The PTPN11 NM_002834.5:c.226G>A (NP_002825.3:p.(Glu76Lys)) missense variant has previously been reported in somatic cancers (COSMIC; COSV61004889, n = 184 times), and lies in a statistically significant hotspot (cancerhotspots.org). Experimental evidence: E76K is listed in the approved PTPN11 SHP-2 phosphatase assay's P/LP/VUS validation controls, satisfying the VCEP one-approved-assay rule. Based on available guidelines, this variant is considered to be a Variant of Uncertain Significance (VUS).
Five-step scale from benign to pathogenic. This variant is uncertain. Select a step to read what it means.
Uncertain.The recorded classification is uncertain significance.
Gene-level background from the recorded interpretation.
Words with a dotted underline have a short definition. Hover or tap them.PTPN11 encodes SHP2, a protein tyrosine phosphatase that helps regulate signaling pathways controlling cell growth, development, metabolism, and movement. Inherited changes in PTPN11 are associated with Noonan syndrome and LEOPARD syndrome, which can increase the risk of juvenile myelomonocytic leukemia and related blood disorders. PTPN11 acts as an oncogene, and acquired changes in the gene occur in several cancers, especially juvenile myelomonocytic leukemia.
The recorded framework is ClinGen PTPN11 VCEP v2.3. The criteria and strengths shown below come from the saved assessment; this page does not recalculate the classification.
The applied criteria and their strengths are shown as assessed under the stated framework.
Met, supporting: E76K is listed in the approved PTPN11 SHP-2 phosphatase assay's P/LP/VUS validation controls, satisfying the VCEP one-approved-assay rule.
Met at Moderate: residue 76 falls within the VCEP-approved directly interacting N-SH2/PTPN domain interval of amino acids 69-77.
Met at Supporting: the variant was absent from all-comers gnomAD v2.1 and v4.1 and from the available non-cancer subsets.
Met (Supporting): REVEL score 0.863 meets the VCEP PP3 missense threshold of >= 0.7.
No benign criterion marked as applied in the recorded assessment.
VUS: PS3 (supporting), PM1 (moderate), PM2 (supporting), and PP3 (supporting) do not satisfy any PTPN11 VCEP combination rule.
Evidence summaries and captured source records, where available. Missing entries should not be interpreted as negative findings.
gnomAD v4.1 allele counts were not recorded for this variant.
Absent from gnomAD v2.1.
Not available in gnomAD-Canada v1.0.
Recorded REVEL score: 0.863. Refer to the recorded PP3/BP4 rationale for interpretation.
8 Pathogenic · 1 Uncertain significance. ClinVar API review status: criteria provided, conflicting classifications.
OncoKB identified variant-specific curated literature and context relevant to functional review; biological-effect context: Gain-of-function; curated oncogenicity label: Oncogenic.
This variant has previously been reported in somatic cancers (COSMIC; COSV61004889, n = 184 times).
This variant lies in a statistically significant hotspot.
ACMG/AMP criteria under ClinGen PTPN11 VCEP v2.3, with the data and sources behind each one.
28 criteria with recorded statuses: 4 met · 5 not met · 9 not assessed · 10 not applicable. Open any row for the full reasoning, the rule and the evidence behind it.
All four requested segregation/de novo criteria are not_assessed because the available evidence does not document parental testing, de novo status, family segregation, non-segregation, or informative meioses.
PS4 is not assessed because the available E76K report is a somatic myeloid-malignancy observation without VCEP-compatible germline RASopathy phenotype-specific case-control data or a point score.
PP4, PP5, and BP6 are not applicable under the PTPN11 VCEP; BP5 is not assessed because no alternate molecular cause or VCEP point score is documented.
No criteria match.
The ClinGen RASopathy VCEP approved-functional-studies table lists the PTPN11 SHP-2 phosphatase activity assay as approved. This gene-specific assay measures substrate dephosphorylation, includes WT and vector controls, three to four independent technical experiments, 16 pathogenic/likely pathogenic validation controls and 17 benign/likely benign validation controls, and defines increased dephosphorylation as abnormal. The queried E76K variant is explicitly included among the P/LP/VUS validation controls for this approved assay. The VCEP PS3 rule assigns Supporting strength when one approved assay is available; therefore PS3 is met at Supporting strength. PMID:14644997 independently reports E76K-associated increased Ba/F3-cell survival after IL-3 withdrawal, but its ERK/Akt phosphorylation results were not uniformly increased and are not used to upgrade the VCEP-calibrated strength.
