive. Based on the available evidence, this alteration is classified as pathogenic.

Published functional studies show that I282V exhibits a gain-of-function effect on the protein (Fragale et al., 2004; Martinelli et al., 2008); The majority of missense variants in this gene are considered pathogenic (Stenson et al., 2014); Not observed in large population cohorts (Lek et al., 2016); This variant is associated with the following publications: (PMID: 24803665, 15985475, 16263833, 21407260, 14974085, 18372317, 15834506, 19077116, 12634870, 11992261, 24183200, 24037001, 22488759, 21784453, 16377799, 11704759, 30541462, 30417923, 30050098, 29907801, 31560489, 32546215, 33300679, 34006472, 33728303)

This variant has been reported in the literature in at least 7 individuals with a clinical diagnosis or suspicion of Noonan syndrome and other RASopathies, including 2 reported de novo cases, and segregating with disease in at least 1 affected family member (selected publications: Tartaglia 2001 PMID:11704759; Jongmans 2011 PMID:21407260; Bessis 2019 PMID:30417923; Lores 2020 PMID:33300679). This variant is present in 0.007% (1/15272) of Latino alleles in the Genome Aggregation Database (https://gnomad.broadinstitute.org/variant/12 112473031 A G?dataset=gnomad_r3). Please note, disease causing variants may be present in control databases at low frequencies, reflective of the general population, carrier status, and/or variable expressivity. This variant is present in ClinVar, with several labs classifying this variant as pathogenic (Variation ID:40525). Of note, this variant occurs in a gene with a high burden of pathogenic missense variants, consistent with a gain of function mechanism (Gelb 2018 PMID:29493581). In vitro functional studies predict that this variant will impact the protein (Fragale 2004 PID:14974085; Martinelli 2008 PMID:18372317). However, these studies may not accurately represent in vivo biological function. Evolutionary conservation and computational predictive tools support that this variant may impact the protein. In summary, this variant is classified as pathogenic.

This sequence change replaces isoleucine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 282 of the PTPN11 protein (p.Ile282Val). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individuals with Noonan syndrome (PMID: 11704759, 15834506, 19077116, 21407260). ClinVar contains an entry for this variant (Variation ID: 40525). Advanced modeling performed at Invitae incorporating data from internal and/or published experimental studies (Invitae) indicates that this missense variant is expected to disrupt PTPN11 function. Experimental studies have shown that this missense change affects PTPN11 function (PMID: 14974085, 15834506, 18372317). For these reasons, this variant has been classified as Pathogenic.

Criteria applied: PS3,PS4_MOD,PM1,PM5,PM2_SUP,PP3