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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 applied · 11 assessed
Applied · 3
Strength Supporting Moderate Strong Very strong
PM1 supporting Pathogenic
The variant results in p.Ala442Pro, which lies within the PIK3CA kinase domain interval AA 322-483, an approved critical functional domain in Table 4 of the Brain Malformations VCEP specification. PM1_Supporting is awarded based on domain membership, independent of hotspot recurrence.
VCEP specification Table 4: PIK3CA kinase domain AA 322-483 approved for PM1_SupportingResidue 442 falls within the AA 322-483 interval
PM2 supporting review Pathogenic
The variant is rare in population databases. gnomAD v2.1 reports 1 allele in 233,204 (AF 4.29e-06), meeting the VCEP threshold of ≤1 allele for PM2_Supporting. gnomAD v4.1 reports 8 alleles in 1,597,406 (AF 5.01e-06). The variant is absent from gnomAD-Canada.
gnomAD v2.1: 1/233204 alleles (AF 4.29e-06)gnomAD v4.1: 8/1
PP2 supporting Pathogenic
PP2 is applicable to PIK3CA per the Brain Malformations VCEP when the missense constraint z-score exceeds 3.09. PIK3CA has a well-established high missense constraint in gnomAD (z-score well above 3.09), supporting that missense variants are a common mechanism of disease in this gene and that benign missense variation is low.
VCEP specification: PP2 Supporting if missense z-score > 3.09applicable to PIK3CAPIK3CA gnomAD missense constraint z-score is well above the 3.09 threshold
Assessed · not applied
Pathogenic
PS1 PS1 requires the same amino acid change (p.Ala442Pro) to have been previously established as pathogenic via a different nucleotide change.
PS2 PS2 requires confirmed de novo occurrence with confirmed maternity and paternity.
PS3 PS3 requires well-established in vitro or in vivo functional studies supportive of a damaging effect.
PS4 PS4 under Brain Malformations VCEP requires phenotype point assignment per Table 2A/2B and is only applicable if PM2 is met.
PM5 PM5 requires a different pathogenic missense change at the same amino acid residue (Ala442).
Benign
BA1 BA1 requires allele frequency >0.0926% per the Brain Malformations VCEP.
BS1 BS1 requires allele frequency >0.0185% per the Brain Malformations VCEP.
BS2 BS2 requires ≥3 homozygotes in gnomAD or ≥3 heterozygous in well-phenotyped family members per the Brain Malformations VCEP.
BS3 BS3 requires well-established in vitro or in vivo functional studies showing no damaging effect.
BP2 BP2 requires observation of the variant in cis or trans with a known pathogenic variant in the same gene.
BP5 BP5 requires the variant to be found in a case with an alternate molecular basis for disease.
N/A · 12 PVS1 · 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
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