Variant classification summary

NM_006218.4:c.397G>A

PIK3CA · NP_006209.2:p.(Asp133Asn) · NM_006218.4

GRCh37: chr3:178917522 G>A · GRCh38: chr3:179199734 G>A

Gene: PIK3CA Transcript: NM_006218.4

Final call

VUS

PM2 supporting PP2 supporting

Variant details

Gene

PIK3CA

Transcript

NM_006218.4

Protein

NP_006209.2:p.(Asp133Asn)

gnomAD AF

ClinVar

OncoKB

Unknown Oncogenic Effect

Classification rationale

Interpretation summary

Generated evidence synthesis

1

NM_006218.4:c.397G>A (p.Asp133Asn) in PIK3CA is absent from gnomAD population databases (v2.1, v4.1), meeting PM2 at supporting strength per the ClinGen Brain Malformations VCEP v1.1.

2

PIK3CA has a high missense constraint z-score exceeding the BMVCEP threshold of 3.09, consistent with a gene where missense variants are a common disease mechanism, meeting PP2 at supporting strength.

3

PVS1 is not applicable because the disease mechanism for PIK3CA-related brain malformations is gain of function, as specified by the BMVCEP v1.1.

4

Residue Asp133 falls outside all Table 4 approved functional domains for PIK3CA (ABD 31-108, Ras-binding 173-292, kinase 322-483, kinase 797-1068); PM1 is not met.

5

No functional data, no de novo reports, no phenotype cases, no ClinVar entries, and no literature citations were identified for this variant. PS1, PS2, PS3, PS4, and PM5 are not met.

6

Applying the BMVCEP Tavtigian point framework (PMID:32720330): PM2_Supporting (+1) + PP2_Supporting (+1) = 2 points total. Score of 2 falls within the VUS range (0-5).

7

No benign criteria are met: BA1 and BS1 population frequency thresholds are not exceeded; BS2 requires homozygotes or well-phenotyped heterozygotes not observed; BS3 lacks functional studies showing no effect; BP2, BP5 lack supporting evidence.

Final determination: Generic ACMG/AMP 2015 fallback rules do not meet benign, likely benign, likely pathogenic, or pathogenic combination thresholds, so the variant is classified as Variant of Uncertain Significance.

Criteria assessment

ACMG/AMP criteria review

Criteria shown when status is available

All criteria require review: For research and educational purposes only.

