NM_006231.4:c.3959G>A

POLE · NP_006222.2:p.(Arg1320Gln) · NM_006231.4

GRCh37: chr12:133225938 C>T · GRCh38: chr12:132649352 C>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.(Arg1320Gln)

gnomAD AF

1.5494055860409713e-05 (v4.1)

ClinVar

Uncertain significance

OncoKB

Unknown Oncogenic Effect

Classification rationale

Interpretation summary

Generated evidence synthesis

NM_006231.4:c.3959G>A (p.Arg1320Gln) in POLE is classified as a Variant of Uncertain Significance (VUS).

This variant is a missense substitution in exon 31 of 49, located in the C-terminal region of POLE, far outside the well-characterized exonuclease domain (residues ~268-471).

The variant is present at very low frequency in population databases: gnomAD v2.1 allele frequency 0.0032% (8/249,426 alleles) and v4.1 allele frequency 0.0016% (25/1,613,522 alleles), with no homozygotes observed (PM2_Supporting).

Multiple in silico tools predict a benign effect: REVEL score 0.225, BayesDel score -0.2976, and SpliceAI max delta 0.02 (BP4_Supporting).

The variant is not one of the five established pathogenic POLE exonuclease-domain hotspot mutations (P286R, V411L, S297F, A456P, S459F) and is absent from the recurrent variant list in the Leon-Castillo et al. 2020 endometrial carcinoma cohort analysis.

ClinVar classifies this variant as Uncertain Significance with 5 clinical laboratory submissions and review status 'criteria provided, single submitter' (1-star). No expert panel review has been performed.

No functional studies, segregation data, de novo observations, or case-control data are available for this variant. The reviewed literature (Karbassi et al. 2016, PMID:26467025; Hampel et al. 2015, PMID:25394175; Nykamp et al. 2017, PMID:28492532) consists of variant classification methodology papers that do not mention this variant.

The net evidence balance is one supporting pathogenic criterion (PM2) and one supporting benign criterion (BP4), resulting in a classification of Uncertain Significance under the ACMG/AMP 2015 framework.

