POLE c.2810A>G, p.Tyr937Cys

Reasoning

PM2 is met at Supporting strength. The exact variant is absent from gnomAD v2.1, gnomAD v4.1, gnomAD v2.1 non-cancer, and gnomAD v3.1 non-cancer. With no VCEP-specific population-source requirement, the default all-comers datasets apply; absence is below the generic PM2 Supporting threshold of <=0.0001.

Rule

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

Evidence considered

• gnomAD v2.1: exact variant absent; observed allele frequency is 0, below the <=0.0001 PM2 Supporting threshold.
• gnomAD v4.1: exact variant absent; observed allele frequency is 0, below the <=0.0001 PM2 Supporting threshold.
• gnomAD v2.1 non-cancer: exact variant absent; the source is concordant but no VCEP-specific non-cancer or exome-only requirement governs this case.
• gnomAD v3.1 non-cancer: exact variant absent; the source is concordant but no VCEP-specific non-cancer requirement governs this case.

Sources

Reasoning

The governing León-Castillo custom POLE framework specifies PM1 only for exact substitutions in three lists: strong p.P286R, p.V411L, p.S297F, p.A456P, and p.S459F; moderate p.F367S, p.L424I, p.M295R, p.P436R, p.M444K, and p.D368Y; and supporting p.A465V, p.L424V, p.T278M, and p.A428T. p.Tyr937Cys/p.Y937C is not in any list. vcep_materials.json has no domain_tables entry for POLE, so there is no additional authoritative domain list to apply. The VCEP PDF and Supplementary Table S1 also contain no c.2810A>G, p.Tyr937Cys, or p.Y937C entry; the supplementary figure text is unavailable.

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 governing PM1_Strong list contains only p.P286R, p.V411L, p.S297F, p.A456P, and p.S459F.
• The governing PM1_Moderate list contains only p.F367S, p.L424I, p.M295R, p.P436R, p.M444K, and p.D368Y.
• The governing PM1_Supporting list contains only p.A465V, p.L424V, p.T278M, and p.A428T.
• vcep_materials.json domain_tables is {} for POLE; no authoritative complete domain table was supplied.
• PATH-250-323.pdf and PATH-250-323-s002.xlsx were searched under all three requested variant notations with no matching entry.

Still missing

• No c.2810A>G entry found in PATH-250-323.pdf after searching that file.
• No p.Tyr937Cys entry found in PATH-250-323.pdf after searching that file.
• No p.Y937C entry found in PATH-250-323.pdf after searching that file.
• No c.2810A>G entry found in PATH-250-323-s002.xlsx after searching that file.
• No p.Tyr937Cys entry found in PATH-250-323-s002.xlsx after searching that file.
• No p.Y937C entry found in PATH-250-323-s002.xlsx after searching that file.
• PATH-250-323-s001.tif was unavailable as searchable text, so its contents could not be checked for the variant.

Sources

Reasoning

BA1 is not met. The variant is absent from gnomAD v2.1 and gnomAD v4.1, with no observed population allele frequency approaching the generic stand-alone benign threshold of >=0.05.

Rule

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

Evidence considered

• gnomAD v2.1: exact variant absent; no allele frequency reported.
• gnomAD v4.1: exact variant absent; no allele frequency reported.
• gnomAD v2.1 non-cancer: exact variant absent.
• gnomAD v3.1 non-cancer: exact variant absent; no VCEP-specific source requirement applies here, so the default all-comers datasets govern.

Sources

Reasoning

BS1 is not met. The variant is absent from gnomAD v2.1 and gnomAD v4.1, so no population frequency greater than expected for the disorder is observed; the supplied generic BS1 threshold is >=0.01.

Rule

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

Evidence considered

• gnomAD v2.1: exact variant absent; no allele frequency reported.
• gnomAD v4.1: exact variant absent; no allele frequency reported.
• gnomAD v2.1 non-cancer: exact variant absent.
• gnomAD v3.1 non-cancer: exact variant absent; no VCEP-specific source requirement applies here, so the default all-comers datasets govern.

Sources

Reasoning

The queried variant is POLE NM_006231.4:c.2810A>G, p.Tyr937Cys (p.Y937C). The governing POLE paper and Supplementary Table S1 were searched for c.2810A>G, p.Tyr937Cys, and p.Y937C; none contains this variant. Those files document established pathogenic hotspot substitutions at other residues, not a previously established pathogenic Tyr937 substitution. The available case PM5 artifact also contains no same-residue comparator, but it explicitly says classic PM5 candidate harvesting was not safely confirmed. Therefore, the available evidence does not establish or exclude a pathogenic variant with the same amino-acid change, and PS1 cannot be assessed conclusively.

