POLE c.1662C>A, p.Ser554Arg

Reasoning

PM2 is met at supporting strength. The supplied generic threshold is allele frequency at most 0.0001. Using the default all-comers population sources because no governing VCEP population-source specification is present, gnomAD v4.1 reports AF=3.09798e-06 (5/1,613,954 alleles, 0 homozygotes), and gnomAD v2.1 reports AF=3.995014222250631e-06 (1/250,312 exome alleles, 0 homozygotes). Both are below 0.0001. The non-cancer subset is also absent in gnomAD v2.1 exomes (0/236,194 alleles), but it is not required for the default determination.

Rule

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

Evidence considered

• gnomAD v4.1 reports AF=3.09798e-06 from 5/1,613,954 total alleles, 0 homozygotes, and grpmax FAF=7.9e-07.
• gnomAD v2.1 reports AF=3.995014222250631e-06 from 1/250,312 exome alleles and 0 homozygotes.
• The separately reported gnomAD v2.1 non-cancer exome subset reports AF=0 from 0/236,194 alleles and 0 homozygotes; no governing VCEP rule requires that subset here, so the default all-comers totals determine PM2.
• The supplied generic PM2 threshold is <=0.0001, and both default all-comers frequencies are below it.

Sources

Reasoning

The governing León-Castillo POLE rule requires the exact missense variant to be recurrent in both COSMIC and TCGA endometrial carcinoma cohorts in Supplementary Table S1, to have a combined EC count >=10, and to belong to the established/pathogenic set highlighted by the paper; it specifically lists p.P286R, p.V411L, p.A456P, and p.S297F. Searches of PATH-250-323.pdf, PATH-250-323-s002.xlsx, and the unavailable PATH-250-323-s001.tif conversion found no c.1662C>A, p.Ser554Arg, or p.S554R entry. The variant is therefore not one of the rule's qualifying recurrent pathogenic variants, and no germline case-control comparison was identified. The literature packet's only candidate paper, PMID:25394175, was verified through its paper extract and does not mention POLE or this variant.

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 framework rule: exact POLE missense variant recurrent in both COSMIC and TCGA endometrial carcinoma cohorts in Supplementary Table S1, combined EC count >=10, and part of the established/pathogenic set; the listed qualifying variants are p.P286R, p.V411L, p.A456P, and p.S297F.
• PATH-250-323.pdf searched for c.1662C>A, p.Ser554Arg, and p.S554R: no matching entry; the paper instead identifies the five established hotspot substitutions as P286R, V411L, S297F, A456P, and S459F and describes a conservative approach for non-hotspot variants.
• PATH-250-323-s002.xlsx, Supplementary Table S1, searched for c.1662C>A, p.Ser554Arg, and p.S554R: no matching row; the extractable matching row visible in the table is p.P286R / c.857C>G, not the queried variant.
• PATH-250-323-s001.tif supplementary figure: full-text conversion unavailable, so it could not provide extractable variant evidence.
• PMID:25394175 paper extract: the paper does not mention POLE or c.1662C>A / p.S554R and provides no variant-specific clinical or case-control information.

Still missing

• No c.1662C>A, p.Ser554Arg, or p.S554R entry was found in PATH-250-323.pdf.
• No c.1662C>A, p.Ser554Arg, or p.S554R entry was found in PATH-250-323-s002.xlsx.
• PATH-250-323-s001.tif was unavailable for text conversion; no visual review was performed.
• No germline case-control counts or matched-ancestry case frequency were available for this exact variant.

Sources

Reasoning

The governing León-Castillo custom POLE framework restricts PM1 to exact listed substitutions: five established hotspots for strong evidence, six exact recurrent pathogenic-tier substitutions for moderate evidence, and four exact recurrent uncertain-tier substitutions for supporting evidence. p.Ser554Arg/p.S554R is not among those lists. The authoritative vcep_materials.json domain_tables key is empty, so there is no additional authoritative domain-table route. PATH-250-323.pdf, PATH-250-323-s002.xlsx, and the unavailable text conversion of PATH-250-323-s001.tif do not contain this variant or residue 554. Therefore PM1 is not met under the governing custom 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

