NM_006231.3:c.4735C>T

POLE · NP_006222.2:p.(Arg1579Cys) · NM_006231.3

GRCh37: chr12:133219309 G>A · GRCh38: chr12:132642723 G>A

Gene: POLE Transcript: NM_006231.3

Final call

VUS

PM2 supporting

Variant details

Gene

POLE

Transcript

NM_006231.3

Protein

NP_006222.2:p.(Arg1579Cys)

gnomAD AF

4.9588723524270585e-06 (v4.1)

ClinVar

Uncertain significance

OncoKB

Unknown Oncogenic Effect

Classification rationale

Interpretation summary

Generated evidence synthesis

NM_006231.3:c.4735C>T (p.Arg1579Cys) is a missense variant in the C-terminal polymerase domain of POLE, distant from the exonuclease domain (residues 1-466) where established pathogenic missense variants cluster.

This variant is present at very low frequency in population databases: gnomAD v2.1 at 0.00319% (1/31,386 alleles), gnomAD v4.1 at 0.00050% (8/1,613,270 alleles), and absent from gnomAD-Canada, meeting PM2 at supporting strength.

Under the León-Castillo et al. 2020 custom POLE framework, this variant does not qualify for PM1 (not an exonuclease-domain hotspot), PS4 (not a recurrent pathogenic variant in endometrial carcinoma cohorts), PP3 (absent from supplementary in silico tables), or BP4 (absent from supplementary in silico tables).

Computational predictors are mixed and do not converge on a pathogenic signal: REVEL 0.412 (intermediate), BayesDel 0.071 (benign-leaning), SpliceAI max delta 0.20 (borderline). PP3 and BP4 are not met.

This variant is reported in ClinVar (VariationID 405672) as 'Uncertain significance' by three clinical laboratories. The associated publications (PMID:25394175, a cancer genetics referral guideline, and PMID:28492532, the Sherloc classification framework) do not provide variant-specific evidence for NM_006231.3:c.4735C>T.

No functional studies, segregation data, de novo observations, or case-control studies are available for this variant. All remaining pathogenic criteria (PS1-PS5, PM1, PM5-PM6, PP1-PP5) and benign criteria (BA1, BS1-BS4, BP1-BP6) are either not met or not applicable.

With only PM2_Supporting met, the overall classification is Uncertain Significance (VUS) per ACMG/AMP 2015 guidelines: insufficient evidence to classify as pathogenic or benign.

Final determination: A single supporting-level criterion (PM2_Supporting) with no other pathogenic or benign criteria met is insufficient to satisfy any Pathogenic, Likely Pathogenic, Benign, or Likely Benign combination under either the León-Castillo et al. 2020 custom POLE framework or generic ACMG/AMP 2015 rules; the variant defaults to VUS.