Criterion	Status	Rationale	Evidence used
PVS1	N/A	Not applicable under the ClinGen Brain Malformations VCEP v1.1. The disease mechanism for PIK3CA is gain of function (GOF); loss of function and/or haploinsufficiency have not been clearly identified as disease mechanisms underlying brain malformations related to these genes.	cspec vcep_clingen_brainmalform_acmg_specifications_v1_1
PS1	Not met	No same amino acid change has been previously established as pathogenic per BMVCEP criteria independent of this point. The variant (p.Asp133Asn) is absent from ClinVar and no prior pathogenic classification at this residue was identified.	clinvar
PS2	Not met	No de novo occurrence data is available for this variant. The BMVCEP requires confirmed maternity and paternity with variant absent from parents (Criteria 1) and presence in affected tissue with lower/absent allelic fraction in another tissue (Criteria 2) for PS2_Strong, or at least one criterion for PS2_Moderate. Neither criterion is met from available evidence.	cspec
PS3	Not met	No functional assay data is available for this specific variant (p.Asp133Asn). OncoKB reports Unknown Oncogenic Effect with no variant-specific reviewed functional evidence. No PMIDs were identified from literature screening. The BMVCEP requires functional assays meeting SVI quality metrics and validation controls (PMID:31892348), which are not available for this variant.	oncokb
PS4	Not met	PS4 requires PM2 first (which is met) and phenotype points per Table 2A/2B of the BMVCEP. No proband phenotype data, no literature cases, no ClinVar submissions, and no COSMIC entries were identified for this variant. Total points = 0, which is below the PS4_Supporting threshold of 0.5 points.	cspec clinvar
PS5	N/A	PS5 is not a recognized ACMG/AMP criterion and is not part of the ClinGen Brain Malformations VCEP v1.1 framework.
PM1	Not met	Residue Asp133 falls outside all approved Table 4 functional domains for PIK3CA. The approved domains are: adaptor binding domain (AA 31-108), kinase Ras-binding domain (AA 173-292), and kinase domains (AA 322-483 and AA 797-1068). Position 133 lies between the ABD and Ras-binding domains and is not within any Table 4 domain. Cancer Hotspots analysis also found no statistically significant hotspot at this residue.	cspec vcep_clingen_brainmalform_acmg_specifications_v1_1
PM2	Met	This variant is absent from gnomAD v2.1 (exomes) and gnomAD v4.1 (exomes/genomes). Under the BMVCEP, PM2 is awarded at supporting strength for variants absent or rare (≤1) in population controls.	gnomad_v2 gnomad_v4
PM5	Not met	No pathogenic missense variants have been established at residue Asp133. The BMVCEP requires that the comparator variant be established as pathogenic per BMVCEP criteria independent of this point. No same-residue ClinVar candidates were identified for this residue.	pm5_candidates clinvar
PM6	N/A	Not applicable under the BMVCEP v1.1. This point is addressed according to PS2 and will not be used separately.	cspec
PP1	N/A	Not applicable under the BMVCEP v1.1. Disease-causing variants are germline mosaic, de novo, or mosaic, making co-segregation analysis inapplicable.	cspec
PP2	Met	PIK3CA has a high gnomAD missense constraint z-score well above the BMVCEP threshold of 3.09, indicating a low rate of benign missense variation. This variant is a missense change in a gene where missense variants are a common disease mechanism. PP2 applies specifically to PIK3CA, MTOR, and AKT3 per the VCEP.	cspec
PP3	N/A	Not applicable under the BMVCEP v1.1. These variants are gain of function, and traditional mutation pathogenicity prediction algorithms focus on loss of function mechanisms. Use may be revisited if algorithms specifically designed to detect GOF mutations emerge.	cspec
PP4	N/A	Not applicable under the BMVCEP v1.1. This criterion is accounted for under PS4.	cspec
PP5	N/A	Not applicable under the BMVCEP v1.1. This criterion is not for use as recommended by the ClinGen Sequence Variant Interpretation VCEP Review Committee.	cspec
BA1	Not met	This variant is absent from gnomAD v2.1 and v4.1 (allele frequency 0%). The BMVCEP BA1 threshold is allele frequency > 0.0926%.	gnomad_v2 gnomad_v4
BS1	Not met	This variant is absent from gnomAD v2.1 and v4.1 (allele frequency 0%). The BMVCEP BS1 threshold is allele frequency > 0.0185%.	gnomad_v2 gnomad_v4
BS2	Not met	No homozygotes are present in gnomAD for this variant, and no well-phenotyped heterozygous family members have been identified. The BMVCEP requires ≥3 homozygotes in gnomAD or ≥3 heterozygous well-phenotyped family members for BS2.	gnomad_v2 gnomad_v4
BS3	Not met	No well-established in vitro or in vivo functional studies show no damaging effect on protein function for this variant. No functional assay data was identified for p.Asp133Asn. The BMVCEP requires functional studies meeting SVI quality metrics and validation controls (PMID:31892348).	oncokb
BS4	N/A	Not applicable under the BMVCEP v1.1. These are de novo, germline mosaic, or post-zygotic mutations, making segregation analysis inapplicable.	cspec
BP1	N/A	Not applicable under the BMVCEP v1.1. Loss of function is not the disease mechanism for PIK3CA-related brain malformations; the mechanism is gain of function.	cspec
BP2	Not met	No evidence that this variant has been observed in cis or trans with a known pathogenic variant in PIK3CA.
BP4	N/A	Not applicable for this variant type under the BMVCEP v1.1. BP4 is restricted to synonymous, intronic (except canonical splice sites), and non-coding variants in UTRs, assessed by two of three splicing prediction tools (varSEAK, SpliceAI, MaxEntScan) predicting no splicing change. This is a missense variant.	cspec
BP5	Not met	No evidence that this variant has been found in a case with an alternate molecular basis for disease in a different gene.
BP6	N/A	Not applicable under the BMVCEP v1.1. This criterion is not for use as recommended by the ClinGen Sequence Variant Interpretation VCEP Review Committee.	cspec
BP7	N/A	Not applicable for this variant type under the BMVCEP v1.1. BP7 is restricted to synonymous, intronic (except canonical splice sites), and non-coding variants in UTRs, assessed by nucleotide conservation (PhyloP score < 0.1). This is a missense variant (c.397G>A, p.Asp133Asn).	cspec

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