PIK3CA c.278G>T, p.(Arg93Leu)

Reasoning

The variant is PIK3CA p.Arg93Leu, affecting residue 93. The authoritative vcep_materials.json domain_tables entry for PIK3CA was checked across every listed approved domain: Kinase Ras-binding domain 173-292 (not overlapping), kinase domains 322-483 and 797-1068 (not overlapping), and adaptor binding domain (PI3K ABD) 31-108 (overlapping). Because residue 93 lies within the approved PI3K ABD critical functional domain, PM1 is met at the VCEP-specified Supporting strength. The VCEP rule does not require hotspot recurrence for domain-based PM1.

Rule

Residues affecting critical functional domains provided in Table 4 for each gene; PIK3CA PM1 is Supporting.

Evidence considered

• The governing Brain Malformations VCEP specifies PM1 at Supporting strength for residues affecting critical functional domains in Table 4.
• The authoritative PIK3CA domain table lists the adaptor binding domain (PI3K ABD) at amino acids 31-108, which contains residue Arg93; the other listed PIK3CA intervals, 173-292, 322-483, and 797-1068, were also checked and do not contain residue 93.
• The VCEP local guidance states that PM1 is domain-based and does not require hotspot recurrence when the variant falls inside an approved domain.

Sources

Reasoning

PM2 Supporting is met. The applicable PIK3CA Brain Malformations VCEP rule permits PM2 Supporting when the variant is absent or rare in an ethnically matched control cohort with at least one qualifying population sample. The variant is absent from gnomAD v2.1 and gnomAD-Canada v1.0 and has 0 alternate alleles among 1,611,098 alleles in gnomAD v4.1, including 0 alleles in the largest listed subpopulation. No population-frequency or homozygote observation weakens PM2.

Rule

PM2 Supporting: absent/rare from controls in an ethnically matched cohort population sample (>=1) under the PIK3CA Brain Malformations VCEP specification.

Evidence considered

• The governing ClinGen Brain Malformations VCEP specifies PM2 at Supporting strength for a variant absent or rare in an ethnically matched control cohort population sample, with at least one qualifying sample.
• gnomAD v2.1 reports the variant absent.
• gnomAD v4.1 reports 0 alternate alleles among 1,611,098 total alleles, total AF 0.0, and 0 homozygotes; the African/African American subgroup, reported as the highest observed-frequency subgroup, also has 0 alternate alleles among 74,682 alleles and AF 0.0.
• gnomAD-Canada v1.0 reports the variant absent.

Sources

Reasoning

BA1 is not met. The PIK3CA Brain Malformations VCEP specifies BA1 at allele frequency >0.0926%; the variant has allele count 0 and allele frequency 0.0 in gnomAD v4.1 and is absent from gnomAD v2.1 and gnomAD-Canada v1.0. These data are far below the BA1 threshold.

Rule

BA1 Stand Alone: allele frequency >0.0926% under the PIK3CA Brain Malformations VCEP specification.

Evidence considered

• The governing ClinGen Brain Malformations VCEP specification for PIK3CA sets BA1 at allele frequency >0.0926%.
• gnomAD v4.1 reports 0 alternate alleles among 1,611,098 total alleles, total AF 0.0, and 0 homozygotes; the highest observed subpopulation AF is also 0.0 in the African/African American group.
• The variant is reported absent from gnomAD v2.1 and gnomAD-Canada v1.0.

Sources

Reasoning

BS1 is not met. The PIK3CA Brain Malformations VCEP specifies BS1 at allele frequency >0.0185%; the variant has allele count 0 and allele frequency 0.0 in gnomAD v4.1 and is absent from gnomAD v2.1 and gnomAD-Canada v1.0. The observed population frequency does not exceed the benign frequency threshold.

Rule

BS1 Strong: allele frequency >0.0185% under the PIK3CA Brain Malformations VCEP specification.

Evidence considered

• The governing ClinGen Brain Malformations VCEP specification for PIK3CA sets BS1 at allele frequency >0.0185%.
• gnomAD v4.1 reports 0 alternate alleles among 1,611,098 total alleles, total AF 0.0, and 0 homozygotes, with AF 0.0 in every listed population subgroup.
• The variant is reported absent from gnomAD v2.1 and gnomAD-Canada v1.0.

Sources

Reasoning

BS2 is not met. The applicable VCEP rule requires at least 3 homozygotes in gnomAD or at least 3 heterozygous occurrences in well-phenotyped family members. gnomAD v4.1 reports 0 homozygotes, and the case bundle contains no qualifying family-member observations.

Rule

BS2 Strong: award only for >=3 gnomAD homozygotes or >=3 heterozygous observations in well-phenotyped family members under the PIK3CA Brain Malformations VCEP specification.

