PIK3CA c.1634A>T, p.(Glu545Val)

Reasoning

The governing Brain Malformations VCEP assigns 0.25 points for each confirmed occurrence of the variant in a tumor sample (Table 2A), and requires PM2 before phenotype points can be used. The case evidence reports NM_006218.4:c.1634A>T / p.Glu545Val / p.E545V absent from gnomAD v2.1 and v4.1, satisfying the VCEP's PM2 prerequisite, and reports four COSMIC occurrences (COSV55892885). Applying the VCEP tumor score gives 4 × 0.25 = 1.00 points. The governing Table 2B range is 0.5–1.25 points for PS4_Supporting, so 1.00 points falls within that range. No exact-variant brain-malformation patient cases were identified in the supplied literature; the score therefore rests on the reported tumor occurrences and should be human-verified against the COSMIC records to confirm that the four countable occurrences are distinct primary tumors and not normal tissue.

Rule

VCEP PS4: phenotype points require PM2; Table 2A tumor occurrence = 0.25 points; Table 2B PS4_Supporting = 0.5–1.25 points.

Evidence considered

• The governing VCEP Table 2A assigns 0.25 points for presence of the variant in a tumor sample and states that each separate primary counts as an occurrence, with normal tissue excluded and a maximum of nine tumor samples.
• The governing VCEP Table 2B defines PS4_Supporting as 0.5–1.25 points.
• The variant is reported absent from gnomAD v2.1 and gnomAD v4.1, satisfying the VCEP requirement that PS4 phenotype points require PM2.
• COSMIC reports PIK3CA c.1634A>T / p.E545V as COSV55892885 with a somatic count of 4; applying the VCEP tumor rule gives 4 × 0.25 = 1.00 points.

Still missing

• The VCEP file contains no exact-variant entry for c.1634A>T, p.Glu545Val, or p.E545V.
• Human verification is needed to confirm that all four COSMIC occurrences are distinct eligible primary tumors and not normal tissue.

Sources

Reasoning

The ClinGen Brain Malformations VCEP specifies PM2_Supporting for an allele absent or rare in an ethnically matched population sample, with one person maximum. The variant is reported absent from gnomAD v2.1, gnomAD v4.1, gnomAD v2.1 non-cancer, and gnomAD v3.1 non-cancer, satisfying the VCEP PM2_Supporting requirement.

Rule

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

Evidence considered

• The governing ClinGen Brain Malformations VCEP defines PM2_Supporting as absent/rare in an ethnically matched cohort population sample with one person maximum.
• The case evidence reports this variant absent from gnomAD v2.1 and gnomAD v4.1.
• The case evidence also reports absence from gnomAD v2.1 non-cancer and gnomAD v3.1 non-cancer subsets.

Still missing

• No variant-specific entry for c.1634A>T, p.Glu545Val, or p.E545V was found in clingen_brainmalform_acmg_specifications_v1_1.pdf.txt; the file provides the governing PM2 rule but not a variant row.
• The case evidence does not provide ancestry-specific allele counts; the available population datasets uniformly report absence.

Sources

Reasoning

The governing VCEP modifies PM1 to PM1_Supporting and authorizes it for residues within the complete PIK3CA Table 4 domain list. The authoritative vcep_materials.json domain_tables entry lists PIK3CA Kinase Ras-binding domain AA 173-292, kinase domains AA 322-483 and AA 797-1068, and adaptor binding domain (PI3K ABD) AA 31-108. The variant is p.Glu545Val at residue 545, which lies outside every approved interval. The VCEP also states that recurrent gain-of-function residues are accounted for by PS4 rather than PM1; hotspot evidence therefore does not alter this domain result.

Rule

PM1_Supporting may be awarded for a PIK3CA residue within an approved Table 4 critical functional domain; use the complete domain_tables list.

Evidence considered

• The VCEP specifies PM1_Supporting for approved Table 4 functional domains and says recurrent gain-of-function residues are addressed under PS4.
• The authoritative PIK3CA domain list contains AA 173-292, AA 322-483, AA 797-1068, and AA 31-108; residue 545 is in none of these intervals.

Sources

Reasoning

The ClinGen Brain Malformations VCEP specifies BA1 when allele frequency is >0.0926%. The variant NM_006218.4:c.1634A>T (p.Glu545Val/p.E545V) is reported absent from gnomAD v2.1, gnomAD v4.1, gnomAD v2.1 non-cancer, and gnomAD v3.1 non-cancer; therefore no allele frequency approaches the BA1 threshold.

Rule

Allele frequency (>0.0926%).

