NM_006231.4:c.1270C>A

POLE · NP_006222.2:p.(Leu424Ile) · NM_006231.4

GRCh37: chr12:133250250 G>T · GRCh38: chr12:132673664 G>T

Gene: POLE Transcript: NM_006231.4

Final call

Likely Pathogenic

PM1 moderate PM2 moderate PM5 moderate PP3 supporting

Variant details

Gene

POLE

Transcript

NM_006231.4

Protein

NP_006222.2:p.(Leu424Ile)

gnomAD AF

ClinVar

Uncertain significance

OncoKB

Likely Oncogenic

Classification rationale

Interpretation summary

Generated evidence synthesis

p.Leu424Ile is an exonuclease-domain missense variant explicitly assigned PM1 at moderate strength in the León-Castillo et al. 2020 custom POLE framework based on recurrence in the TCGA endometrial carcinoma cohort (n=2) and classification in the pathogenic POLE-score tier.

The variant is absent from gnomAD v2.1, v4.1, and gnomAD-Canada population databases, meeting the PM2 threshold of <0.1% allele frequency.

A different pathogenic missense variant at the same codon, c.1270C>G (p.Leu424Val), is established as a high-penetrance germline cause of polymerase proofreading-associated polyposis across multiple independent cohorts (Palles et al. 2013, Valle et al. 2014, Elsayed et al. 2014, Spier et al. 2015), satisfying PM5 at moderate strength.

In silico assessment from Supplementary Table S2 shows REVEL class 'likely disease causing' with only 1 benign result (SIFT=Deleterious, PANTHER=Probably damaging, SNAP2=effect, PolyPhen2=Probably damaging, PROVEAN=Neutral), meeting the custom POLE PP3_Supporting rule.

No variant-specific functional data, de novo observations, segregation data, or germline case-control evidence exist for c.1270C>A; eight publications citing POLE codon 424 all refer to the sister variant c.1270C>G (p.Leu424Val) and do not mention c.1270C>A.

Final determination: >=3 moderate-strength pathogenic criteria qualifies as Likely Pathogenic under the standard ACMG/AMP 2015 combination rules retained by the León-Castillo et al. 2020 custom POLE framework.

Criteria assessment

ACMG/AMP criteria review

Criteria shown when status is available

All criteria require review: For research and educational purposes only.

