PIK3CA c.317G>C, p.(Gly106Ala)

Reasoning

The PIK3CA Brain Malformations VCEP specifies PM2 at Supporting strength for a variant absent/rare from controls in an ethnically matched cohort population sample, with one person maximum. NM_006218.4:c.317G>C is absent from gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada v1.0, with no observed control carriers in the available population datasets.

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 when the variant is absent/rare in an ethnically matched cohort population sample, allowing a maximum of one person.
• Direct variant queries report NM_006218.4:c.317G>C as absent from gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada v1.0; the available control datasets therefore show zero observed carriers, within the VCEP maximum of one person.

Sources

Reasoning

The applicable VCEP limits PM1 to Supporting evidence for residues affecting critical functional domains listed in its Table 4. For PIK3CA, the approved intervals are kinase-domain amino acids 322-483 and 797-1068. The variant affects Gly106, which is outside both intervals. Although the case bundle reports a Cancer Hotspots hit for G106, that finding does not satisfy the VCEP's specified domain-based PM1 rule.

Rule

PM1_Supporting: residues affecting critical functional domains provided in VCEP Table 4; PIK3CA domains 322-483 and 797-1068.

Evidence considered

• The Brain Malformations VCEP specification defines PM1_Supporting by Table 4 critical functional-domain membership.
• For PIK3CA, the bundle identifies the approved PM1 domains as amino acids 322-483 and 797-1068; p.Gly106Ala is at residue 106 and is outside both domains.
• Cancer Hotspots reports a statistically significant PIK3CA G106 hotspot, but hotspot status alone does not override the applicable VCEP domain-based PM1 specification.

Sources

Reasoning

The PIK3CA Brain Malformations VCEP specifies BA1 at an allele frequency greater than 0.0926%. The variant is absent from gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada v1.0; therefore no population allele frequency reaches the BA1 threshold.

Rule

Allele frequency (>0.0926%).

Evidence considered

• The governing Brain Malformations VCEP specification sets BA1 at allele frequency >0.0926%.
• Direct variant queries report NM_006218.4:c.317G>C as absent from gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada v1.0, so an allele frequency above 0.0926% is not observed.

Sources

Reasoning

The PIK3CA Brain Malformations VCEP specifies BS1 at an allele frequency greater than 0.0185%. The variant is absent from gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada v1.0; therefore no population allele frequency reaches the BS1 threshold.

Rule

Allele frequency (>0.0185%).

Evidence considered

• The governing Brain Malformations VCEP specification sets BS1 at allele frequency >0.0185%.
• Direct variant queries report NM_006218.4:c.317G>C as absent from gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada v1.0, so an allele frequency above 0.0185% is not observed.

Sources

Reasoning

The VCEP requires at least 3 homozygotes in gnomAD or at least 3 heterozygous observations in well-phenotyped family members. The variant is absent from the queried gnomAD datasets, and the case bundle contains no qualifying well-phenotyped family observations; therefore BS2 is not met.

Rule

Award BS2 if ≥3 homozygotes are present in gnomAD or ≥3 heterozygous observations are present in well-phenotyped family members.

Evidence considered

• The governing Brain Malformations VCEP rule requires ≥3 homozygotes in gnomAD or ≥3 heterozygous observations in well-phenotyped family members.
• The variant is reported absent from gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada v1.0, providing no homozygous observations, and no qualifying family-member observations are present in the case evidence bundle.

Sources

Reasoning

The variant is PIK3CA NM_006218.4:c.317G>C, p.Gly106Ala. The applicable Brain Malformations VCEP retains PS1 unchanged and requires the same amino acid change to have been previously established as pathogenic regardless of nucleotide change. The case bundle reports no ClinVar record, no literature PMIDs, and no variant-specific pathogenic comparator, so PS1 cannot be applied.

Rule

Same amino acid change as a previously established pathogenic variant regardless of nucleotide change; no VCEP change.

Evidence considered

• The Brain Malformations VCEP specification states that PS1 is applicable as originally described, with no change: the same amino acid change as a previously established pathogenic variant regardless of nucleotide change.
• The case bundle reports that NM_006218.4:c.317G>C is absent from ClinVar and that no literature PMIDs were found across the collected evidence sources.
• The normalized protein consequence is NP_006209.2:p.(Gly106Ala).