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	This is a missense variant (c.4735C>T, p.Arg1579Cys), not a null variant (nonsense, frameshift, or canonical ±1/2 splice site). PVS1 is not applicable to missense substitutions.	pvs1_variant_assessment pvs1_gene_context
PS1	Not met	No known pathogenic variant at the same amino acid position (Arg1579) with the same nucleotide change has been identified in ClinVar or the literature.	clinvar pm5_candidates
PS2	Not met	No de novo data are available for this variant. No publications report de novo occurrence of NM_006231.3:c.4735C>T.
PS3	Not met	No well-established functional studies demonstrating a damaging effect have been identified for this variant. OncoKB classifies this variant as 'Unknown Oncogenic Effect.' No publications with variant-specific functional data were found.	oncokb
PS4	Not met	Under the León-Castillo et al. 2020 custom POLE framework, PS4_Supporting applies only to four specific hotspot variants (P286R, V411L, A456P, S297F) with combined endometrial carcinoma count ≥10 in Supplementary Table S1. R1579C is not among these variants and is absent from Table S1. Under generic ACMG, no case-control studies demonstrating statistically significant enrichment in affected individuals are available. The variant has been observed in COSMIC (n=2) but this somatic recurrence is insufficient for germline PS4.	vcep_path_250_323_s002 clinvar
PS5	Not met	No reputable source has reported this variant as pathogenic. ClinVar classification is 'Uncertain significance' (VariationID 405672, three clinical laboratories, review status: criteria provided, single submitter).	clinvar
PM1	Not met	Under the León-Castillo et al. 2020 custom POLE framework, PM1 applies only to specific exonuclease-domain hotspot variants listed in Supplementary Table S1. R1579C is at residue 1579, far outside the POLE exonuclease domain (residues ~1-466), and is not among the specified variants at any strength tier (Strong: P286R/V411L/S297F/A456P/S459F; Moderate: F367S/L424I/M295R/P436R/M444K/D368Y; Supporting: A465V/L424V/T278M/A428T). The variant is absent from Supplementary Table S1. Under generic ACMG, this residue is not located in a well-established mutational hotspot or critical functional domain.	vcep_path_250_323 vcep_path_250_323_s002 final_classification_framework
PM2	Met	This variant is present at very low frequency in population databases, meeting PM2 at supporting strength. gnomAD v2.1 AF = 0.00319% (1/31,386 alleles), gnomAD v4.1 AF = 0.00050% (8/1,613,270 alleles, grpmax FAF = 2.92e-06), and the variant is absent from gnomAD-Canada. All frequencies are well below the 0.1% threshold. No homozygotes have been observed in any population database.	gnomad_v2 gnomad_v4 gnomad_canada
PM5	N/A	No same-residue comparator variants with confirmed pathogenicity were identified at Arg1579. The automated PM5 candidate harvest found zero candidates and recommended not_applicable.	pm5_candidates
PM6	Not met	No de novo data are available for this variant. PM6 requires confirmed de novo occurrence with confirmed maternity and paternity.
PP1	Not met	No segregation data are available for this variant. PP1 requires cosegregation with disease in multiple affected family members.
PP2	Not assessed	PP2 requires demonstration that the gene has a low rate of benign missense variation (high missense Z-score) and that missense variants are a common disease mechanism. POLE is a large gene with both missense and truncating pathogenic variants. Region-specific missense constraint data for the C-terminal domain (where R1579 resides) are not established. This criterion is deferred for lack of domain-specific constraint metrics.
PP3	Not met	Under the León-Castillo et al. 2020 custom POLE framework, PP3_Supporting requires the variant to appear in Supplementary Table S2 or S3 with REVEL class 'likely disease causing' and benign in silico results ≤1. R1579C is absent from both tables. Under generic ACMG, the computational evidence is mixed and does not support a deleterious effect: REVEL score is 0.412 (intermediate, below typical pathogenic threshold of 0.5), BayesDel score is 0.071 (benign-leaning), and SpliceAI max delta is 0.20 (borderline). Multiple lines of computational evidence do not converge on a damaging prediction.	vcep_path_250_323_s003 vcep_path_250_323_s004 revel bayesdel spliceai
PP4	Not met	No specific patient phenotype or clinical information is available for this variant to assess whether the phenotype is highly specific for POLE-related disease.
PP5	Not met	This variant is reported in ClinVar (VariationID 405672) as 'Uncertain significance' by three clinical laboratories with review status 'criteria provided, single submitter.' The ClinVar-associated PMIDs do not provide variant-specific evidence: PMID 25394175 (Hampel et al. 2015) is a general cancer genetics referral guideline that does not mention NM_006231.3:c.4735C>T; PMID 28492532 (Nykamp et al. 2017, Sherloc) describes a variant classification framework and does not contain variant-specific evidence. No reputable source has classified this variant as pathogenic.	clinvar
BA1	Not met	Variant frequency in population databases is well below the 1% threshold for BA1. Maximum observed frequency is 0.00649% in gnomAD v2.1 European (non-Finnish) and 0.00050% overall in gnomAD v4.1.	gnomad_v2 gnomad_v4
BS1	Not met	Variant frequency is well below the 0.3% threshold for BS1. Maximum population frequency is 0.00649% in gnomAD v2.1 European (non-Finnish).	gnomad_v2 gnomad_v4
BS2	Not met	No evidence of this variant being observed in a healthy adult individual for a fully penetrant disorder. No homozygous observations in population databases.
BS3	Not met	No well-established functional studies showing no damaging effect on protein function or splicing have been identified for this variant.	oncokb
BS4	Not met	No segregation data are available to demonstrate lack of cosegregation with disease.
BP1	Not met	BP1 applies to missense variants in genes where primarily truncating variants cause disease. POLE has well-established pathogenic missense variants in the exonuclease domain (e.g., P286R, V411L, S297F, A456P, S459F) and disease is not exclusively caused by truncating variants. Therefore BP1 is not applicable to POLE missense variants.	pvs1_gene_context vcep_path_250_323
BP2	Not met	No evidence of this variant being observed in trans with a known pathogenic POLE variant. POLE-associated disease (polymerase proofreading-associated polyposis, PPAP) is autosomal dominant with incomplete penetrance; observation in trans with a pathogenic variant would be informative but none is reported.
BP4	Not met	Under the León-Castillo et al. 2020 custom POLE framework, BP4_Supporting requires the variant to appear in Supplementary Table S2 or S3 with REVEL class 'Likely benign' and benign in silico results ≥4. R1579C is absent from both tables. Under generic ACMG, computational evidence is mixed rather than showing a consensus benign prediction: REVEL 0.412 (intermediate), BayesDel 0.071 (benign-leaning but not strongly so), SpliceAI max delta 0.20. Multiple lines of evidence do not converge on a benign prediction.	vcep_path_250_323_s003 vcep_path_250_323_s004 revel bayesdel spliceai
BP5	Not met	No evidence that this variant is found in a case with an alternate molecular basis for disease. No reports of this variant co-occurring with a solved molecular diagnosis.
BP6	Not met	No reputable source has reported this variant as benign. ClinVar classification is 'Uncertain significance' (VariationID 405672), not benign or likely benign.	clinvar
BP7	N/A	BP7 applies to synonymous (silent) variants not predicted to affect splicing. This is a missense variant (c.4735C>T, p.Arg1579Cys) and therefore BP7 is not applicable.
BP3	N/A	Skipped per instructions — trivially not applicable (in-frame deletions/insertions in non-repeat regions).
PM3	N/A	Skipped per instructions — trivially not applicable (no recessive inheritance context for POLE).
PM4	N/A	Skipped per instructions — trivially not applicable (not an in-frame deletion/insertion or stop-loss variant).

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