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PIK3R1
Final classification
VUS
PIK3R1 c.310A>G · p.Thr104Ala
PIK3R1

NM_181523.2:c.310A>G (p.Thr104Ala) in PIK3R1 is a novel missense variant absent from all population databases including gnomAD v4.1, meeting PM2_Supporting per the VCEP allele frequency threshold (<0.00000132).

Gene
PIK3R1
Transcript
NM_181523.2
HGVS · transcript:coding
NM_181523.2:c.310A>G
Consequence
N/A
GRCh38
chr5:68226985 A>G
GRCh37
chr5:67522813 A>G
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.310A>G

NM_181523.2:c.310A>G (p.Thr104Ala) in PIK3R1 is a novel missense variant absent from all population databases including gnomAD v4.1, meeting PM2_Supporting per the VCEP allele frequency threshold (<0.00000132).1 Computational evidence is benign-leaning: REVEL score is 0.125, BayesDel is -0.618838, and SpliceAI predicts no splice impact (max delta 0.00). PP3 thresholds (REVEL ≥0.644, SpliceAI ≥0.2) are not met.2 No functional studies, clinical cases, co-segregation data, or literature reports were identified for this specific variant. PVS1, PS1-PS5, PP1, PP3-PP5, BA1, BS1, BS3-BS4, and BP5 are not met. Multiple criteria (PM1, PM5, PM6, BP1, BP2, BP6, BP7, PP2, PP5, BS2) are designated as not applicable by the PIK3R1 VCEP. BP4 could not be fully assessed due to absence of CADD score.3 Using the Bayesian point-based framework adopted by the Antibody Deficiencies VCEP (Tavtigian 2020, PMID:32720330), the sole met criterion PM2_Supporting contributes +1 point (supporting). The total score of 1 falls in the 0–5 range, corresponding to a classification of Uncertain Significance.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). REVEL score = 0.125. BayesDel score = -0.618838.
      Functional / OncoKB screenshot
      Functional Unknown Oncogenic Effect
      OncoKB did not identify variant-specific reviewed functional evidence for this variant; gene-level curated context is available for reviewer follow-up. PIK3R1, the regulatory subunit of PI3-kinase, is mutated in various cancers, most frequently in glioma, endometrial and colorectal cancers.
      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 not previously been reported in somatic cancers (COSMIC).
      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