POLE c.6380G>A, p.(Arg2127Gln)

Reasoning

The variant is NM_006231.4:c.6380G>A, p.Arg2127Gln (p.R2127Q). No previously established pathogenic variant producing the same Arg2127Gln amino-acid change by a different nucleotide substitution was identified in the consulted case records. The ClinVar record is uncertain significance, not an established pathogenic record, and the governing POLE files contain no entry for c.6380G>A, p.Arg2127Gln, or p.R2127Q. Therefore PS1 is not met.

Rule

Same amino acid change as a previously established pathogenic variant regardless of nucleotide change.

Evidence considered

• ClinVar variation 645558 reports NM_006231.4:c.6380G>A (p.Arg2127Gln) as Uncertain significance with criteria provided by a single submitter; this is not an established pathogenic comparator.
• PATH-250-323.pdf, PATH-250-323-s002.xlsx, and PATH-250-323-s001.tif were checked for c.6380G>A, p.Arg2127Gln, and p.R2127Q; the first two text files had no matching entry and the TIFF text conversion was unavailable.

Still missing

• No entry for c.6380G>A, p.Arg2127Gln, or p.R2127Q was found in PATH-250-323.pdf.
• No entry for c.6380G>A, p.Arg2127Gln, or p.R2127Q was found in PATH-250-323-s002.xlsx.
• PATH-250-323-s001.tif was unavailable for text search; its visual content was not used to assume variant absence.

Sources

Reasoning

The governing POLE rule requires the exact missense variant to be recurrent in both COSMIC and TCGA endometrial carcinoma cohorts, have a combined EC count >=10, and belong to the established/pathogenic set highlighted by León-Castillo et al. 2020; it specifically assigns PS4_Supporting only to p.P286R, p.V411L, p.A456P, and p.S297F. The exact variant c.6380G>A / p.Arg2127Gln / p.R2127Q was not found in PATH-250-323.pdf or Supplementary Table S1 (PATH-250-323-s002.xlsx), and the case evidence reports only COSMIC recurrence of 2 with no qualifying TCGA-plus-COSMIC table entry. Therefore the exact-variant recurrence, combined-count, and established/pathogenic-set requirements are not satisfied.

VCEP rule

Apply PS4_Supporting only when the exact POLE missense variant is recurrent in both the COSMIC and TCGA endometrial carcinoma cohorts in Supplementary Table S1, has a combined EC count >=10, and belongs to the established/pathogenic set highlighted by León-Castillo et al. 2020. Under the current package this supports p.P286R, p.V411L, p.A456P, and p.S297F. Do not upgrade above Supporting because the evidence source is somatic recurrence context rather than germline case-control evidence.

Evidence considered

• León-Castillo et al. 2020 custom PS4 rule: "Apply PS4_Supporting only when the exact POLE missense variant is recurrent in both the COSMIC and TCGA endometrial carcinoma cohorts in Supplementary Table S1, has a combined EC count >=10, and belongs to the established/pathogenic set highlighted by León-Castillo et al. 2020. Under the current package this supports p.P286R, p.V411L, p.A456P, and p.S297F. Do not upgrade above Supporting because the evidence source is somatic recurrence context rather than germline case-control evidence."
• PATH-250-323.pdf searched for c.6380G>A, p.Arg2127Gln, and p.R2127Q: no exact entry found.
• PATH-250-323-s002.xlsx, Supplementary Table S1 searched for c.6380G>A, p.Arg2127Gln, and p.R2127Q: no exact entry found; the table's qualifying established variants are different substitutions.
• Case COSMIC result: COSV109664922, somatic count n = 2; this does not establish recurrence in both COSMIC and TCGA or a combined EC count >=10.

Still missing

• No exact c.6380G>A, p.Arg2127Gln, or p.R2127Q entry was found in PATH-250-323.pdf.
• No exact c.6380G>A, p.Arg2127Gln, or p.R2127Q entry was found in PATH-250-323-s002.xlsx Supplementary Table S1.
• PATH-250-323-s001.tif has no converted searchable text and was not independently visually reviewed; this does not establish evidence for the variant.

Sources

Reasoning

The governing León-Castillo et al. 2020 POLE framework assigns PM1 only to its exact listed hotspot or recurrent exonuclease-domain substitutions: p.P286R, p.V411L, p.S297F, p.A456P, p.S459F, p.F367S, p.L424I, p.M295R, p.P436R, p.M444K, p.D368Y, p.A465V, p.L424V, p.T278M, and p.A428T. p.Arg2127Gln is not one of these substitutions. vcep_materials.json has no domain_tables entry for POLE, so there is no additional authoritative domain list to apply. PM1 is therefore not met under the local framework.