Still missing

• A previously established pathogenic PIK3CA variant producing p.Gly106Ala through a different nucleotide change is not documented in the collected evidence.

Sources

Reasoning

The applicable PIK3CA Brain Malformations VCEP rule requires evidence that the variant is present in the proband and absent from parental samples with confirmed maternity and paternity for PS2_Moderate; PS2_Strong additionally requires detectable variant in an affected tissue and absence or lower allele fraction in another tissue. The case bundle contains no proband genotype, parental testing, maternity/paternity confirmation, tissue-specific allele fractions, or comparable de novo evidence. Therefore PS2 cannot be assessed.

Rule

ClinGen Brain Malformations VCEP v1.1: PS2_Strong requires Criteria 1 and 2; Criterion 1 is detectable variant in the proband and absence from parental samples with confirmed maternity and paternity, and Criterion 2 is detectable variant in affected tissue with absence or lower allele fraction in another tissue. PS2_Moderate requires Criterion 1, or Criterion 2 when parents are unavailable.

Evidence considered

• The ClinGen Brain Malformations VCEP specification for PIK3CA defines PS2_Moderate as requiring the variant to be detectable in the proband and absent from parental samples with confirmed maternity and paternity, or the affected-tissue criterion when parents are unavailable; PS2_Strong requires both criteria.
• The consolidated case-evidence bundle provides no segregation/de novo family data, parental testing results, maternity/paternity confirmation, or tissue-specific allele-fraction data for this variant.

Still missing

• Proband variant detection and allele fraction are not documented.
• Parental variant testing results are not documented.
• Confirmed maternity and paternity are not documented.
• Affected-tissue and comparison-tissue allele fractions are not documented for the VCEP PS2_Strong requirement.

Sources

Reasoning

No variant-specific functional assay or animal-model evidence was identified in the case-evidence bundle for NM_006218.4:c.317G>C (p.Gly106Ala). Therefore PS3 cannot be assessed. The applicable Brain Malformations VCEP specification requires functional evidence to meet SVI/BMVCEP assay acceptability criteria, including appropriate validation controls for evidence above Supporting; those requirements cannot be evaluated without an assay report.

Rule

Follow the applicable Brain Malformations VCEP/SVI recommendations for assay quality metrics and minimum validation controls; assign PS3 only when variant-specific functional evidence satisfies those requirements.

Evidence considered

• The applicable ClinGen Brain Malformations VCEP specification states that PS3 follows SVI recommendations with BMVCEP quality metrics and minimum validation controls; it describes phosphorylation, DEPTOR binding, cell survivability, and cell proliferation assays as accepted assay classes and requires positive and negative validation controls for evidence above Supporting.
• The consolidated bundle reports no literature PMIDs, contains no paper extracts, and provides no variant-specific functional assay results for NM_006218.4:c.317G>C (p.Gly106Ala).

Still missing

• Variant-specific functional study report is absent.
• Assay type, biological relevance, quantitative result, replicate structure, and positive/negative control performance are unavailable.
• The number of independently evaluated variants and whether the assay meets the VCEP minimum validation requirements are unavailable.

Sources

Reasoning

The applicable Brain Malformations VCEP specification requires PM2 eligibility plus phenotype-point accumulation from affected individuals under Tables 2A/2B. No affected-individual phenotype data, eligible literature cases, or case-control enrichment data are present for PIK3CA p.(Gly106Ala), so no PS4 point total or strength can be assigned.

Rule

ClinGen Brain Malformations VCEP PS4: after PM2 eligibility, assign affected cases to the single highest Table 2A category and use the aggregate Table 2B point thresholds.

Evidence considered

• The Brain Malformations VCEP PS4 specification requires PM2 eligibility and assigns PS4 strength from the aggregate Table 2A phenotype-point total: Supporting 0.5-1.25, Moderate 1.5-3.25, Strong 3.5-15.75, and Very Strong at least 16 points.
• The evidence bundle reports no PMIDs or literature cases for this exact variant and no phenotype data from affected individuals.
• The variant is reported absent from gnomAD v2.1 and v4.1, but PM2 itself is outside this group's adjudication and was not independently assigned here.

Still missing

• Variant-specific affected-individual reports with phenotype details sufficient for Table 2A point assignment are needed.
• A documented PM2 assessment is needed before phenotype points may be used under the VCEP PS4 rule.

