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PIK3CA
Final classification
Uncertain Significance
PIK3CA c.1255_1264delinsA · p.His419_Leu422delinsMet
PIK3CA

The PIK3CA c.1255_1264delinsA (p.His419_Leu422delinsMet; p.H419_L422delinsM) variant has not been reported in ClinVar, while OncoKB classifies it as Likely Oncogenic.

Gene
PIK3CA
Transcript
NM_006218.4
HGVS · transcript:coding
NM_006218.4:c.1255_1264delinsA
Consequence
N/A
GRCh38
chr3:179210189 CACTGTCCAT>A
GRCh37
chr3:178927977 CACTGTCCAT>A
Basis Brain Malformations Specification Tavtigian point framework: PM1_Supporting (+1) and PM2_Supporting (+1) yield 2 total points, which falls within the 0-5 Uncertain Significance range.
Brain Malformations Specification Tavtigian point framework: PM1_Supporting (+1) and PM2_Supporting (+1) yield 2 total points, which falls within the 0-5 Uncertain Significance range.
Classification rationale
PM1PM2 Uncertain Significance
PIK3CA c.1255_1264delinsA

The PIK3CA c.1255_1264delinsA (p.His419_Leu422delinsMet; p.H419_L422delinsM) variant has not been reported in ClinVar, while OncoKB classifies it as Likely Oncogenic.1 This variant is absent from gnomAD v2.1 and gnomAD v4.1, supporting that it is absent or extremely rare in population controls.2 The altered residues fall within the PIK3CA kinase domain spanning amino acids 322 to 483, which is an approved Brain Malformations VCEP critical functional domain and supports PM1 at Supporting strength.3 SpliceAI predicts no significant splice impact for this variant, with a maximum delta score of 0.01.4

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 = 0.01).
      Functional / OncoKB screenshot
      Functional Likely Oncogenic
      OncoKB classifies this variant as 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 not previously been reported in somatic cancers (COSMIC).
      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