VCEP rule

Apply PM1_Strong to the five established POLE exonuclease-domain hotspot missense variants emphasized by León-Castillo et al. 2020: p.P286R, p.V411L, p.S297F, p.A456P, and p.S459F. These are the exact hotspot substitutions repeatedly treated in the paper as pathogenic for the POLE-ultramutated phenotype in endometrial carcinoma. ... Apply PM1_Moderate to the exact non-hotspot exonuclease-domain missense variants identified in the paper as recurrent and POLE-score >=4 / classified as pathogenic in the TCGA-based analysis: p.F367S, p.L424I, p.M295R, p.P436R, p.M444K, and p.D368Y. Use this only for these exact substitutions, not all substitutions at the same codon. ... Apply PM1_Supporting to exact recurrent exonuclease-domain missense variants that the paper places in the POLE-score 3 / uncertain tier rather than the pathogenic tier: p.A465V, p.L424V, p.T278M, and p.A428T. This captures hotspot/domain context without promoting them to the paper's pathogenic set.

Evidence considered

• The local POLE framework lists PM1_Strong for p.P286R, p.V411L, p.S297F, p.A456P, and p.S459F; PM1_Moderate for p.F367S, p.L424I, p.M295R, p.P436R, p.M444K, and p.D368Y; and PM1_Supporting for p.A465V, p.L424V, p.T278M, and p.A428T.
• p.Arg2127Gln does not match any exact substitution in those framework lists; vcep_materials.json domain_tables is empty for POLE.

Still missing

• No entry for c.6380G>A, p.Arg2127Gln, or p.R2127Q was found in PATH-250-323.pdf.
• No entry for c.6380G>A, p.Arg2127Gln, or p.R2127Q was found in PATH-250-323-s002.xlsx.
• PATH-250-323-s001.tif was unavailable for text search; its visual content was not used to assume variant absence.

Sources

Reasoning

PM2 is not met under the supplied generic threshold because the variant is observed in controls rather than absent. It occurs at AF 8.45816e-06 in gnomAD v2.1 non-cancer exomes, 4.33739e-06 in gnomAD v4.1 all-comers, and 2.0279e-05 in gnomAD v3.1 non-cancer genomes; the 1KG:CHB subset reaches 0.00490196, above the <=0.0001 PM2 supporting threshold. No governing VCEP or disease-specific population rule changes this generic assessment.

Rule

PM2 (supporting): <= 0.0001 — SVI recommendation to downgrade PM2 to Supporting (ClinGen SVI 2020) (PMID:25741868)

Evidence considered

• gnomAD v2.1 non-cancer exomes: 2/236458 alleles, AF 8.45816e-06, homozygotes 0.
• gnomAD v4.1 all-comers: 7/1613874 alleles, AF 4.33739e-06, homozygotes 0.
• gnomAD v3.1 non-cancer genomes: 3/147936 alleles, AF 2.0279e-05, homozygotes 0; 1KG:CHB subset AF 0.00490196 (1/204), an ancestry-specific threshold artifact that prevents treating the variant as absent or extremely rare across controls.
• Applied the published generic PM2 threshold supplied for this case: <= 0.0001, SVI recommendation to downgrade PM2 to Supporting (ClinGen SVI 2020; PMID:25741868).

Sources

Reasoning

The variant is a missense substitution, so the POLE custom PP3 rule applies only if the exact variant appears in Supplementary Table S2 or S3, has REVEL class 'likely disease causing' (including minor spelling variants), and has no more than one benign in silico result. Searches of PATH-250-323-s003.xlsx and PATH-250-323-s004.xlsx found no c.6380G>A, p.Arg2127Gln, or p.R2127Q entry. Therefore the custom rule cannot be applied and the generic missense fallback is used: REVEL only, with PP3 requiring REVEL > 0.750. The observed REVEL score is 0.313, so PP3 is not met. SpliceAI is not used because the governing generic missense path specifies REVEL only.

VCEP rule

Apply PP3_Supporting when the exact missense variant appears in Supplementary Table S2 or S3, the REVEL class is 'likely disease causing' (including minor spelling variants), and the number of benign in silico results is <=1. If the variant is absent from the supplementary tables, do not use this custom PP3 rule and fall back to the project's generic in-silico workflow.