Final determination: One pathogenic supporting criterion (PM2) and one benign supporting criterion (BP4) do not meet any Pathogenic, Likely Pathogenic, Benign, or Likely Benign combination rule under the Leon-Castillo et al. 2020 custom POLE framework, which applies standard ACMG/AMP 2015 final-classification thresholds; all other combinations default 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	PVS1 is not applicable. NM_006231.4:c.3959G>A is a missense substitution (p.Arg1320Gln) and does not fall into any null-variant bucket (nonsense, frameshift, or canonical +/-1,2 splice consensus). The variant lies in exon 31 of 49, outside the exonuclease domain, and the ClinGen SVI PVS1 framework does not support PVS1 for missense variants.	pvs1_generic_framework pvs1_variant_assessment
PS1	Not assessed	No evidence is available regarding a different pathogenic nucleotide change at the same amino acid position (Arg1320). No literature or database entries describe a pathogenic missense change at codon 1320 with a different nucleotide substitution.
PS2	Not assessed	No de novo data are available for this variant. No published reports of de novo occurrence were identified in ClinVar submissions or the reviewed literature.
PS3	Not met	No functional data exist for NM_006231.4:c.3959G>A or a systematically characterized range that includes position 1320. The variant is absent from OncoKB curated functional evidence and is not in COSMIC. The variant lies outside the well-characterized exonuclease domain (residues ~268-471), and no experimental studies have tested this variant or a saturation mutagenesis range covering residue 1320.	oncokb
PS4	Not met	Under the Leon-Castillo et al. 2020 custom POLE framework, PS4_Supporting applies only when the exact missense variant is recurrent in both COSMIC and TCGA endometrial carcinoma cohorts with a combined EC count >=10. NM_006231.4:c.3959G>A (p.Arg1320Gln) is absent from Supplementary Table S1 and is not one of the established pathogenic hotspots. No germline case-control evidence is available to support generic PS4 application.	vcep_path_250_323_s002
PS5	Not assessed	No data are available to support PS5. This criterion requires a different pathogenic variant at the same codon, supported by functional or clinical evidence independent of PM5. No such evidence was identified for codon 1320.
PM1	Not met	Under the Leon-Castillo et al. 2020 custom POLE framework, PM1 applies only to specified exonuclease-domain hotspot and recurrent variants. p.Arg1320Gln lies at the C-terminus of POLE, far outside the exonuclease domain (residues ~268-471), and is not one of the five established pathogenic hotspots (P286R, V411L, S297F, A456P, S459F) or the listed recurrent non-hotspot variants. No other well-characterized critical functional domain has been described at position 1320.	vcep_path_250_323 vcep_path_250_323_s002
PM2	Met	NM_006231.4:c.3959G>A is present at extremely low frequency in population databases. In gnomAD v2.1, the allele frequency is 3.21e-05 (0.0032%, 8/249,426 alleles, 0 homozygotes; grpmax FAF=8.51e-05). In gnomAD v4.1, the frequency is 1.55e-05 (0.0016%, 25/1,613,522 alleles, 0 homozygotes; grpmax FAF=1.10e-04). Both are well below the 0.1% PM2 threshold. The variant is absent from gnomAD-Canada v1.0. Highest subpopulation frequency is in South Asians (v2.1: 0.020%, v4.1: 0.018%).	gnomad_v2 gnomad_v4 gnomad_canada
PM5	N/A	PM5 cannot be applied. The automated PM5 candidate harvesting pipeline was unable to identify same-residue comparator variants for position Arg1320. No ClinVar entries describe a different pathogenic missense change at this codon.	pm5_candidates
PM6	Not assessed	No de novo data are available for this variant. No published reports of de novo occurrence were identified.
PP1	Not assessed	No segregation data are available for this variant. No family studies or co-segregation analyses were identified in ClinVar or the reviewed literature.
PP2	Not assessed	PP2 requires demonstration that the gene has a low rate of benign missense variation and that missense variants are a common mechanism of disease. While POLE exonuclease domain missense variants are a known disease mechanism, the variant at position 1320 lies outside this domain. Insufficient gene-level missense constraint data are available to confidently apply PP2 across the entire POLE coding sequence.
PP3	Not met	Under the Leon-Castillo et al. 2020 custom POLE framework, PP3_Supporting applies only when the exact missense variant appears in Supplementary Table S2 or S3 with REVEL class 'likely disease causing' and <=1 benign in silico results. R1320Q is absent from both supplementary tables, so the custom rule does not apply. Under generic fallback, multiple lines of computational evidence predict a benign effect: REVEL score 0.225 (below the 0.5 pathogenic threshold), BayesDel score -0.2976 (negative = benign), and SpliceAI max delta 0.02 (no splicing impact). These results do not support a deleterious effect.	revel bayesdel spliceai vcep_path_250_323_s003 vcep_path_250_323_s004
PP4	Not assessed	No patient phenotype or family history data are provided for this case. PP4 requires that the patient's phenotype or family history is highly specific for the disease associated with the gene.
PP5	Not met	ClinVar reports this variant as Uncertain Significance with review status 'criteria provided, single submitter' (1-star). The PP5/BP6 rule requires a 3-star expert panel review for supporting-level application. No expert panel has reviewed this variant, and the single submitter classification does not meet the threshold for PP5.	clinvar
BA1	Not met	The variant is present at very low frequency in gnomAD. v2.1 AF=3.21e-05 (0.0032%), v4.1 AF=1.55e-05 (0.0016%). Both are well below the 1% BA1 threshold. The highest subpopulation frequency is 0.020% in South Asians (v2.1), also far below 1%.	gnomad_v2 gnomad_v4
BS1	Not met	The variant is present at very low frequency in gnomAD. v2.1 AF=3.21e-05 (0.0032%), v4.1 AF=1.55e-05 (0.0016%). Both are well below the 0.3% BS1 threshold. The highest subpopulation frequency is 0.020% in South Asians (v2.1), also far below 0.3%.	gnomad_v2 gnomad_v4
BS2	Not assessed	No data are available regarding homozygous or hemizygous observations of this variant in healthy individuals. BS2 requires observation in a homozygous or hemizygous state without disease.
BS3	Not assessed	No functional studies have been performed on this variant to demonstrate a benign effect. While in silico tools predict a benign outcome (REVEL 0.225, BayesDel -0.298), these are computational predictions (BP4 territory), not experimental functional evidence meeting BS3 standards.
BS4	Not assessed	No segregation data are available for this variant. BS4 requires lack of segregation with disease in affected family members.
BP1	Not met	BP1 is not met. BP1 applies when a missense variant occurs in a gene where only truncating variants are known to cause disease. POLE has well-established pathogenic missense variants, particularly in the exonuclease domain (e.g., P286R, V411L, S297F, A456P, S459F), which cause ultramutated phenotype in endometrial carcinoma. Therefore, POLE does not meet the BP1 requirement that only truncating variants cause disease.	vcep_path_250_323
BP2	Not assessed	No data are available regarding observations of this variant in trans with a known pathogenic variant. BP2 requires observation in trans with a pathogenic variant in a gene for which fully penetrant dominant disease is the established mechanism.
BP4	Met	Under the Leon-Castillo et al. 2020 custom POLE framework, BP4_Supporting applies when the variant appears in Supplementary Table S2 or S3 with REVEL class 'Likely benign' and >=4 benign in silico results. R1320Q is absent from both tables, so the custom rule does not apply. Under generic fallback, multiple lines of computational evidence predict no impact: REVEL score 0.225 (below 0.5, benign-leaning), BayesDel score -0.2976 (negative, predicting benign), and SpliceAI max delta 0.02 (no splicing impact). These results support a lack of deleterious effect at the supporting evidence level.	revel bayesdel spliceai vcep_path_250_323_s003 vcep_path_250_323_s004
BP5	Not assessed	No data are available regarding an alternate molecular basis for disease in this case. BP5 requires that an alternate cause of disease has been identified.
BP6	Not met	ClinVar reports this variant as Uncertain Significance with review status 'criteria provided, single submitter' (1-star). The PP5/BP6 rule requires a 3-star expert panel review for supporting-level application. No expert panel has reviewed this variant, and the current classification does not support a benign assertion through BP6.	clinvar
BP7	N/A	BP7 applies to silent/intronic variants outside the splice consensus. NM_006231.4:c.3959G>A is a missense variant (p.Arg1320Gln), not a silent or intronic change.

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