POLE c.122C>T, p.(Thr41Met)

Reasoning

PM2 is met at Moderate strength under the generic non-VCEP population rule. The variant is rare in gnomAD v4.1 (overall AF 1.9825e-05; 32/1,614,120 alleles) and remains below 0.1% in the highest-frequency ancestry group (East Asian AF 0.000512409; grpmax FAF 0.0003497); no homozygotes are observed. gnomAD v2.1 provides concordant rare-frequency data (overall AF 3.53527e-05; grpmax FAF 0.00022756; no homozygotes).

Rule

Generic non-VCEP PM2: apply at Moderate strength when the variant is absent or rare below 0.1% in appropriate population databases, with no homozygote observation that conflicts with the disease model. No POLE-specific PM2 rule was retrieved.

Evidence considered

• gnomAD v4.1 reports 32/1,614,120 alleles, overall AF 1.9825e-05, maximum subgroup AF 0.000512409 in East Asian individuals, grpmax FAF 0.0003497, and zero homozygotes.
• gnomAD v2.1 reports 10/282,864 alleles, overall AF 3.53527e-05, maximum subgroup AF 0.000350842 in East Asian individuals, grpmax FAF 0.00022756, and zero homozygotes.
• gnomAD-Canada v1.0 reports the variant as absent, providing an additional ancestry/population dataset consistent with rarity.
• The case uses the generic non-VCEP PM2 threshold of AF <0.1% in population databases; the highest observed subgroup frequency in either gnomAD release is below this threshold.

Sources

Reasoning

BP4_Supporting is met by the generic missense workflow: REVEL is 0.177, below the calibrated benign supporting threshold (<0.250). The local POLE table-specific BP4 rule does not apply because p.(Thr41Met) is absent from Supplementary Tables S2 and S3.

Rule

Local POLE BP4 rule: exact Table S2/S3 presence plus likely-benign REVEL class and >=4 benign in-silico results; otherwise generic missense fallback: REVEL <0.250 for BP4 supporting.

Evidence considered

• The governing local POLE framework directs a generic in-silico fallback for exact missense variants absent from Supplementary Table S2 or S3. Direct inspection found no T41M, Thr41Met, c.122C>T, or T41 entry in either table.
• REVEL is 0.177, below the generic BP4 supporting threshold of <0.250. These REVEL calibration cutoffs are from ClinGen SVI Bayesian calibration work (PMID:36413997).
• SpliceAI maximum delta is 0.014 and predicts no significant splice impact, but it is not used to adjudicate this missense variant under the generic missense workflow. BayesDel is not used because no verified published threshold is available in this pipeline.

Sources

Reasoning

The applicable local POLE PS4 specification permits only PS4_Supporting for exact variants recurrent in both COSMIC and TCGA endometrial-carcinoma cohorts, with combined count at least 10 and membership in the established/pathogenic set. p.(Thr41Met) is not among the four variants specified as qualifying.

Rule

Local POLE PS4_Supporting: exact missense variant recurrent in both COSMIC and TCGA endometrial-carcinoma cohorts, combined count >=10, and in the established/pathogenic set; no greater strength is permitted.

Evidence considered

• The applicable local POLE framework caps PS4 at Supporting and identifies p.P286R, p.V411L, p.A456P, and p.S297F as the currently qualifying exact variants; p.(Thr41Met) is not included.
• The case evidence search reported no COSMIC result for POLE c.122C>T, so there is no somatic-recurrence basis for the framework's required COSMIC-and-TCGA condition.

Sources

Reasoning

The applicable local POLE framework specifies PM1 only for exact POLE exonuclease-domain recurrent/hotspot substitutions: Strong for p.P286R, p.V411L, p.S297F, p.A456P, and p.S459F; Moderate for p.F367S, p.L424I, p.M295R, p.P436R, p.M444K, and p.D368Y; and Supporting for p.A465V, p.L424V, p.T278M, and p.A428T. p.Thr41Met is not one of these exact substitutions, and the case hotspot search was negative. Therefore the custom PM1 rule is not met.

Rule

Local POLE PM1 rule: apply only to the exact listed exonuclease-domain hotspot/recurrent substitutions and at the specified strength; do not generalize the rule to all substitutions at a codon or to all POLE missense variants.

Evidence considered

• The local POLE framework is explicitly literature-derived and not an official ClinGen CSPEC/VCEP specification; its exact-variant PM1 rules do not include p.Thr41Met.
• The Cancer Hotspots result for POLE T41 was no result, with the case bundle stating that the variant does not lie in a statistically significant hotspot.