Evidence considered

• The governing ClinGen Brain Malformations VCEP specifies BA1 for allele frequency >0.0926%.
• The case evidence reports this variant absent from gnomAD v2.1 and gnomAD v4.1.
• The case evidence also reports absence from gnomAD v2.1 non-cancer and gnomAD v3.1 non-cancer subsets; no population allele count or frequency was provided.

Still missing

• No variant-specific entry for c.1634A>T, p.Glu545Val, or p.E545V was found in clingen_brainmalform_acmg_specifications_v1_1.pdf.txt; the file provides the governing BA1 rule but not a variant row.

Sources

Reasoning

The ClinGen Brain Malformations VCEP specifies BS1 when allele frequency is >0.0185%. The variant is reported absent from gnomAD v2.1, gnomAD v4.1, gnomAD v2.1 non-cancer, and gnomAD v3.1 non-cancer, so no allele frequency exceeds the VCEP BS1 threshold.

Rule

Allele frequency (>0.0185%).

Evidence considered

• The governing ClinGen Brain Malformations VCEP specifies BS1 for allele frequency >0.0185%.
• The case evidence reports this variant absent from gnomAD v2.1 and gnomAD v4.1.
• The case evidence also reports absence from gnomAD v2.1 non-cancer and gnomAD v3.1 non-cancer subsets; no population allele count or frequency was provided.

Still missing

• No variant-specific entry for c.1634A>T, p.Glu545Val, or p.E545V was found in clingen_brainmalform_acmg_specifications_v1_1.pdf.txt; the file provides the governing BS1 rule but not a variant row.

Sources

Reasoning

The ClinGen Brain Malformations VCEP requires at least 3 homozygotes in gnomAD or at least 3 heterozygous observations in well-phenotyped family members for BS2. The variant is absent from the reported gnomAD datasets, and the case evidence contains no qualifying healthy-adult family observations; the threshold is not met.

Rule

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

Evidence considered

• The governing ClinGen Brain Malformations VCEP requires >=3 homozygotes in gnomAD or >=3 heterozygous observations in well-phenotyped family members.
• The case evidence reports the variant absent from gnomAD v2.1, gnomAD v4.1, gnomAD v2.1 non-cancer, and gnomAD v3.1 non-cancer.
• No qualifying healthy-adult family-member observations are present in the reviewed case evidence.

Still missing

• No variant-specific entry for c.1634A>T, p.Glu545Val, or p.E545V was found in clingen_brainmalform_acmg_specifications_v1_1.pdf.txt; the file provides the governing BS2 rule but not a variant row.

Sources

Reasoning

The variant is PIK3CA p.Glu545Val (p.E545V). The governing Brain Malformations VCEP specification defines PS1 as the same amino-acid change as a previously established pathogenic variant and provides no variant-specific PS1 entry. Searches of the complete VCEP text for c.1634A>T, p.Glu545Val, and p.E545V found no entry. ClinVar reported no record. The reviewed literature sources did not identify this exact variant or a previously established pathogenic variant producing the same amino-acid change. Therefore, the available evidence does not establish the required PS1 comparator.

Rule

Same amino acid change as a previously established pathogenic variant regardless of nucleotide change; previously established variant must meet VCEP pathogenic criteria independently.

Evidence considered

• The governing VCEP states that PS1 requires the same amino-acid change as a previously established pathogenic variant; its specification for PS1 is unchanged.
• The complete governing VCEP text was searched under c.1634A>T, p.Glu545Val, and p.E545V without finding a variant-specific entry.
• ClinVar reported no record for NM_006218.4:c.1634A>T.
• PMID:19349352 was directly reviewed; it reports recurrent activating PIK3CA mutations in ovarian clear cell carcinoma but does not identify p.Glu545Val or a same-amino-acid pathogenic comparator.
• PMID:24504419 extraction reports that the specific PIK3CA variants were not identified in the available text and searched terms did not find this variant.

Still missing

• The complete governing file clingen_brainmalform_acmg_specifications_v1_1.pdf.txt was searched for c.1634A>T, p.Glu545Val, and p.E545V; no variant-specific entry was found.
• A curated expert-panel pathogenic comparator for the same amino-acid change was not identified in the available evidence.

Sources

Reasoning

The governing Brain Malformations VCEP requires PS2_Strong only when both criteria are fulfilled: the variant is detected in the affected proband/tissue and absent from parental samples with confirmed maternity and paternity, and it is detected in affected tissue but absent or lower in another tissue. PS2_Moderate requires the parental criterion alone or the affected-tissue criterion when parents are unavailable. The supplied case evidence contains no proband phenotype, allelic-fraction result, parental test result, maternity/paternity confirmation, tissue comparison, or family-history assessment for NM_006218.4:c.1634A>T (p.Glu545Val/p.E545V), so no PS2 strength can be assigned.

