Starting
Initialising…
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PIK3CA
Final classification
Likely Pathogenic
PIK3CA c.2176G>A · p.Glu726Lys
PIK3CA

NM_006218.3:c.2176G>A (p.Glu726Lys) is a missense variant in PIK3CA exon 14 that is absent from gnomAD population databases (PM2_Supporting).

Gene
PIK3CA
Transcript
NM_006218.3
HGVS · transcript:coding
NM_006218.3:c.2176G>A
Consequence
N/A
GRCh38
chr3:179221146 G>A
GRCh37
chr3:178938934 G>A
Basis Brain Malformations Specification Tavtigian point framework v1.1.0 point-based framework: PS2 moderate (+2) + PS4 strong (+4) + PM2 supporting (+1) + PP5 supporting (+1) = 8 points, which maps to Likely Pathogenic.
Brain Malformations Specification Tavtigian point framework v1.1.0 point-based framework: PS2 moderate (+2) + PS4 strong (+4) + PM2 supporting (+1) + PP5 supporting (+1) = 8 points, which maps to Likely Pathogenic.
Classification rationale
PS2PS4PM2PP5 Likely Pathogenic
PIK3CA c.2176G>A

NM_006218.3:c.2176G>A (p.Glu726Lys) is a missense variant in PIK3CA exon 14 that is absent from gnomAD population databases (PM2_Supporting).1 The variant was identified as a confirmed de novo event in one MCAP patient and as a postzygotic mosaic mutation in two additional unrelated MCAP patients, consistent with the known gain-of-function disease mechanism (PS2_Moderate).2 Four independently reported patients with megalencephaly-capillary malformation syndrome and brain overgrowth phenotypes carry this variant, with strong phenotype specificity for the disorder (PS4_Strong).3 This variant has been classified as Pathogenic by the ClinGen Brain Malformations Variant Curation Expert Panel after expert panel review (ClinVar Variation ID: 376476).4 Using the Brain Malformations VCEP Tavtigian point framework (Path Supporting +1, Path Moderate +2, Path Strong +4, Path Very Strong +8), the assigned criteria yield a total of 7 points, which falls within the Likely Pathogenic range (6 to 9 points). The expert panel classification of Pathogenic likely reflects additional criteria such as PM1 or PS3 applied with access to the VCEP functional assay spreadsheet and Table 2A phenotype point values.5

