rs121918466

chr12-112450416-A-Gchr12-112450416-A-T

Variant summary

Our verdict is Pathogenic. Variant got 19 ACMG points: 19P and 0B. PM1 PM2 PM5 PP2 PP3_Strong PP5_Very_Strong

The NM_002834.5(PTPN11):c.236A>G(p.Gln79Arg) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,582 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. Q79K) has been classified as Likely pathogenic.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 6.8e-7 (0 hom.)
• Consequence: PTPN11 NM_002834.5 missense
• Clinical Significance: Pathogenic criteria provided, multiple submitters, no conflicts P:27
• Conservation: PhyloP100: 9.31

Genes affected

PTPN11 (HGNC:9644): (protein tyrosine phosphatase non-receptor type 11) The protein encoded by this gene is a member of the protein tyrosine phosphatase (PTP) family. PTPs are known to be signaling molecules that regulate a variety of cellular processes including cell growth, differentiation, mitotic cycle, and oncogenic transformation. This PTP contains two tandem Src homology-2 domains, which function as phospho-tyrosine binding domains and mediate the interaction of this PTP with its substrates. This PTP is widely expressed in most tissues and plays a regulatory role in various cell signaling events that are important for a diversity of cell functions, such as mitogenic activation, metabolic control, transcription regulation, and cell migration. Mutations in this gene are a cause of Noonan syndrome as well as acute myeloid leukemia. [provided by RefSeq, Aug 2016]

ACMG classification

Verdict is Pathogenic. Variant got 19 ACMG points.

• PM1: In a hotspot region, there are 4 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 0 benign, 3 uncertain in NM_002834.5
• PM2: Very rare variant in population databases, with high coverage
• PM5: Other missense variant is known to change same aminoacid residue: Variant chr12-112450415-C-A is described in ClinVar as [Likely_pathogenic]. Clinvar id is 44605.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• PP2: Missense variant where missense usually causes diseases, PTPN11
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.964
• PP5: Variant 12-112450416-A-G is Pathogenic according to our data. Variant chr12-112450416-A-G is described in ClinVar as [Pathogenic]. Clinvar id is 13340.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr12-112450416-A-G is described in Lovd as [Likely_pathogenic]. Variant chr12-112450416-A-G is described in Lovd as [Pathogenic]. Variant chr12-112450416-A-G is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PTPN11	NM_002834.5	c.236A>G	p.Gln79Arg	missense_variant	3/16	ENST00000351677.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PTPN11	ENST00000351677.7	c.236A>G	p.Gln79Arg	missense_variant	3/16	1	NM_002834.5	A1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 6.84e-7 AC: 1 AN: 1461582 Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1 AN XY: 727120

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 8.99e-7

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:27

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Noonan syndrome 1 Pathogenic:10