Rule

Award the PS2_Strong point if Criteria 1 AND Criteria 2 are fulfilled. Criteria 1: the variant is present at a detectable allele fraction but is absent from parental samples with confirmed maternity and paternity. Criteria 2: the variant is present at a detectable allele fraction in an affected tissue sample but is absent from or detected at a lower allelic fraction in another tissue. Award PS2_Moderate if Criteria 1 is fulfilled, OR if parents are not available but Criteria 2 is fulfilled.

Evidence considered

• The VCEP specification states that PS2_Strong requires both parental absence with confirmed maternity and paternity and the affected-tissue versus another-tissue criterion; PS2_Moderate requires the parental criterion or the affected-tissue criterion when parents are unavailable.
• The consolidated case-evidence bundle and directly checked prefetch.json and vcep_materials.json provide no case-specific proband, parental, de novo, tissue-mosaicism, or segregation results for this variant.
• The on-record VCEP full-text file was searched for c.1634A>T, p.Glu545Val, and p.E545V; no variant-specific row or pre-assigned code was found.

Still missing

• No case-level proband phenotype, variant allelic fraction, parental testing, maternity/paternity confirmation, tissue comparison, or family-history data was located.
• No entry for c.1634A>T, p.Glu545Val, or p.E545V was found in clingen_brainmalform_acmg_specifications_v1_1.pdf.txt.

Sources

Reasoning

The governing Brain Malformations VCEP requires PS3 functional evidence to meet SVI acceptability criteria, including appropriate assay quality metrics and validation controls. The case materials provide no assay directly testing PIK3CA c.1634A>T / p.Glu545Val / p.E545V. PMID:19349352 reports activating PIK3CA mutations as a group and increased phosphorylated AKT in mutation-positive ovarian clear cell carcinomas, but does not identify or experimentally test this variant; PMID:24504419 reports drug-response and signaling assays in ovarian clear cell cell lines, but its extracted findings do not identify this variant. These data are not sufficient for variant-specific PS3, and no strength above supporting can be assigned without documented positive and negative controls and direct variant testing.

Rule

Follow recommendations set forth by the SVI in conjunction with specifications added by the BMVCEP for quality metrics and minimum validation controls required.

Evidence considered

• The governing VCEP specifies that PS3 follows SVI functional-assay acceptability recommendations and requires assay quality metrics and minimum validation controls; publications with evidence above supporting require positive and negative validation controls.
• PMID:19349352 studied PIK3CA mutations collectively in ovarian clear cell carcinoma and reported phosphorylated AKT, but the reviewed text does not identify p.Glu545Val or test it directly.
• PMID:24504419 evaluated DS-7423 response, pathway phosphorylation, proliferation, apoptosis, and xenografts in ovarian clear cell carcinoma cell lines, but the extracted paper finding states that the specific PIK3CA variants were not identified and p.Glu545Val was not mentioned.

Still missing

• The governing VCEP file clingen_brainmalform_acmg_specifications_v1_1.pdf was searched for c.1634A>T, p.Glu545Val, and p.E545V; no variant-specific entry was found.
• No variant-specific assay results for PIK3CA c.1634A>T / p.Glu545Val / p.E545V were available, including documented assay controls, replicate data, and calibration against known pathogenic and benign variants.

Sources

Reasoning

The governing VCEP leaves PM5 unchanged: a missense change at an amino-acid residue where a different missense change independently determined to be pathogenic has been seen before. The collected PM5 candidate artifact identified eight total candidates but zero same-residue candidates and records an HTTP 429 failure during candidate harvesting. The complete VCEP text contained no entry for c.1634A>T, p.Glu545Val, or p.E545V. Because the retrieval was incomplete and no validated same-residue comparator was available, PM5 cannot be adjudicated as met or not met from the current evidence.

Rule

Missense change at an amino-acid residue where a different missense change determined to be pathogenic has been seen before; previously established variant must meet VCEP pathogenic criteria independently.

Evidence considered

• The VCEP defines PM5 as a different missense change at the same amino-acid residue that has independently been determined pathogenic.
• The PM5 candidate artifact reports 8 candidates reviewed, 0 same-residue candidates, 0 expert-panel P/LP candidates, and an HTTP 429 retrieval error.
• The complete governing VCEP text was searched under c.1634A>T, p.Glu545Val, and p.E545V without finding a variant-specific entry.
• PMID:19349352 was reviewed for residue-level PIK3CA comparators but does not identify the exact variant or a validated pathogenic alternate at residue 545.
• PMID:24504419 extraction did not identify the specific PIK3CA variants in the available text.

