Starting
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PIK3CA
Final classification
VUS
PIK3CA c.1324G>C · p.Ala442Pro
PIK3CA

The variant NM_006218.4:c.1324G>C (p.Ala442Pro) lies within the PIK3CA kinase domain (AA 322-483), an approved critical functional domain per the Brain Malformations VCEP Table 4, supporting PM1 at Supporting strength (+1 point).

Gene
PIK3CA
Transcript
NM_006218.4
HGVS · transcript:coding
NM_006218.4:c.1324G>C
Consequence
N/A
GRCh38
chr3:179210258 G>C
GRCh37
chr3:178928046 G>C
Basis Brain Malformations Specification Tavtigian point framework v1.1.0 point-based framework: PM1 supporting (+1) + PM2 supporting (+1) + PP2 supporting (+1) = 3 points, which maps to VUS.
Brain Malformations Specification Tavtigian point framework v1.1.0 point-based framework: PM1 supporting (+1) + PM2 supporting (+1) + PP2 supporting (+1) = 3 points, which maps to VUS.
Classification rationale
PM1PM2PP2 VUS
PIK3CA c.1324G>C

The variant NM_006218.4:c.1324G>C (p.Ala442Pro) lies within the PIK3CA kinase domain (AA 322-483), an approved critical functional domain per the Brain Malformations VCEP Table 4, supporting PM1 at Supporting strength (+1 point).1 The variant is rare in population databases: gnomAD v2.1 reports 1 allele in 233,204 (AF 4.29e-06) and v4.1 reports 8 alleles in 1,597,406 (AF 5.01e-06). The variant meets the VCEP PM2_Supporting threshold of ≤1 allele based on v2.1 data (+1 point). gnomAD v4.1 showing 8 alleles is noted for reviewer consideration.2 PIK3CA has a high missense constraint z-score in gnomAD (well above the 3.09 threshold specified by the VCEP), supporting PP2 at Supporting strength (+1 point). Missense variants are a recognized mechanism of disease in this gene, and the rate of benign missense variation is low.3 No variant-specific functional studies were identified: OncoKB reports Unknown Oncogenic Effect, COSMIC has no entry, and none of the six reviewed publications contained variant-specific functional data. PS3 is not met.4 No affected individuals with this variant have been reported in ClinVar (single submitter, Uncertain significance, no case-level detail) or the literature. PS4 cannot be assessed without phenotype data.5 Under the Brain Malformations VCEP Tavtigian point framework (page 12), the total evidence score is +3 points (PM1_Supporting +1, PM2_Supporting +1, PP2_Supporting +1), which falls in the VUS range (0 to 5 points). The variant is classified as Uncertain Significance.6

PM1 + PM2 + PP2 VUS
1 cspec ↗vcep_clingen_brainmalform_acmg_specifications_v1_1
6 cspec ↗final_classification_framework
Gene diagram · NM_006218.4 · variants mapped to exon structure
PIK3CA NM_006218.4
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
      This variant is present in gnomAD v4.1 (AF= 5.00812e-06; MAF= 0.00050%, 8/1597406 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 6.8033e-06; MAF= 0.00068%, 8/1175900 alleles, homozygotes = 0); grpmax FAF= 2.93e-06.
      v2.1
      This variant is present in gnomAD v2.1 (AF= 4.28809e-06; MAF= 0.00043%, 1/233204 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 9.18139e-06; MAF= 0.00092%, 1/108916 alleles, homozygotes = 0).
      🇨🇦 CA
      This variant is present in gnomAD-Canada v1.0 (AF= 0.00027150304083405736, 5/18416 alleles, homozygotes = 0).
      Allele frequency by ancestry
      three datasets · side by side
      gnomAD v4.1
      0.0005% · 8 / 1,597,406
      0 hom · FAF 0.00029%
      European (non-Finnish)
      8 / 1,175,900
      0.00068%
      + 9 not observed (Remaining individuals, Admixed American, European (Finnish), Amish, East Asian, Middle Eastern, South Asian, Ashkenazi Jewish, African/African American)
      gnomAD v2.1
      0.00043% · 1 / 233,204
      0 hom
      European (non-Finnish)
      1 / 108,916
      0.00092%
      + 7 not observed (African/African American, Admixed American, Ashkenazi Jewish, East Asian, European (Finnish), Remaining individuals, South Asian)
      gnomAD Canada 🇨🇦
      0.027% · 5 / 18,416
      0 hom · FAF 0.017%
      European (non-Finnish)
      5 / 11,740
      0.043%
      + 8 not observed (African/African American, Latino/Admixed American, Ashkenazi Jewish, East Asian, European (Finnish), Middle Eastern, Remaining individuals, South Asian)
      ClinVar screenshot
      ClinVar
      This variant has been reported in ClinVar as Uncertain significance (1 clinical laboratory). (ClinVarID = 570411)
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.01). REVEL score = 0.636. BayesDel score = 0.269546.
      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. PIK3CA, the catalytic subunit of PI3-kinase, is frequently mutated in a diverse range of cancers including breast, endometrial and cervical cancers.
      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 not previously been reported in somatic cancers (COSMIC).
      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
      Triaged references · 5 PMIDs not cited in assessment
      23519317 ↗ Clinical genetics evaluation in identifying the etiology of autism spectrum disorders: 2013 guideline revisions. CLINVAR
      25190698 ↗ Genetic/familial high-risk assessment: breast and ovarian, version 1.2014. CLINVAR
      26389210 ↗ Genetics of Breast and Gynecologic Cancers (PDQ®): Health Professional Version. CLINVAR
      26389258 ↗ Cancer Genetics Risk Assessment and Counseling (PDQ®): Health Professional Version. CLINVAR
      26389333 ↗ Genetics of Skin Cancer (PDQ®): Health Professional Version. CLINVAR