Well-established in vitro or in vivo functional studies supportive of a damaging effect on the gene or gene product. Approved assays are available in the supplemental materials. ... One approved assay.
The VCEP limits PM1 to critical, well-established functional domains listed in its supplementary table and specifies directly interacting residues between the N-SH2 and PTPN domains, including amino acids 69-77. The variant is p.Glu76Lys at residue 76, which lies within the explicitly listed 69-77 interval; no domain_tables entry is present for PTPN11 in vcep_materials.json. The variant is not excluded as a specific residue under PM1 because the rule's exclusion refers to the separate PM5 route, while the applicable evidence here is domain membership.
Applicable only to critical and well-established functional domains available in the supplementary table (Directly interacting residues between N-SH2 and PTPN domains [AA 4, AA 7-9, AA 58-63, AA 69-77, AA 247, AA 251, AA 255, AA 256, AA 258, AA 261, AA 265, AA 278-281, AA 284]). Not applicable to specific amino acid residues (see PM5).
The PTPN11 VCEP applies PM2 at Supporting strength when the variant is absent from controls in gnomAD. NM_002834.5:c.226G>A (p.Glu76Lys) was absent from all-comers gnomAD v2.1 and v4.1, and was also absent from gnomAD v2.1 non-cancer exomes and gnomAD v3.1 non-cancer genomes; PM2 Supporting is met.
The variant must be absent from controls (gnomAD).
The variant is missense, NP_002825.3:p.(Glu76Lys), so the VCEP's missense PP3 path applies. The governing rule requires REVEL >= 0.7 for missense variants. The available REVEL score is 0.863, which meets that threshold; this is sufficient for PP3 Supporting. The SpliceAI result (maximum delta score 0.021) is not used for PP3 because the missense path is independently satisfied by the named REVEL predictor, and the same splice prediction is not double-counted in another criterion.
For missense variants: REVEL >= 0.7. For splicing impact, predicted outcome must match disease mechanism.
The VCEP requires the same amino acid change as a previously established pathogenic PTPN11 variant regardless of nucleotide change. The available literature and ClinVar material document the queried NM_002834.5:c.226G>A, p.(Glu76Lys) variant itself, including its occurrence in leukemia, but do not document a different nucleotide change producing the same p.Glu76Lys amino acid change as a previously established pathogenic variant. Therefore PS1 is not met.
Same amino acid change as a previously established pathogenic variant in _PTPN11_ regardless of nucleotide change.
The VCEP assigns PM5 at Moderate strength for one likely pathogenic residue change at the same codon, and Strong strength only for at least two different likely pathogenic residue changes at the same codon observed in at least five probands. The supplied PM5 comparator collection contains eight candidates but zero same-residue candidates, so neither PM5 threshold is met.
≥2 different [likely] pathogenic residues changes at the same codon observed in ≥5 probands. ... 1 [likely] pathogenic residue change at the same codon.
The PTPN11 VCEP requires a gnomAD filtering allele frequency of at least 0.05% for BA1. NM_002834.5:c.226G>A (p.Glu76Lys) was absent from all-comers gnomAD v2.1 and v4.1, and also absent from gnomAD v2.1 non-cancer exomes and gnomAD v3.1 non-cancer genomes; therefore the BA1 frequency threshold is not met.
GnomAD filtering allele frequency ≥0.05%.
The PTPN11 VCEP requires a gnomAD filtering allele frequency of at least 0.025% for BS1. NM_002834.5:c.226G>A (p.Glu76Lys) was absent from all-comers gnomAD v2.1 and v4.1, and also absent from gnomAD v2.1 non-cancer exomes and gnomAD v3.1 non-cancer genomes; therefore the BS1 frequency threshold is not met.
GnomAD filtering allele frequency ≥0.025%.