• vcep_materials.json, León-Castillo et al. 2020 custom POLE framework: PM1 Strong is limited to p.P286R, p.V411L, p.S297F, p.A456P, and p.S459F; PM1 Moderate to p.F367S, p.L424I, p.M295R, p.P436R, p.M444K, and p.D368Y; PM1 Supporting to p.A465V, p.L424V, p.T278M, and p.A428T.
• vcep_materials.json domain_tables is an empty object, so no authoritative POLE domain list adds residue 554 as a PM1 route.
• PATH-250-323.pdf, León-Castillo et al. 2020: 'For the five most common POLE mutations (P286R, V411L, S297F, A456P, and S459F), pathogenicity (in this sense meaning causal for tumour ultramutation) has been confirmed.'
• PATH-250-323-s002.xlsx, Supplementary Table S1: the listed recurrent variants include p.P286R, p.V411L, p.A456P, p.S297F, p.S459F, and other specified residues, but not p.S554R or residue 554.
• Cancer Hotspots reports no statistically significant hotspot for POLE S554; this source cannot create a PM1 route because the governing POLE framework does not name a hotspot-source route.

Still missing

• PATH-250-323.pdf was searched for c.1662C>A, p.Ser554Arg, p.S554R, and residue 554 with no entry.
• PATH-250-323-s002.xlsx was searched for c.1662C>A, p.Ser554Arg, p.S554R, and residue 554 with no entry.
• PATH-250-323-s001.tif full-text conversion is unavailable and its visual content was not searchable; this is a review gap, not evidence that the file is empty.

Sources

Reasoning

PP3 is applicable only to missense variants represented in POLE Supplementary Table S2 or S3, with REVEL classified as likely disease causing and no more than one benign in silico result. The exact variant was not found when searching PATH-250-323-s003.xlsx for c.1662C>A, p.Ser554Arg, or p.S554R, and was likewise not found in PATH-250-323-s004.xlsx. Therefore the custom lookup rule cannot be used. Under the generic fallback for a missense variant, REVEL is the named predictor; the REVEL score is 0.393, which lies in the gray-zone interval [0.250, 0.750], so PP3 is not met. SpliceAI max delta 0.243 is not used for this missense PP3 path.

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 entry found for c.1662C>A, p.Ser554Arg, or p.S554R.
• PATH-250-323-s004.xlsx, Supplementary Table S3: no entry found for c.1662C>A, p.Ser554Arg, or p.S554R.
• Local REVEL predictor lookup: score 0.393; the generic missense PP3 threshold is REVEL >0.750, while scores from 0.250 through 0.750 are gray zone.
• SpliceAI result: maximum delta score 0.243; not used because the governing generic fallback assigns missense variants to REVEL rather than the splice predictor path.

Sources

Reasoning

ClinVar records the exact variant NM_006231.4:c.1662C>A (p.Ser554Arg) as Uncertain significance from two clinical laboratories, with zero expert-panel submissions. Therefore there is no exact-variant ClinVar expert-panel Pathogenic or Likely pathogenic classification to support PP5. The literature packet's candidate PMID:25394175 was checked through its paper extract and does not mention POLE or this variant.

Rule

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

Evidence considered

• ClinVar exact-variant record 944903: classification Uncertain significance, two clinical-laboratory submissions, and expert_panels empty; ordinary laboratory submissions do not meet the exact-variant expert-panel requirement.
• PMID:25394175 paper extract: the paper does not mention POLE or c.1662C>A / p.S554R and does not provide a reputable exact-variant pathogenic classification.

Sources

Reasoning

BA1 is not met. The governing default requires an allele frequency of at least 0.05. The largest adequately sampled gnomAD v4.1 population has only 1/62,484 observed alleles (point estimate 1.60041e-05), and the required filtering measure is grpmax FAF=7.9e-07, far below 0.05. The population exceeds the 2,000-observed-allele minimum, so this is not an isolate-sample artifact. gnomAD v2.1 also shows only 1/250,312 alleles (3.99501e-06).

Rule

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

Evidence considered

• gnomAD v4.1 reports 5/1,613,954 total alleles, AF=3.09798e-06, homozygotes=0; the highest observed subgroup is Remaining individuals at 1/62,484 alleles, AF=1.60041e-05, while grpmax FAF=7.9e-07.
• The frequency-bearing population has 62,484 observed alleles, exceeding the 2,000-allele minimum; the subgroup point estimate was not used as the decision metric.
• gnomAD v2.1 reports 1/250,312 exome alleles, AF=3.995014222250631e-06, homozygotes=0.

Sources

Reasoning

BS1 is not met. The generic default threshold is allele frequency at least 0.01, but the appropriate filtering metric is gnomAD v4.1 grpmax FAF=7.9e-07, not the highest subgroup point estimate. This is more than four orders of magnitude below 0.01. The observed frequency is therefore not greater than expected for the disorder on the supplied generic rule, and no maximum-credible-frequency calculation is needed to rescue or reject an elevated-frequency signal.

