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PIK3CA
Final classification
VUS
PIK3CA c.112C>T · p.Arg38Cys
PIK3CA

This variant is completely absent from population databases including gnomAD v2.1 (0/248,624 alleles) and gnomAD v4.1 (0/1,611,102 alleles), meeting PM2_Supporting per the Brain Malformations VCEP.

Gene
PIK3CA
Transcript
NM_006218.4
HGVS · transcript:coding
NM_006218.4:c.112C>T
Consequence
N/A
GRCh38
chr3:179198937 C>T
GRCh37
chr3:178916725 C>T
Basis Brain Malformations Specification Tavtigian point framework v1.1.0 point-based framework: PM2 supporting (+1) = 1 points, which maps to VUS.
Brain Malformations Specification Tavtigian point framework v1.1.0 point-based framework: PM2 supporting (+1) = 1 points, which maps to VUS.
Classification rationale
PM2 VUS
PIK3CA c.112C>T

This variant is completely absent from population databases including gnomAD v2.1 (0/248,624 alleles) and gnomAD v4.1 (0/1,611,102 alleles), meeting PM2_Supporting per the Brain Malformations VCEP.1 No other pathogenic or benign criteria are met under the Brain Malformations VCEP v1.1.0 framework. PVS1, PP3, PP4, PP5, BS4, PM6, BP1, BP4, BP6, BP7, and PP1 are explicitly not applicable per the VCEP. Most remaining criteria lack variant-specific evidence in the published literature.2 OncoKB curates p.Arg38Cys as Likely Oncogenic with Likely Gain-of-function biological context; however, no variant-specific functional data was identified in the reviewed full-text publications, and the Brain Malformations VCEP PS3 criterion requires validated functional assays meeting specific quality metrics.3 This variant has been reported in ClinVar as Uncertain significance by two clinical laboratories (ClinVarID 376493). No de novo reports, segregation data, or brain malformation phenotype cases were identified.4 Variant has been observed in somatic cancers (COSMIC, n=39 occurrences) but this does not independently support germline brain malformation pathogenicity under the VCEP PS4 framework.

PM2 VUS
Gene diagram · NM_006218.4 · variants mapped to exon structure
PIK3CA NM_006218.4
Fetching transcript structure from UCSC…
Applied criteria · 1 applied · 13 assessed
Applied · 1
Strength Supporting Moderate Strong Very strong
PM2 supporting Pathogenic
This variant is completely absent from all gnomAD population databases: gnomAD v2.1 (0/248,624 alleles), gnomAD v4.1 (0/1,611,102 alleles), and gnomAD-Canada v1.0. Per the Brain Malformations VCEP, PM2_Supporting is awarded when the variant is absent or rare (≤1) in ethnically-matched population cohorts.
gnomAD v2.1: 0/248624 allelesgnomAD v4.1: 0/1
Assessed · not applied
Pathogenic
PS1 No previously established pathogenic variant causing the same amino acid change (p.Arg38Cys) via a different nucleotide change was identified.
PS2 No de novo observation of this variant has been identified in any reviewed publication or ClinVar submission.
PS3 No variant-specific functional data confirming a damaging effect was identified in any reviewed full-text publication.
PS4 No published cases of this variant in individuals with brain malformation phenotypes were identified in the reviewed literature.
PM1 Residue Arg38 lies outside the Table 4 PIK3CA critical functional domains (kinase domain AA 322–483 and AA 797–1068) per the Brain Malformations VCEP.
PM5 No pathogenic comparator variant at residue Arg38 was identified in ClinVar or the literature.
PP2 The Brain Malformations VCEP specifies PP2_Supporting for PIK3CA if the missense constraint z-score from ExAC/gnomAD exceeds 3.09.
Benign
BA1 Variant is completely absent from all gnomAD populations (0/248,624 in v2.1, 0/1,611,102 in v4.1).
BS1 Variant is completely absent from all gnomAD populations.
BS2 No homozygotes present in gnomAD (0/248,624 in v2.1, 0/1,611,102 in v4.1) and no well-phenotyped heterozygous family members without disease have been reported.
BS3 No well-established in vitro or in vivo functional studies demonstrate a benign effect.
BP2 No evidence that this variant has been observed in cis or in trans with a known pathogenic variant in PIK3CA.
BP5 No evidence that this variant has been found in a case with an alternative 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%, 0/1611102 alleles, homozygotes = 0) and has highest observed frequency in the African/African American population (AF= 0; MAF= 0.00000%, 0/74900 alleles, homozygotes = 0).
v2.1
This variant is present in gnomAD v2.1 (AF= 0; MAF= 0.00000%, 0/248624 alleles, homozygotes = 0) and has highest observed frequency in the African/African American population (AF= 0; MAF= 0.00000%, 0/15466 alleles, homozygotes = 0).
🇨🇦 CA
Absent from gnomAD-Canada v1.0.
Allele frequency by ancestry
three datasets · side by side
gnomAD v4.1
Absent · 0 / 1,611,102
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 / 248,624
0 hom
Not observed in any ancestry group.
+ 8 not observed (African/African American, Admixed American, Ashkenazi Jewish, East Asian, European (Finnish), European (non-Finnish), Remaining individuals, South Asian)
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 = 376493)
SpliceAI screenshot
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.05). REVEL score = 0.737. BayesDel score = 0.244629.
Functional / OncoKB screenshot
Functional Likely Oncogenic
OncoKB identified variant-specific curated literature and context relevant to functional review; biological-effect context: Likely Gain-of-function; curated oncogenicity label: Likely Oncogenic.
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; COSV55874617, n = 39 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 · 6 PMIDs not cited in assessment
29533785 ↗ Systematic Functional Annotation of Somatic Mutations in Cancer. ONCOKB
26122737 ↗ Oncogenic mutations weaken the interactions that stabilize the p110α-p85α heterodimer in phosphatidylinositol 3-kinase α. CLINVAR
28966033 ↗ Integrated Molecular Meta-Analysis of 1,000 Pediatric High-Grade and Diffuse Intrinsic Pontine Glioma. CLINVAR
24705252 ↗ Recurrent activating ACVR1 mutations in diffuse intrinsic pontine glioma. CLINVAR
26389258 ↗ Cancer Genetics Risk Assessment and Counseling (PDQ®): Health Professional Version. CLINVAR
26389333 ↗ Genetics of Skin Cancer (PDQ®): Health Professional Version. CLINVAR