The variant is missense, so BP4 is within the VCEP rule's stated scope. The governing rule requires REVEL <= 0.3 for missense variants. The available REVEL score is 0.863, which does not meet the <= 0.3 benign-prediction threshold. Therefore BP4 is not met. The low SpliceAI score is not substituted for the VCEP's named missense predictor and is not independently used for BP4.
For missense variants: REVEL <= 0.3.
The available case evidence does not document that the PTPN11 c.226G>A (p.Glu76Lys) variant is de novo, does not identify parental genotypes, and does not provide a VCEP de novo point count. Therefore, the VCEP PS2 strength cannot be assigned.
4 Points. ... 2 Points. ... 1 Point.
The PTPN11 VCEP defines PS4 using point-based scoring for autosomal-dominant cases with RASopathy phenotypic specifications. Its governing rule requires that the prevalence of the variant in affected individuals be significantly increased versus controls; the VCEP reproduces the ACMG/AMP case-control guidance that RR or OR must be >5.0 with a confidence interval excluding 1.0, while multiple unrelated patients with the same phenotype and absence from controls may support moderate evidence in very rare variants. PMID:14644997 verifies NM_002834.5:c.226G>A (p.Glu76Lys) in 3 JMML specimens and 1 AML specimen, but this is a somatic myeloid-malignancy mutation cohort, not a germline RASopathy case-control comparison, and it supplies no affected/control counts, OR or RR, confidence interval, or VCEP PS4 point score. The available evidence therefore cannot evaluate PS4 under this VCEP; no case-control conclusion or strength assignment is made.
Strength adjustment using point-based scoring for autosomal dominant cases with phenotypic specifications: full points awarded with RASopathy phenotypes, reduced points applicable to cases with minimal phenotypic information (i.e. prenatal cases, cases with a clinical order of a RASopathy panel without clinical information, and cases with limited clinical information in other global tests (such as WES)). ... The prevalence of the variant in affected individuals is significantly increased compared to the prevalence in controls. ... Note 1: Relative risk (RR) or odds ratio (OR), as obtained from case-control studies, is >5.0 and the confidence interval around the estimate of RR or OR does not include 1.0. See manuscript for detailed guidance. ... Note 2: In instances of very rare variants where case-control studies may not reach statistical significance, the prior observation of the variant in multiple unrelated patients with the same phenotype, and its absence in controls, may be used as moderate level of evidence. ... ≥5 points. ... ≥3 points. ... ≥1 points.
The available evidence does not document an apparently de novo occurrence without parental testing, nor does it provide the VCEP point assignment for such evidence. The VCEP PM6 criterion therefore cannot be evaluated.
2 Points. ... 1 Point. ... 0.5 Points.
The available case evidence contains no documented affected relatives, family segregation results, or informative meioses for NM_002834.5:c.226G>A (p.Glu76Lys). The VCEP PP1 thresholds therefore cannot be evaluated.
≥7 informative meioses. ... ≥5 informative meioses. ... ≥3 informative meioses.
The VCEP requires a missense z score greater than 3.09 in gnomAD. The supplied case evidence contains no PTPN11 missense z score, so the criterion cannot be evaluated under the VCEP rule without substituting an unapproved metric.
Missense z score is >3.09 in gnomAD.
The PTPN11 VCEP evaluates BS2 using point-based scoring from healthy homozygote or heterozygote observations, with reduced points for apparently unaffected heterozygotes and applicability to parent or sibling samples during clinical family evaluations. The available population evidence documents absence from gnomAD but does not document a qualifying healthy homozygote or heterozygote, unaffected parent or sibling, phenotype assessment, or BS2 point assignment; therefore BS2 cannot be assessed.
Strength adjustment using point-based scoring based on phenotypic specifications. Phenotypic specifications: based on healthy homozygote or heterozygote individuals, reduced points for apparently unaffected heterozygous individuals, applicable to parent or sibling samples during clinical family evaluations.
The available case evidence does not document an unaffected relative who carries the variant, a non-segregation observation, or any informative meiosis. The VCEP BS4 requirement cannot therefore be evaluated.
Requires only one informative meiosis.