Evidence considered

• PATH-250-323-s003.xlsx, Supplementary Table S2: no row was found for c.6380G>A, p.Arg2127Gln, or p.R2127Q.
• PATH-250-323-s004.xlsx, Supplementary Table S3: no row was found for c.6380G>A, p.Arg2127Gln, or p.R2127Q.
• Local REVEL lookup: missense REVEL score 0.313.
• Generic missense fallback: REVEL >0.750 is required for PP3 supporting; REVEL 0.250–0.750 is a gray zone yielding neither PP3 nor BP4.

Still missing

• No exact-variant entry for c.6380G>A, p.Arg2127Gln, or p.R2127Q was found in PATH-250-323-s003.xlsx (Supplementary Table S2).
• No exact-variant entry for c.6380G>A, p.Arg2127Gln, or p.R2127Q was found in PATH-250-323-s004.xlsx (Supplementary Table S3).

Sources

Reasoning

The generic PP5 rule requires a reputable source to recently report the exact variant as pathogenic when the evidence is unavailable to the laboratory for independent evaluation. The exact ClinVar record is Uncertain significance from two clinical laboratories, with zero expert-panel submissions; therefore no qualifying expert-panel pathogenic or likely pathogenic classification is present.

Rule

Reputable source recently reports variant as pathogenic, but the evidence is not available to the laboratory to perform an independent evaluation.

Evidence considered

• Exact ClinVar match NM_006231.4(POLE):c.6380G>A (p.Arg2127Gln): overall classification Uncertain significance, two clinical laboratories, criteria provided, and zero expert-panel submissions.
• The two exact matched submissions are both Uncertain significance from individual clinical laboratories; neither is a qualifying expert-panel pathogenic or likely pathogenic classification.

Sources

Reasoning

BA1 is not met. The variant is rare in the evaluated population datasets: AF 8.45816e-06 in gnomAD v2.1 non-cancer exomes, 4.33739e-06 in gnomAD v4.1 all-comers, and 2.0279e-05 in gnomAD v3.1 non-cancer genomes; the highest reported ancestry-specific value is 0.00490196 in the small 1KG:CHB subset, still below the 0.05 stand-alone threshold.

Rule

BA1 (stand-alone): >= 0.05 — ACMG/AMP 2015 stand-alone benign allele frequency (PMID:25741868)

Evidence considered

• gnomAD v2.1 non-cancer exomes: 2/236458 alleles, AF 8.45816e-06, homozygotes 0.
• gnomAD v4.1 all-comers: 7/1613874 alleles, AF 4.33739e-06, homozygotes 0; highest reported all-comers population AF 4.99800e-05 in Admixed American individuals.
• gnomAD v3.1 non-cancer genomes: 3/147936 alleles, AF 2.0279e-05, homozygotes 0; 1KG:CHB subset AF 0.00490196 (1/204), which remains below 0.05.
• Applied the published generic BA1 threshold supplied for this case: >= 0.05, ACMG/AMP 2015 stand-alone benign allele frequency (PMID:25741868).

Sources

Reasoning

BS1 is not met under the supplied generic threshold. The observed AF is 8.45816e-06 in gnomAD v2.1 non-cancer exomes, 4.33739e-06 in gnomAD v4.1 all-comers, and 2.0279e-05 in gnomAD v3.1 non-cancer genomes, all below the generic BS1 threshold of 0.01; even the small 1KG:CHB ancestry subset is 0.00490196.

Rule

BS1 (strong): >= 0.01 — Generic SVI default; per-gene derivation preferred (Whiffin et al. 2017) (PMID:28518168)

Evidence considered

• gnomAD v2.1 non-cancer exomes: AF 8.45816e-06 overall and 0.000113071 in the highest reported East Asian subgroup.
• gnomAD v4.1 all-comers: AF 4.33739e-06 overall and 4.99800e-05 in the highest reported Admixed American subgroup.
• gnomAD v3.1 non-cancer genomes: AF 2.0279e-05 overall and 0.00490196 in the 1KG:CHB subset (1/204 alleles).
• Applied the published generic BS1 threshold supplied for this case: >= 0.01; generic SVI default, with per-gene derivation preferred (Whiffin et al. 2017, PMID:28518168).

Sources

Reasoning

The variant is a missense substitution, so the POLE custom BP4 rule applies only if the exact variant appears in Supplementary Table S2 or S3, has REVEL class 'Likely benign' or 'Likely-benign', and has at least four benign in silico results. Searches of PATH-250-323-s003.xlsx and PATH-250-323-s004.xlsx found no c.6380G>A, p.Arg2127Gln, or p.R2127Q entry. Therefore the custom rule cannot be applied and the generic missense fallback is used: REVEL only, with BP4 requiring REVEL < 0.250. The observed REVEL score is 0.313, so BP4 is not met. SpliceAI is not used because the governing generic missense path specifies REVEL only.

