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Initialising…
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PIK3CA
Final classification
Uncertain Significance
PIK3CA c.1265del · p.Leu422TrpfsTer6
PIK3CA

The PIK3CA c.1265del (p.(Leu422TrpfsTer6)) variant has not been reported in ClinVar.

Gene
PIK3CA
Transcript
NM_006218.4
HGVS · transcript:coding
NM_006218.4:c.1265del
Consequence
N/A
GRCh38
chr3:179210197 AT>A
GRCh37
chr3:178927985 AT>A
Basis Brain Malformations Specification Tavtigian point framework from the CSPEC/VCEP final-classification framework: PM1_Supporting (+1) and PM2_Supporting (+1) for a total of 2 points.
Brain Malformations Specification Tavtigian point framework from the CSPEC/VCEP final-classification framework: PM1_Supporting (+1) and PM2_Supporting (+1) for a total of 2 points.
Classification rationale
PM1PM2 Uncertain Significance
PIK3CA c.1265del

The PIK3CA c.1265del (p.(Leu422TrpfsTer6)) variant has not been reported in ClinVar.1 This variant is absent from gnomAD v2.1 and gnomAD v4.1, supporting PM2 at Supporting strength, and its observed population frequency of 0% is below the VCEP BS1 threshold of >0.0185% and BA1 threshold of >0.0926%.2 The altered residue lies within the approved PIK3CA kinase-domain interval spanning amino acids 322-483, which is a Brain Malformations VCEP critical functional domain and supports PM1_Supporting.3 SpliceAI predicts no significant splice impact for this variant, with a maximum delta score of 0.07, although computational pathogenicity criteria are not applied for PIK3CA gain-of-function interpretation in this VCEP framework.4

PM1 + PM2 Uncertain Significance
3 cspec ↗vcep_c_l_i_n_g_e_n___b_r_a_i_n_m_a_l_f_o_r_m___a_c_m_g___s_p_e_c_i_f_i_c_a_t_i_o_n_s___v_1___1
Gene diagram · NM_006218.4 · variants mapped to exon structure
PIK3CA NM_006218.4
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.
      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.
      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 = 0.07).
      Functional / OncoKB screenshot
      Functional Unknown Oncogenic Effect
      OncoKB oncogenicity for this specific variant: Unknown Oncogenic Effect (variant has not been individually curated).
      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; COSV104381249, n = 1 times).
      Hotspots
      This variant does not lie in a statistically significant hotspot.
      Sources & reference links
      8Sources
      CSpec VCEP
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      SpliceAI
      OncoKB
      COSMIC
      Cancer hotspots