Starting
Initialising…
0%
POLE
Final classification
VUS
POLE c.2778G>C · p.Glu926Asp
POLE

NM_006231.4:c.2778G>C (p.Glu926Asp) is a missense variant in exon 24 of POLE, located within the DNA polymerase domain (residues 393-1191). It is absent from gnomAD v2.1, v4.1, and gnomAD-Canada population databases (PM2_Supporting).

Gene
POLE
Transcript
NM_006231.4
HGVS · transcript:coding
NM_006231.4:c.2778G>C
Consequence
N/A
GRCh38
chr12:132661613 C>G
GRCh37
chr12:133238199 C>G
Classification rationale
PM2 VUS
POLE c.2778G>C

NM_006231.4:c.2778G>C (p.Glu926Asp) is a missense variant in exon 24 of POLE, located within the DNA polymerase domain (residues 393-1191). It is absent from gnomAD v2.1, v4.1, and gnomAD-Canada population databases (PM2_Supporting).1 The variant is not one of the established exonuclease-domain hotspot mutations (P286R, V411L, S297F, A456P, S459F) and does not appear in the León-Castillo et al. 2020 supplementary recurrence or in silico tables. It does not meet the custom POLE framework criteria for PM1, PS4, PP3, or BP4.2 Computational predictions are equivocal: REVEL score of 0.281 is below pathogenic thresholds, BayesDel score of -0.171963 is benign-leaning, and SpliceAI predicts no splicing impact (max delta 0.01). Multiple lines of in silico evidence do not support a deleterious effect (PP3 not met) but also do not convincingly support a benign effect (BP4 not met).3 This variant has been reported in ClinVar as Uncertain significance (Variation ID 3225427) by a single clinical laboratory. No variant-specific functional studies, segregation data, or case-control evidence were identified.4 The only publication associated with this variant (PMID:25394175) is an ACMG/NSGC practice guideline on cancer predisposition referral indications that does not mention this specific variant and does not provide variant-level evidence (PP5 not met).5 With only PM2_Supporting met and no other pathogenic or benign criteria triggered, this variant remains a Variant of Uncertain Significance (VUS) under the León-Castillo 2020 custom POLE framework and generic ACMG/AMP 2015 combination rules.6

PM2 VUS
2 vcep_path_250_323_s002vcep_path_250_323_s003vcep_path_250_323_s004vcep_path_250_323
3 revelbayesdelspliceai ↗
6 final_classification_framework
Gene diagram · NM_006231.4 · variants mapped to exon structure
POLE NM_006231.4
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 has been reported in ClinVar as Uncertain significance (1 clinical laboratory). (ClinVarID = 3225427)
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.01). REVEL score = 0.281. BayesDel score = -0.171963.
      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. POLE, the catalytic subunit of DNA polymerase epsilon, is an enzyme involved in DNA replication and repair. Select POLE mutations lead to ultra-high m
      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
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      gnomAD-Canada
      SpliceAI
      OncoKB
      COSMIC
      Cancer hotspots
      Triaged references · 1 PMID not cited in assessment
      25394175 ↗ A practice guideline from the American College of Medical Genetics and Genomics and the National Society of Genetic Counselors: referral indications for cancer predisposition assessment. CLINVAR