The VCEP permits BP2 when an alternative molecular cause of a RASopathy is present in the same gene and the phenotype is consistent with the expected severity, with point-based strength thresholds. The available case evidence does not document a second pathogenic variant in cis or trans with NM_002834.5:c.226G>A, establish phase, or provide a qualifying alternative molecular cause and phenotype assessment; therefore no BP2 strength can be assigned.
Points are awarded for an alternative molecular cause of a RASopathy in the same gene (and/or in conjunction with BP5) and the phenotype is consistent with expected severity of the RASopathy.
BP5 is applicable under the PTPN11 VCEP when an alternative molecular cause of a RASopathy in a different gene is present, with a phenotype consistent with the expected severity, or when a phenotype inconsistent with RASopathy is fully explained by a different causative variant. The case evidence contains no alternative causative variant, no alternate-gene molecular diagnosis, no documented phenotype fully explained by another variant, and no BP5 point score. The criterion therefore cannot be evaluated under the VCEP and is not assessed.
Points are awarded for an alternative molecular cause of a RASopathy in a different gene (and/or in conjunction with BP2) and the phenotype is consistent with expected severity of the RASopathy. Points are also awarded for phenotypes inconsistent with a RASopathy and fully explained by a different causative variant (e.g. WES testing). ... ≥ (-4) Points. ... ≥ (-2) Points. ... ≥ (-1) Point.
PVS1 is not applicable under the PTPN11 RASopathy VCEP specification. The assessed variant is NM_002834.5:c.226G>A, a missense change producing p.(Glu76Lys) in exon 3, not a null variant of the types listed in the VCEP's PVS1 summary. The VCEP also explicitly marks PVS1 as not applicable for these RASopathy-specific criteria.
LOF and/or haploinsufficiency has not been clearly identified as disease mechanisms for these genes relative to the RASopathy spectrum phenotype, therefore in general this rule is not applicable. Note that PTPN11 is currently the only gene with a confirmed association to another non-RASopathy disorder due to LOF alleles. Variants in PTPN11 with predicted LOF should not be evaluated by these RASopathy specific criteria, but should defer to non-adjusted criteria.
The ClinGen RASopathy Expert Panel PTPN11 Version 2.3 specification explicitly marks PM3 as not applicable; therefore phase, affected-proband observations, and trans/cis observations cannot activate PM3 in this framework.
Not applicable.
PM4 is not applicable because the VCEP limits this criterion to protein length changes caused by in-frame deletions or insertions in a non-repeat region, or to stop-loss variants. NM_002834.5:c.226G>A is a missense variant, p.(Glu76Lys), with no protein-length change and no stop-loss or in-frame indel consequence.
Protein length changes due to in-frame deletions/insertions in a non-repeat region or stop-loss variants. ... No known repetitive areas in gene. Use as described.
The PTPN11 VCEP explicitly marks PP4 as not applicable and directs evaluation to PS4 instead. PP4 is therefore not used independently.
Not applicable, see PS4.
The PTPN11 VCEP marks PP5 as not applicable and states that the criterion is not for use as recommended by the ClinGen Sequence Variant Interpretation VCEP Review Committee. Independent literature evidence is not converted to PP5.
This criterion is not for use as recommended by the ClinGen Sequence Variant Interpretation VCEP Review Committee.
The PTPN11 Version 2.3 VCEP CSPEC entry explicitly marks BS3 as Not Applicable. BS3 therefore cannot be assigned, regardless of the available functional assay data.
Well-established in vitro or in vivo functional studies show no damaging effect on protein function or splicing.
The VCEP's BP1 rule restricts use to truncating variants, specifically nonsense, frameshift, canonical splice-site, initiation-codon, entire-gene, or multi-exon deletions in genes without established loss-of-function correlation. This variant is a missense substitution, NM_002834.5:c.226G>A p.(Glu76Lys), and does not fall within any named BP1 variant type.
This rule has contraindications for use with RASopathies. Given the disease mechanism is gain-of-function for RASopathies, BP1 should be used for any truncating variant (nonsense, frameshift, affects canonical splice sites, initiation codon, entire gene or multi exon deletion) in genes without established LOF correlation to disease. See the supplemental material regarding dosage sensitivity information for each individual gene and potential association to disorders associated with LOF variants.