Pathogenic, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Feb 26, 2019	Across a selection of the available literature, the PTPN11 c.236A>G (p.Gln79Arg) missense variant has been identified in a heterozygous state in at least 13 individuals from four unrelated families affected with Noonan syndrome (Schollen et al. 2003; Niihori et al. 2005; Atik et al. 2016). Schollen et al. (2003) reported a large four generation Belgian family with ten affected members, in whom the p.Gln79Arg variant segregated with Noonan syndrome. The p.Gln79Arg variant was absent from 100 healthy controls and is not reported in the Genome Aggregation Database in a region of good sequence coverage, suggesting that it is rare. The Gln79 residue in present in the N-SH2 domain, which functions as an intra-molecular switch to control the protein's catalytic activity (Schollen et al. 2003; Nakamura et al. 2007). Functional studies in HEK293 cells, rat cardiomyocytes and chick valve explants found that the p.Gln79Arg is a gain-of-function variant resulting in increased MAPK 1/2 signaling and thereby increased growth, which can be reversed by use of MAPK 1/2 inhibitors (Niihori et al. 2005; Krenz et al. 2005). In addition, transgenic mice expressing the p.Gln79Arg variant protein in cardiomyocytes during gestation, showed altered cardiomyocyte cell cycling, ventricular noncompaction, and ventricular septal defects (Nakamura et al. 2007). Based on the collective evidence and application of the ACMG criteria, the p.Gln79Arg variant is classified as pathogenic for Noonan syndrome. -
Pathogenic, no assertion criteria provided	literature only	OMIM	Jan 01, 2003	- -
Pathogenic, no assertion criteria provided	clinical testing	Zotz-Klimas Genetics Lab, MVZ Zotz Klimas	Oct 09, 2023	- -
Pathogenic, criteria provided, single submitter	clinical testing	Institute for Genomic Statistics and Bioinformatics, University Hospital Bonn	-	- -
Pathogenic, criteria provided, single submitter	clinical testing	3billion	Jan 03, 2022	he variant has been previously reported as de novo in a similarly affected individual (PMID: 22848035, PS2_S). Same nucleotide change resulting in same amino acid change has been previously reported as pathogenic/likely pathogenic with strong evidence (ClinVar ID: VCV000013340, PS1_S). The variant was co-segregated with Noonan syndrome 1 in multiple affected family members (PMID: 11704759, PP1_P). In silico tool predictions suggest damaging effect of the variant on gene or gene product (REVEL: 0.933, 3CNET: 0.973, PP3_P). A missense variant is a common mechanism associated with Noonan syndrome 1 (PP2_P). It is not observed in the gnomAD v2.1.1 dataset (PM2_M). The variant is located in a well-established functional domain or exonic hotspot, where pathogenic variants have frequently reported (PM1_M). A different missense change at the same codon has been reported as pathogenic/likely pathogenic with strong evidence (ClinVar ID: VCV000044605, PM5_M). TTherefore, this variant is classified as pathogenic according to the recommendation of ACMG/AMP guideline. -
Pathogenic, no assertion criteria provided	research	Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Peking Union Medical College Hospital	May 31, 2019	- -
Pathogenic, criteria provided, single submitter	clinical testing	Center for Human Genetics, Inc, Center for Human Genetics, Inc	Nov 01, 2016	- -
Pathogenic, criteria provided, single submitter	clinical testing	Laboratory of Medical Genetics, National & Kapodistrian University of Athens	Oct 01, 2021	PM1, PM2, PM5, PP3, PP4, PP5 -
Pathogenic, criteria provided, single submitter	clinical testing	Victorian Clinical Genetics Services, Murdoch Childrens Research Institute	Feb 02, 2022	Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as Pathogenic. Following criteria are met: 0103 - Loss of function and gain of function are known mechanisms of disease in this gene. Metachondromatosis (MIM#156250) and Noonan syndrome with multiple lentigines (MIM#151100) are associated with loss of function while Noonan syndrome 1 (MIM#163950) is associated with gain of function (OMIM). (I) 0107 - This gene is associated with autosomal dominant disease. (I) 0115 - Variants in this gene are known to have variable expressivity and associated with Noonan syndrome (GeneReviews). (I) 0200 - Variant is predicted to result in a missense amino acid change from glutamine to arginine. (I) 0251 - This variant is heterozygous. (I) 0301 - Variant is absent from gnomAD (both v2 and v3). (SP) 0309 - An alternative amino acid change at the same position has been observed in gnomAD (v2) (p.(Gln79His): 1 heterozygote, 0 homozygotes). (I) 0502 - Missense variant with conflicting in silico predictions and uninformative conservation. (I) 0602 - Variant is located in a hotspot region or cluster of pathogenic variants (Decipher) within the N terminal SH2 domain (Decipher, NCBI). (SP) 0703 - Other missense variants comparable to the one identified in this case have moderate previous evidence for pathogenicity. The p.(Gln79Lys) and p.(Gln79Pro) variants have been reported in individuals with Noonan syndrome (PMID: 12960218; ClinVar). (SP) 0801 - This variant has strong previous evidence of pathogenicity in unrelated individuals. This variant has been identified in at least ten individuals diagnosed with Noonan syndrome and has been classified as pathogenic by multiple clinical diagnostic laboratories (PMIDs: 16358218, 32164556; ClinVar). (SP) 1203 - This variant has been shown to be de novo in the proband (parental status confirmed) (by trio analysis). (SP) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign -
Pathogenic, criteria provided, single submitter	clinical testing	Genesolutions, Medical Genetics Institutes, Ho Chi Minh City, Vietnam	Jun 22, 2022	- -

not provided Pathogenic:7

Pathogenic, criteria provided, single submitter	clinical testing	Institute for Clinical Genetics, University Hospital TU Dresden, University Hospital TU Dresden	Aug 17, 2022	- -
Pathogenic, criteria provided, single submitter	clinical testing	Mayo Clinic Laboratories, Mayo Clinic	Mar 14, 2022	PP2, PP3, PM1, PM2_supporting, PS2, PS3, PS4 -
Pathogenic, criteria provided, single submitter	clinical testing	Molecular Diagnostics Lab, Nemours Children's Health, Delaware	Sep 29, 2015	- -
Pathogenic, criteria provided, single submitter	clinical testing	Blueprint Genetics	Nov 13, 2018	- -
Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	May 03, 2022	In vitro expression of PTPN11-Q79R in cardiac cell cushions from chick embryos resulted in increased phosphatase activity and significantly increased outgrowth of cushion cells compared to wild-type protein expression (Krenz et al., 2005); Not observed in large population cohorts (gnomAD); Missense variants in this gene are often considered pathogenic (HGMD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Located in the N-SH2 domain (Gelb 2018); This variant is associated with the following publications: (PMID: 22848035, 19017799, 17641779, 11704759, 24803665, 17020470, 16987887, 26855057, 11992261, 29396779, 12529711, 16166557, 19251646, 26607044, 22681964, 27521173, 27348588, 26817465, 12634870, 29084544, 29766225, 30417923, 30050098, 29907801, 31219622, 31560489, 32164556, 33318624, 34008892, 34006472, 35440950, 35178568, 29493581) -
Pathogenic, no assertion criteria provided	clinical testing	Greenwood Genetic Center Diagnostic Laboratories, Greenwood Genetic Center	Jan 15, 2015	- -
Pathogenic, criteria provided, single submitter	clinical testing	Revvity Omics, Revvity	May 07, 2019	- -