Sources

Reasoning

The applicable VCEP retains the classic PM5 rule: a novel missense change at a residue where a different missense change has been determined to be pathogenic. The collected PM5 candidate summary contains six candidates but zero same-residue candidates for Gly106, so no qualifying comparator was identified.

Rule

Novel missense change at an amino acid residue where a different missense change determined to be pathogenic has been seen before; no VCEP change.

Evidence considered

• The Brain Malformations VCEP specification states that PM5 is applicable as originally described, with no change.
• The PM5 candidate summary reports total_candidates_seen = 6, same_residue_candidates = 0, expert_panel_plp_candidates = 0, and non_expert_majority_plp_candidates = 0.
• The target missense consequence is p.Gly106Ala; no alternate missense change at residue Gly106 meeting the PM5 requirement is documented.

Still missing

• No qualifying pathogenic or likely pathogenic alternate missense variant at PIK3CA residue Gly106 was identified in the collected PM5 comparator set.

Sources

Reasoning

The applicable VCEP permits PP2_Supporting for PIK3CA when the ExAC/gnomAD missense-constraint z-score is greater than 3.09. The case bundle does not provide a PIK3CA missense-constraint z-score or an equivalent qualifying value, so PP2 cannot be adjudicated from the available evidence.

Rule

Award PP2_Supporting for PIK3CA if the ExAC/gnomAD missense-constraint z-score is greater than 3.09.

Evidence considered

• The Brain Malformations VCEP rule for PP2_Supporting requires a missense-constraint z-score greater than 3.09 and applies to PIK3CA.
• The collected case evidence contains no missense-constraint z-score for PIK3CA; the available gnomAD entries only report absence of the queried variant.

Still missing

• PIK3CA ExAC/gnomAD missense-constraint z-score is not available in the case bundle.

Sources

Reasoning

No variant-specific functional assay or animal-model evidence demonstrating no damaging effect on protein function or splicing was identified in the case-evidence bundle for NM_006218.4:c.317G>C (p.Gly106Ala). Therefore BS3 cannot be assessed. The applicable Brain Malformations VCEP specification requires the SVI/BMVCEP assay quality metrics and minimum validation controls to be evaluated before assigning BS3.

Rule

Follow the applicable Brain Malformations VCEP/SVI recommendations for assay quality metrics and minimum validation controls; assign BS3 only when variant-specific functional evidence demonstrates no damaging effect and satisfies those requirements.

Evidence considered

• The applicable ClinGen Brain Malformations VCEP specification defines BS3 as well-established in vitro or in vivo evidence showing no damaging effect and directs curators to apply SVI/BMVCEP quality metrics and minimum validation controls.
• The consolidated bundle reports no literature PMIDs, contains no paper extracts, and provides no variant-specific benign functional assay results for NM_006218.4:c.317G>C (p.Gly106Ala).

Still missing

• Variant-specific benign functional study report is absent.
• Assay result demonstrating preserved function, assay controls, replicates, and validation status are unavailable.
• There is no evidence establishing that the tested assay is biologically relevant and sufficiently validated for BS3 strength assignment.

Sources

Reasoning

The applicable 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 or family observations, phase results, or co-occurring known pathogenic PIK3CA variant, so BP2 cannot be assessed.

Rule

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

Evidence considered

• The ClinGen Brain Malformations VCEP specification states that BP2 is Supporting when the variant is observed in cis or trans with a known pathogenic variant in the same gene.
• The consolidated case-evidence bundle provides no phase information, no family or affected-proband allelic observations, and no co-occurring known pathogenic PIK3CA variant for NM_006218.4:c.317G>C (p.Gly106Ala).

Still missing

• A documented co-occurring known pathogenic PIK3CA variant is needed.
• Phase of NM_006218.4:c.317G>C relative to that pathogenic variant (cis or trans) is needed.
• Affected-proband or family-level segregation/inheritance observations supporting the phase are not available in the case bundle.

Sources

Reasoning

BP5 remains applicable as originally described by the VCEP, but the bundle contains no affected case with a documented alternate molecular diagnosis explaining the phenotype.

Rule

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

Evidence considered

• The VCEP retains BP5 without modification: 'Variant found in a case with an alternate molecular basis for disease.'
• No patient-level molecular diagnostic or phenotype data are present in the evidence bundle.

Still missing

• Case-level molecular testing and phenotype information demonstrating an alternative diagnosis are needed to assess BP5.

Sources