Sources

Reasoning

PP3 is not met. POLE p.(Thr41Met) is absent from the local León-Castillo Supplementary Tables S2 and S3, so the custom PP3 rule does not apply. Under the generic missense fallback, REVEL is 0.177, below the pathogenic supporting threshold (>0.750).

Rule

Local POLE PP3 rule: exact Table S2/S3 presence plus likely disease-causing REVEL class and <=1 benign in-silico result; otherwise generic missense fallback: REVEL >0.750 for PP3 supporting.

Evidence considered

• The governing local POLE framework has no official ClinGen CSPEC and directs a generic in-silico fallback when an exact missense variant is absent from Supplementary Table S2 or S3. Direct inspection found no T41M, Thr41Met, c.122C>T, or T41 entry in either table.
• REVEL is 0.177. The generic missense workflow uses REVEL only; its PP3 supporting threshold is >0.750 and its BP4 supporting threshold is <0.250. These REVEL calibration cutoffs are from ClinGen SVI Bayesian calibration work (PMID:36413997).
• SpliceAI maximum delta is 0.014 and predicts no significant splice impact, but it is not used to adjudicate this missense variant under the generic missense workflow. BayesDel is not used because no verified published threshold is available in this pipeline.

Sources

Reasoning

No exact-variant ClinVar expert-panel Pathogenic or Likely pathogenic assertion is present. Therefore PP5 is not triggered.

Rule

Apply PP5 only for an exact-variant ClinVar expert-panel Pathogenic or Likely pathogenic classification.

Evidence considered

• ClinVar Variation ID 405900 is uncertain significance with six submissions and no expert-panel submissions; all listed submissions are non-expert laboratory submissions.

Sources

Reasoning

BA1 is not met. The highest observed population frequency is 0.000512409 in the East Asian subgroup in gnomAD v4.1, with a maximum group frequency of 0.0003497; the overall frequency is 0.000019825. These values are far below the generic non-VCEP BA1 threshold of 1% used for this case.

Rule

Generic non-VCEP BA1: apply only when the allele frequency is greater than 1% in a suitable population database. No POLE-specific BA1 rule was retrieved.

Evidence considered

• gnomAD v4.1 reports 32/1,614,120 alleles, overall AF 1.9825e-05, no homozygotes, and maximum observed subgroup AF 0.000512409 in East Asian individuals; grpmax FAF is 0.0003497.
• gnomAD v2.1 independently reports 10/282,864 alleles, overall AF 3.53527e-05, no homozygotes, and grpmax FAF 0.00022756.
• The case uses the generic non-VCEP population thresholds BA1 >1% and BS1 >0.3% when no applicable POLE specification exists; neither threshold is approached here.

Sources

Reasoning

BS1 is not met. The maximum observed subgroup frequency is 0.000512409 in gnomAD v4.1, and the maximum group frequency is 0.0003497 (0.03497%), both below the generic non-VCEP BS1 threshold of 0.3% used for this case. The overall allele frequency is substantially lower at 0.0019825%.

Rule

Generic non-VCEP BS1: apply when the allele frequency is greater than 0.3% and exceeds the maximum credible frequency for the relevant disease context. No POLE-specific BS1 rule was retrieved.

Evidence considered

• gnomAD v4.1 reports the highest subgroup AF as 0.000512409 in East Asian individuals and grpmax FAF as 0.0003497; no homozygotes were observed.
• gnomAD v2.1 reports grpmax FAF 0.00022756 and no homozygotes.
• The case uses the generic non-VCEP BS1 threshold of greater than 0.3%; the observed frequencies remain below that threshold even in the highest-frequency ancestry group.

Sources

Reasoning

No exact-variant ClinVar expert-panel Benign or Likely benign assertion is present. Therefore BP6 is not triggered.

Rule

Apply BP6 only for an exact-variant ClinVar expert-panel Benign or Likely benign classification.

Evidence considered

• ClinVar Variation ID 405900 is uncertain significance with six submissions and no expert-panel submissions; ordinary laboratory submissions and the aggregate label were not used for BP6.

Sources

Reasoning

The variant is POLE NP_006222.2:p.(Thr41Met) (T41M). The reviewed case evidence does not document a pathogenic or likely pathogenic POLE variant producing the same amino-acid change through a different nucleotide change. ClinVar classifies the queried variant as uncertain significance, which cannot be used to establish PS1.