Noonan syndrome Pathogenic:3

Pathogenic, no assertion criteria provided	clinical testing	Clinical Molecular Genetics Laboratory, Johns Hopkins All Children's Hospital	Jul 06, 2016	- -
Pathogenic, criteria provided, single submitter	clinical testing	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	Jul 16, 2015	The p.Gln79Arg variant in PTPN11 has been reported in >30 individuals with clini cal features of Noonan syndrome and segregated with disease in >10 affected rela tives (Tartaglia 2001, Tartaglia 2002, Schollen 2003, Musante 2003, Yoshida 2004 , Zenker 2004, Chan 2006, Bertola 2006, LMM unpublished data). This variant has also occurred de novo in multiple affected individuals (LMM unpublished data). I t has not been identified in large population studies. In-vivo animal models and in-vitro studies provide evidence that the p.Gln79Arg variant impacts protein f unction (Krenz 2005, Nakamura 2007). In summary, this variant meets our criteria to be classified as pathogenic for Noonan syndrome in an autosomal dominant man ner based upon segregation studies, de novo occurrences in affected individuals, extremely low frequency in the general population, and functional evidence. -
Pathogenic, no assertion criteria provided	clinical testing	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	May 02, 2014	- -

PTPN11-related condition Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

Feb 13, 2024

The PTPN11 c.236A>G variant is predicted to result in the amino acid substitution p.Gln79Arg. This variant has been identified in many individuals with Noonan syndrome (Tartaglia et al. 2001. PubMed ID: 11704759; Tartaglia et al. 2006. PubMed ID: 16358218; Karbach et al. 2012. PubMed ID: 22848035; van Trier et al. 2016. PubMed ID: 27521173; Xu et al. 2017. PubMed ID: 29084544; Athota et al. 2020. PubMed ID: 32164556). In one family it was found to segregate in 3 affected individuals (Tartaglia et al. 2001. PubMed ID: 11704759) and has been noted as a de novo event in at least two cases (Karbach et al. 2012. PubMed ID: 22848035; Fan et al. 2021. PubMed ID: 34006472). This variant has been interpreted as pathogenic by multiple clinical labs in the ClinVar database (https://www.ncbi.nlm.nih.gov/clinvar/variation/13340/). 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. -

Noonan syndrome 3 Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

Aug 15, 2016

Variant summary: The PTPN11 c.236A>G (p.Gln79Arg) variant involves the alteration of a conserved nucleotide. 3/4 in silico tools predict a damaging outcome for this variant. It is located at N-SH2 domain of the protein (InterPro) which is a known functionally important domain in PTPN11 protein. This variant is absent in 121794 control chromosomes. This variant has been widely reported as a pathogenic variant in literature found in many Noonan Syndrome (NS) and/or Noonan Syndrome and Related Conditions (NSRD), including reports of de novo occurrences and co-segregation with disease (Tartaglia_2001, Schollen_2003, Niihori_2005, Ezquieta_2012, Karback_2012). In vitro studies show that this mutant results in significantly elevated phosphatase activity and endocardial cushion growth (Krenz_2005). Furthermore, in vivo mice expression model showed that this mutant leads to embryonic lethality and the embryonic hearts showed altered cardiomyocyte cell cycling ventricular noncompaction, and ventricular septal defects. Fetal expression of Q79R led to the specific activation of the ERK1/2 pathway, and breeding Q79R transgenics into Erk1/2-null backgrounds confirmed that the pathway was necessary and sufficient for mediating the effects of mutant Shp2 (Nakamura_2007). Another variant at the same residue, p.Q79K, has also been reported in NSRD patients (PMIDs: 12960218, 22848035, 16358218) and is classified as likely pathogenic by a clinical lab in ClinVar. Several clinical diagnostic laboratories/reputable databases have classified this variant as pathogenic. Taken together, this variant is classified as Pathogenic. -

Cardiovascular phenotype Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Ambry Genetics

