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PTPN11
Final classification
VUS
PTPN11 c.200G>A · p.Gly67Glu
PTPN11

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.

Gene
PTPN11
Transcript
NM_002834.4
HGVS · transcript:coding
NM_002834.4:c.200G>A
Consequence
N/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 met · select any tile
Met
Not met
Not assessed
N/A
Strength very strong supporting
Pathogenic evidence
PVS
PS
PM
PP
Benign evidence
BA
BS
BP
Rationale
Select a criterion.
Sources
Evidence used
    Gaps remaining
      Rule
      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