PIK3CA c.268T>C, p.(Cys90Arg)

Reasoning

The governing Brain Malformations VCEP specifies PM1 at Supporting strength for residues affecting critical functional domains in Table 4. The authoritative vcep_materials.json domain_tables entry for PIK3CA lists the adaptor binding domain (PI3K ABD) at amino acids 31-108, the kinase Ras-binding domain at 173-292, and kinase domains at 322-483 and 797-1068. The variant is p.Cys90Arg, so residue 90 falls within the approved PI3K ABD interval 31-108; the other approved intervals were also checked and do not contain residue 90. PM1_Supporting is therefore met.

Rule

Residues affecting critical functional domains provided in Table 4 for each gene.

Evidence considered

• The VCEP PM1 rule awards Supporting evidence for residues affecting critical functional domains provided in Table 4.
• The authoritative PIK3CA domain table lists PI3K ABD residues 31-108, kinase Ras-binding residues 173-292, and kinase-domain intervals 322-483 and 797-1068.
• The case protein consequence is p.Cys90Arg; residue 90 is within the approved PI3K ABD interval 31-108 and outside the other listed intervals.

Sources

Reasoning

PM2_Supporting is met under the governing ClinGen Brain Malformations VCEP specification. NM_006218.4:c.268T>C (p.Cys90Arg) is absent from gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada v1.0. The case does not document the patient's ancestry, so the ethnically matched-cohort component cannot be independently confirmed; this is retained as a human-review caveat rather than downgrading the VCEP population absence evidence.

Rule

Absent/rare from controls in an ethnically-matched cohort population sample (>=1).

Evidence considered

• The governing Brain Malformations VCEP specifies PM2 at Supporting strength for a variant absent/rare from controls in an ethnically matched cohort population sample, with one population sample sufficient.
• The variant is reported absent from gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada v1.0. These independent population resources provide concordant absence evidence, although the case does not state the patient's ancestry or provide detailed coverage metrics.

Still missing

• Patient ancestry is not documented, so an ethnically matched population cohort cannot be specifically verified.
• The population records provide absence statements but no explicit allele-number, allele-count, or coverage metrics.

Sources

Reasoning

BA1 is not met. The ClinGen Brain Malformations VCEP threshold for PIK3CA is allele frequency >0.0926%. NM_006218.4:c.268T>C (p.Cys90Arg) is absent from gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada v1.0; therefore no population frequency approaches the BA1 threshold.

Rule

Allele frequency (>0.0926%).

Evidence considered

• The governing Brain Malformations VCEP specification sets BA1 at allele frequency >0.0926% for this disease context.
• The variant is reported absent from gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada v1.0, with no allele count or allele frequency reported in any of these sources.

Sources

Reasoning

BS1 is not met. The ClinGen Brain Malformations VCEP threshold for PIK3CA is allele frequency >0.0185%. The variant is absent from gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada v1.0, so no observed frequency exceeds the BS1 threshold.

Rule

Allele frequency (>0.0185%).

Evidence considered

• The governing Brain Malformations VCEP specification sets BS1 at allele frequency >0.0185% for this disease context.
• The variant is reported absent from gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada v1.0; no population allele frequency exceeds the VCEP BS1 threshold.

Sources

Reasoning

BS2 is not met. The PIK3CA VCEP requires at least 3 homozygotes in gnomAD or at least 3 heterozygous observations in well-phenotyped family members. The available population sources report the variant as absent, and the case contains no qualifying homozygote observations or well-phenotyped family-member observations.

Rule

Award BS2 if >=3 homozygotes present in gnomAD or >=3 heterozygous in well phenotyped family members.

Evidence considered

• The governing Brain Malformations VCEP BS2 rule requires >=3 homozygotes in gnomAD or >=3 heterozygous observations in well-phenotyped family members.
• gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada v1.0 each report the variant as absent; no homozygote count is available and no qualifying family observations are provided.

Sources

Reasoning

The governing Brain Malformations VCEP applies PS1 at Strong strength without modification when the same amino-acid change has been previously established as pathogenic. The case variant is PIK3CA p.Cys90Arg, but the available bundle does not provide a previously established pathogenic variant with the same amino-acid change. The single ClinVar submission is uncertain significance and cannot establish PS1.

Rule

No change.

Evidence considered

• The Brain Malformations VCEP specifies PS1 as applicable as originally described at Strong strength: same amino-acid change as a previously established pathogenic variant regardless of nucleotide change.
• The case variant is NM_006218.4:c.268T>C, NP_006209.2:p.(Cys90Arg).
• ClinVar reports one single-submitter classification of uncertain significance, which is not evidence that the same amino-acid change is established pathogenic.