Jul 03, 2023

The c.236A>G (p.Q79R) alteration is located in exon 3 (coding exon 3) of the PTPN11 gene. This alteration results from an A to G substitution at nucleotide position 236, causing the glutamine (Q) at amino acid position 79 to be replaced by an arginine (R). This clinical significance of this variant is unclear for metachondromatosis; however, it would be expected to be causative of PTPN11-related RASopathy based on mechanism of disease. This variant was not reported in population-based cohorts in the Genome Aggregation Database (gnomAD). This mutation segregated in 3 individuals with Noonan syndrome and was absent from 2 unaffected individuals in one family (Tartaglia, 2001); it was also identified in a sporadic case (Tartaglia, 2001) and de novo in another affected individual (Karbach, 2012). This amino acid position is highly conserved in available vertebrate species. Activity studies in rat neonatal cardiomyocytes showed this alteration results in a gain-of-function of the protein, with a 4.5 times higher activity compared to wild type (Krenz, 2005). This alteration is predicted to be deleterious by in silico analysis. Based on the available evidence, this alteration is classified as pathogenic. -

Juvenile myelomonocytic leukemia;C0410530:Metachondromatosis;C4551484:LEOPARD syndrome 1;C4551602:Noonan syndrome 1 Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Fulgent Genetics, Fulgent Genetics

May 18, 2017

- -

RASopathy Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Invitae

Jan 25, 2024

This sequence change replaces glutamine, which is neutral and polar, with arginine, which is basic and polar, at codon 79 of the PTPN11 protein (p.Gln79Arg). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individual(s) with Noonan syndrome (PMID: 11704759, 11992261, 12529711, 12634870, 17020470, 22848035). In at least one individual the variant was observed to be de novo. It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 13340). 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: 16166557, 17641779, 19017799). For these reasons, this variant has been classified as Pathogenic. -

Noonan syndrome and Noonan-related syndrome Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Genome Diagnostics Laboratory, The Hospital for Sick Children

May 27, 2021

- -

PTPN11 Related Disorders Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Rady Children's Institute for Genomic Medicine, Rady Children's Hospital San Diego

-

This variant has been previously reported as a heterozygous change in patients with Noonan syndrome (PMID: 11704759, 11992261, 12529711, 12634870, 17020470, 22848035). This variant is located in a mutational hotspot for pathogenic variants associated with Noonan syndrome. Pathogenic missense variants at the same amino acid residue (p.Gln79Pro) and nearby amnio acid residues (p.Glu76Asp, p.Glu76Gln, p.Glu76Gly, p.Glu76Val) have been reported in association with Noonan syndrome (PMID: 12960218, 24803665, 3279447, 20308328). Functional studies showed that the c.236A>G (p.Gln79Arg) variant is a gain-of-function variant that induces an increase of phosphatase activity and endocardial cushion growth (PMID: 16166557, 15834506). Animal studies in mice showed altered cardiomyocyte cell cycling, ventricular noncompaction, and ventricular septal defects when the c.236A>G (p.Gln79Arg) variant is present (PMID: 17641779). The c.236A>G (p.Gln79Arg) variant is absent from the gnomAD population database and thus is presumed to be rare. In silico tools used to predict the effect of this variant on protein function yield discordant results. Analysis of the parental samples was negative for the variant, indicating this variant likely occurred as a de novo event. Based on the available evidence, the c.236A>G (p.Gln79Arg) variant is classified as Pathogenic. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.96
CardioboostCm	Uncertain	0.82
BayesDel_addAF	Pathogenic	0.52	D
BayesDel_noAF	Pathogenic	0.50
Cadd	Pathogenic	26
Dann	Uncertain	1.0
Eigen	Uncertain	0.67
Eigen_PC	Pathogenic	0.73
FATHMM_MKL	Pathogenic	0.99	D
LIST_S2	Benign	0.70	T;T;T;T
M_CAP	Pathogenic	0.30	D
MetaRNN	Pathogenic	0.96	D;D;D;D
MetaSVM	Pathogenic	0.98	D
MutationAssessor	Benign	1.4	L;L;.;L
MutationTaster	Benign	1.0	A;A
PrimateAI	Pathogenic	0.88	D
PROVEAN	Uncertain	-3.0	D;D;.;.
REVEL	Pathogenic	0.93
Sift	Uncertain	0.0040	D;D;.;.
Sift4G	Benign	0.11	T;T;.;T
Polyphen		0.85	P;D;.;.
Vest4		0.93
MutPred		0.90		Loss of helix (P = 0.1299);Loss of helix (P = 0.1299);Loss of helix (P = 0.1299);Loss of helix (P = 0.1299);
MVP		1.0
MPC		1.9
ClinPred		0.97	D
GERP RS		5.9
Varity_R		0.89
gMVP		0.72

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs121918466; hg19: chr12-112888220; COSMIC: COSV61005872; COSMIC: COSV61005872;