POLE encodes the catalytic subunit of DNA polymerase epsilon, the enzyme that replicates the leading strand of DNA during cell division and participates in DNA repair. It contains a proofreading domain that corrects replication errors, keeping the accumulation of mutations in check. Germline mutations in POLE cause polyposis and predispose to colorectal cancer, and are also linked to a rare syndrome of facial dysmorphism, immunodeficiency, livedo, and short stature. Somatic mutations, particularly in the proofreading domain, occur in colorectal and endometrial cancers, where they drive an ultra-mutated tumor phenotype and are associated with better responses to immune checkpoint inhibitors.
This variant
POLE mutations cause polyposis, colorectal cancer predisposition, and, through proofreading-domain changes, an ultra-mutated tumor phenotype; this synonymous variant alters no amino acid and shows no splice impact, so it does not engage any known POLE disease mechanism. Its VUS classification reflects extreme rarity in population databases but no functional, segregation, or case-level evidence linking it to disease, leaving its clinical relevance unresolved.
Transcript
NM_006231.4
HGVS · transcript:coding
NM_006231.4:c.4275C>T
GRCh38
chr12:132643852 G>A
GRCh37
chr12:133220438 G>A
BasisVUS: only PM2 (Supporting) and BP4 (Supporting) are met, and one supporting pathogenic versus one supporting benign factor does not reach any combined classification threshold.▾
VUS: only PM2 (Supporting) and BP4 (Supporting) are met, and one supporting pathogenic versus one supporting benign factor does not reach any combined classification threshold.
Classification rationale
PM2BP4VUS
POLE c.4275C>Tsynonymous · exon 33
PM2 (Supporting): extremely rare in population databases (gnomAD v4.1 AF 1.86e-06, 0 homozygotes), below the 0.1% rarity threshold. BP4 (Supporting): SpliceAI max delta 0.037 predicts no splice impact, below the <0.1 benign-splice threshold. VUS: the single supporting pathogenic factor (PM2) conflicts with the single supporting benign factor (BP4), which does not reach any LP/LB or P/B combination.
PM2 + BP4→VUS
Gene diagram
· NM_006231.4 · variants mapped to exon structure
POLENM_006231.4
Fetching transcript structure from UCSC…
Exons
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Transcript span
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Strand
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Variants mapped
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Source
UCSC ncbiRefSeqCurated
All variants in POLE—click a row to locate it on the plot · use the link column to open its page
Variant ↕
Protein
Location
Classification
Link
Applied criteria · 2 applied · 17 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
✓
PM2supportingPathogenic
Met (Supporting): extremely rare in gnomAD v4.1 at AF 1.86e-06 (3/1,614,022 alleles), below the 0.1% rarity threshold.
gnomAD v4.1: 3/1,614,022 total alleles, AF 1.85871e-06 (0.000185871%), grpmax FAF 6.8e-07, and 0 homozygotes; the highest population AF is 2.54254e-06 in European non-Finnish individuals.gnomAD v2.1: 1/251,190 total alleles, AF 3.98105e-06 (0.000398105%), highest population AF 8.80483e-06 in European non-Finnish individuals, and 0 homozygotes.gnomAD-Canada v1.0: absent.
Met (Supporting): SpliceAI max delta 0.037 is below the <0.1 benign-splice threshold.
SpliceAI evidence_sentence: 'SpliceAI predicts no significant splice impact for this variant (max delta score = 0.04)'; underlying scores DS_AG=0.01, DS_AL=0.013, DS_DG=0.037, DS_DL=0.008, max_delta=0.037.Generic fallback rule (generic_acmg_classification_rules.md, cited as generic_acmg_combination_rules) specifies: for intronic/synonymous/non-canonical-splice-position variants, use SpliceAI only, and SpliceAI max delta < 0.1 triggers BP4 (supporting).Custom POLE literature-derived PP3/BP4 rule (Le\u00f3n-Castillo et al. 2020 supplementary Tables S2/S3, REVEL-class based) was checked but does not apply because it is scoped to exact missense variants present in those tables, and this variant is synonymous and absent from them.
This variant is present in gnomAD v4.1 (AF= 1.85871e-06; MAF= 0.00019%, 3/1614022 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 2.54254e-06; MAF= 0.00025%, 3/1179922 alleles, homozygotes = 0); grpmax FAF= 6.8e-07.
v2.1
This variant is present in gnomAD v2.1 (AF= 3.98105e-06; MAF= 0.00040%, 1/251190 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 8.80483e-06; MAF= 0.00088%, 1/113574 alleles, homozygotes = 0).
🇨🇦 CA
Absent from gnomAD-Canada v1.0.
Allele frequency by ancestry
three datasets · side by side
gnomAD v4.1
0.00019%
· 3 / 1,614,022
0 hom · FAF 6.8e-05%
European (non-Finnish)
3 / 1,179,922
0.00025%
+ 9 not observed (Remaining individuals, Admixed American, European (Finnish), Amish, East Asian, Middle Eastern, South Asian, Ashkenazi Jewish, African/African American)
gnomAD v2.1
0.0004%
· 1 / 251,190
0 hom
European (non-Finnish)
1 / 113,574
0.00088%
+ 7 not observed (African/African American, Admixed American, Ashkenazi Jewish, East Asian, European (Finnish), Remaining individuals, South Asian)
This variant does not lie in a statistically significant hotspot. This variant has previously been reported in somatic cancers (COSMIC; COSV57674767, n = 3 times).
Hotspots
This variant does not lie in a statistically significant hotspot.
Triaged references · 2 PMIDs 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
28492532 ↗Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.CLINVAR