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PIK3CA
Final classification
VUS
PM1PM2
PIK3CA
c.1346C>T
p.Pro449Leu
missense · exon 8

PIK3CA encodes the p110α catalytic subunit of phosphoinositide 3-kinase (PI3K), an enzyme that converts the membrane lipid PIP2 into PIP3, thereby activating signaling cascades such as the AKT-mTOR pathway that promote cell survival, proliferation, growth, and motility. It is among the most commonly mutated genes in cancer, and aberrant activation of PI3K signaling is a driving event in tumor development, with the gene implicated in cancers including cervical cancer. Because this pathway is central to tumor growth, it is a major target of cancer therapies, although drug-induced pathway activation can also contribute to treatment resistance.

This variant

PIK3CA is a well-established cancer driver whose activating mutations promote tumor growth and are central to cancer therapy decisions. Although p.Pro449Leu falls within the gene's kinase domain, it remains a VUS because no variant-specific functional, segregation, or recurrence evidence confirms an effect - the only functional data concern a different substitution at the same residue.

Transcript
NM_006218.4
HGVS · transcript:coding
NM_006218.4:c.1346C>T
GRCh38
chr3:179210280 C>T
GRCh37
chr3:178928068 C>T
Basis VUS: under generic ACMG/AMP 2015 rules (the gene-specific ruleset was incomplete), only PM1 and PM2 at Supporting strength were met, and two supporting criteria do not combine to Likely Pathogenic or Pathogenic.
VUS: under generic ACMG/AMP 2015 rules (the gene-specific ruleset was incomplete), only PM1 and PM2 at Supporting strength were met, and two supporting criteria do not combine to Likely Pathogenic or Pathogenic.
Classification rationale
PM1PM2 VUS
PIK3CA c.1346C>T missense · exon 8

PM1 (Supporting): residue 449 lies in the VCEP-approved PIK3CA kinase-domain interval (AA 322-483). PM2 (Supporting): the variant is absent from gnomAD v2.1, v4.1, and gnomAD-Canada v1.0. Overall: VUS - PM1 and PM2 at Supporting strength are the only met criteria, and two supporting pathogenic criteria do not satisfy the ACMG/AMP 2015 Likely Pathogenic combination.

PM1 + PM2 VUS
Gene diagram · NM_006218.4 · variants mapped to exon structure
PIK3CA NM_006218.4
Fetching transcript structure from UCSC…
Applied criteria · 2 applied · 12 assessed
MetEvidence satisfies this criterion.
Not metEvaluated against available evidence; threshold not reached.
Not assessedApplies in principle, but no evidence was found to evaluate it.
N/ADoesn't apply to this variant type.
Applied · 2
Strength Supporting Moderate Strong Very strong
PM1 supporting Pathogenic
Met (Supporting): residue 449 lies in the PIK3CA kinase-domain interval AA 322-483 approved in the VCEP specification.
The governing ClinGen Brain Malformations VCEP specification lists PIK3CA kinase-domain AA 322-483 as an approved critical functional domain for PM1_Supporting; residue 449 is within this interval.
PM2 supporting Pathogenic
Met (Supporting): the variant is absent from gnomAD v2.1, v4.1, and gnomAD-Canada v1.0, meeting the VCEP rarity threshold.
The governing Brain Malformations VCEP specifies PM2 at Supporting strength for a variant absent/rare from controls in an ethnically matched cohort population sample, with a maximum of one person.The exact variant NM_006218.4:c.1346C>T (p.Pro449Leu) is reported absent from gnomAD v2.1.The exact variant is reported absent from gnomAD v4.1.
Assessed · not applied · 4 not met · 8 not assessed
Pathogenic
PS1 Not assessed: the known same-residue variant is p.Pro449Thr, a different amino-acid change from this p.Pro449Leu.
PS2 Not assessed: no proband assay details, parental genotypes, or allele-fraction data were available to confirm a de novo origin.
PS3 Not assessed: the functional paper tested p.Pro449Thr, not p.Pro449Leu, so its gain-of-function result cannot be transferred to this variant.
PS4 Not met: tumor observations contribute only 0.25 point per category, below the 0.5-point PS4 supporting threshold.
PM5 Not assessed: p.Pro449Thr is not established as a pathogenic clinical variant, and no qualifying same-residue candidate was found.
PP2 Not assessed: no PIK3CA missense-constraint z-score was available to test the >3.09 requirement.
Benign
BA1 Not met: absent from gnomAD, so allele frequency is far below the >0.0926% BA1 threshold.
BS1 Not met: absent from gnomAD, so allele frequency is far below the >0.0185% BS1 threshold.
BS2 Not met: no homozygotes or well-phenotyped family-member observations meet the required three occurrences.
BS3 Not assessed: no assay directly testing p.Pro449Leu demonstrated a benign effect; the available study tested p.Pro449Thr.
BP2 Not assessed: no second pathogenic PIK3CA variant or phase information was available to establish co-occurrence.
BP5 Not assessed: no evidence of an alternate molecular diagnosis explaining the presenting disease was available.
N/A · 14 PVS1 · PM3 · PM4 · PM6 · PP1 · PP3 · PP4 · PP5 · BS4 · BP1 · BP3 · BP4 · BP6 · BP7
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 Pathogenic (1 clinical laboratory) and as Likely pathogenic (1 clinical laboratory). (ClinVarID = 1804026)
SpliceAI screenshot
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.01). REVEL score = 0.617. BayesDel score = 0.0927074.
Functional / OncoKB screenshot
Functional Likely Oncogenic
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 Hotspot
COSMIC
This variant lies in a statistically significant hotspot. This variant has previously been reported in somatic cancers (COSMIC; COSV55899150, n = 2 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 · 4 PMIDs not cited in assessment
20530683 ↗ Correlating phosphatidylinositol 3-kinase inhibitor efficacy with signaling path ONCOKB
23946963 ↗ PIK3CA-Related Overgrowth Spectrum. CLINVAR
27631024 ↗ PIK3CA-associated developmental disorders exhibit distinct classes of mutations with variable expression and tissue distribution. CLINVAR
39434542 ↗ Modified Rules for Classification of Variants Associated With Disorders of Somatic Mosaicism. CLINVAR