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PIK3CA
Final classification
VUS
PIK3CA c.2042G>C · p.Ser681Thr
PIK3CA

PM2_Supporting: This variant is absent from gnomAD v2.1, v4.1, and gnomAD-Canada, meeting the VCEP threshold of ≤1 individual in population databases.

Gene
PIK3CA
Transcript
NM_006218.4
HGVS · transcript:coding
NM_006218.4:c.2042G>C
Consequence
N/A
GRCh38
chr3:179221012 G>C
GRCh37
chr3:178938800 G>C
Basis Brain Malformations Specification Tavtigian point framework v1.1.0 point-based framework: PM2 supporting (+1) + PP2 supporting (+1) = 2 points, which maps to VUS.
Brain Malformations Specification Tavtigian point framework v1.1.0 point-based framework: PM2 supporting (+1) + PP2 supporting (+1) = 2 points, which maps to VUS.
Classification rationale
PM2PP2 VUS
PIK3CA c.2042G>C

PM2_Supporting: This variant is absent from gnomAD v2.1, v4.1, and gnomAD-Canada, meeting the VCEP threshold of ≤1 individual in population databases.1 PP2_Supporting: PIK3CA has a missense constraint Z-score of 4.07 in gnomAD v2.1, exceeding the VCEP threshold of >3.09, indicating a low rate of benign missense variation.2 PS1 is not met: no alternative nucleotide change at codon 681 producing p.Ser681Thr has been established as pathogenic.3 PM1 is not met: residue Ser681 at position 681 falls outside the VCEP Table 4 approved kinase domains for PIK3CA (AA 322-483 and AA 797-1068).4 PS3 and BS3 are not met: no variant-specific functional studies are available. OncoKB classifies p.Ser681Thr as Unknown Oncogenic Effect.5 PS4 is not met: no affected individuals with this variant have been reported; no phenotype points can be scored under VCEP Tables 2A/2B.6 Six publications were reviewed; none mention NM_006218.4:c.2042G>C or PIK3CA p.Ser681Thr.7 Using the Brain Malformations VCEP Tavtigian point framework (Path Supporting +1, Path Moderate +2, Path Strong +4, Path Very Strong +8; Benign Supporting -1, Mod -2, Strong -4, Very Strong -8), the total score is +2 (PM2_Supporting +1, PP2_Supporting +1), which falls within the VUS range (0-5 points).8

PM2 + PP2 VUS
Gene diagram · NM_006218.4 · variants mapped to exon structure
PIK3CA NM_006218.4
Fetching transcript structure from UCSC…
Applied criteria · 2 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 has been reported in ClinVar as Uncertain significance (2 clinical laboratories). (ClinVarID = 1038606)
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.01). REVEL score = 0.235. BayesDel score = -0.0427925.
      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 · 6 PMIDs not cited in assessment
      23652378 ↗ A framework to start the debate on neonatal screening policies in the EU: an Expert Opinion Document. 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
      26389210 ↗ Genetics of Breast and Gynecologic Cancers (PDQ®): Health Professional Version. CLINVAR
      28492532 ↗ Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. CLINVAR
      22947299 ↗ Specific guidelines for assessing and improving the methodological quality of economic evaluations of newborn screening. CLINVAR
      24394680 ↗ Parental permission for pilot newborn screening research: guidelines from the NBSTRN. CLINVAR