Rule

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

Evidence considered

• PATH-250-323.pdf was searched for c.2810A>G, p.Tyr937Cys, and p.Y937C; no matching entry was found. The paper instead names P286R, V411L, S297F, A456P, and S459F as the five common pathogenic POLE mutations.
• PATH-250-323-s002.xlsx was searched for c.2810A>G, p.Tyr937Cys, and p.Y937C; no matching row was found.
• The case PM5 candidate artifact reports zero same-residue candidates and states that classic PM5 semantics could not be safely confirmed; it was not used as proof of absence.

Still missing

• No c.2810A>G entry found in PATH-250-323.pdf after searching that file.
• No p.Tyr937Cys entry found in PATH-250-323.pdf after searching that file.
• No p.Y937C entry found in PATH-250-323.pdf after searching that file.
• No c.2810A>G entry found in PATH-250-323-s002.xlsx after searching that file.
• No p.Tyr937Cys entry found in PATH-250-323-s002.xlsx after searching that file.
• No p.Y937C entry found in PATH-250-323-s002.xlsx after searching that file.
• PATH-250-323-s001.tif was unavailable as searchable text, so its contents could not be checked for the variant.
• A comprehensive same-amino-acid pathogenic comparator review outside the listed VCEP files is not available in the case evidence.

Sources

Reasoning

The available case evidence does not document that the proband has the relevant disease, does not provide parental testing establishing both maternity and paternity, and does not state that there is no family history. Therefore, the requirements for PS2 cannot be assessed.

Rule

PS2: De novo (both maternity and paternity confirmed) in a patient with the disease and no family history.

Evidence considered

• No proband phenotype, parental segregation results, maternity/paternity confirmation, or family-history assessment was found in the reviewed case evidence.

Still missing

• Documented disease phenotype in the proband
• Parental genotypes showing the variant is absent in both biological parents
• Confirmation of both maternity and paternity
• Documented absence of family history

Reasoning

No variant-specific, validated in vitro or in vivo functional assay for POLE NM_006231.4:c.2810A>G (p.Tyr937Cys) was identified in the supplied evidence. OncoKB explicitly reports no variant-specific reviewed functional evidence, and the available computational predictions and gene-level context do not establish functional assay evidence. Therefore PS3 cannot be assessed.

Rule

Well-established in vitro or in vivo functional studies supportive of a damaging effect on the gene or gene product.

Evidence considered

• OncoKB reports: "OncoKB did not identify variant-specific reviewed functional evidence for this variant"; the available record is gene-level context rather than a functional assay.
• No functional, biochemical, cellular, splicing, or in vivo assay result for POLE p.Tyr937Cys is present in the supplied case evidence.

Still missing

• A variant-specific in vitro or in vivo assay demonstrating a damaging effect, with appropriate controls, reproducibility, and biologic relevance, is needed.

Sources

Still missing

• attempt 1: evidence_refs must contain only source_registry keys
• attempt 2: evidence_refs must contain only source_registry keys
• attempt 3: evidence_refs must contain only source_registry keys

Reasoning

Not assessed: the available evidence does not document a recessive disease context, an affected proband, a pathogenic variant in trans, or parental/offspring testing establishing phase for NM_006231.4:c.2810A>G (p.Tyr937Cys).

Rule

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

Evidence considered

• The case evidence documents NM_006231.4:c.2810A>G (p.Tyr937Cys) and ClinVar uncertainty, but provides no affected-proband observation, pathogenic allele in trans, parental or offspring testing, or phase result.
• No source in the reviewed case materials supplies the inheritance mode needed to determine whether the recessive PM3 pathway applies.

Still missing

• Confirm the relevant disease and inheritance mode.
• Document an affected proband carrying the variant.
• Identify a pathogenic or likely pathogenic allele in trans.
• Obtain parental or offspring testing establishing phase.

Reasoning

The queried change is p.Tyr937Cys/p.Y937C. The governing VCEP files contain no p.Tyr937Cys, p.Y937C, or c.2810A>G entry and therefore provide no different pathogenic missense change at Tyr937. The case PM5 candidate artifact reports no same-residue candidates but warns that classic PM5 semantics were not safely confirmed. Without a validated comprehensive same-residue pathogenic comparator review, PM5 is not assessable.

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 VCEP PDF and Supplementary Table S1 were searched for all requested representations; neither contains the queried variant or a Tyr937 comparator row.
• The case PM5 candidate artifact lists zero same-residue candidates and explicitly instructs that PM5 must not be applied from that artifact alone.