VCEP rule

Apply BP4_Supporting when the exact missense variant appears in Supplementary Table S2 or S3, the REVEL class is 'Likely benign' or 'Likely-benign', and the number of benign in silico results is >=4. If the variant is absent from the supplementary tables, do not use this custom BP4 rule and fall back to the project's generic in-silico workflow.

Evidence considered

• PATH-250-323-s003.xlsx, Supplementary Table S2: no row was found for c.6380G>A, p.Arg2127Gln, or p.R2127Q.
• PATH-250-323-s004.xlsx, Supplementary Table S3: no row was found for c.6380G>A, p.Arg2127Gln, or p.R2127Q.
• Local REVEL lookup: missense REVEL score 0.313.
• Generic missense fallback: REVEL <0.250 is required for BP4 supporting; REVEL 0.250–0.750 is a gray zone yielding neither PP3 nor BP4.

Still missing

• No exact-variant entry for c.6380G>A, p.Arg2127Gln, or p.R2127Q was found in PATH-250-323-s003.xlsx (Supplementary Table S2).
• No exact-variant entry for c.6380G>A, p.Arg2127Gln, or p.R2127Q was found in PATH-250-323-s004.xlsx (Supplementary Table S3).

Sources

Reasoning

The generic BP6 rule requires a reputable source to recently report the exact variant as benign when the evidence is unavailable to the laboratory for independent evaluation. The exact ClinVar record is Uncertain significance from two clinical laboratories, with zero expert-panel submissions; therefore no qualifying expert-panel benign or likely benign classification is present.

Rule

Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation.

Evidence considered

• Exact ClinVar match NM_006231.4(POLE):c.6380G>A (p.Arg2127Gln): overall classification Uncertain significance, two clinical laboratories, criteria provided, and zero expert-panel submissions.
• The two exact matched submissions are both Uncertain significance from individual clinical laboratories; neither is a qualifying expert-panel benign or likely benign classification.

Sources

Reasoning

No case-level evidence establishes that NM_006231.4:c.6380G>A is de novo in an affected proband. The available materials do not document the proband's disease, family history, testing of both biological parents, or confirmed maternity and paternity.

Rule

De novo (both maternity and paternity confirmed) in a patient with the disease and no family history.

Evidence considered

• No case-level proband, parental-testing, family-history, or de novo evidence was identified in the reviewed case materials.

Still missing

• Affected proband and disease phenotype are not documented.
• Family history is not documented.
• Parental testing results are not documented.
• Maternity and paternity confirmation are not documented.

Reasoning

No validated, variant-specific in vitro or in vivo functional assay evidence was identified for NM_006231.4:c.6380G>A (NP_006222.2:p.(Arg2127Gln)). OncoKB explicitly reports no variant-specific reviewed functional evidence, and the only extracted publication is a general referral guideline that does not mention POLE or this variant. Therefore, the evidence is insufficient to assess PS3 or calibrate its strength.

Rule

PS3: Well-established in vitro or in vivo functional studies supportive of a damaging effect on the gene or gene product. Note: Functional studies that have been validated and shown to be reproducible and robust in a clinical diagnostic laboratory setting are considered the most well-established.

Evidence considered

• OncoKB reports no variant-specific reviewed functional evidence for POLE p.Arg2127Gln.
• The extracted PMID:25394175 publication is a general cancer-genetic referral guideline and does not mention POLE, c.6380G>A, or p.Arg2127Gln; it provides no functional assay evidence.

Still missing

• Variant-specific functional testing with appropriate positive and negative controls and a biologically relevant assay has not been identified.
• No reproducibility or clinical diagnostic laboratory validation data are available.

Sources

Reasoning

PM3 cannot be assessed because the available evidence does not establish that POLE-related disease in this case is recessive, does not report an affected proband carrying NM_006231.4:c.6380G>A with a pathogenic variant, and provides no parental or offspring testing to demonstrate the variants are in trans.

Rule

PM3: For recessive disorders, detected in trans with a pathogenic variant ... Note: This requires testing of parents (or offspring) to determine phase.

Evidence considered

• The reviewed case materials contain no documented affected-proband allelic observation involving NM_006231.4:c.6380G>A and a pathogenic POLE variant.
• No parental or offspring testing, phase result, or cis/trans relationship is reported for this variant.

