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PIK3CA
Final classification
VUS
PIK3CA c.112C>T · p.Arg38Cys
PIK3CA

This variant is completely absent from population databases including gnomAD v2.1 (0/248,624 alleles) and gnomAD v4.1 (0/1,611,102 alleles), meeting PM2_Supporting per the Brain Malformations VCEP.

Gene
PIK3CA
Transcript
NM_006218.4
HGVS · transcript:coding
NM_006218.4:c.112C>T
Consequence
N/A
GRCh38
chr3:179198937 C>T
GRCh37
chr3:178916725 C>T
Basis Brain Malformations Specification Tavtigian point framework v1.1.0 point-based framework: PM2 supporting (+1) = 1 points, which maps to VUS.
Brain Malformations Specification Tavtigian point framework v1.1.0 point-based framework: PM2 supporting (+1) = 1 points, which maps to VUS.
Classification rationale
PM2 VUS
PIK3CA c.112C>T

This variant is completely absent from population databases including gnomAD v2.1 (0/248,624 alleles) and gnomAD v4.1 (0/1,611,102 alleles), meeting PM2_Supporting per the Brain Malformations VCEP.1 No other pathogenic or benign criteria are met under the Brain Malformations VCEP v1.1.0 framework. PVS1, PP3, PP4, PP5, BS4, PM6, BP1, BP4, BP6, BP7, and PP1 are explicitly not applicable per the VCEP. Most remaining criteria lack variant-specific evidence in the published literature.2 OncoKB curates p.Arg38Cys as Likely Oncogenic with Likely Gain-of-function biological context; however, no variant-specific functional data was identified in the reviewed full-text publications, and the Brain Malformations VCEP PS3 criterion requires validated functional assays meeting specific quality metrics.3 This variant has been reported in ClinVar as Uncertain significance by two clinical laboratories (ClinVarID 376493). No de novo reports, segregation data, or brain malformation phenotype cases were identified.4 Variant has been observed in somatic cancers (COSMIC, n=39 occurrences) but this does not independently support germline brain malformation pathogenicity under the VCEP PS4 framework.

PM2 VUS
Gene diagram · NM_006218.4 · variants mapped to exon structure
PIK3CA NM_006218.4
Fetching transcript structure from UCSC…
Applied criteria · 1 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
      This variant is present in gnomAD v4.1 (AF= 0; MAF= 0.00000%, 0/1611102 alleles, homozygotes = 0) and has highest observed frequency in the African/African American population (AF= 0; MAF= 0.00000%, 0/74900 alleles, homozygotes = 0).
      v2.1
      This variant is present in gnomAD v2.1 (AF= 0; MAF= 0.00000%, 0/248624 alleles, homozygotes = 0) and has highest observed frequency in the African/African American population (AF= 0; MAF= 0.00000%, 0/15466 alleles, homozygotes = 0).
      🇨🇦 CA
      Absent from gnomAD-Canada v1.0.
      Allele frequency by ancestry
      three datasets · side by side
      gnomAD v4.1
      Absent · 0 / 1,611,102
      0 hom
      Not observed in any ancestry group.
      + 10 not observed (Remaining individuals, Admixed American, European (Finnish), Amish, East Asian, Middle Eastern, South Asian, Ashkenazi Jewish, African/African American, European (non-Finnish))
      gnomAD v2.1
      Absent · 0 / 248,624
      0 hom
      Not observed in any ancestry group.
      + 8 not observed (African/African American, Admixed American, Ashkenazi Jewish, East Asian, European (Finnish), European (non-Finnish), Remaining individuals, South Asian)
      gnomAD Canada 🇨🇦
      Absent · 0 / ?
      0 hom
      Not observed in any ancestry group.
      ClinVar screenshot
      ClinVar
      This variant has been reported in ClinVar as Uncertain significance (2 clinical laboratories). (ClinVarID = 376493)
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.05). REVEL score = 0.737. BayesDel score = 0.244629.
      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; COSV55874617, n = 39 times).
      Hotspots
      This variant lies 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
      Triaged references · 6 PMIDs not cited in assessment
      29533785 ↗ Systematic Functional Annotation of Somatic Mutations in Cancer. ONCOKB
      26122737 ↗ Oncogenic mutations weaken the interactions that stabilize the p110α-p85α heterodimer in phosphatidylinositol 3-kinase α. CLINVAR
      28966033 ↗ Integrated Molecular Meta-Analysis of 1,000 Pediatric High-Grade and Diffuse Intrinsic Pontine Glioma. CLINVAR
      24705252 ↗ Recurrent activating ACVR1 mutations in diffuse intrinsic pontine glioma. CLINVAR
      26389258 ↗ Cancer Genetics Risk Assessment and Counseling (PDQ®): Health Professional Version. CLINVAR
      26389333 ↗ Genetics of Skin Cancer (PDQ®): Health Professional Version. CLINVAR