NM_006231.4:c.6150C>A

POLE · NP_006222.2:p.(Phe2050Leu) · NM_006231.4

GRCh37: chr12:133209081 G>T · GRCh38: chr12:132632495 G>T

Gene: POLE Transcript: NM_006231.4

Final call

VUS

PM2 supporting BP4 supporting

Variant details

Gene

POLE

Transcript

NM_006231.4

Protein

NP_006222.2:p.(Phe2050Leu)

gnomAD AF

ClinVar

Uncertain significance

OncoKB

Unknown Oncogenic Effect

Classification rationale

Interpretation summary

Generated evidence synthesis

NM_006231.4:c.6150C>A (p.Phe2050Leu) is a missense variant in the C-terminal region of POLE, far outside the exonuclease domain (residues ~268-471) where established pathogenic hotspot mutations cluster.

This variant is absent from gnomAD v2.1, v4.1, and gnomAD-Canada population databases (PM2_Supporting).

Multiple lines of computational evidence (REVEL 0.228, BayesDel -0.046, SpliceAI max delta 0.15) suggest no significant impact on the gene product (BP4_Supporting).

ClinVar reports this variant as Uncertain significance (VariationID 3004425) with review status 'criteria provided, single submitter' (1-star); no expert panel classification is available.

No published functional studies, segregation analyses, de novo observations, or case-control data exist for this variant.

The variant has not been observed in COSMIC and is not listed as a recurrent variant in the Leon-Castillo et al. 2020 endometrial carcinoma cohort analysis.

With one supporting pathogenic criterion (PM2) and one supporting benign criterion (BP4), the evidence is insufficient for classification; the variant remains a Variant of Uncertain Significance.

Final determination: Under ACMG/AMP 2015 (PMID:25741868), any combination of criteria that does not meet the specified thresholds for Pathogenic, Likely Pathogenic, Likely Benign, or Benign defaults to Variant of Uncertain Significance. One supporting pathogenic and one supporting benign criterion falls into this default category.