Evidence considered

• The governing ClinGen Brain Malformations VCEP specifies BS2 only when at least 3 homozygotes are present in gnomAD or at least 3 heterozygotes are present in well-phenotyped family members.
• gnomAD v4.1 reports homozygotes = 0 and total_hom = 0 for the variant.
• No well-phenotyped family-member data meeting the VCEP threshold are provided in the case-evidence bundle.

Sources

Reasoning

The variant is PIK3CA p.Arg93Leu (NM_006218.4:c.278G>T). The governing Brain Malformations VCEP applies PS1 at Strong strength without modification, but the case bundle contains no ClinVar record, no literature PMIDs, and no documented previously established pathogenic variant producing the same amino-acid change. PS1 cannot be awarded from the available evidence.

Rule

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

Evidence considered

• The VCEP rule states that PS1 is the same amino-acid change as a previously established pathogenic variant regardless of nucleotide change and specifies no change to the Strong strength.
• The case bundle reports that this variant is absent from ClinVar and that no PMIDs were found across evidence sources; therefore no qualifying same-amino-acid pathogenic comparator was documented.

Still missing

• A reliable clinical or published record establishing PIK3CA p.Arg93Leu as pathogenic, or an equivalent same-amino-acid substitution caused by another nucleotide change, is needed.

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, and additionally requires affected-tissue detection with absent or lower detection in another tissue for PS2_Strong. The case-evidence bundle contains no proband-level variant result, parental testing results, maternity/paternity confirmation, allele fraction, tissue source, or phenotype-linked de novo documentation. Therefore PS2 cannot be adjudicated from the available case evidence.

Rule

VCEP PS2: PS2_Strong requires Criteria 1 and Criteria 2; Criteria 1 is detectable variant in the affected individual absent from parental samples with confirmed maternity and paternity, and Criteria 2 is detectable variant in affected tissue absent from or at lower allelic fraction in another tissue. PS2_Moderate requires Criteria 1, or Criteria 2 when parents are unavailable.

Evidence considered

• The ClinGen Brain Malformations VCEP specification for PIK3CA defines PS2_Moderate when the variant is detected in the affected individual and absent from parental samples with confirmed maternity and paternity, and PS2_Strong when this is combined with affected-tissue detection and absent or lower detection in another tissue.
• The consolidated case-evidence bundle provides no proband, parental, maternity/paternity, tissue, allele-fraction, or segregation/de novo observations for NM_006218.4:c.278G>T (NP_006209.2:p.Arg93Leu).

Still missing

• Proband variant detection and assay quality/allele fraction
• Maternal and paternal testing results
• Confirmed maternity and paternity
• Affected tissue and comparison-tissue testing if considering PS2_Strong
• Clinical phenotype documentation for the proband

Sources

Reasoning

No variant-specific in vitro or in vivo functional assay evidence is present in the case-evidence bundle for NM_006218.4:c.278G>T (PIK3CA p.Arg93Leu). The applicable Brain Malformations VCEP specification requires validated functional assays with appropriate quality metrics and minimum validation controls; the bundle contains no functional publication, assay result, positive control, negative control, replicate information, or animal-model result from which PS3 can be assigned or calibrated.

Rule

Apply PS3 only when a well-established functional assay satisfies the Brain Malformations VCEP/SVI quality-metric and minimum-validation-control requirements; strength calibration requires the specified validation controls and assay evidence.

Evidence considered

• The Brain Malformations VCEP specification applies to PIK3CA and states that PS3 requires a functional assay meeting the specified SVI/BMVCEP acceptability criteria, including quality metrics and minimum validation controls.
• The consolidated case-evidence bundle reports zero literature PMIDs and an empty paper_extracts object; therefore no variant-specific functional study was available for review.
• The bundle contains only non-functional context such as a curated likely gain-of-function label and population/cancer-database observations; these were not used to infer PS3.

Still missing

• Variant-specific functional assay results are absent.
• Assay methodology, biological relevance, controls, replication, and validation metrics are unavailable.
• No evidence is available to determine PS3 supporting, moderate, or strong strength.

Sources

Reasoning

The applicable Brain Malformations VCEP PS4 framework requires a phenotype-point total for affected individuals and requires the PM2 rarity prerequisite. Although this variant is absent from the reported gnomAD datasets, the bundle contains no affected individual, phenotype, case-control, or literature case evidence from which to assign Table 2A points or establish enrichment.

Rule

ClinGen Brain Malformations VCEP v1.1 PS4: assign each reported case only its highest Table 2A category, total the points, and apply the Table 2B threshold only when the PM2 rarity prerequisite is satisfied.