Still missing

• No independently evaluated pathogenic PIK3CA p.Cys90Arg comparator was identified in the supplied evidence bundle.

Sources

Reasoning

The applicable PIK3CA Brain Malformations VCEP rule requires de novo evidence. Strong PS2 requires the variant to be detectable in affected tissue, absent from parental samples with confirmed maternity and paternity, and absent or at a lower allelic fraction in another tissue; Moderate PS2 requires confirmed parental absence or, if parents are unavailable, the affected-tissue distribution criterion. The case-evidence bundle contains no proband variant allele fraction, parental testing results, maternity/paternity confirmation, tissue comparison, or other de novo documentation, so PS2 cannot be awarded or excluded.

Rule

VCEP PS2: Strong requires Criteria 1 AND Criteria 2; Criteria 1 is detectable variant in the proband affected tissue absent from parents with confirmed maternity and paternity, and Criteria 2 is detectable variant in affected tissue absent from or at a lower allelic fraction in another tissue. Moderate requires Criteria 1 OR, if parents are unavailable, Criteria 2.

Evidence considered

• The ClinGen Brain Malformations VCEP specification for PIK3CA defines PS2_Strong using both parental absence with confirmed maternity/paternity and tissue-distribution criteria, and PS2_Moderate using confirmed parental absence or the tissue criterion when parents are unavailable.
• The consolidated case-evidence bundle provides no proband, parental, maternity/paternity, allele-fraction, or tissue-segregation data for NM_006218.4:c.268T>C (p.Cys90Arg).

Still missing

• Proband variant detection and allele fraction are not documented.
• Maternal and paternal testing results and confirmation of maternity/paternity are not documented.
• Affected-tissue and other-tissue variant fractions are not documented.

Sources

Reasoning

The applicable ClinGen Brain Malformations VCEP specification requires a validated functional assay with the specified quality metrics and controls. The case bundle provides no assay result for the exact variant NM_006218.4:c.268T>C (p.Cys90Arg). PMID:29975751 tested other PIK3CA ABD variants, including C90Y, but did not test C90R; results from a different amino-acid substitution cannot establish PS3 for this variant. Therefore PS3 cannot be assigned at any strength.

Rule

Applicable VCEP PS3 rule: follow ClinGen SVI recommendations and BMVCEP specifications for functional-assay quality metrics and minimum validation controls; the assay must meet the acceptability criteria cited by the VCEP (PMID:31892348).

Evidence considered

• The applicable Brain Malformations VCEP specification states that PS3 follows ClinGen SVI recommendations with BMVCEP quality metrics and minimum validation controls; evidence above Supporting requires independent positive and negative controls and variant-count thresholds.
• The bundle's extracted finding for PMID:29975751 reports experiments on PIK3CA C90Y and R88Q, not the case variant p.Cys90Arg, so those results were not used to assign PS3.
• The case variant is NM_006218.4:c.268T>C, NP_006209.2:p.(Cys90Arg).

Still missing

• No variant-specific in vitro or in vivo functional assay result for PIK3CA p.Cys90Arg.
• No documented assay validation controls, replicate data, or quantitative result for the exact variant.

Sources

Reasoning

The PIK3CA Brain Malformations VCEP PS4 specification requires PM2 eligibility and phenotype-point accumulation under Tables 2A/2B. Although the variant is absent from the available population datasets, the bundle supplies no affected cerebral-malformation cases with usable phenotype-point assignments or case-control enrichment data. One somatic cancer occurrence is insufficient to reach the VCEP PS4_Supporting threshold.

Rule

PIK3CA Brain Malformations VCEP PS4: phenotype points under Tables 2A/2B may be used only with PM2; PS4_Supporting requires 0.5–1.25 points.

Evidence considered

• The governing Brain Malformations VCEP specification requires PM2 eligibility and assigns PS4 only after summing phenotype points: Supporting 0.5–1.25, Moderate 1.5–3.25, Strong 3.5–15.75, and Very Strong at least 16 points.
• The variant is absent from gnomAD v2.1 and v4.1, satisfying the population-data prerequisite but not supplying affected-case evidence.
• The evidence bundle records one COSMIC somatic cancer occurrence; the VCEP material states tumor evidence contributes only 0.25 point per occurrence category, below the PS4_Supporting threshold.

Still missing

• Variant-specific, phenotyped cerebral-malformation cases sufficient to calculate the VCEP Table 2A total are unavailable.
• No case-control study or odds-ratio analysis for c.268T>C (p.Cys90Arg) is available.

Sources

Reasoning

The governing Brain Malformations VCEP applies PM5 at Moderate strength as originally described: a novel missense change at a residue where a different missense change determined to be pathogenic has been seen before. The bundle identifies one same-residue comparator, PIK3CA C90Y, in a functional paper, but that study does not establish C90Y as pathogenic and instead reports no increased activity or tumorigenic phenotype over wild type in its tested models. The supplied PM5 candidate summary also reports no useful same-residue candidates. PM5 cannot be met from the available evidence.