Rule

Generic PS1: same amino-acid change as a previously established pathogenic variant, with a different nucleotide change; the comparator must itself be established pathogenic and must not be inferred from a final classification alone.

Evidence considered

• The case normalization identifies NM_006231.4:c.122C>T as NP_006222.2:p.(Thr41Met), and the ClinVar record reports Uncertain significance.
• No same-amino-acid-change pathogenic comparator was identified in the consolidated bundle or reviewed paper extraction.

Still missing

• A validated pathogenic or likely pathogenic comparator with the same p.Thr41Met amino-acid change is not available in the reviewed evidence.

Sources

Reasoning

No proband-level de novo observation is documented in the case-evidence bundle. There is no documented parental testing, maternity/paternity confirmation, trio result, or phenotype information establishing that NM_006231.4:c.122C>T (NP_006222.2:p.(Thr41Met)) arose de novo in an affected proband.

Rule

Generic ACMG/AMP PS2: confirmed de novo occurrence in an affected proband with confirmed maternity and paternity; strength depends on the quality and completeness of de novo and phenotype evidence.

Evidence considered

• The consolidated case-evidence bundle contains no family-level de novo observation, parental genotype result, trio analysis, or proband phenotype suitable for PS2 assessment.

Still missing

• Affected proband phenotype and diagnostic fit
• Variant presence in the proband
• Maternal and paternal genotypes with confirmed maternity/paternity
• Trio-based or equivalent de novo testing result

Reasoning

No validated variant-specific functional assay demonstrating a damaging effect was identified for POLE NM_006231.4:c.122C>T (NP_006222.2:p.(Thr41Met)). OncoKB reports no variant-specific reviewed functional evidence, and the available literature does not describe an assay for this variant. PS3 is therefore not assessed.

Rule

Generic ACMG/AMP PS3: functional studies must be well established, appropriately controlled, and demonstrate a damaging effect relevant to the gene/disease mechanism. No such variant-specific evidence is available.

Evidence considered

• OncoKB states that it did not identify variant-specific reviewed functional evidence for this variant and labels the oncogenic effect unknown.
• The ACMG/AMP standards paper provides general interpretation guidance but does not mention POLE or this variant and contains no functional assay result; therefore it cannot establish PS3.
• The POLE custom framework is not an official CSPEC/VCEP specification and does not define a PS3 rule; generic ACMG/AMP functional-evidence requirements were used.

Still missing

• A validated functional assay for p.(Thr41Met) with appropriate positive, negative, and wild-type controls is not available in the case evidence.
• No assay result establishing a biologically relevant loss of POLE function or other disease-relevant damaging effect was identified.

Sources

Reasoning

No applicable POLE-specific PM3 rule was identified. The case bundle contains no affected-proband observations, second pathogenic or likely pathogenic allele, phase information, parental testing, compound-heterozygous genotype, or inheritance assignment establishing a recessive context for this variant. PM3 therefore cannot be applied.

Rule

Generic ACMG/AMP PM3: apply only when the variant is observed in trans with a pathogenic or likely pathogenic variant in an affected individual with a recessive condition, with phase and disease context adequately established. No POLE-specific PM3 rule was available.

Evidence considered

• The consolidated case-evidence bundle identifies the variant as NM_006231.4:c.122C>T (NP_006222.2:p.(Thr41Met)) in POLE but provides no family, proband, second-allele, phase, or segregation observations.
• The available local POLE framework customizes PM1, PS4, PP3, and BP4 only; it provides no PM3 specification. Generic ACMG/AMP PM3 requires evidence that the variant is observed in trans with a pathogenic variant in an affected individual in a recessive disorder context, which is not documented here.

Still missing

• Affected-proband genotype and phenotype details are unavailable.
• No pathogenic or likely pathogenic second allele is documented.
• No cis/trans phase or parental-origin testing is documented.
• The relevant POLE disease inheritance mode for this case is not established.

Reasoning

No same-residue POLE comparator variants were collected or documented in the case evidence. The PM5 candidate artifact reports zero total candidates and zero same-residue candidates and states that classic PM5 semantics could not be confirmed safely. PM5 therefore cannot be applied from the available evidence.

Rule

Generic PM5: a different missense change at the same amino-acid residue has been established as pathogenic; the comparator must be independently established and the same-residue relationship must be verified.