Rule

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

Evidence considered

• gnomAD v4.1 reports grpmax FAF=7.9e-07 and total AF=3.09798e-06 from 5/1,613,954 alleles; its highest subgroup point estimate is 1.60041e-05 from 1/62,484 alleles.
• Under the supplied ClinGen SVI-based instruction, the filtering allele frequency (grpmax FAF) was used and the popmax point estimate was not used.
• The available population frequency is far below the generic BS1 default of 0.01; no ancestry-confined elevated-frequency or reduced-penetrance exception is present in these data.

Sources

Reasoning

BP4 is applicable only to missense variants represented in POLE Supplementary Table S2 or S3, with REVEL classified as Likely benign or Likely-benign and at least four benign in silico results. The exact variant was not found when searching PATH-250-323-s003.xlsx for c.1662C>A, p.Ser554Arg, or p.S554R, and was likewise not found in PATH-250-323-s004.xlsx. Therefore the custom lookup rule cannot be used. Under the generic fallback for a missense variant, REVEL is the named predictor; the REVEL score is 0.393, which lies in the gray-zone interval [0.250, 0.750], so BP4 is not met. SpliceAI max delta 0.243 is not used for this missense BP4 path.

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 entry found for c.1662C>A, p.Ser554Arg, or p.S554R.
• PATH-250-323-s004.xlsx, Supplementary Table S3: no entry found for c.1662C>A, p.Ser554Arg, or p.S554R.
• Local REVEL predictor lookup: score 0.393; the generic missense BP4 threshold is REVEL <0.250, while scores from 0.250 through 0.750 are gray zone.
• SpliceAI result: maximum delta score 0.243; not used because the governing generic fallback assigns missense variants to REVEL rather than the splice predictor path.

Sources

Reasoning

ClinVar records the exact variant as Uncertain significance from two clinical laboratories and shows zero expert-panel submissions. No exact-variant ClinVar expert-panel Benign or Likely benign classification is present, so BP6 cannot be applied. The candidate literature PMID:25394175 was verified through its paper extract and does not mention POLE or this variant.

Rule

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

Evidence considered

• ClinVar exact-variant record 944903: Uncertain significance from two clinical laboratories, expert_panels empty; no expert-panel Benign or Likely benign classification is present.
• PMID:25394175 paper extract: the paper does not mention POLE or c.1662C>A / p.S554R and does not provide a reputable exact-variant benign classification.

Sources

Reasoning

The case materials establish POLE NM_006231.4:c.1662C>A as p.Ser554Arg/p.S554R, but they do not provide an established pathogenic variant producing the same amino-acid change through a different nucleotide change. The governing VCEP files PATH-250-323.pdf and PATH-250-323-s002.xlsx contain no c.1662C>A, p.Ser554Arg, p.S554R, or residue-554 entry, and the available PM5 candidate record contains no comparator candidates. This is insufficient to conclude that no same-amino-acid pathogenic variant exists outside the reviewed materials, so PS1 is not assessed.

Rule

Same amino acid change as a previously established pathogenic variant regardless of nucleotide change. ... Caveat: Beware of changes that impact splicing rather than at the amino acid/protein level.

Evidence considered

• The normalized case variant is NM_006231.4:c.1662C>A, NP_006222.2:p.(Ser554Arg), also p.(S554R).
• PATH-250-323.pdf: the paper identifies the established pathogenic substitutions P286R, V411L, S297F, A456P, and S459F, but contains no queried c.1662C>A, p.Ser554Arg, p.S554R, or residue-554 entry.
• PATH-250-323-s002.xlsx, Supplementary Table S1: the recurrent-variant table contains no queried c.1662C>A, p.Ser554Arg, p.S554R, or residue-554 entry.
• The supplementary figure PATH-250-323-s001.tif has no converted searchable text and therefore cannot establish a same-amino-acid comparator.
• The case PM5 candidate record reports zero same-residue candidates and zero candidates overall; it is not treated as proof that no external comparator exists.

Still missing

• A confirmed pathogenic variant causing the same p.Ser554Arg amino-acid change through a different nucleotide change is not documented.
• PATH-250-323.pdf was searched for c.1662C>A, p.Ser554Arg, p.S554R, and residue 554 with no entry.
• PATH-250-323-s002.xlsx was searched for c.1662C>A, p.Ser554Arg, p.S554R, and residue 554 with no entry.
• PATH-250-323-s001.tif text conversion is unavailable; its visual content was not searchable.

