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PIK3CA
Final classification
VUS
PIK3CA c.370C>T · p.Pro124Ser
PIK3CA

NM_006218.3:c.370C>T (p.Pro124Ser) is a missense variant in PIK3CA, a gene in which gain-of-function missense variants cause brain malformations including megalencephaly and focal cortical dysplasia.

Gene
PIK3CA
Transcript
NM_006218.3
HGVS · transcript:coding
NM_006218.3:c.370C>T
Consequence
N/A
GRCh38
chr3:179199707 C>T
GRCh37
chr3:178917495 C>T
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.370C>T

NM_006218.3:c.370C>T (p.Pro124Ser) is a missense variant in PIK3CA, a gene in which gain-of-function missense variants cause brain malformations including megalencephaly and focal cortical dysplasia.1 This variant is absent from gnomAD v4.1 (0/1,608,782 alleles) and gnomAD v2.1, supporting PM2_Supporting under the Brain Malformations VCEP population criterion.2 PIK3CA has high missense constraint (gnomAD missense z-score >3.09), meeting PP2_Supporting under the VCEP specification.3 Residue Pro124 lies within the adaptor-binding domain region, outside the VCEP Table 4 approved critical functional domains (AA 322-483 and AA 797-1068 kinase domains); PM1_Supporting is therefore not met.4 No functional study has directly tested P124S. PMID:22430209 tested P124L (a different missense at the same residue) in a somatic cancer context and demonstrated gain-of-function activity, but this evidence is not transferable to P124S and does not satisfy VCEP PS3 requirements.5 Total Tavtigian points: PM2_Supporting (+1) + PP2_Supporting (+1) = 2 points. Under the VCEP point framework (>10 Pathogenic, 6-9 Likely Pathogenic, 0-5 VUS), a score of 2 falls within the VUS range.6 This variant is classified as a Variant of Uncertain Significance (VUS) under the ClinGen Brain Malformations Expert Panel specifications version 1.1.0.7

PM2 + PP2 VUS
6 cspec ↗final_classification_framework
7 cspec ↗final_classification_framework
Gene diagram · NM_006218.3 · variants mapped to exon structure
PIK3CA NM_006218.3
Fetching transcript structure from UCSC…
Applied criteria · 2 applied · 12 assessed
Applied · 2
Strength Supporting Moderate Strong Very strong
PM2 supporting Pathogenic
The variant is absent from gnomAD v4.1 (0/1,608,782 alleles, 0 homozygotes) and absent from gnomAD v2.1, meeting the VCEP PM2_Supporting criterion of absence or rarity in an ethnically-matched cohort population sample (≥1 individual threshold).
Absent from gnomAD v2.1 exomesabsent from gnomAD v4.1 (0/1608
PP2 supporting review Pathogenic
PIK3CA has a high missense constraint z-score in gnomAD (z > 3.09), meeting the VCEP PP2_Supporting criterion for genes where missense variants are a common mechanism of disease and benign missense variation is depleted. The VCEP explicitly lists PIK3CA as applicable for PP2.
VCEP specification awards PP2 if missense z-score > 3.09PIK3CA missense z-score in gnomAD is approximately 4.11well above the threshold. PIK3CA is explicitly listed as eligible for PP2 in the VCEP rule.
Assessed · not applied
Pathogenic
PS1 No previously established pathogenic variant with the same amino acid change (P124S) has been identified.
PS2 No de novo observation has been reported for this variant.
PS3 No functional study has directly tested P124S (NM_006218.3:c.370C>T).
PS4 No probands with brain malformation phenotypes have been reported for this variant.
PM1 Residue Pro124 falls within the p85-binding/adaptor-binding domain (ABD) region of PIK3CA, outside the VCEP Table 4 approved critical functional domains for PM1_Supporting (AA 322–483 kinase domain and AA 797–1068 kinase domain).
PM5 No different missense variant at residue Pro124 has been classified as pathogenic in ClinVar.
Benign
BA1 The variant is absent from gnomAD v4.1 (allele frequency 0.00%).
BS1 The variant is absent from gnomAD v4.1 (allele frequency 0.00%).
BS2 No homozygotes are present in gnomAD (0 homozygotes in v4.1), and no well-phenotyped heterozygous family members have been reported.
BS3 No functional study has demonstrated that P124S has no damaging effect on protein function.
BP2 No evidence that this variant has been observed in cis or trans with a known pathogenic variant in PIK3CA.
BP5 No case has been reported in which this variant was found in an individual with an alternate molecular basis for disease.
N/A · 11 PVS1 · PM6 · PP1 · PP3 · PP4 · PP5 · BS4 · BP1 · 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= 0; MAF= 0.00000%, 0/1608782 alleles, homozygotes = 0) and has highest observed frequency in the African/African American population (AF= 0; MAF= 0.00000%, 0/74876 alleles, homozygotes = 0).
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 / 1,608,782
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 / ?
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 is absent from ClinVar.
SpliceAI screenshot
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.06). REVEL score = 0.189. BayesDel score = -0.0235373.
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 Not in COSMIC / hotspots
COSMIC
This variant does not lie in a statistically significant hotspot. This variant has previously been reported in somatic cancers (COSMIC; COSV55888156, n = 2 times).
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 · 1 PMID not cited in assessment
22430209 ↗ PIK3CA mutation spectrum in urothelial carcinoma reflects cell context-dependent signaling and phenotypic outputs. ONCOKB