Evidence considered

• The PM5 candidate artifact reports pm5_mode as unknown, zero total candidates, and zero same-residue candidates.
• The artifact specifically instructs that PM5 should not be applied from that artifact alone.

Still missing

• A same-residue variant at POLE codon 41 with an independently established pathogenic or likely pathogenic classification is not available.

Sources

Reasoning

No unconfirmed de novo observation is documented for this variant. The case-evidence bundle does not report a proband, parental genotypes, assumed de novo status, or evidence addressing maternity/paternity confirmation.

Rule

Generic ACMG/AMP PM6: assumed de novo occurrence in an affected proband when maternity and/or paternity is not confirmed; it requires documented de novo-related case evidence and appropriate phenotype assessment.

Evidence considered

• The consolidated case-evidence bundle contains no assumed-de-novo clinical observation or parental testing information for NM_006231.4:c.122C>T.

Still missing

• A documented affected proband carrying the variant
• Parental testing or an explicit statement that the variant was assumed de novo
• Confirmation status for maternity and paternity
• Phenotype consistency with a POLE-related disorder

Reasoning

No segregation data are provided. The case-evidence bundle contains no affected relatives, unaffected relatives, variant-positive relatives, variant-negative relatives, pedigree, phase information, or informative meioses from which co-segregation can be evaluated.

Rule

Generic ACMG/AMP PP1: co-segregation with disease in multiple affected family members, with strength determined by the number and informativeness of meioses and the specificity of the phenotype.

Evidence considered

• The consolidated case-evidence bundle contains no family segregation observations or meiosis-count data for this variant.

Still missing

• Pedigree and family structure
• Phenotype status of relatives
• Genotypes of informative affected and unaffected relatives
• Number of informative meioses and segregation pattern
• Assessment of phenotype specificity and possible phenocopies

Reasoning

The reviewed evidence does not establish that POLE has a high proportion of pathogenic missense variants together with a low rate of benign missense variation under a validated gene-specific PP2 rule. The local POLE framework does not specify PP2, and gene-level enzyme function or the presence of selected POLE hotspot mutations is insufficient to apply PP2.

Rule

Generic PP2: a missense mechanism is established for the gene, with a high proportion of pathogenic missense variants and low benign missense variation; this requires gene-level validation and is not inferred from a single variant or gene-function description.

Evidence considered

• The local POLE framework customizes PM1, PS4, PP3, and BP4, but provides no PP2 specification.
• The available OncoKB entry supplies only gene-level biological context and is not variant-specific or a validated PP2 calibration.

Still missing

• A validated POLE-specific missense-mechanism rule or suitable gene-wide pathogenic-versus-benign missense distribution analysis is not available.

Reasoning

No phenotype, clinical diagnosis, or phenotype-to-disease specificity evidence for the individual is present in the consolidated bundle. PP4 cannot be assessed from a ClinVar condition list or from gene-level disease associations.

Rule

Generic ACMG/AMP PP4: apply only when the individual's phenotype or family history is highly specific for a disease with a single genetic etiology.

Evidence considered

• No POLE-specific PP4 specification was retrieved; the generic ACMG/AMP phenotype-specificity criterion is the applicable fallback.
• ClinVar lists several condition labels for this exact variant, but the record is classified as uncertain significance and supplies no individual phenotype evidence establishing specificity.

Still missing

• Structured proband phenotype and diagnosis information, including age of onset and relevant negative findings.
• Evidence that the observed phenotype is highly specific for a POLE-related disorder and lacks a more likely alternative molecular explanation.

Reasoning

BS2 cannot be established from the available evidence. gnomAD v2.1 and v4.1 each report zero homozygotes, so there is no observation of this variant in healthy homozygous individuals. The available population records also do not provide phenotype ascertainment, age-related penetrance, or disease-status confirmation sufficient to evaluate the BS2 healthy-adult criterion.

Rule

Generic BS2: requires observation of the variant in healthy adults, typically in the homozygous state for a recessive condition or in multiple healthy adults for a dominant condition with high penetrance. No POLE-specific BS2 rule was retrieved.

Evidence considered

• gnomAD v4.1 reports homozygotes = 0 overall and in the listed ancestry groups.
• gnomAD v2.1 reports homozygotes = 0 overall and in the listed ancestry groups.
• Zero observed homozygotes is absence of positive BS2 evidence, not evidence that the variant occurs in healthy homozygous adults; the datasets do not establish clinical health or penetrance for carriers.

