ClinVar Genomic variation as it relates to human health

This de novo mutation identified in the PTPN11 gene is one of the well-described mutations causing the LEOPARD syndrome.

The PTPN11 c.836A>G; p.Tyr279Cys variant (rs121918456) is reported in the literature in numerous individuals affected with Noonan syndrome and LEOPARD syndrome, also known as Noonan syndrome with multiple lentigines (Begic 2014, Digilio 2004, Legius 2002, Quaio 2013, Sarkozy 2004, Tartaglia 2002, Wang 2014). This is a recurrent variant reported to cosegregate with disease in families (Begic 2014, Legius 2002) and also observed de novo (Begic 2014, Digilio 2004, Wang 2014). This variant is reported as pathogenic by multiple laboratories in ClinVar (Variation ID: 13328), and it is absent from general population databases (Exome Variant Server, Genome Aggregation Database), indicating it is not a common polymorphism. The tyrosine at codon 279 is highly conserved and interacts with an active site loop required for catalysis (Kontaridis 2006, Qiu 2014), and biochemical analyses demonstrate strongly reduced phosphatase activity of the p.Tyr279Cys variant (Hanna 2006, Qiu 2014). In both cultured cells and mice, the p.Tyr279Cys variant exhibits a dominant negative effect on Erk/MAPK signaling (Kontaridis 2006, Marin 2011), and the mouse model of PTPN11 p.Tyr279Cys recapitulates physiological symptoms of human LEOPARD syndrome, including skeletal abnormalities and hypertrophic cardiomyopathy (Marin 2011). Additionally, another variant at this codon (p.Tyr279Ser) has been reported in an individual with symptoms of LEOPARD syndrome (Sarkozy 2004), reiterating its functional importance. Based on available information, the p.Tyr279Cys variant is considered to be pathogenic. References: Begic F et al. Leopard syndrome: a report of five cases from one family in two generations. Eur J Pediatr. 2014 Jun;173(6):819-22. Digilio MC et al. Familial aggregation of genetically heterogeneous hypertrophic cardiomyopathy: a boy with LEOPARD syndrome due to PTPN11 mutation and his nonsyndromic father lacking PTPN11 mutations. Birth Defects Res A Clin Mol Teratol. 2004 Feb;70(2):95-8. Hanna N et al. Reduced phosphatase activity of SHP-2 in LEOPARD syndrome: consequences for PI3K binding on Gab1. FEBS Lett. 2006 May 1;580(10):2477-82. Kontaridis MI et al. PTPN11 (Shp2) mutations in LEOPARD syndrome have dominant negative, not activating, effects. J Biol Chem. 2006 Mar 10;281(10):6785-92. Legius E et al. PTPN11 mutations in LEOPARD syndrome. J Med Genet. 2002 Aug;39(8):571-4. Marin TM et al. Rapamycin reverses hypertrophic cardiomyopathy in a mouse model of LEOPARD syndrome-associated PTPN11 mutation. J Clin Invest. 2011 Mar;121(3):1026-43. Qiu W et al. Structural insights into Noonan/LEOPARD syndrome-related mutants of protein-tyrosine phosphatase SHP2 (PTPN11). BMC Struct Biol. 2014 Mar 14;14:10. Quaio CR et al. Tegumentary manifestations of Noonan and Noonan-related syndromes. Clinics (Sao Paulo). 2013;68(8):1079-83. Sarkozy A et al. Clinical and molecular analysis of 30 patients with multiple lentigines LEOPARD syndrome. J Med Genet. 2004 May;41(5):e68. 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. Wang Y et al. Leopard syndrome caused by heterozygous missense mutation of Tyr 279 Cys in the PTPN11 gene in a sporadic case of Chinese Han. Int J Cardiol. 2014 Jul 1;174(3):e101-4.

This variant was classified as: Pathogenic. The following ACMG criteria were applied in classifying this variant: PS1,PM1,PM2,PM5,PP2,PP3.

This variant has been reported to occur de novo in multiple individuals with clinical features associated with this gene (PMID: 30732632, 24820750, 14991917, 33258288). Furthermore, it has been reported in multiple unrelated symptomatic individuals (PMID: 12058348, 12161596, 15520399, 11992261, 16172598, 32164556, 24037001, 24401936, 26918529, 28483241, 30692697, 31560489, 31722741). Assessment of experimental evidence suggests this variant results in abnormal protein function (PMID: 16358218, 16638574, 16377799, 18372317). This variant has not been reported in large, multi-ethnic general populations (http://gnomad.broadinstitute.org).This observation is not an independent occurrence and has been identified in the same individual by RCIGM, the other laboratory participating in the GEMINI study.