Sources

Reasoning

No case-specific evidence establishes that NM_006231.4:c.1662C>A (p.Ser554Arg) is de novo, that both maternity and paternity were confirmed, that the proband has the relevant disease, or that there is no family history. The available records contain no parental genotypes, trio testing, maternity or paternity confirmation, proband phenotype assessment, or family-history data; therefore PS2 cannot be assessed.

Rule

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

Evidence considered

• The available case evidence does not report parental testing, trio results, maternity or paternity confirmation, proband phenotype details, or family history for NM_006231.4:c.1662C>A.
• ClinVar records the variant as Uncertain significance but provides no variant-specific segregation or de novo evidence; classification was not used as evidence for PS2.

Still missing

• Documented proband diagnosis and phenotype consistency
• Maternal and paternal testing results for the variant
• Confirmation of maternity and paternity
• Family history and assessment for alternative inheritance or parental mosaicism

Sources

Reasoning

No variant-specific in vitro or in vivo functional assay, assay-control result, or validated diagnostic-laboratory functional study was identified for POLE NM_006231.4:c.1662C>A (p.Ser554Arg). OncoKB explicitly reports no variant-specific reviewed functional evidence, and PMID:25394175 does not mention POLE or this variant. Therefore the evidence is insufficient to assess PS3 rather than supporting a damaging effect.

Rule

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

Evidence considered

• OncoKB variant record for POLE S554R: no variant-specific reviewed functional evidence was identified; only gene-level context was available.
• PMID:25394175 paper extract: the paper does not mention POLE or NM_006231.4:c.1662C>A / NP_006222.2:p.(S554R), so it provides no functional evidence for this variant.

Still missing

• Variant-specific functional evidence measuring POLE protein or cellular function, with appropriate positive and negative controls, is unavailable.
• Independent replication or clinical diagnostic-laboratory validation is unavailable.

Sources

Reasoning

PM3 cannot be assessed because the available case evidence documents no affected proband with a recessive POLE disorder, no pathogenic allelic partner, and no parental or offspring testing establishing that NM_006231.4:c.1662C>A (p.Ser554Arg) is in trans with a pathogenic variant. The ClinVar record is an uncertain-significance germline submission and provides no phase or affected-proband compound-heterozygosity evidence.

Rule

For recessive disorders, detected in trans with a pathogenic variant.

Evidence considered

• The available case evidence contains no affected-proband report, pathogenic allelic partner, parental genotypes, offspring genotypes, or phase determination for NM_006231.4:c.1662C>A.
• ClinVar records the variant as uncertain significance and provides no variant-specific phase or compound-heterozygosity evidence; this classification was not used as evidence for PM3.

Still missing

• Affected proband with a documented recessive POLE disorder
• Pathogenic allelic partner identified in the same proband
• Parental or offspring genotypes establishing phase

Reasoning

The target is a missense variant at residue 554, but no different missense substitution at Ser554 that was established as pathogenic is documented in the reviewed case materials or the governing VCEP files. The recurrent POLE table and paper contain no residue-554 entry, and the available PM5 candidate record contains zero same-residue candidates. Because this does not exclude a pathogenic Ser554 comparator in sources outside the reviewed materials, PM5 is not assessed.

Rule

Novel missense change at an amino acid residue where a different missense change determined to be pathogenic has been seen before. ... Caveat: Beware of changes that impact splicing rather than at the amino acid/protein level.

Evidence considered

• PATH-250-323.pdf and PATH-250-323-s002.xlsx contain no p.Ser554Arg, p.S554R, c.1662C>A, or alternate missense substitution at residue 554.
• The case PM5 candidate record reports zero same-residue candidates and zero candidates overall; it is not treated as proof that no external comparator exists.

Still missing

• A different missense variant at Ser554 with an established pathogenic classification is not documented.
• PATH-250-323.pdf was searched for c.1662C>A, p.Ser554Arg, p.S554R, and residue 554 with no entry.
• PATH-250-323-s002.xlsx was searched for c.1662C>A, p.Ser554Arg, p.S554R, and residue 554 with no entry.
• PATH-250-323-s001.tif text conversion is unavailable; its visual content was not searchable.

Sources

Reasoning

No case-specific evidence establishes an assumed de novo occurrence of NM_006231.4:c.1662C>A (p.Ser554Arg). The available records contain no parental genotypes or report of a de novo event, so it is not possible to determine whether maternity and paternity were unconfirmed rather than untested or undocumented.