Rule

No change.

Evidence considered

• The VCEP PM5 rule requires a different missense change at the same amino-acid residue that has been determined to be pathogenic; the default strength is Moderate.
• The supplied PM5 candidate summary reports one candidate seen overall but zero same-residue candidates and no useful candidates for PM5.
• PMID:29975751 experimentally evaluated PIK3CA C90Y as a same-residue comparator but reported that ABD mutants did not increase PI3K signaling, migration, or colony formation more than wild-type PIK3CA in the tested models and did not establish C90Y as pathogenic.

Still missing

• A different PIK3CA missense variant at residue 90 established as pathogenic by eligible clinical evidence is not available in the supplied bundle.

Sources

Reasoning

The governing Brain Malformations VCEP allows PP2 at Supporting strength for PIK3CA when the ExAC/gnomAD missense-constraint z-score is greater than 3.09. The supplied bundle confirms that PP2 is applicable to PIK3CA and provides no missense-constraint z-score for the gene. The available population records are variant-frequency absence results and do not establish the required gene-level constraint threshold, so PP2 is not assessed.

Rule

Missense constraint computed in ExAC/gnomAD was utilized. Award PP2 if the z-score > 3.09. (applicable to MTOR, PIK3CA and AKT3 but not PIK3R2).

Evidence considered

• The VCEP PP2 rule specifies Supporting evidence for MTOR, PIK3CA, and AKT3 when the ExAC/gnomAD missense-constraint z-score is greater than 3.09.
• The case bundle contains no PIK3CA missense-constraint z-score, so the VCEP threshold cannot be evaluated.

Still missing

• PIK3CA ExAC/gnomAD missense-constraint z-score is not provided; the required value must be verified as greater than 3.09.

Sources

Reasoning

The applicable ClinGen Brain Malformations VCEP specification requires well-established functional evidence showing no damaging effect, assessed under the specified SVI/BMVCEP assay quality metrics and validation controls. No qualifying functional study of the exact PIK3CA p.Cys90Arg variant is present in the case bundle. PMID:29975751 evaluated other ABD substitutions, including C90Y, and therefore cannot establish a benign functional effect for C90R. BS3 is not assigned.

Rule

Applicable VCEP BS3 rule: follow ClinGen SVI recommendations together with Brain Malformation Group specifications for functional-assay quality metrics and minimum validation controls.

Evidence considered

• The applicable Brain Malformations VCEP specification defines BS3 as well-established in vitro or in vivo functional evidence showing no damaging effect and directs review under SVI/BMVCEP quality metrics and minimum validation controls.
• The bundle's extracted finding for PMID:29975751 reports experiments on PIK3CA C90Y and R88Q, not the case variant p.Cys90Arg; those non-identical substitutions were not used to assign BS3.
• The case variant is NM_006218.4:c.268T>C, NP_006209.2:p.(Cys90Arg).

Still missing

• No variant-specific functional result demonstrating preserved PIK3CA function for p.Cys90Arg.
• No documented assay validation controls, replicate data, or quantitative benign-effect result for the exact variant.

Sources

Reasoning

The applicable PIK3CA VCEP rule permits BP2 at Supporting strength when the variant is observed in cis or trans with a known pathogenic variant in the same gene. The case bundle contains no affected-proband observation, second PIK3CA variant, pathogenic partner variant, parental testing, or phase information establishing cis or trans, so BP2 cannot be assessed from the available evidence.

Rule

Observed in cis or trans with a known pathogenic variant in the same gene.

Evidence considered

• The PIK3CA Brain Malformations VCEP rule for BP2 is: observed in cis or trans with a known pathogenic variant in the same gene.

Still missing

• Document a known pathogenic PIK3CA partner variant in the same individual and confirm whether the variants are in cis or trans using parental, offspring, or equivalent phasing data.

Sources

Reasoning

BP5 remains applicable as originally described by the VCEP, but the bundle contains no individual-level report showing this variant in a person whose phenotype has an established alternate molecular basis.

Rule

Brain Malformations VCEP BP5: applicable as originally described; variant found in a case with an alternate molecular basis for disease.

Evidence considered

• The Brain Malformations VCEP retains BP5 without modification: it requires a variant to be found in a case with an alternate molecular basis for disease.
• No supplied case-level or publication evidence documents an alternate molecular diagnosis for a carrier of c.268T>C (p.Cys90Arg).

Still missing

• An individual-level case report documenting an alternate molecular diagnosis that explains the phenotype is unavailable.

Sources