Variant classification summary

NM_006218.4:c.1324G>C

PIK3CA · NP_006209.2:p.(Ala442Pro) · NM_006218.4

GRCh37: chr3:178928046 G>C · GRCh38: chr3:179210258 G>C

Gene: PIK3CA Transcript: NM_006218.4

Final call

VUS

PM1 supporting PM2 supporting PP2 supporting

Variant details

Gene

PIK3CA

Transcript

NM_006218.4

Protein

NP_006209.2:p.(Ala442Pro)

gnomAD AF

5.008119413599298e-06 (v4.1)

ClinVar

Uncertain significance

OncoKB

Unknown Oncogenic Effect

Classification rationale

Interpretation summary

Generated evidence synthesis

1

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).

2

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.

3

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.

4

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.

5

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.

6

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.

Final determination: Brain Malformations Specification Tavtigian point framework v1.1.0 point-based framework yields a total score of 3, which maps to VUS under the specified Tavtigian-style ranges.

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 per Brain Malformations VCEP v1.1.0: loss of function and/or haploinsufficiency have not been clearly identified as disease mechanisms underlying brain malformations related to PIK3CA; the disease mechanism is gain of function (GOF).	cspec
PS1	Not met	PS1 requires the same amino acid change (p.Ala442Pro) to have been previously established as pathogenic via a different nucleotide change. No prior pathogenic classification was identified for p.Ala442Pro from any nucleotide change in ClinVar or the literature reviewed.	cspec clinvar
PS2	Not met	PS2 requires confirmed de novo occurrence with confirmed maternity and paternity. No de novo report or parental testing data was identified for this variant in ClinVar submissions, the literature reviewed, or any other source.	cspec
PS3	Not met	PS3 requires well-established in vitro or in vivo functional studies supportive of a damaging effect. OncoKB reports no variant-specific reviewed functional evidence for NM_006218.4:c.1324G>C (p.Ala442Pro). No variant-specific functional data were identified in any of the six publications reviewed. COSMIC has no entry for this variant.	cspec oncokb
PS4	Not met	PS4 under Brain Malformations VCEP requires phenotype point assignment per Table 2A/2B and is only applicable if PM2 is met. No case reports describing affected individuals with this specific variant were identified in ClinVar, the literature, or COSMIC. Without any reported cases, phenotype points cannot be assigned.	cspec clinvar
PS5	N/A	Not in the ONLY ASSESS list; adjudication not required for this criterion.
PM1	Met	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.	cspec vcep_clingen_brainmalform_acmg_specifications_v1_1
PM2	Met	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 gnomad_v4 gnomad_canada cspec
PM5	Not met	PM5 requires a different pathogenic missense change at the same amino acid residue (Ala442). The PM5 candidate search identified zero comparator variants at residue 442 with pathogenic classification. No same-residue pathogenic missense comparator is available.	pm5_candidates cspec
PM6	N/A	Not applicable per Brain Malformations VCEP v1.1.0: this criterion is addressed according to PS2 and will not be used separately.	cspec
PP1	N/A	Not applicable per Brain Malformations VCEP v1.1.0: disease-causing variants are germline mosaic, de novo, or mosaic, making co-segregation analysis inapplicable.	cspec
PP2	Met	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.	cspec gnomad_v2
PP3	N/A	Not applicable per Brain Malformations VCEP v1.1.0: traditional mutation pathogenicity prediction algorithms focus on LOF mechanisms, while PIK3CA disease mechanism is GOF. Use of this criterion can be revisited if algorithms specifically designed to detect GOF mutations emerge.	cspec
PP4	N/A	Not applicable per Brain Malformations VCEP v1.1.0: this criterion is accounted for under PS4 in this framework.	cspec
PP5	N/A	Not applicable per recommendation of the ClinGen Sequence Variant Interpretation VCEP Review Committee: this criterion is not for use.	cspec
BA1	Not met	BA1 requires allele frequency >0.0926% per the Brain Malformations VCEP. The highest observed frequency is 9.18e-06 (0.00092%) in the European (non-Finnish) subpopulation in gnomAD v2.1 and 6.80e-06 in v4.1, far below the BA1 threshold.	gnomad_v2 gnomad_v4 cspec
BS1	Not met	BS1 requires allele frequency >0.0185% per the Brain Malformations VCEP. The highest observed frequency is 9.18e-06 (0.00092%) in gnomAD v2.1, well below the BS1 threshold.	gnomad_v2 gnomad_v4 cspec
BS2	Not met	BS2 requires ≥3 homozygotes in gnomAD or ≥3 heterozygous in well-phenotyped family members per the Brain Malformations VCEP. Zero homozygotes are observed in gnomAD v2.1 or v4.1. No well-phenotyped heterozygous family members were identified.	gnomad_v2 gnomad_v4 cspec
BS3	Not met	BS3 requires well-established in vitro or in vivo functional studies showing no damaging effect. No variant-specific functional studies were identified for this variant. OncoKB reports no reviewed functional evidence. No benign functional data are available.	cspec oncokb
BS4	N/A	Not applicable per Brain Malformations VCEP v1.1.0: disease-causing variants in these genes are de novo, germline mosaic, or post-zygotic mutations, making lack of segregation analysis inapplicable.	cspec
BP1	N/A	Not applicable per Brain Malformations VCEP v1.1.0: LOF is not the disease mechanism for PIK3CA.	cspec
BP2	Not met	BP2 requires observation of the variant in cis or trans with a known pathogenic variant in the same gene. No such observation has been reported.	cspec
BP3	N/A	Not applicable: in-frame deletions/insertions in repetitive regions without known function are not relevant to this missense substitution variant.
BP4	N/A	Not applicable per Brain Malformations VCEP v1.1.0: BP4 is restricted to synonymous, intronic (except canonical splice sites), and non-coding UTR variants. NM_006218.4:c.1324G>C is a missense variant and does not qualify.	cspec
BP5	Not met	BP5 requires the variant to be found in a case with an alternate molecular basis for disease. No such finding has been reported for this variant.	cspec
BP6	N/A	Not applicable per recommendation of the ClinGen Sequence Variant Interpretation VCEP Review Committee: this criterion is not for use.	cspec
BP7	N/A	Not applicable per Brain Malformations VCEP v1.1.0: BP7 is restricted to synonymous, intronic (except canonical splice sites), and non-coding UTR variants with PhyloP score <0.1. NM_006218.4:c.1324G>C is a missense variant and does not qualify.	cspec

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