Still missing

• Confirm the relevant POLE disease inheritance model.
• Document an affected proband carrying NM_006231.4:c.6380G>A and a pathogenic variant.
• Obtain parental or offspring testing establishing the variants are in trans.

Reasoning

PM5 requires a different missense substitution at Arg2127 that has been determined to be pathogenic. The available PM5 candidate artifact contains zero same-residue candidates and explicitly does not establish classic PM5 semantics. The available ClinVar record for p.Arg2127Gln is uncertain significance, and no governing-file entry for the queried variant was found. A defensible pathogenic Arg2127 comparator was not available, so PM5 cannot be assessed.

Rule

Novel missense change at an amino acid residue where a different missense change determined to be pathogenic has been seen before.

Evidence considered

• The available PM5 candidate record reports total_candidates_seen=0, same_residue_candidates=0, and no candidate variants.
• ClinVar variation 645558 reports the queried p.Arg2127Gln as Uncertain significance rather than providing a pathogenic alternate-allele comparator.

Still missing

• No validated pathogenic alternate missense comparator at residue Arg2127 was identified in the available case evidence.
• No entry for c.6380G>A, p.Arg2127Gln, or p.R2127Q was found in PATH-250-323.pdf.
• No entry for c.6380G>A, p.Arg2127Gln, or p.R2127Q was found in PATH-250-323-s002.xlsx.
• PATH-250-323-s001.tif was unavailable for text search; its visual content was not used to assume variant absence.

Sources

Reasoning

No case-level evidence establishes an assumed de novo occurrence of NM_006231.4:c.6380G>A in an affected proband. The available materials do not document the proband's disease, family history, or parental testing, including whether either parent was untested or whether paternity or maternity was unconfirmed.

Rule

Assumed de novo, but without confirmation of paternity and maternity.

Evidence considered

• No case-level proband, parental-testing, family-history, or assumed de novo evidence was identified in the reviewed case materials.

Still missing

• Affected proband and disease phenotype are not documented.
• Family history is not documented.
• Parental testing status and results are not documented.
• Whether maternity or paternity was unconfirmed is not documented.

Reasoning

No case-level family data document affected relatives carrying NM_006231.4:c.6380G>A, the number of informative meioses, or phenotype-consistent co-segregation. Therefore, co-segregation cannot be assessed or assigned a strength.

Rule

Co-segregation with disease in multiple affected family members in a gene definitively known to cause the disease.

Evidence considered

• No pedigree, affected-relative testing, informative-meiosis count, or phenotype-consistent segregation evidence was identified in the reviewed case materials.

Still missing

• Pedigree and affected-relative phenotypes are not documented.
• Variant testing results in relatives are not documented.
• Number of informative meioses is not documented.
• Co-segregation strength cannot be determined.

Reasoning

The generic PP2 rule requires evidence that POLE has a low rate of benign missense variation and that missense variants are a common disease mechanism. The case materials provide no validated gene-level benign-missense-rate analysis or disease-mechanism dataset suitable for this criterion. The León-Castillo materials address somatic POLE exonuclease-domain hotspots and do not establish the generic PP2 requirements for germline interpretation. PP2 is not assessed.

Rule

Missense variant in a gene that has a low rate of benign missense variation and where missense variants are a common mechanism of disease.

Evidence considered

• The León-Castillo et al. 2020 package concerns somatic POLE mutations in endometrial carcinoma and does not supply the generic PP2 gene-level thresholds or analyses.
• No case source supplied the two gene-level facts required by PP2.

Still missing

• A validated POLE-specific benign missense variation analysis is not available in the consulted case evidence.
• A validated germline disease-mechanism analysis showing missense variants are a common POLE disease mechanism is not available.

Reasoning

The generic PP4 rule requires a phenotype or family history highly specific for a disease with a single genetic etiology. The reviewed case evidence does not provide a patient phenotype or family history that can be assessed against this requirement.

Rule

Patient’s phenotype or family history is highly specific for a disease with a single genetic etiology.

Evidence considered

• No patient phenotype or family-history evidence was supplied that establishes a highly specific phenotype for a disease with a single genetic etiology.

Still missing

• Patient phenotype and family-history information sufficient for PP4 assessment is not available in the reviewed case evidence.

Sources

Reasoning

BS2 cannot be assessed from the available population data. The variant has zero observed homozygotes in gnomAD v2.1 non-cancer exomes, gnomAD v3.1 non-cancer genomes, and gnomAD v4.1 all-comers, but these aggregate databases do not document that a specific healthy adult carried the variant or establish the relevant disease inheritance, expected age of onset, penetrance, or phenotype.