The PTPN11 c.836A>G variant is predicted to result in the amino acid substitution p.Tyr279Cys. This variant has been well documented in multiple unrelated individuals to be causative for both Noonan and Leopard Syndromes (see for example - Legius et al. 2002. PubMed ID: 12161596; Tartaglia et al. 2002. PubMed ID: 11992261; Sarkozy et al. 2004. PubMed ID: 15121796; Tartaglia and Gelb. 2005. PubMed ID: 16124853). Functional studies demonstrate increased p-MEK/ERK levels, consistent with a gain-of-function mechanism that results in the hyperactivation of the RAS pathway (Kontaridis et al. 2006. PubMed ID: 16377799; Hanna et al. 2006. PubMed ID: 16638574; Martinelli et al. 2008. PubMed ID: 18372317; Schramm et al. 2013. PubMed ID: 23673659; Yu et al. 2014. PubMed ID: 24935154). Additionally, a knockin mouse model of this variant demonstrates features consistent with Noonan syndrome (Marin et al. 2011. PubMed ID: 21339643). This variant has not been reported in a large population database (http://gnomad.broadinstitute.org), indicating this variant is rare. This variant is interpreted as pathogenic.

The variant was detected in a neonate with congenital intrauterine revealed myocardial hypertrophy. The main clinical sign was myocardial hypertrophy and cardiac output deficit due to reduced LV cavity. No morphological signs of Noonan syndrome were observed. The variant was detected in combination with CBL NM_005188: exon11: c.G1754T :p.R585L variant in RAS-pathway (PMID 25731833).

The p.Tyr279Cys variant in PTPN11 has previously been reported in several indivi duals with clinical features of Noonan or LEOPARD syndrome, segregated with dis ease in multiple families, and occured as a de novo variant in sporadic cases (F roster 2003, Tartaglia 2006, Martinelli 2008, Tang 2009, Digilio 2002, Kalev 200 9, Legius 2002, Legius 2002, Oishi 2009). It was absent from large population st udies. In summary, this variant meets our criteria to be classified as pathogeni c for Noonan syndrome and LEOPARD syndrome in an autosomal dominant manner (http ://www.partners.org/personalizedmedicine/LMM).

Variant summary: PTPN11 c.836A>G (p.Tyr279Cys) results in a non-conservative amino acid change located in the Tyrosine specific protein phosphatases domain of the encoded protein sequence. Four of five in-silico tools predict a damaging effect of the variant on protein function. The variant was absent in 245584 control chromosomes (gnomAD). c.836A>G has been reported in the literature in multiple individuals affected with Noonan Syndrome/Leopard Syndrome (Keren_2004, Harakmi_2016). These data indicate that the variant is very likely to be associated with disease. Multiple functional studies have indicated the variant abolishes enzymatic activity of PTPN11 and increases AKT, the variant's mechanism causes a gain of function (Yu_2014). The variant has been established to be a common disease variant by multiple publications. In addition, nine ClinVar submissions from clinical diagnostic laboratories (evaluation after 2014) cite the variant as likely pathogenic/pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic.

Same nucleotide change resulting in same amino acid change has been previously reported as pathogenic/likely pathogeic with strong evidence (ClinVar ID:VCV000013328.26, PS1). The variant has been observed in at least two similarly affected unrelated individuals (3billion dataset, PS4_M). The missense variant is located in a mutational hot spot and/or well-established functional domain in which established pathogenic variants have been reported (PM1). It is not observed in the gnomAD v2.1.1 dataset (PM2). A different missense change at the same codon (p.Tyr279Ser) has been reported as pathogenic/likely pathogenic with strong evidence (ClinVar ID: VCV000065666.4, PMID: 24820750 and 25917897, PM5). The variant was observed as assumed (i.e. paternity and maternity not confirmed) de novoo (3billion dataset, PM6). In silico tool predictions suggest damaging effect of the variant on gene or gene product (REVEL: 0.973, 3Cnet: 0.607, PP3). 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.