Criterion	Status	Rationale	Evidence used
PVS1	N/A	NM_006231.4:c.1270C>A is a missense variant (p.Leu424Ile) and does not fall into the generic PVS1 null-variant buckets of nonsense, frameshift, or canonical ±1,2 splice consensus variants.	pvs1_variant_assessment pvs1_gene_context
PS1	N/A	No previously established pathogenic variant produces the same amino acid change (p.Leu424Ile) via a different nucleotide substitution.
PS2	Not met	No de novo occurrence of NM_006231.4:c.1270C>A has been reported in the reviewed literature. Published de novo reports at codon 424 all refer to the sister variant c.1270C>G (p.Leu424Val), not c.1270C>A.	PMID:24501277 PMID:25370038
PS3	Not met	No variant-specific functional data exist for NM_006231.4:c.1270C>A (p.Leu424Ile) in the reviewed literature. No systematic range characterization (tiling screen, saturation mutagenesis, systematic truncation series) covering position 424 that includes this exact substitution was identified. The OncoKB 'Likely Oncogenic' annotation reflects somatic curation context and does not constitute germline PS3 functional evidence.	oncokb
PS4	Not met	The custom POLE PS4 rule requires recurrence in both COSMIC and TCGA with combined EC count >=10 and membership in the established pathogenic hotspot set. p.L424I has 0 COSMIC cases and 2 TCGA cases (total 2), does not meet the >=10 threshold, and is not one of the five established hotspot mutations (P286R, V411L, S297F, A456P, S459F). No germline case-control evidence exists for this variant.	vcep_path_250_323_s002 vcep_path_250_323
PS5	Not met	No reputable source has classified NM_006231.4:c.1270C>A as pathogenic. ClinVar classification is Uncertain significance (single submitter).	clinvar
PM1	Met	p.Leu424Ile is explicitly listed in the León-Castillo et al. 2020 custom POLE framework as a non-hotspot exonuclease-domain missense variant qualifying for PM1_Moderate. The variant falls within the exonuclease proofreading domain (residues 268-471) and was classified in the pathogenic tier (POLE-score >=4) in the TCGA-based analysis.	vcep_path_250_323 vcep_path_250_323_s002
PM2	Met	NM_006231.4:c.1270C>A is absent from gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada v1.0, meeting the non-VCEP PM2 threshold of allele frequency <0.1%.	gnomad_v2 gnomad_v4 gnomad_canada
PM5	Met	A different pathogenic missense variant at the same codon — c.1270C>G (p.Leu424Val) — is established as a high-penetrance germline pathogenic variant causing polymerase proofreading-associated polyposis (PPAP), confirmed across multiple independent cohorts (Palles et al. 2013, Valle et al. 2014, Elsayed et al. 2014, Spier et al. 2015). The novel c.1270C>A (p.Leu424Ile) substitution at the same residue therefore meets PM5 at moderate strength.	PMID:23263490 PMID:24501277 PMID:25370038 PMID:25529843 clinvar
PM6	Not met	No de novo observation has been reported for NM_006231.4:c.1270C>A specifically. De novo reports at codon 424 are for c.1270C>G (p.Leu424Val) only.	PMID:24501277 PMID:25370038
PP1	Not met	No segregation data are available for NM_006231.4:c.1270C>A in any reviewed publication.
PP2	Not met	Insufficient data to determine whether POLE has a low rate of benign missense variation; no gene-level missense constraint metric (e.g., gnomAD Z-score, HCI prior) was available for this assessment.
PP3	Met	p.L424I appears in Supplementary Table S2 of León-Castillo et al. 2020 with REVEL class 'likely disease causing' and only 1 benign in silico result (<=1), meeting the custom POLE PP3_Supporting rule. SpliceAI predicts no splicing impact (max delta score = 0.00).	vcep_path_250_323_s003 vcep_path_250_323 revel spliceai
PP4	Not met	No specific phenotypic data are available for any individual carrying NM_006231.4:c.1270C>A. The variant's phenotype cannot be assessed from the available evidence.
PP5	Not met	No reputable source has classified NM_006231.4:c.1270C>A as pathogenic. The single ClinVar submission classifies it as Uncertain significance.	clinvar
BA1	Not met	The variant is absent from gnomAD v2.1, v4.1, and gnomAD-Canada. Allele frequency is 0%, far below the BA1 threshold of >1%.	gnomad_v2 gnomad_v4 gnomad_canada
BS1	Not met	The variant is absent from gnomAD. Allele frequency is 0%, far below the BS1 threshold of >0.3%.	gnomad_v2 gnomad_v4 gnomad_canada
BS2	Not met	No observation of this variant in healthy adult controls; the variant is absent from population databases.	gnomad_v2 gnomad_v4
BS3	Not met	No functional studies demonstrating no deleterious effect for NM_006231.4:c.1270C>A (p.Leu424Ile) exist in the reviewed literature.
BS4	Not met	No segregation data demonstrating lack of cosegregation with disease are available for this variant.
BP1	Not met	Missense variants in POLE, particularly in the exonuclease domain, are a well-established mechanism of disease (PPAP). BP1 is contraindicated because the gene's disease spectrum includes pathogenic missense variants.	PMID:23263490
BP2	Not met	No observation of this variant in trans with a pathogenic POLE variant has been reported.
BP4	Not met	The custom POLE BP4_Supporting rule requires REVEL class 'Likely benign' and >=4 benign in silico results. p.L424I has REVEL class 'likely disease causing' and only 1 benign result in Table S2, so it does not meet the custom BP4 rule. Under generic ACMG, the in silico evidence is mixed (REVEL 0.593 is indeterminate; BayesDel -0.085 leans benign but is not strongly predictive; SpliceAI = 0.00), which does not reach the threshold for BP4_Supporting.	vcep_path_250_323_s003 revel bayesdel spliceai
BP5	Not met	No alternative molecular cause for the observed phenotype has been identified in any individual carrying this variant.
BP6	Not met	ClinVar classification is 'Uncertain significance' (single submitter), not 'Benign' or 'Likely benign' from a reputable source.	clinvar
BP7	Not met	NM_006231.4:c.1270C>A is a missense variant, not a synonymous variant. BP7 applies only to synonymous variants predicted to have no splicing impact.

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