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PIK3R1
Final classification
VUS
PIK3R1 c.1345_1347del · p.Leu449del
PIK3R1

NM_181523.2:c.1345_1347del (p.Leu449del) is an in-frame deletion of a single amino acid in exon 11 of PIK3R1, which encodes the p85-alpha regulatory subunit of PI3K. The variant has not been reported in ClinVar and is absent from gnomAD v2.1, v4.1, and gnomAD-Canada, meeting PM2_Supporting under the Antibody Deficiencies VCEP framework (total AF = 0; threshold <0.00000132).

Gene
PIK3R1
Transcript
NM_181523.2
HGVS · transcript:coding
NM_181523.2:c.1345_1347del
Consequence
N/A
GRCh38
chr5:68293752 AATT>A
GRCh37
chr5:67589580 AATT>A
Basis ClinGen Antibody Deficiencies Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for PIK3R1 Version 1.0.0 v1.0.0 point-based framework: PM2 supporting (+1) = 1 points, which maps to VUS.
ClinGen Antibody Deficiencies Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for PIK3R1 Version 1.0.0 v1.0.0 point-based framework: PM2 supporting (+1) = 1 points, which maps to VUS.
Classification rationale
PM2 VUS
PIK3R1 c.1345_1347del

NM_181523.2:c.1345_1347del (p.Leu449del) is an in-frame deletion of a single amino acid in exon 11 of PIK3R1, which encodes the p85-alpha regulatory subunit of PI3K. The variant has not been reported in ClinVar and is absent from gnomAD v2.1, v4.1, and gnomAD-Canada, meeting PM2_Supporting under the Antibody Deficiencies VCEP framework (total AF = 0; threshold <0.00000132).1 The variant has been observed in somatic cancers (COSMIC COSV57127217, n=5) and is annotated as Likely Oncogenic / Likely Loss-of-function by OncoKB. However, no variant-specific germline functional data are available from VCEP-approved assays (lipid kinase activity, AKT kinase activity, protein binding, conformational dynamics, mouse knock-in, or pS6/pAKT T-cell enrichment assay). PS3 and BS3 are not met.2 PVS1, PS1, PM1, PM5, PM6, PP2, PP5, BS2, BP1, BP2, BP3, BP6, and BP7 are not applicable under the Antibody Deficiencies VCEP specifications. PM4 is not met because the deletion removes only one amino acid (threshold: >=2 amino acids). PP3 and BP4 do not apply to in-frame deletions under current VCEP rules. BA1 and BS1 are not met as the variant is absent from population databases.3 PS2, PS4, PP1, PP4, BS4, and BP5 cannot be assessed due to absence of proband phenotype data, family segregation studies, and alternative molecular diagnoses in the available literature and case materials. Applying the PIK3R1 VCEP Bayesian point-based classification framework (Tavtigian 2020 adaptation): the only met criterion is PM2_Supporting (+1 point). Total = 1 point, which falls in the VUS range (0-5 points). The evidence is insufficient to classify this variant as pathogenic or benign at this time.4

PM2 VUS
Gene diagram · NM_181523.2 · variants mapped to exon structure
PIK3R1 NM_181523.2
Fetching transcript structure from UCSC…
Applied criteria · 1 met · select any tile
Met
Not met
Not assessed
N/A
Strength very strong supporting
Pathogenic evidence
PVS
PS
PM
PP
Benign evidence
BA
BS
BP
Rationale
Select a criterion.
Sources
Evidence used
    Gaps remaining
      Rule
      Research & evidence
      Population frequency
      gnomAD v4.1 screenshot
      gnomAD v4.1
      gnomAD v2.1 screenshot
      gnomAD v2.1
      v4.1
      Absent from gnomAD v4.1.
      v2.1
      Absent from gnomAD v2.1.
      🇨🇦 CA
      Absent from gnomAD-Canada v1.0.
      Allele frequency by ancestry
      three datasets · side by side
      gnomAD v4.1
      Absent · 0 / ?
      0 hom
      Not observed in any ancestry group.
      gnomAD v2.1
      Absent · 0 / ?
      0 hom
      Not observed in any ancestry group.
      gnomAD Canada 🇨🇦
      Absent · 0 / ?
      0 hom
      Not observed in any ancestry group.
      ClinVar screenshot
      ClinVar
      This variant is absent from ClinVar.
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00).
      Functional / OncoKB screenshot
      Functional Likely Oncogenic
      OncoKB identified variant-specific curated literature and context relevant to functional review; biological-effect context: Likely Loss-of-function; curated oncogenicity label: Likely Oncogenic.
      OncoKB ↗
      COSMIC screenshot
      COSMIC
      Cancer hotspots screenshot
      Cancer hotspots
      Somatic evidence Not in COSMIC / hotspots
      COSMIC
      This variant does not lie in a statistically significant hotspot. This variant has previously been reported in somatic cancers (COSMIC; COSV57127217, n = 5 times).
      Hotspots
      This variant does not lie in a statistically significant hotspot.
      Sources & reference links
      9Sources
      CSpec VCEP
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      gnomAD-Canada
      SpliceAI
      OncoKB
      COSMIC
      Cancer hotspots
      Triaged references · 2 PMIDs not cited in assessment
      28481359 ↗ Mutational landscape of metastatic cancer revealed from prospective clinical sequencing of 10,000 patients. ONCOKB
      29636360 ↗ A First-in-Human Phase 1 Study of LY3023414, an Oral PI3K/mTOR Dual Inhibitor, in Patients with Advanced Cancer. ONCOKB