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PTPN11
Final classification
Pathogenic
PTPN11 c.215C>T · p.Ala72Val
PTPN11

PS1 (Strong): p.Ala72Val is an established pathogenic amino acid substitution in PTPN11, meeting the RASopathy VCEP criterion for same amino acid change as a previously established pathogenic variant.

Gene
PTPN11
Transcript
NM_001330437.1
HGVS · transcript:coding
NM_001330437.1:c.215C>T
Consequence
N/A
GRCh38
chr12:112450395 C>T
GRCh37
chr12:112888199 C>T
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: matched Rule8 (1 Pathogenic.Strong + 1 Pathogenic.Moderate + Pathogenic.Supporting >=4) with applied criteria: PS1 strong, PS3 supporting, PS4 supporting, PM1 moderate, PM2 supporting, PP2 supporting, PP3 supporting; maps to Pathogenic.
ClinGen RASopathy Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for PTPN11 Version 2.3.0 v2.3.0 criteria-combination framework: matched Rule8 (1 Pathogenic.Strong + 1 Pathogenic.Moderate + Pathogenic.Supporting >=4) with applied criteria: PS1 strong, PS3 supporting, PS4 supporting, PM1 moderate, PM2 supporting, PP2 supporting, PP3 supporting; maps to Pathogenic.
Classification rationale
PS1PS3PS4PM1PM2PP2PP3 Pathogenic
PTPN11 c.215C>T

PS1 (Strong): p.Ala72Val is an established pathogenic amino acid substitution in PTPN11, meeting the RASopathy VCEP criterion for same amino acid change as a previously established pathogenic variant.1 PM1 (Moderate): Residue 72 lies within the N-SH2/PTPN domain interaction interface (amino acids 69-77), a critical functional domain defined by the RASopathy VCEP as a known mutational hotspot.2 PM2 (Supporting): The variant is absent from gnomAD population controls (v2.1 and v4.1), meeting the VCEP threshold for absence from controls.3 PP2 (Supporting): PTPN11 has a low rate of benign missense variation with a gnomAD missense Z-score >3.09, consistent with a gene where missense variants are a common disease mechanism.4 PP3 (Supporting): In silico prediction with a REVEL score of 0.921 supports a deleterious effect on protein function, exceeding the VCEP threshold of ≥0.7.5 PS3_Supporting: Functional studies demonstrate gain-of-function activity of the p.Ala72Val SHP-2 mutant, as curated by OncoKB and reported in published functional analyses of PTPN11 mutations.6 PS4_Supporting: The variant has been observed in multiple individuals with Noonan syndrome/RASopathy phenotypes, meeting the VCEP threshold of ≥1 point for PS4 at Supporting strength.7 Final classification: Pathogenic per RASopathy VCEP v2.3.0, Rule8 (1 Strong criterion [PS1] + 1 Moderate criterion [PM1] + ≥4 Supporting criteria [PS3_Supporting, PS4_Supporting, PM2_Supporting, PP2, PP3]).8

PS1 + PS3 + PS4 + PM1 + PM2 + PP2 + PP3 Pathogenic
Gene diagram · NM_001330437.1 · variants mapped to exon structure
PTPN11 NM_001330437.1
Fetching transcript structure from UCSC…
Applied criteria · 7 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 · supports pathogenic
      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
      This variant is absent from gnomAD-Canada.
      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 has been reported in ClinVar as Pathogenic (2 clinical laboratories) and as Uncertain significance (1 clinical laboratory) and as Likely pathogenic (1 clinical laboratory). (ClinVarID = 41443)
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.02). REVEL score = 0.921. BayesDel score = 0.282132.
      Functional / OncoKB screenshot
      Functional Likely Oncogenic
      OncoKB identified variant-specific curated literature and context relevant to functional review; biological-effect context: Likely Gain-of-function; curated oncogenicity label: Likely Oncogenic.
      OncoKB ↗
      COSMIC screenshot
      COSMIC
      Cancer hotspots screenshot
      Cancer hotspots
      Somatic evidence Hotspot
      COSMIC
      This variant lies in a statistically significant hotspot. This variant has previously been reported in somatic cancers (COSMIC; COSV61005613, n = 108 times).
      Hotspots
      This variant lies in a statistically significant hotspot.
      Literature · how each cited paper was used
      3papers cited
      Each card is an audit: what was searched, what was found, whether it names the variant, which criteria it fed, and why. 4 further PMIDs triaged but not cited — see Sources & References.
      PTPN11 (protein-tyrosine phosphatase, nonreceptor-type 11) mutations in seven Japanese patients with Noonan syndrome.
      Found
      (Kosaki et al.
      Applied to
      PS4 supports · met
      Functional analysis of PTPN11/SHP-2 mutants identified in Noonan syndrome and childhood leukemia.
      Found
      (Niihori et al.
      Applied to
      PS3 supports · met
      Diversity and functional consequences of germline and somatic PTPN11 mutations in human disease.
      Found
      (Tartaglia et al.
      Applied to
      PS3 supports · met
      Sources & reference links
      8Sources
      CSpec VCEP
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      SpliceAI
      OncoKB
      COSMIC
      Cancer hotspots
      Triaged references · 4 PMIDs not cited in assessment
      31179415 ↗ Rare Pediatric Invasive Gliofibroma Has BRAFV600E Mutation and Transiently Responds to Targeted Therapy Before Progressive Clonal Evolution. ONCOKB
      12717436 ↗ Somatic mutations in PTPN11 in juvenile myelomonocytic leukemia, myelodysplastic syndromes and acute myeloid leukemia. CLINVAR
      14982869 ↗ Genetic evidence for lineage-related and differentiation stage-related contribution of somatic PTPN11 mutations to leukemogenesis in childhood acute leukemia. CLINVAR
      28492532 ↗ Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. CLINVAR