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PTPN11
Final classification
VUS
PM2PP2PP3
PTPN11
c.200G>A
p.Gly67Glu
This variant

NM_002834.4:c.200G>A (p.Gly67Glu) in PTPN11 is absent from all population databases including gnomAD v2.1, v4.1, and gnomAD-Canada.

Transcript
NM_002834.4
HGVS · transcript:coding
NM_002834.4:c.200G>A
GRCh38
chr12:112450380 G>A
GRCh37
chr12:112888184 G>A
Basis ClinGen RASopathy Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for PTPN11 Version 2.3.0 v2.3.0 criteria-combination framework was evaluated deterministically with applied criteria: PM2 supporting, PP2 supporting, PP3 supporting; no rule matched the adjudicated criteria.
ClinGen RASopathy Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for PTPN11 Version 2.3.0 v2.3.0 criteria-combination framework was evaluated deterministically with applied criteria: PM2 supporting, PP2 supporting, PP3 supporting; no rule matched the adjudicated criteria.
Classification rationale
PM2PP2PP3 VUS
PTPN11 c.200G>A

NM_002834.4:c.200G>A (p.Gly67Glu) in PTPN11 is absent from all population databases including gnomAD v2.1, v4.1, and gnomAD-Canada.1 PTPN11 has a gnomAD missense z-score >3.09, indicating strong constraint against missense variation and supporting pathogenicity under PP2 at Supporting strength per RASopathy VCEP specifications.2 REVEL in silico prediction score is 0.89, exceeding the VCEP threshold of 0.70 for PP3 at Supporting strength, consistent with a deleterious effect on protein function.3 The variant does not meet criteria for PS1 (no known pathogenic G67E), PM1 (position 67 is outside the VCEP-defined critical functional domain residue set), PM5 (no pathogenic comparators at codon 67), or any other pathogenic criterion above Supporting strength.4 With PM2_Supporting, PP2_Supporting, and PP3_Supporting met (three Supporting-level pathogenic criteria), the variant does not satisfy any Pathogenic or Likely Pathogenic combination rule in the RASopathy VCEP Version 2.3.0 framework. No Likely Pathogenic rule is triggered with fewer than four Supporting criteria in the absence of Moderate or Strong evidence. The variant is classified as a Variant of Uncertain Significance (VUS).5

PM2 + PP2 + PP3 VUS
Gene diagram · NM_002834.4 · variants mapped to exon structure
PTPN11 NM_002834.4
Fetching transcript structure from UCSC…
Applied criteria · 3 applied · 15 assessed
MetEvidence satisfies this criterion.
Not metEvaluated against available evidence; threshold not reached.
Not assessedApplies in principle, but no evidence was found to evaluate it.
N/ADoesn't apply to this variant type.
Applied · 3
Strength Supporting Moderate Strong Very strong
PM2 supporting Pathogenic
The variant is absent from all population databases: gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada v1.0. Per RASopathy VCEP specifications, PM2 is downgraded to Supporting strength when the variant is absent from controls.
Absent from gnomAD v2.1 (0 alleles).Absent from gnomAD v4.1 (0 alleles).Absent from gnomAD-Canada v1.0 (0 alleles).
PP2 supporting Pathogenic
PTPN11 has a gnomAD missense z-score substantially exceeding 3.09, indicating strong constraint against missense variation. Per RASopathy VCEP specifications, a missense z-score >3.09 qualifies for PP2 at Supporting strength.
PTPN11 gnomAD missense z-score >3.09consistent with a gene where missense variants are a common disease mechanism and benign missense variation is depleted.
PP3 supporting Pathogenic
REVEL score is 0.89, which exceeds the RASopathy VCEP threshold of ≥0.7 for PP3 at Supporting strength. Additionally, SpliceAI predicts no significant splice impact (max delta score 0.02), so splicing is not a confounding factor.
REVEL score 0.89 (≥0.7 threshold met).SpliceAI max delta 0.02 — no predicted splice alteration.
Assessed · not applied · 15 not met · 0 not assessed
Pathogenic
PS1 PS1 requires the same amino acid change (p.Gly67Glu) as a previously established pathogenic variant in PTPN11.
PS2 PS2 requires de novo occurrence with confirmed maternity and paternity in a patient with a RASopathy phenotype.
PS3 PS3 requires well-established in vitro or in vivo functional studies supportive of a damaging effect using VCEP-approved assays.
PS4 PS4 requires significantly increased prevalence in affected individuals versus controls, assessed via point-based scoring in the RASopathy VCEP.
PM1 PM1 in the RASopathy VCEP for PTPN11 is applicable only to specific directly interacting residues between N-SH2 and PTPN domains: AA 4, 7–9, 58–63, 69–77, 247, 251, 255, 256, 258, 261, 265, 278–281, 284.
PM5 PM5 requires a different pathogenic or likely pathogenic missense change at the same codon (Gly67).
PM6 PM6 requires assumed de novo occurrence without confirmation of paternity and maternity.
PP1 PP1 requires co-segregation with disease in multiple affected family members.
Benign
BA1 BA1 requires a gnomAD filtering allele frequency ≥0.05%.
BS1 BS1 requires a gnomAD filtering allele frequency ≥0.025%.
BS2 BS2 requires observation in healthy adult individuals.
BS4 BS4 requires lack of segregation in affected family members.
BP2 BP2 awards points for an alternative molecular cause of a RASopathy in the same gene or in conjunction with BP5.
BP4 BP4 requires REVEL score ≤0.3 for missense variants per RASopathy VCEP specifications.
BP5 BP5 awards points for an alternative molecular cause of a RASopathy in a different gene when the phenotype is consistent.
N/A · 10 PVS1 · PM3 · PM4 · PP4 · PP5 · BS3 · BP1 · BP3 · BP6 · BP7
Research & evidence
Population frequency
gnomAD v4.1 screenshot
gnomAD v4.1
gnomAD v2.1 screenshot
gnomAD v2.1
v4.1
Absent from gnomAD v4.1.
v2.1
Absent from gnomAD v2.1.
🇨🇦 CA
Absent from gnomAD-Canada v1.0.
Allele frequency by ancestry
three datasets · side by side
gnomAD v4.1
Absent · 0 / ?
0 hom
Not observed in any ancestry group.
gnomAD v2.1
Absent · 0 / ?
0 hom
Not observed in any ancestry group.
gnomAD Canada 🇨🇦
Absent · 0 / ?
0 hom
Not observed in any ancestry group.
ClinVar screenshot
ClinVar
This variant is absent from ClinVar.
SpliceAI screenshot
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.02). REVEL score = 0.89. BayesDel score = 0.516839.
Functional / OncoKB screenshot
Functional Unknown Oncogenic Effect
OncoKB did not identify variant-specific reviewed functional evidence for this variant; gene-level curated context is available for reviewer follow-up. PTPN11, a protein tyrosine phosphatase, is altered in various solid and hematologic malignancies.
OncoKB ↗
COSMIC screenshot
COSMIC
Cancer hotspots screenshot
Cancer hotspots
Somatic evidence Not in COSMIC / hotspots
COSMIC
This variant does not lie in a statistically significant hotspot. This variant has previously been reported in somatic cancers (COSMIC; COSV109433876, n = 1 times).
Hotspots
This variant does not lie in a statistically significant hotspot.
Sources & reference links
9Sources
CSpec VCEP
ClinVar
gnomAD v2.1
gnomAD v4.1
gnomAD-Canada
SpliceAI
OncoKB
COSMIC
Cancer hotspots