Still missing

• The complete governing file clingen_brainmalform_acmg_specifications_v1_1.pdf.txt was searched for c.1634A>T, p.Glu545Val, and p.E545V; no variant-specific entry was found.
• Independent confirmation of pathogenicity for any alternate missense variant at PIK3CA residue 545 remains unavailable because PM5 candidate harvesting failed with HTTP 429.

Sources

Reasoning

The governing VCEP applies PP2 to PIK3CA and requires a missense-constraint z-score greater than 3.09. The case evidence confirms that this is a missense PIK3CA variant, but it does not provide the applicable ExAC/gnomAD missense-constraint z-score. The z-score threshold is therefore not evaluable from the available evidence, so PP2 is not assessed.

Rule

Award PP2 for PIK3CA when the ExAC/gnomAD missense-constraint z-score is >3.09.

Evidence considered

• The VCEP specifically states that PP2 applies to PIK3CA and is awarded when the ExAC/gnomAD missense-constraint z-score is greater than 3.09.
• The normalized consequence is missense for PIK3CA p.Glu545Val, but no ExAC/gnomAD missense-constraint z-score is supplied.

Still missing

• An ExAC/gnomAD missense-constraint z-score for PIK3CA is not present in the available case evidence.

Sources

Reasoning

The governing Brain Malformations VCEP defines BS3 as well-established in vitro or in vivo functional evidence showing no damaging effect and requires the SVI assay-quality and validation-control recommendations. No reviewed study directly tested PIK3CA c.1634A>T / p.Glu545Val / p.E545V in a benign or function-preserving assay. PMID:19349352 provides group-level tumor observations rather than a neutral functional result for this variant, while PMID:24504419 does not mention the variant and its drug-response experiments cannot establish preserved PIK3CA function. Therefore BS3 cannot be assigned at strong or supporting strength.

Rule

Follow recommendations set forth by the SVI in conjunction with specifications added by the Brain Malformation Group for quality metrics and minimum validation controls required.

Evidence considered

• The governing VCEP requires BS3 functional studies to follow SVI recommendations for assay quality metrics and minimum validation controls.
• PMID:19349352 reports pathway activation associated with PIK3CA mutation-positive tumors at the group level and does not provide a no-damaging-effect result for p.Glu545Val.
• PMID:24504419 reports pharmacologic inhibition of ovarian clear cell carcinoma cell lines, not direct functional preservation of the queried PIK3CA variant.

Still missing

• The governing VCEP file clingen_brainmalform_acmg_specifications_v1_1.pdf was searched for c.1634A>T, p.Glu545Val, and p.E545V; no variant-specific entry was found.
• No directly tested variant-specific benign functional result was available with appropriate wild-type, negative, and other validation controls or replicate documentation.

Sources

Reasoning

The governing 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 reviewed case-evidence materials contain no documented phase, affected-proband genotype, parental testing, or other evidence establishing that NM_006218.4:c.1634A>T (p.Glu545Val/p.E545V) is in cis or trans with a known pathogenic PIK3CA variant, so BP2 cannot be adjudicated.

Rule

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

Evidence considered

• The governing VCEP rule permits BP2 only for an observation in cis or trans with a known pathogenic variant in the same gene.
• The available case materials provide no phase or paired-variant observation that would establish BP2 for this PIK3CA variant.

Still missing

• No documented cis/trans phase, paired pathogenic PIK3CA variant, parental testing, or affected-proband genotype was found in the reviewed case-evidence materials.
• No exact occurrence of c.1634A>T, p.Glu545Val, or p.E545V was found in clingen_brainmalform_acmg_specifications_v1_1.pdf.

Sources

Reasoning

The governing VCEP leaves BP5 unchanged and specifies that it applies when the variant is observed in a case with an alternate molecular basis for disease in a different gene. The supplied evidence documents COSMIC tumor observations and no exact-variant brain-malformation case with a documented alternate molecular diagnosis; it therefore does not establish or exclude BP5.

Rule

VCEP BP5: observed in a case with an alternate molecular basis for disease in a different gene.

Evidence considered

• The governing VCEP BP5 rule is: variant found in a case with an alternate molecular basis for disease; the brain-malformation recommendation specifies a different gene.
• The available case evidence reports tumor database occurrences but does not document an eligible patient case with an alternate molecular diagnosis in a different gene.

Still missing

• No eligible exact-variant case with a documented alternate molecular basis in a different gene was supplied.

Sources