Published functional studies demonstrate weakened interactions between the N-SH2 and PTP domains leading to sustained RAS-ERK1/2 activation (Yu et al., 2014; Kontaridis et al., 2006); 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); Not observed in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 15121796, 23312806, 26337637, 12161596, 15520399, 16358218, 20308328, 16172598, 16679933, 24820750, 24628801, 16377799, 16638574, 18372317, 18849586, 24037001, 11992261, 24034393, 24775816, 14991917, 24803665, 22822385, 25917897, 26377839, 19768645, 19725129, 28483241, 20493809, 21339643, 23457302, 23673659, 12058348, 19520282, 30732632, 30692697, 30417923, 26918529, 30050098, 31446693, 29907801, 31560489, 31722741, 32164556, 24935154, 24401936, 32866449, 33318624, 31589614, 33258288, 28252636, 9491886, 16053901, 29493581, 33855281)

PTPN11 NM_002834.4 exon 7 p.Tyr279Cys (c.836A>G): This variant is a well established and commonly reported pathogenic variant in the literature, identified in several individuals with Noonan syndrome/LEOPARD syndrome, including a GeneReviews entry. This variant has been published as segregating with disease in multiple affected family members, and as a de novo occurence (Legius 2002 PMID:12161596, Tartaglia 2002 PMID:11992261, Kalev 2010 PMID:19768645, Begic 2014 PMID:24401936, Gelb 2015 PMID:20301557). This variant is not present in large control databases. This variant is present in ClinVar, with several labs classifying this variant as pathogenic (Variation ID:13328). Evolutionary conservation and computational predictive tools support that this variant may impact the protein. In addition, functional studies (including a drosophila model) have shown a deleterious effect of this variant (Kontaridis 2006 PMID: 16377799, Martinelli 2008 PMID:18372317, Oishi 2009 PMID:18849586). In summary, this variant is classified as pathogenic.

This sequence change replaces tyrosine, which is neutral and polar, with cysteine, which is neutral and slightly polar, at codon 279 of the PTPN11 protein (p.Tyr279Cys). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individuals with Noonan syndrome with multiple lentigines (NSML, also known as LEOPARD syndrome) (PMID: 15520399, 17020470, 22681964, 22822385, 24401936, 24820750, 25917897). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 13328). 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 with a positive predictive value of 95%. Experimental studies have shown that this missense change affects PTPN11 function (PMID: 16377799, 16638574, 18372317, 21339643, 23673659). For these reasons, this variant has been classified as Pathogenic.

The p.Y279C pathogenic mutation (also known as c.836A>G), located in coding exon 7 of the PTPN11 gene, results from an A to G substitution at nucleotide position 836. The tyrosine at codon 279 is replaced by cysteine, an amino acid with highly dissimilar properties. This mutation has been reported in multiple patients and families with a clinical diagnosis of Noonan syndrome or related disorder, most of whom had skin findings including multiple lentigines and/or cafe-au-lait spots, and several patients had hypertrophic cardiomyopathy or other cardiac findings (Tartaglia M, Am. J. Hum. Genet. 2002 Jun; 70(6):1555-63; Keren B, J. Med. Genet. 2004 Nov; 41(11):e117; Carcavilla A, Rev Esp Cardiol (Engl Ed) 2013 May; 66(5):350-6; Conboy E et al. J Med Genet. 2016;53(2):123-6). One study reported this mutation had occurred de novo in the index case, and co-segregated with disease in four affected offspring (Begi F, Eur. J. Pediatr. 2014 Jun; 173(6):819-22). The p.Y279C mutation is one of the most common mutations reported in Noonan syndrome and related disorders, it is in the protein tyrosine phosphatase (PTP) functional domain, and another pathogenic variant at the same codon, p.Y279S, has been reported in affected individuals (Tartaglia M, Eur J Med Genet. 2005 Apr; 48(2):81-96). In addition, a functional study of fibroblasts from individuals heterozygotes for this mutation, and HEK293 cells transfected with this mutation, showed significantly stronger EGF-induced phosphorylation of downstream targets when compared to normal controls (Edouard T, Mol. Cell. Biol. 2010 May; 30(10):2498-507). This variant is considered to be rare based on population cohorts in the Genome Aggregation Database (gnomAD). Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation.

PTPN11: PS1, PM1, PM2, PP2, PP3

Variant classified using ACMG guidelines