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	PVS1 is not applicable to missense variants. NM_006231.4:c.6150C>A is a missense substitution (p.Phe2050Leu) and does not fall into the null-variant buckets of nonsense, frameshift, or canonical ±1,2 splice consensus variants as defined by the ClinGen SVI PVS1 recommendations (PMC6185798).	pvs1_generic_framework
PS1	Not met	No known pathogenic variant at the same nucleotide position (c.6150) with the same amino acid change (p.Phe2050Leu) has been identified. ClinVar reports no pathogenic or likely pathogenic submissions for any variant at this codon.	clinvar
PS2	Not met	No de novo observation has been reported for this variant. Neither the ClinVar submissions nor the reviewed literature include a de novo report with confirmed maternity and paternity.	clinvar
PS3	Not met	No functional data exists for NM_006231.4:c.6150C>A (p.Phe2050Leu). The variant has not been directly tested in any published functional assay, nor does it fall within a systematically characterized range (e.g., saturation mutagenesis, CRISPR tiling screen). The position 2050 is in the C-terminal region of POLE, far outside the exonuclease domain (residues ~268-471). REVEL score of 0.228 and BayesDel score of -0.046 do not support a deleterious functional effect. The Leon-Castillo et al. 2020 supplementary tables do not include this variant. OncoKB reports no variant-specific functional evidence.	revel bayesdel oncokb
PS4	Not met	The variant is absent from COSMIC and was not identified in the TCGA endometrial carcinoma cohorts summarized in Leon-Castillo et al. 2020 Supplementary Table S1. The custom POLE framework requires variant-specific recurrence with a combined EC count >=10 for PS4_Supporting. The ClinVar submissions (VUS, 2 clinical laboratories) do not provide case-control or cohort evidence for PS4.	vcep_path_250_323_s002 clinvar
PS5	Not met	No reputable source reports this variant as pathogenic. ClinVar classification is Uncertain significance with review status 'criteria provided, single submitter' (1-star). The variant has not been reported as pathogenic by an expert panel or in a peer-reviewed publication.	clinvar
PM1	Not met	PM1 is not met. The variant p.Phe2050Leu is located at amino acid position 2050 in the C-terminal region of POLE, far outside the exonuclease domain (residues ~268-471) where established pathogenic hotspot missense mutations cluster (P286R, V411L, S297F, A456P, S459F). The custom POLE framework defines PM1_Strong for the five established exonuclease-domain hotspot mutations, PM1_Moderate for specific non-hotspot exonuclease-domain variants with POLE-score >=4, and PM1_Supporting for specific POLE-score 3 variants. F2050L is not in any of these lists. The variant also does not lie in a statistically significant cancer hotspot by cancerhotspots.org. No characterized functional domain encompasses position 2050.	vcep_path_250_323_s002 vcep_path_250_323
PM2	Met	NM_006231.4:c.6150C>A is absent from all large population databases, including gnomAD v2.1 (exomes), gnomAD v4.1 (exomes/genomes), and gnomAD-Canada v1.0. This satisfies PM2_Supporting under the generic ACMG/AMP framework (allele frequency <0.1% and absent from controls).	gnomad_v2 gnomad_v4 gnomad_canada
PM5	Not met	No same-residue comparator variants with a pathogenic or likely pathogenic classification were identified for codon 2050. The automated PM5 candidate search returned zero same-residue candidates, and a manual ClinVar review confirms no pathogenic missense variants at p.Phe2050 with a different amino acid change.	pm5_candidates clinvar
PM6	Not met	No de novo observation has been reported for this variant. Neither the ClinVar submissions nor the reviewed literature provide evidence of a de novo occurrence with confirmed maternity and paternity.	clinvar
PP1	Not met	No segregation data are available for this variant. No published family studies or cosegregation analyses involving NM_006231.4:c.6150C>A have been identified.
PP2	Not met	PP2 requires a low rate of benign missense variation and demonstration that missense variants are a common disease mechanism for the gene. While pathogenic POLE missense variants are well-established in the exonuclease domain (P286R, V411L, etc.), this variant lies at position 2050 in the C-terminal region, outside the exonuclease domain. No HCI prior score is available to quantify missense constraint for this gene region. Without evidence that missense variants across the full POLE protein are a common mechanism (rather than localized to the exonuclease domain), PP2 cannot be applied.
PP3	Not met	Multiple lines of computational evidence do not support a deleterious effect. REVEL score is 0.228 (below the 0.5 pathogenic threshold; in the benign-leaning range <0.3). BayesDel score is -0.046 (negative, consistent with a benign/neutral prediction). SpliceAI max delta score is 0.15 (below the 0.2 threshold for significant splice impact). The custom POLE PP3 rule requires the variant to appear in Leon-Castillo et al. 2020 Supplementary Table S2 or S3 with REVEL class 'likely disease causing' and <=1 benign in silico result; the variant is absent from both tables, so the custom rule is not triggered and generic ACMG/AMP fallback applies, which also does not support PP3.	revel bayesdel spliceai vcep_path_250_323_s003 vcep_path_250_323_s004
PP4	Not met	No specific phenotypic or family history data are available for this variant. The ClinVar submissions (VariationID 3004425) are classified as VUS and do not provide detailed phenotypic information. No published case reports describing the phenotype of individuals carrying this variant were identified.	clinvar
PP5	Not met	ClinVar reports this variant as Uncertain significance (VariationID 3004425) with review status 'criteria provided, single submitter' (1-star). The reviewing clinical laboratories did not classify it as pathogenic or likely pathogenic. No expert panel (3-star) classification is available, and the override rule for PP5 at 3-star expert panel does not apply at this review level. Neither of the two associated publications (PMID:25394175, PMID:28492532) mentions this specific variant.	clinvar PMID:25394175 PMID:28492532
BA1	Not met	BA1 requires an allele frequency >1% in population databases. This variant is absent from gnomAD v2.1, v4.1, and gnomAD-Canada, with an observed allele frequency of 0.	gnomad_v2 gnomad_v4 gnomad_canada
BS1	Not met	BS1 requires an allele frequency >0.3% in population databases. This variant is absent from all queried population databases (gnomAD v2.1, v4.1, Canada), with an observed allele frequency of 0.	gnomad_v2 gnomad_v4 gnomad_canada
BS2	Not met	BS2 requires observation of the variant in a healthy adult individual for a fully penetrant disorder. This variant has not been observed in any individual in gnomAD, and no published reports describe observation in a healthy control.	gnomad_v2 gnomad_v4
BS3	Not met	No published functional studies have assessed NM_006231.4:c.6150C>A (p.Phe2050Leu) in a well-established assay demonstrating no deleterious effect. While REVEL (0.228) and BayesDel (-0.046) predict a benign/neutral effect, in silico predictions alone are not sufficient to satisfy BS3, which requires experimental functional data.	revel bayesdel
BS4	Not met	No segregation data are available to assess non-segregation with disease. No published family studies involving this variant were identified.
BP1	Not met	BP1 applies to missense variants in genes for which primarily truncating variants are known to cause disease. POLE has well-established pathogenic missense variants in the exonuclease domain (P286R, V411L, S297F, A456P, S459F) that are recognized as a pathogenic mechanism, particularly in the context of polymerase proofreading deficiency and ultramutated tumor phenotypes. Because both truncating and missense variants can be pathogenic in POLE, BP1 does not apply.	vcep_path_250_323
BP2	Not met	BP2 requires observation of the variant in trans with a known pathogenic variant in a gene for a fully penetrant dominant disorder, or in cis with a pathogenic variant in a recessive disorder. No such observations have been reported for this variant.
BP4	Met	Multiple lines of computational evidence suggest no impact on the gene product. REVEL score is 0.228 (below the 0.3 benign-leaning threshold), BayesDel score is -0.046 (negative, consistent with a benign prediction), and SpliceAI max delta score is 0.15 (below the 0.2 threshold for significant splice impact). The variant is absent from the Leon-Castillo et al. Supplementary Tables S2/S3, so the custom POLE BP4 rule is not triggered; generic ACMG/AMP BP4 applies at supporting strength based on concordant benign predictions from multiple algorithms.	revel bayesdel spliceai
BP5	Not met	BP5 requires observation of the variant in a case with an alternative molecular cause of disease. No such observation has been reported for this variant.
BP6	Not met	BP6 requires a reputable source to report the variant as benign. ClinVar classification is Uncertain significance with review status 'criteria provided, single submitter' (1-star). No expert panel (3-star) classification is available. The associated publications (PMID:25394175, PMID:28492532) are general guideline/framework papers that do not mention this specific variant. The PP5/BP6 3-star expert panel override rule does not apply at this review level.	clinvar PMID:25394175 PMID:28492532
BP7	N/A	BP7 applies to synonymous (silent) variants with no predicted impact on splicing. NM_006231.4:c.6150C>A is a missense variant resulting in p.Phe2050Leu, an amino acid change. BP7 is therefore not applicable.

Disclaimer: The content and results provided by LYFE Sciences are for research and educational purposes only and must not be used as a substitute for professional medical judgment, diagnosis, or treatment. Always consult a qualified healthcare professional before making any clinical decisions.