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NM_006231.3:c.1763T>C
p.Val588Ala · POLE
León-Castillo et al. 2020 custom POLE framework · vleon-castillo-2020-custom-framework-v1
0%
complete
Final classification
Unclassified
PM2BP4
POLE
c.1763T>C
p.Val588Ala
· exon NC_000012.11
This variant

NM_006231.3:c.1763T>C (p.Val588Ala) is a missense variant in POLE, the catalytic subunit of DNA polymerase epsilon. It is absent from gnomAD v2.1, v4.1, and gnomAD-Canada (PM2_Supporting).

Transcript
NM_006231.3
HGVS · transcript:coding
NM_006231.3:c.1763T>C
GRCh38
chr12:132672246 A>G
GRCh37
chr12:133248832 A>G
Classification rationale
PM2 BP4 Unclassified
POLE c.1763T>C · exon NC_000012.11

NM_006231.3:c.1763T>C (p.Val588Ala) is a missense variant in POLE, the catalytic subunit of DNA polymerase epsilon. It is absent from gnomAD v2.1, v4.1, and gnomAD-Canada (PM2_Supporting).1 Multiple computational predictors suggest a benign effect: REVEL score 0.26, BayesDel score -0.437986, and SpliceAI delta score 0.00 (BP4_Supporting).2 Residue 588 lies outside the POLE exonuclease domain (residues ~268–471) and is not one of the established pathogenic hotspot residues identified by León-Castillo et al. 2020. The variant is absent from COSMIC and has not been reported as a recurrent somatic mutation in endometrial carcinoma.3 No variant-specific functional data, de novo observations, co-segregation data, or ClinVar classifications were identified for this variant. OncoKB reports an unknown oncogenic effect with no variant-level curated evidence.4 The overall evidence profile yields PM2_Supporting (1 pathogenic supporting criterion) and BP4_Supporting (1 benign supporting criterion). These offset to a variant of uncertain significance (VUS) per ACMG/AMP 2015 classification rules.

PM2 + BP4 Unclassified
LYFE Sciences is an AI system, and it can make mistakes. Criteria may be applied incorrectly, sources may be misread, and a confident-looking classification can still be wrong. Double-check every criterion and its underlying evidence before relying on any call.
Gene diagram · NM_006231.3 · variants mapped to exon structure
POLE NM_006231.3
Fetching transcript structure from UCSC…
Applied criteria · 2 applied · 8 assessed
MetEvidence satisfies this criterion.
Not metEvaluated against available evidence; threshold not reached.
Not assessedApplies in principle, but no evidence was found to evaluate it.
N/ADoesn't apply to this variant type.
Applied · 2
Strength Supporting Moderate Strong Very strong
PM2 supporting Pathogenic
This variant is absent from gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada v1.0. Under generic ACMG/AMP, absence from large population databases supports pathogenicity at supporting strength for a gene where pathogenic missense variants are an established disease mechanism.
Absent from gnomAD v2.1 (0 alleles)gnomAD v4.1 (0 alleles)and gnomAD-Canada v1.0 (0 alleles).
BP4 supporting Benign
Multiple lines of computational evidence suggest no impact on the gene product. REVEL score 0.26 (below 0.5 pathogenic threshold, consistent with benign), BayesDel score -0.437986 (negative, indicating tolerated/benign), and SpliceAI max delta score 0.00 (predicting no splice alteration). Three independent computational predictors converge on a benign interpretation, meeting the BP4 threshold.
REVEL 0.26 (benign)BayesDel -0.437986 (benign)SpliceAI max delta 0.00 (no splice impact).
Assessed · not applied · 7 not met · 1 not assessed
Pathogenic
PS3 No variant-specific functional data identified.
PS4 Under the Leon-Castillo custom framework, PS4_Supporting requires the exact variant to be recurrent in both COSMIC and TCGA endometrial carcinoma cohorts with a combined count ≥10, which V588A does not satisfy (absent from COSMIC and supplementary tables).
PM1 Residue 588 lies outside the POLE exonuclease domain (residues ~268–471).
PP2 While POLE has established pathogenic missense variants (exonuclease domain hotspots) supporting that missense changes are a disease mechanism, the HCI prior constraint data is unavailable for this transcript, precluding reliable assessment of the gene's rate of benign missense variation.
PP3 V588A is absent from León-Castillo Supplementary Tables S2 and S3, so the custom PP3_Supporting rule does not apply.
Benign
BA1 Variant is absent from gnomAD v2.1, v4.1, and gnomAD-Canada (allele frequency 0%).
BS1 Variant is absent from gnomAD (allele frequency 0%).
BS3 No functional studies demonstrating a neutral or benign effect for this variant.
N/A · 15 PVS1 · PS1 · PS2 · PM5 · PM6 · PP1 · PP4 · PP5 · BS2 · BS4 · BP1 · BP2 · BP5 · BP6 · BP7
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
In progress — evidence not uploaded yet.
SpliceAI screenshot
In silico
In progress — evidence not uploaded yet.
Functional / OncoKB screenshot
Functional Unknown Oncogenic Effect
In progress — evidence not uploaded yet.
OncoKB ↗
COSMIC screenshot
COSMIC
Cancer hotspots screenshot
Cancer hotspots
Somatic evidence Not in COSMIC / hotspots
COSMIC
In progress — evidence not uploaded yet.
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