Variant classification summary

NM_006218.3:c.370C>T

PIK3CA · NP_006209.2:p.(Pro124Ser) · NM_006218.3

GRCh37: chr3:178917495 C>T · GRCh38: chr3:179199707 C>T

Gene: PIK3CA Transcript: NM_006218.3

Final call

VUS

PM2 supporting PP2 supporting

Variant details

Gene

PIK3CA

Transcript

NM_006218.3

Protein

NP_006209.2:p.(Pro124Ser)

gnomAD AF

0.0 (v4.1)

ClinVar

OncoKB

Likely Oncogenic

Classification rationale

Interpretation summary

Generated evidence synthesis

1

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.

2

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.

3

PIK3CA has high missense constraint (gnomAD missense z-score >3.09), meeting PP2_Supporting under the VCEP specification.

4

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.

5

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.

6

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.

7

This variant is classified as a Variant of Uncertain Significance (VUS) under the ClinGen Brain Malformations Expert Panel specifications version 1.1.0.

Final determination: Brain Malformations Specification Tavtigian point framework v1.1.0 point-based framework yields a total score of 2, 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	PVS1 is not applicable under the ClinGen Brain Malformations VCEP because the disease mechanism for PIK3CA is gain of function, not loss of function or haploinsufficiency.	cspec
PS1	Not met	No previously established pathogenic variant with the same amino acid change (P124S) has been identified. The variant is absent from ClinVar, and no published report describes P124S as a pathogenic variant in any context.	clinvar
PS2	Not met	No de novo observation has been reported for this variant. The VCEP PS2 criteria require confirmed maternity and paternity with absent parental variant (Strong) or at minimum evidence of tissue-specific mosaicism (Moderate). Neither is available.
PS3	Not met	No functional study has directly tested P124S (NM_006218.3:c.370C>T). The only functional study of the same residue tested P124L (a different amino acid substitution) in a somatic cancer context using NIH3T3 and NHUC cell lines; that study demonstrated gain-of-function activity for P124L but did not examine P124S. Under VCEP PS3 criteria, the exact variant must be tested unless a systematic range characterization including the variant position is available, which is not the case here.
PS4	Not met	No probands with brain malformation phenotypes have been reported for this variant. The VCEP PS4 is point-based and requires PM2 as a prerequisite. COSMIC reports two somatic occurrences, which under Table 2A would contribute at most 0.25 points each (0.50 total), falling below the PS4_Supporting threshold of 0.5–1.25 points. No germline case reports with relevant phenotypes exist.	gnomad_v4
PS5	N/A	PS5 is not a recognized criterion in the ClinGen Brain Malformations VCEP specification and is not included in the CSPEC criteria list for PIK3CA.	cspec
PM1	Not met	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). Although the literature supports functional relevance of position 124 for p85α interaction, it does not meet the VCEP domain criteria for PM1 application.	cspec PMID:22430209
PM2	Met	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).	gnomad_v2 gnomad_v4 cspec
PM5	Not met	No different missense variant at residue Pro124 has been classified as pathogenic in ClinVar. P124L was reported in PMID:22430209 as a rare somatic variant in urothelial carcinoma with gain-of-function activity, but has never been classified as pathogenic in a germline context and lacks a ClinVar pathogenic assertion. The VCEP PM5 (Moderate, 'No change' from original ACMG) requires a previously established pathogenic missense at the same residue, which is not available.	clinvar PMID:22430209
PM6	N/A	PM6 is not applicable under the ClinGen Brain Malformations VCEP: 'This point is addressed according to PS2 and will not be used.'	cspec
PP1	N/A	PP1 is not applicable under the ClinGen Brain Malformations VCEP: 'Not applicable since disease-causing variants are germline mosaic, de novo or mosaic.'	cspec
PP2	Met	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.	cspec gnomad_v4
PP3	N/A	PP3 is not applicable under the ClinGen Brain Malformations VCEP: 'This criterion is not applicable since these variants are GOF, and traditional mutation pathogenicity prediction algorithms focus on LOF mechanisms.'	cspec
PP4	N/A	PP4 is not applicable under the ClinGen Brain Malformations VCEP: 'Not applicable since this criterion is accounted for under PS4.'	cspec
PP5	N/A	PP5 is not applicable: 'This criterion is not for use as recommended by the ClinGen Sequence Variant Interpretation VCEP Review Committee.'	cspec
BA1	Not met	The variant is absent from gnomAD v4.1 (allele frequency 0.00%). The VCEP BA1 Stand Alone threshold is >0.0926%, which is not met.	gnomad_v2 gnomad_v4 cspec
BS1	Not met	The variant is absent from gnomAD v4.1 (allele frequency 0.00%). The VCEP BS1 Strong threshold is >0.0185%, which is not met.	gnomad_v2 gnomad_v4 cspec
BS2	Not met	No homozygotes are present in gnomAD (0 homozygotes in v4.1), and no well-phenotyped heterozygous family members have been reported. The VCEP BS2 Strong requires ≥3 homozygotes in gnomAD or ≥3 heterozygous well-phenotyped family members.	gnomad_v4 cspec
BS3	Not met	No functional study has demonstrated that P124S has no damaging effect on protein function. The only functional study at this residue (PMID:22430209) tested P124L and demonstrated gain-of-function activity, which would be in the opposite direction of BS3. No well-established in vitro or in vivo studies show a benign functional effect for P124S.
BS4	N/A	BS4 is not applicable under the ClinGen Brain Malformations VCEP: 'Not applicable as these are de novo, germline mosaic or post-zygotic mutations.'	cspec
BP1	N/A	BP1 is not applicable under the ClinGen Brain Malformations VCEP: 'Not applicable as LOF is not the disease mechanism.'	cspec
BP2	Not met	No evidence that this variant has been observed in cis or trans with a known pathogenic variant in PIK3CA. No phase information is available.
BP4	N/A	BP4 under this VCEP is restricted to synonymous variants, intronic positions (except canonical splice sites), and non-coding variants in UTRs. NM_006218.3:c.370C>T is a missense variant and does not qualify for BP4 application.	cspec
BP5	Not met	No case has been reported in which this variant was found in an individual with an alternate molecular basis for disease. The VCEP BP5 (Supporting, 'No change') requires evidence of an alternate molecular diagnosis in a case harboring this variant.
BP6	N/A	BP6 is not applicable: 'This criterion is not for use as recommended by the ClinGen Sequence Variant Interpretation VCEP Review Committee.'	cspec
BP7	N/A	BP7 under this VCEP is restricted to synonymous variants, intronic positions (except canonical splice sites), and non-coding variants in UTRs. NM_006218.3:c.370C>T is a missense variant and does not qualify for BP7 application.	cspec

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