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PIK3CB
Final classification
VUS
PIK3CB c.3200A>T · p.Asp1067Val
PIK3CB

NM_006219.2:c.3200A>T (p.Asp1067Val) is absent from all population databases including gnomAD v2.1, v4.1, and gnomAD-Canada (allele frequency 0.0).

Gene
PIK3CB
Transcript
NM_006219.2
HGVS · transcript:coding
NM_006219.2:c.3200A>T
Consequence
N/A
GRCh38
chr3:138655402 T>A
GRCh37
chr3:138374244 T>A
Basis gene-specific framework lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: PM1 moderate, PM2 moderate; combination = 2 moderate, which maps to VUS.
gene-specific framework lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: PM1 moderate, PM2 moderate; combination = 2 moderate, which maps to VUS.
Classification rationale
PM1PM2 VUS
PIK3CB c.3200A>T

NM_006219.2:c.3200A>T (p.Asp1067Val) is absent from all population databases including gnomAD v2.1, v4.1, and gnomAD-Canada (allele frequency 0.0).1 The variant is absent from ClinVar and has no germline classification from any submitter.2 Asp1067 resides in the C-terminal kinase domain of PIK3Cβ and lies within a statistically significant mutational hotspot (cancerhotspots.org). PMID:25982275 reports that D1067V is the most recurrent missense mutation in the PIK3Cβ kinase domain, accounting for ~15% of kinase domain missense mutations, and that D1067 is highly conserved across species.3 Functional studies in PMID:25982275 demonstrate that PIK3Cβ/D1067V is a gain-of-function activating mutation in somatic cancer models (enhanced AKT/S6 phosphorylation, increased cell growth in vitro, tumor formation in vivo, erlotinib resistance). This evidence was not applied toward PS3 because the demonstrated gain-of-function mechanism does not align with the reported germline loss-of-function disease mechanism.4 REVEL score of 0.65 suggests possible pathogenicity, but BayesDel (0.313) is borderline and SpliceAI predicts no splicing impact (max delta = 0.00). In silico evidence does not provide multiple converging lines for PP3 or BP4.5 The variant has been observed 16 times in somatic cancers (COSMIC COSV56683107) and is classified as Oncogenic by OncoKB, but these pertain to somatic context and are not directly applicable to germline classification.6 Two moderate pathogenicity criteria are met: PM1 (kinase domain hotspot) and PM2 (absent from population databases). No benign criteria are met. Per generic ACMG/AMP 2015 combination rules, two moderate criteria in the absence of benign criteria yields a classification of Likely Pathogenic.7

PM1 + PM2 VUS
Gene diagram · NM_006219.2 · variants mapped to exon structure
PIK3CB NM_006219.2
Fetching transcript structure from UCSC…
Applied criteria · 2 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 = 0.65. BayesDel score = 0.312683.
      Functional / OncoKB screenshot
      Functional Oncogenic
      OncoKB identified variant-specific curated literature and context relevant to functional review; biological-effect context: Gain-of-function; curated oncogenicity label: Oncogenic.
      OncoKB ↗
      COSMIC screenshot
      COSMIC
      Cancer hotspots screenshot
      Cancer hotspots
      Somatic evidence Hotspot
      COSMIC
      This variant lies in a statistically significant hotspot. This variant has previously been reported in somatic cancers (COSMIC; COSV56683107, n = 16 times).
      Hotspots
      This variant lies in a statistically significant hotspot.
      Literature · how each cited paper was used
      1papers cited
      Each card is an audit: what was searched, what was found, whether it names the variant, which criteria it fed, and why.
      Oncogenic activation of the PI3-kinase p110β isoform via the tumor-derived PIK3Cβ(D1067V) kinase domain mutation.
      Searched
      c.3200A>Tp.Asp1067ValD1067VPIK3CβD1067VPIK3Cbeta D1067V
      Found
      PIK3Cβ/D1067V demonstrated gain-of-function activation of PI3K pathway signaling (increased phosphorylated AKT and S6 kinase compared to wild-type), enhanced cell growth in vitro in NIH-3T3 cells, and was sufficient for tumor formation in vivo in immunocompromised mice. In patient-derived A498 renal-cell carcinoma cells with endogenous PIK3Cβ/D1067V, genetic and pharmacologic inhibition of p110β suppressed growth and PI3K signaling. Expression of PIK3Cβ/D1067V in EGFR-mutant H3255 NSCLC cells sustained AKT/S6 phosphorylation during erlotinib treatment and promoted drug resistance. D1067V was identified as the most recurrent missense mutation in the PIK3Cβ kinase domain (~15% of mutations) and was observed across multiple tumor types (NSCLC, RCC, GBM, HNSCC, melanoma, thyroid, endometrial).
      Variant
      ✓ Names this variant — characterised directly
      Applied to
      PM1 supports · met
      Why
      Variant-specific functional data confirmed gain-of-function oncogenic activation in somatic context. Cited for PM1 (kinase domain localization, recurrence as hotspot mutation). Not cited for PS3 because demonstrated gain-of-function mechanism does not align with reported germline loss-of-function disease mechanism.
      PIK3CβD1067V activated PI3K pathway downstream signaling, as measured by the levels of phosphorylated AKT and S6 kinase, to a greater degree than PIK3CβWT
      Location Abstract; Results and Discussion, pages 1-7; Figures 1-4  ·  Context NIH-3T3 fibroblasts (stable retroviral transduction), H3255 EGFR-mutant NSCLC cells, A498 renal-cell carcinoma cells (endogenous heterozygous D1067V); immunoblot, CellTiterGLO viability assays, tumor allograft assays in immunocompromised mice, pharmacologic inhibition with TGX-221 (p110β-selective) and BKM-120 (pan-PI3K)  ·  full text
      Sources & reference links
      8Sources
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      gnomAD-Canada
      SpliceAI
      OncoKB
      COSMIC
      Cancer hotspots