Still missing

• No c.2810A>G entry found in PATH-250-323.pdf after searching that file.
• No p.Tyr937Cys entry found in PATH-250-323.pdf after searching that file.
• No p.Y937C entry found in PATH-250-323.pdf after searching that file.
• No c.2810A>G entry found in PATH-250-323-s002.xlsx after searching that file.
• No p.Tyr937Cys entry found in PATH-250-323-s002.xlsx after searching that file.
• No p.Y937C entry found in PATH-250-323-s002.xlsx after searching that file.
• PATH-250-323-s001.tif was unavailable as searchable text, so its contents could not be checked for the variant.
• A validated comprehensive pathogenic alternate-missense search at Tyr937 is not available in the case evidence.

Sources

Reasoning

The available case evidence does not document a de novo variant in a patient with the disease. It also provides no parental testing or information establishing whether maternity or paternity was confirmed, so assumed de novo status cannot be evaluated.

Rule

PM6: Assumed de novo, but without confirmation of paternity and maternity.

Evidence considered

• No proband phenotype, parental test results, or de novo/assumed-de-novo observation was found in the reviewed case evidence.

Still missing

• Documented disease phenotype in the proband
• Evidence that the variant is absent from tested parent(s)
• Parental testing and confirmation status for maternity and paternity

Reasoning

The available case evidence identifies no affected family members with genotype-phenotype co-segregation and provides no meiosis or segregation data. Consequently, PP1 cannot be assessed.

Rule

PP1: Co-segregation with disease in multiple affected family members in a gene definitively known to cause the disease.

Evidence considered

• No family pedigree, affected-relative genotypes, phenotype concordance, or informative segregation observations was found in the reviewed case evidence.

Still missing

• Affected relatives with a phenotype relevant to the disease
• Variant testing results for affected relatives
• Phenotype concordance and clinical ascertainment details
• Number of informative meioses or segregation observations

Reasoning

The available evidence identifies POLE as an enzyme and describes somatic exonuclease-domain hotspot biology, but it does not establish the two required generic PP2 components for germline interpretation: a low rate of benign missense variation and missense as a common disease mechanism. The available gnomAD absence and predictor values do not answer those gene-level requirements. PP2 therefore remains 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

• OncoKB supplies only general gene-level context that POLE is the catalytic subunit of DNA polymerase epsilon; it does not establish the PP2 requirements.
• The León-Castillo paper concerns somatic POLE exonuclease-domain mutations in endometrial carcinoma and is not sufficient to establish the generic germline PP2 rule.

Still missing

• No validated gene-level benign-missense constraint assessment for POLE was supplied.
• No validated evidence establishing missense variants as a common POLE disease mechanism for this generic PP2 rule was supplied.

Reasoning

The governing POLE rule applies PP3_Supporting only when the exact missense 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. c.2810A>G / p.Tyr937Cys / p.Y937C was not found in PATH-250-323-s003.xlsx or PATH-250-323-s004.xlsx. The available REVEL score is 0.709, and SpliceAI max delta is 0.009, but neither predictor result can establish this VCEP PP3 rule without the required exact table entry; generic PP3 thresholds are not applied to this VCEP-governed criterion.

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 matched c.2810A>G, p.Tyr937Cys, or p.Y937C.
• PATH-250-323-s004.xlsx, Supplementary Table S3: no row matched c.2810A>G, p.Tyr937Cys, or p.Y937C.
• Case evidence: REVEL score 0.709 was available, but the VCEP rule requires the exact variant to be present in Table S2 or S3 and uses the table's REVEL class plus benign-result count.
• Case evidence: SpliceAI max delta score was 0.009; splice prediction is not the named predictor path in the POLE missense PP3 rule.

Still missing

• No exact c.2810A>G entry found in PATH-250-323-s003.xlsx full text.
• No exact p.Tyr937Cys entry found in PATH-250-323-s003.xlsx full text.
• No exact p.Y937C entry found in PATH-250-323-s003.xlsx full text.
• No exact c.2810A>G entry found in PATH-250-323-s004.xlsx full text.
• No exact p.Tyr937Cys entry found in PATH-250-323-s004.xlsx full text.
• No exact p.Y937C entry found in PATH-250-323-s004.xlsx full text.

Sources

Still missing

• attempt 1: evidence_refs must contain only source_registry keys
• attempt 2: evidence_refs must contain only source_registry keys
• attempt 3: evidence_refs must contain only source_registry keys

Still missing

• attempt 1: evidence_refs must contain only source_registry keys
• attempt 2: evidence_refs must contain only source_registry keys
• attempt 3: evidence_refs must contain only source_registry keys

Reasoning

BS2 cannot be assessed from the available evidence. No reliable observation is provided of this variant in a healthy adult individual, and the case materials do not establish the relevant inheritance model or full penetrance at an early age.

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.

Still missing

• No documented healthy adult carrier observation for the exact variant.
• Inheritance model and expectation of full early-age penetrance are not established in the available evidence.