Evidence considered

• The Brain Malformations VCEP specifies PS4 phenotype-point thresholds of Supporting 0.5-1.25, Moderate 1.5-3.25, Strong 3.5-15.75, and Very Strong at least 16 points; phenotype points require the PM2 rarity prerequisite.
• The bundle reports no literature PMIDs or patient-level phenotype/case evidence for PIK3CA p.(Arg93Leu).
• The reported population lookups show zero alternate alleles in gnomAD v2.1 and 0/1,611,098 alleles in gnomAD v4.1; this does not substitute for affected-case evidence.

Still missing

• Variant-specific affected-case reports with the VCEP Table 2A phenotype categories and sufficient details to assign non-duplicative points.
• A case-control analysis or a completed VCEP phenotype-point total after confirming the PM2 prerequisite.

Sources

Reasoning

The governing VCEP applies PM5 at Moderate strength without modification. The case bundle's PM5 candidate collection found four candidates overall but zero same-residue candidates and reports no clearly useful comparator variants. Thus the available evidence does not establish a different pathogenic missense change at Arg93, and PM5 cannot be awarded.

Rule

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

Evidence considered

• The VCEP rule defines PM5 as a missense change at an amino-acid residue where a different missense change determined to be pathogenic has been seen before and specifies Moderate strength.
• The case bundle reports zero same-residue candidates and no clearly useful comparator variants; the PM5 artifact is not itself sufficient to apply PM5.

Still missing

• A validated pathogenic or likely pathogenic missense variant at PIK3CA residue Arg93, with a source supporting that classification independently of PM5, is needed.

Sources

Reasoning

The governing VCEP permits PP2 for PIK3CA at Supporting strength when the ExAC/gnomAD missense-constraint z-score is greater than 3.09. The case bundle provides population observations for the variant but does not provide the PIK3CA missense-constraint z-score or an equivalent gene-level constraint value. PP2 therefore cannot be assessed.

Rule

Award PP2 if the ExAC/gnomAD missense-constraint z-score is >3.09; applicable to PIK3CA; Supporting.

Evidence considered

• The VCEP rule states to award PP2 for PIK3CA when the ExAC/gnomAD missense-constraint z-score is greater than 3.09.
• The bundle reports the variant's gnomAD v2.1 absence and gnomAD v4.1 allele count/frequency, but contains no PIK3CA gene-level missense-constraint z-score. Variant rarity alone does not establish PP2.

Still missing

• The applicable ExAC/gnomAD PIK3CA missense-constraint z-score is required to determine whether it exceeds 3.09.

Sources

Reasoning

No variant-specific in vitro or in vivo functional assay evidence is present in the case-evidence bundle showing no damaging effect on PIK3CA function or splicing. The applicable Brain Malformations VCEP specification requires validated functional evidence with appropriate quality metrics and minimum validation controls; without an assay result and its controls, BS3 cannot be assigned at supporting or strong strength.

Rule

Apply BS3 only when a well-established in vitro or in vivo functional study demonstrates no damaging effect and satisfies the Brain Malformations VCEP/SVI quality-metric and minimum-validation-control requirements.

Evidence considered

• The Brain Malformations VCEP specification defines BS3 as well-established functional evidence showing no damaging effect and directs application according to the SVI/BMVCEP quality-metric and minimum-validation-control requirements.
• The consolidated case-evidence bundle reports zero literature PMIDs and an empty paper_extracts object; therefore no variant-specific benign functional study was available for review.
• Absence of functional evidence was treated as not assessed, not as evidence of a benign effect.

Still missing

• Variant-specific benign functional assay results are absent.
• Assay methodology, biological relevance, controls, replication, and validation metrics are unavailable.
• No evidence is available to determine BS3 supporting or strong strength.

Sources

Reasoning

The VCEP 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-evidence bundle contains no affected-proband, family, parental, phase, or second-PIK3CA-variant observation for NM_006218.4:c.278G>T (p.Arg93Leu), so BP2 cannot be adjudicated.

Rule

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

Evidence considered

• The governing ClinGen Brain Malformations VCEP specification defines BP2 as Supporting when a variant is observed in cis or trans with a known pathogenic variant in the same gene.
• The consolidated case-evidence bundle reports no literature PMIDs and provides no phase, parental, family, or second-variant observations for this case.

Still missing

• Documented observation of the variant with a known pathogenic PIK3CA variant
• Phase determination as cis or trans
• Affected-proband or family-level genotype context

Sources

Reasoning

BP5 remains applicable as originally described by the VCEP, but the bundle contains no patient-level molecular workup showing an alternate molecular basis for the relevant phenotype.

Rule

ClinGen Brain Malformations VCEP v1.1 BP5: apply at Supporting only when the case has an alternate molecular basis for disease.

Evidence considered

• The VCEP retains BP5 without modification: a variant found in a case with an alternate molecular basis for disease.

Still missing

• A variant-specific patient report documenting a molecular diagnosis that fully explains the phenotype independently of PIK3CA p.(Arg93Leu).

Sources