Rule

Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age.

Evidence considered

• gnomAD v2.1 non-cancer exomes: homozygotes 0.
• gnomAD v3.1 non-cancer genomes: homozygotes 0.
• gnomAD v4.1 all-comers: homozygotes 0.
• Absence of homozygotes in an aggregate population database is not, by itself, documented observation of this variant in a healthy adult individual.

Still missing

• Documented healthy-adult carrier status for this exact variant is unavailable.
• The disease inheritance model, expected age of onset, and full-penetrance assumption needed for BS2 are not established in the available case evidence.

Sources

Reasoning

No validated, variant-specific in vitro or in vivo functional assay evidence demonstrating a lack of damaging effect was identified for NM_006231.4:c.6380G>A (NP_006222.2:p.(Arg2127Gln)). The absence of variant-specific reviewed functional evidence in OncoKB and the absence of relevant functional data in the extracted publication do not establish a benign functional effect. Therefore, BS3 cannot be assessed or strength-calibrated.

Rule

BS3: Well-established in vitro or in vivo functional studies show no damaging effect on protein function or splicing.

Evidence considered

• OncoKB reports no variant-specific reviewed functional evidence for POLE p.Arg2127Gln; this is an evidence gap and does not demonstrate preserved function.
• The extracted PMID:25394175 publication is a general cancer-genetic referral guideline and does not mention POLE, c.6380G>A, or p.Arg2127Gln; it provides no functional assay evidence.

Still missing

• Variant-specific functional testing showing no damaging effect, with appropriate controls and a biologically relevant assay, has not been identified.
• No reproducibility or clinical diagnostic laboratory validation data are available.

Sources

Reasoning

No case-level family data identify affected relatives who lack NM_006231.4:c.6380G>A. Consequently, lack of segregation cannot be distinguished from an uninformative or undocumented pedigree, and BS4 cannot be applied.

Rule

Lack of segregation in affected members of a family.

Evidence considered

• No affected-relative testing, pedigree, phenotype, or non-segregation evidence was identified in the reviewed case materials.

Still missing

• Affected relatives and their phenotypes are not documented.
• Variant testing results for affected relatives are not documented.
• Pedigree information is not documented.
• Potential phenocopies or multiple pathogenic variants cannot be evaluated.

Reasoning

The generic BP1 rule requires evidence that POLE disease is caused primarily by truncating variants. The case materials do not provide a validated gene-level assessment demonstrating that truncating variants are the predominant known disease mechanism, and the León-Castillo package focuses on somatic missense hotspot biology rather than establishing this germline rule. BP1 is not assessed.

Rule

Missense variant in a gene for which primarily truncating variants are known to cause disease.

Evidence considered

• The León-Castillo et al. 2020 package addresses somatic POLE exonuclease-domain missense mutations and is not a gene-level germline truncating-variant mechanism analysis.
• No case source established that truncating variants are the primary known cause of POLE-related disease.

Still missing

• A validated POLE-specific assessment of the predominant disease-causing variant mechanism is not available in the consulted case evidence.
• The available León-Castillo materials do not establish the generic BP1 germline requirement.

Reasoning

BP2 cannot be assessed because the available evidence does not establish a fully penetrant dominant POLE disorder, does not document this variant in trans with a pathogenic variant, and does not document this variant in cis with a pathogenic variant.

Rule

BP2: Observed in trans with a pathogenic variant for a fully penetrant dominant gene/disorder or observed in cis with a pathogenic variant in any inheritance pattern.

Evidence considered

• The reviewed case materials contain no documented cis or trans phase result between NM_006231.4:c.6380G>A and a pathogenic variant.
• No qualifying fully penetrant dominant inheritance context is established for this interpretation.

Still missing

• Confirm whether the relevant POLE disorder is fully penetrant and dominant.
• Document a pathogenic variant and phase it relative to NM_006231.4:c.6380G>A.

Reasoning

The generic BP5 rule requires the variant to be found in a case with an alternate molecular basis for disease. No alternate molecular diagnosis or molecular basis for the relevant disease is documented in the reviewed case evidence.

Rule

Variant found in a case with an alternate molecular basis for disease.

Evidence considered

• No alternate molecular basis for disease was documented in the reviewed case evidence.

Still missing

• An alternate molecular diagnosis or molecular basis for the patient's disease is not documented.

Sources