BP3 is explicitly marked not applicable by the PTPN11 RASopathy VCEP because there are no known benign repetitive areas in RASopathy genes. The assessed variant is also a missense substitution rather than an in-frame deletion or insertion in a repetitive region.
No known benign repetitive areas in RASopathy genes.
The PTPN11 VCEP marks BP6 as not applicable and states that the criterion is not for use as recommended by the ClinGen Sequence Variant Interpretation VCEP Review Committee. Benign reports are not converted to BP6.
This criterion is not for use as recommended by the ClinGen Sequence Variant Interpretation VCEP Review Committee.
The VCEP BP7 rule applies to synonymous variants and also to intronic positions except canonical splice sites or non-coding variants. This variant is a missense coding variant, NP_002825.3:p.(Glu76Lys), so it lies outside BP7's stated scope. BP7 is therefore not_applicable without evaluating splice-prediction or conservation evidence.
A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved. This rule is also applicable for intronic positions (except canonical splice sites) or non-coding variants and should be used in conjunction with BP4.
Every interpreted variant in PTPN11, mapped onto the exon structure of NM_002834.5. Select a row to find it on the plot.
| Protein | Location | Classification | Link |
|---|
Absent from gnomAD v4.1.
Absent from gnomAD v2.1.
Not available in gnomAD-Canada v1.0.
The variant is missense, NP_002825.3:p.(Glu76Lys), so the VCEP's missense PP3 path applies. The governing rule requires REVEL >= 0.7 for missense variants. The available REVEL score is 0.863, which meets that threshold; this is sufficient for PP3 Supporting. The SpliceAI result (maximum delta score 0.021) is not used for PP3 because the missense path is independently satisfied by the named REVEL predictor, and the same splice prediction is not double-counted in another criterion.
For missense variants: REVEL >= 0.7. For splicing impact, predicted outcome must match disease mechanism.
The variant is missense, so BP4 is within the VCEP rule's stated scope. The governing rule requires REVEL <= 0.3 for missense variants. The available REVEL score is 0.863, which does not meet the <= 0.3 benign-prediction threshold. Therefore BP4 is not met. The low SpliceAI score is not substituted for the VCEP's named missense predictor and is not independently used for BP4.
For missense variants: REVEL <= 0.3.
The VCEP BP7 rule applies to synonymous variants and also to intronic positions except canonical splice sites or non-coding variants. This variant is a missense coding variant, NP_002825.3:p.(Glu76Lys), so it lies outside BP7's stated scope. BP7 is therefore not_applicable without evaluating splice-prediction or conservation evidence.
A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved. This rule is also applicable for intronic positions (except canonical splice sites) or non-coding variants and should be used in conjunction with BP4.
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.02). REVEL score = 0.863. BayesDel score = 0.484499.
7 paper records listed. 1 cited in the classification.
226 G→A Glu76Lys 3
Location Table 1, PTPN11 mutations detected in JMML; Table 3, PTPN11 mutations detected in myeloid malignancies; Results, Functional and biochemical studies in Ba/F3 cells
Context PTPN11 mutation screening in JMML and other myeloid malignancies; retroviral expression of wild-type or mutant SHP-2 in Ba/F3 cells followed by IL-3 withdrawal, survival counting, and ERK/Akt phosphorylation assays.
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The evidence statements recorded by the interpretation pipeline. They have not been reinterpreted by the page.
Absent from gnomAD v4.1.
Absent from gnomAD v2.1.
Not available in gnomAD-Canada v1.0.
This variant has been reported in ClinVar as Pathogenic (8 clinical laboratories) and as Uncertain significance (1 clinical laboratory). (ClinVarID = 13336)
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.02). REVEL score = 0.863. BayesDel score = 0.484499.
OncoKB identified variant-specific curated literature and context relevant to functional review; biological-effect context: Gain-of-function; curated oncogenicity label: Oncogenic.
This variant lies in a statistically significant hotspot. This variant has previously been reported in somatic cancers (COSMIC; COSV61004889, n = 184 times).
This variant lies in a statistically significant hotspot.