Still missing

• No confirmed healthy homozygous individuals are reported.
• No phenotype, age, penetrance, or disease-status information is available for carriers in the population datasets.

Sources

Reasoning

No validated variant-specific functional assay demonstrating a normal or benign effect was identified for POLE NM_006231.4:c.122C>T (NP_006222.2:p.(Thr41Met)). OncoKB reports no variant-specific reviewed functional evidence, and the available literature does not describe an assay for this variant. BS3 is therefore not assessed.

Rule

Generic ACMG/AMP BS3: a well-established, appropriately controlled functional study showing a normal or benign effect relevant to the gene/disease mechanism is required. No such variant-specific evidence is available.

Evidence considered

• OncoKB states that it did not identify variant-specific reviewed functional evidence for this variant and labels the oncogenic effect unknown.
• The ACMG/AMP standards paper provides general interpretation guidance but does not mention POLE or this variant and contains no functional assay result; therefore it cannot establish BS3.
• The POLE custom framework is not an official CSPEC/VCEP specification and does not define a BS3 rule; generic ACMG/AMP functional-evidence requirements were used.

Still missing

• A validated functional assay for p.(Thr41Met) with appropriate controls demonstrating preserved POLE function is not available in the case evidence.
• No biologically relevant assay result supports a benign functional effect for this variant.

Sources

Reasoning

No non-segregation observation is documented. The case-evidence bundle does not identify affected relatives who lack the variant, nor does it provide a pedigree, relatives tested, phenotype definitions, penetrance considerations, or informative meioses needed to evaluate BS4.

Rule

Generic ACMG/AMP BS4: lack of segregation in affected members of a family; it requires reliable genotype and phenotype data in informative affected relatives and consideration of reduced penetrance and phenocopies.

Evidence considered

• The consolidated case-evidence bundle contains no affected relative with a documented negative result for NM_006231.4:c.122C>T and no non-segregation analysis.

Still missing

• Affected relatives tested for the variant
• Reliable negative genotype results in affected relatives
• Pedigree and number of informative meioses
• Phenotype verification and consideration of reduced penetrance or phenocopy

Reasoning

The reviewed evidence does not establish that POLE-related disease is primarily caused by truncating or other non-missense variants such that a missense variant would qualify for BP1. The local POLE framework does not specify BP1, and the available gene-level context does not provide a validated benign-missense rule.

Rule

Generic BP1: a missense variant occurs in a gene for which primarily truncating or other non-missense variants are known to cause disease; this requires an established gene-level mechanism and is not inferred from the variant's uncertain classification.

Evidence considered

• The local POLE framework does not specify BP1.
• The available evidence does not provide a validated POLE-specific assessment of the relative pathogenicity of missense versus truncating variants.

Still missing

• A validated POLE disease-mechanism analysis showing that pathogenic variation is predominantly non-missense and that missense variants are generally benign is not available.

Reasoning

No applicable POLE-specific BP2 rule was identified. The case bundle contains no observation of this variant in cis with a pathogenic variant or in trans with a benign variant, and no phase-resolved family or proband genotype data. BP2 therefore cannot be applied.

Rule

Generic ACMG/AMP BP2: apply only when the variant is observed in cis with a pathogenic variant or in trans with a benign variant, with the phase and classifications adequately established. No POLE-specific BP2 rule was available.

Evidence considered

• The consolidated case-evidence bundle contains no phase-resolved allelic observations involving NM_006231.4:c.122C>T and another pathogenic or benign variant.
• The available local POLE framework customizes PM1, PS4, PP3, and BP4 only; it provides no BP2 specification. Generic ACMG/AMP BP2 requires a documented cis or trans relationship with another variant of appropriate classification, which is absent here.

Still missing

• No additional pathogenic or benign variant is documented in the same individual.
• No cis/trans phase information is documented.
• No parental or family testing is documented.

Reasoning

The consolidated bundle contains no individual-level phenotype or second molecular diagnosis that could be assessed as a fully explanatory alternative cause.

Rule

Generic ACMG/AMP BP5: apply only when a variant is found in an individual with an alternate molecular cause that fully explains the phenotype.

Evidence considered

• No POLE-specific BP5 specification was retrieved; the generic ACMG/AMP alternate-molecular-cause criterion is the applicable fallback.

Still missing

• Individual-level phenotype and diagnostic information.
• Comprehensive molecular results establishing whether an alternative diagnosis fully explains the phenotype.