PS2 + PS4 + PM2 + PP5 Likely Pathogenic
Gene diagram · NM_006218.3 · variants mapped to exon structure
PIK3CA NM_006218.3
Fetching transcript structure from UCSC…
Applied criteria · 4 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
      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 has been reported in ClinVar as Pathogenic (8 clinical laboratories) and as Pathogenic by ClinGen Brain Malformations Variant Curation Expert Panel (expert panel). (ClinVarID = 376476)
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.02). REVEL score = 0.442. BayesDel score = 0.266518.
      Functional / OncoKB screenshot
      Functional Inconclusive
      OncoKB identified variant-specific curated literature and context relevant to functional review; biological-effect context: Inconclusive; curated oncogenicity label: Inconclusive.
      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; COSV55875460, n = 167 times).
      Hotspots
      This variant lies in a statistically significant hotspot.
      Literature · how each cited paper was used
      2papers cited
      Each card is an audit: what was searched, what was found, whether it names the variant, which criteria it fed, and why. 8 further PMIDs triaged but not cited — see Sources & References.
      De novo germline and postzygotic mutations in AKT3, PIK3R2 and PIK3CA cause a spectrum of related megalencephaly syndromes.
      Searched
      c.2176G>Ap.Glu726LysE726K2176
      Found
      NM_006218.3:c.2176G>A (p.Glu726Lys) identified as a de novo or postzygotic mosaic mutation in three unrelated MCAP patients (162-001P, LR08-261, LR06-333). Deep sequencing confirmed mosaicism with mutant allele fractions ranging from 12% to 41% across tissues. Functional assays on lymphoblastoid lines from other PIK3CA mutation carriers demonstrated increased PIP3 levels and elevated PI3K-mTOR signaling, consistent with gain of function.
      Variant
      ✓ Names this variant — characterised directly
      Applied to
      PS2 supports · met PS4 supports · met
      Why
      Variant directly reported as de novo and mosaic in MCAP patients; provides strong evidence for PS2_Moderate and case-level evidence for PS4.
      MCAP 162-001P PIK3CA chr3:178938934 G>A c.2176G>A p.Glu726Lys De novo
      Location Table 1 (mutation list, 3 occurrences of c.2176G>A); Table 2 (deep sequencing confirmation of mosaicism for LR08-261 and LR06-333); Results para 2  ·  Context Lymphoblastoid cell lines from MCAP patients with other PIK3CA mutations; PIP3 immunostaining, S6/4E-BP1 phosphorylation western blots; PI3K inhibitor PI-103 treatment  ·  full text
      In vitro efficacy of ARQ 092, an allosteric AKT inhibitor, on primary fibroblast cells derived from patients with PIK3CA-related overgrowth spectrum (PROS).
      Searched
      c.2176G>Ap.Glu726LysE726K2176
      Found
      NM_006218.3:c.2176G>A identified in Patient 3 (MCAP), a 17-year-old boy with focal hemimegalencephaly, perisylvian polymicrogyria, capillary malformations, and refractory seizures. Mutation present at 37% allele frequency in cultured primary fibroblasts from affected skin. The paper focused functional characterization on Patient 1 (H1047R) and did not report variant-specific functional data for E726K.
      Variant
      ✓ Names this variant — characterised directly
      Applied to
      PS4 supports · met
      Why
      Variant directly identified in a fourth independent MCAP patient, contributing to PS4 case count. No variant-specific functional data reported; not cited for PS3.
      3 MCAP c.2176G > A p.Glu726Gly 37 37 N/A N/A
      Location Table 1 (Patient 3: MCAP, c.2176G>A, p.Glu726Gly [sic - likely typo for Lys], 37% in biopsy/cells); Subjects and Methods, Patient 3 description  ·  Context Primary fibroblasts from affected skin biopsies; targeted deep sequencing of 21 PI3K/AKT/mTOR pathway genes; AKT inhibitor ARQ 092 treatment; WST-1 proliferation assays; western blot for pAKT/pAKT1S1/pRPS6  ·  full text
      Sources & reference links
      9Sources
      CSpec VCEP
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      gnomAD-Canada
      SpliceAI
      OncoKB
      COSMIC
      Cancer hotspots
      Triaged references · 8 PMIDs not cited in assessment
      29533785 ↗ Systematic Functional Annotation of Somatic Mutations in Cancer. ONCOKB
      24497998 ↗ Megalencephaly syndromes: exome pipeline strategies for detecting low-level mosaic mutations. CLINVAR
      25626707 ↗ Whole-genome sequencing in newborn screening? A statement on the continued importance of targeted approaches in newborn screening programmes. CLINVAR
      25730230 ↗ Expanded carrier screening in reproductive medicine-points to consider: a joint statement of the American College of Medical Genetics and Genomics, American College of Obstetricians and Gynecologists, National Society of Genetic Counselors, Perinatal Quality Foundation, and Society for Maternal-Fetal Medicine. CLINVAR
      25741868 ↗ Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. CLINVAR
      23246288 ↗ Germline PIK3CA and AKT1 mutations in Cowden and Cowden-like syndromes. CLINVAR
      23037933 ↗ Including the initial newborn screening bloodspot collection device serial number on birth certificates: basis and recommendations from the Secretary of Health and Human Services' Advisory Committee on Heritable Disorders in Newborns and Children. CLINVAR
      24394680 ↗ Parental permission for pilot newborn screening research: guidelines from the NBSTRN. CLINVAR