Reasoning

No variant-specific, validated in vitro or in vivo functional assay for POLE NM_006231.4:c.2810A>G (p.Tyr937Cys) demonstrating no damaging effect on protein function or splicing was identified in the supplied evidence. The absence of reported functional evidence cannot be treated as a benign functional result. Therefore BS3 cannot be assessed.

Rule

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 this variant; it does not provide a benign functional assay result.
• No functional, biochemical, cellular, splicing, or in vivo assay result for POLE p.Tyr937Cys is present in the supplied case evidence.

Still missing

• A variant-specific well-established assay showing no damaging effect on POLE protein function or splicing, with suitable controls and biologic relevance, is needed.

Sources

Reasoning

The available case evidence does not identify affected family members who were tested for the variant and does not report any discordant genotype-phenotype observations. Lack of segregation therefore cannot be evaluated.

Rule

BS4: Lack of segregation in affected members of a family.

Evidence considered

• No affected-relative testing, pedigree-based non-segregation observation, or genotype-phenotype discordance was found in the reviewed case evidence.

Still missing

• Affected relatives evaluated for the disease
• Genotypes of affected relatives
• Phenotypes and diagnostic certainty of those relatives
• Evidence of variant absence in affected relatives

Reasoning

The available case evidence does not establish that POLE disease is caused primarily by truncating variants. The León-Castillo materials address somatic missense exonuclease-domain variants and do not provide a gene-level germline loss-of-function-versus-missense mechanism assessment. BP1 therefore remains not assessed rather than being applied from incomplete gene context.

Rule

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

Evidence considered

• The León-Castillo paper and Supplementary Table S1 focus on somatic POLE missense and other recurrent variants in endometrial carcinoma, not the generic germline BP1 mechanism requirement.
• The case's PVS1 context is not a validated POLE-specific mechanism source for BP1 and was not used to infer this criterion.

Still missing

• No validated gene-level disease-mechanism review establishing primarily truncating POLE disease was supplied.
• The governing León-Castillo materials are somatic missense-focused and do not answer the generic BP1 mechanism question.

Reasoning

Not assessed: the available evidence does not document a fully penetrant dominant disease context with a pathogenic variant in trans, nor a pathogenic variant in cis in any inheritance pattern, and phase is not established.

Rule

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 case evidence documents NM_006231.4:c.2810A>G (p.Tyr937Cys) and ClinVar uncertainty, but provides no pathogenic paired variant or cis/trans phase result.
• No inheritance or affected-proband evidence is available to establish the dominant fully penetrant pathway.

Still missing

• Confirm whether the relevant disorder is fully penetrant and dominant.
• Document a pathogenic variant in trans or cis with this variant.
• Obtain testing that establishes phase.

Reasoning

The governing POLE rule applies BP4_Supporting only when the exact missense 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. c.2810A>G / p.Tyr937Cys / p.Y937C was not found in PATH-250-323-s003.xlsx or PATH-250-323-s004.xlsx. The available REVEL score is 0.709, and SpliceAI max delta is 0.009, but neither predictor result can establish this VCEP BP4 rule without the required exact table entry; generic BP4 thresholds are not applied to this VCEP-governed criterion.

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 matched c.2810A>G, p.Tyr937Cys, or p.Y937C.
• PATH-250-323-s004.xlsx, Supplementary Table S3: no row matched c.2810A>G, p.Tyr937Cys, or p.Y937C.
• Case evidence: REVEL score 0.709 was available, but the VCEP rule requires the exact variant to be present in Table S2 or S3 and uses the table's REVEL class plus benign-result count.
• Case evidence: SpliceAI max delta score was 0.009; splice prediction is not the named predictor path in the POLE missense BP4 rule.

Still missing

• No exact c.2810A>G entry found in PATH-250-323-s003.xlsx full text.
• No exact p.Tyr937Cys entry found in PATH-250-323-s003.xlsx full text.
• No exact p.Y937C entry found in PATH-250-323-s003.xlsx full text.
• No exact c.2810A>G entry found in PATH-250-323-s004.xlsx full text.
• No exact p.Tyr937Cys entry found in PATH-250-323-s004.xlsx full text.
• No exact p.Y937C entry found in PATH-250-323-s004.xlsx full text.

Sources

Still missing

• attempt 1: evidence_refs must contain only source_registry keys
• attempt 2: evidence_refs must contain only source_registry keys
• attempt 3: evidence_refs must contain only source_registry keys

Still missing

• attempt 1: evidence_refs must contain only source_registry keys
• attempt 2: evidence_refs must contain only source_registry keys
• attempt 3: evidence_refs must contain only source_registry keys