Rule

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

Evidence considered

• The available case evidence does not report a de novo event, parental genotypes, maternity or paternity confirmation, or proband phenotype details for NM_006231.4:c.1662C>A.
• The only fetched paper relevant to the case-evidence packet does not mention POLE or this variant and therefore provides no de novo evidence.

Still missing

• A case report or laboratory record identifying the variant as de novo
• Parental genotypes and whether maternity or paternity were confirmed
• Documented proband disease and phenotype consistency

Sources

Reasoning

No affected relatives, family pedigree, segregation results, or meioses are documented for NM_006231.4:c.1662C>A (p.Ser554Arg). Consequently, there is no evidence of co-segregation with disease in one or more affected family members and no basis to assign a PP1 strength.

Rule

Co-segregation with disease in multiple affected family members in a gene definitively known to cause the disease. ... May be used as stronger evidence with increasing segregation data.

Evidence considered

• The available case evidence contains no family pedigree, affected relatives, relative genotypes, phenotype assessments, or segregation data for NM_006231.4:c.1662C>A.
• No informative meioses or family-level co-segregation observations are reported.

Still missing

• Pedigree identifying affected and unaffected relatives
• Variant testing results for relatives
• Phenotype and disease-status assessment for tested relatives
• Number of informative meioses and segregation pattern

Sources

Reasoning

The available evidence does not establish both PP2 prerequisites for POLE: a low rate of benign missense variation and missense variation as a common disease mechanism. The León-Castillo materials document somatic POLE exonuclease-domain hotspot mutations in endometrial carcinoma, but they do not provide a gene-wide benign-missense rate or a germline mechanism analysis sufficient for the generic PP2 rule. PP2 is therefore 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

• PATH-250-323.pdf describes somatic POLE exonuclease-domain mutations and the POLE-ultramutated endometrial-carcinoma phenotype, but does not quantify benign missense variation or establish the generic germline PP2 prerequisites.
• PATH-250-323-s002.xlsx is a somatic COSMIC/TCGA recurrence table and does not provide a gene-wide benign missense rate or germline missense-mechanism assessment.

Still missing

• A validated gene-level assessment of POLE's benign missense variation rate is unavailable in the reviewed materials.
• A gene-level assessment establishing missense variants as a common mechanism of the relevant disease is unavailable in the reviewed materials.

Sources

Reasoning

No patient phenotype or family history specific enough to evaluate PP4 was provided. The available records contain variant normalization and database evidence but do not document a patient diagnosis, phenotype, or family history that can be assessed against a disease with a single genetic etiology.

Rule

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

Still missing

• Patient phenotype and family-history details are unavailable.
• A disease diagnosis and assessment of whether it has a single genetic etiology are unavailable.

Reasoning

BS2 cannot be assessed from the available evidence. gnomAD provides aggregate control-population observations, including zero homozygotes in gnomAD v2.1 and v4.1, but it does not identify an individual as a healthy adult, establish the relevant inheritance state, or document age and phenotype sufficient to show that the variant is tolerated in a healthy adult. No individual-level healthy-adult observation or penetrance/age-of-onset evidence was supplied.

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 v4.1 reports 5/1,613,954 total alleles and 0 homozygotes; gnomAD v2.1 reports 1/250,312 exome alleles and 0 homozygotes.
• These are aggregate population-control counts and do not document an identified healthy adult individual or the individual's age, clinical status, inheritance state, or penetrance.

Still missing

• Individual-level observation in a healthy adult with documented age, phenotype, and relevant zygosity/hemizygosity is unavailable.

Sources

Reasoning

No variant-specific in vitro or in vivo functional assay, assay-control result, or validated diagnostic-laboratory functional study was identified for POLE NM_006231.4:c.1662C>A (p.Ser554Arg). OncoKB explicitly reports no variant-specific reviewed functional evidence, and PMID:25394175 does not mention POLE or this variant. Therefore the evidence is insufficient to assess BS3 rather than supporting a normal protein-function or splicing effect.

Rule

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

Evidence considered

• OncoKB variant record for POLE S554R: no variant-specific reviewed functional evidence was identified; only gene-level context was available.
• PMID:25394175 paper extract: the paper does not mention POLE or NM_006231.4:c.1662C>A / NP_006222.2:p.(S554R), so it provides no functional evidence for this variant.

Still missing

• Variant-specific functional evidence demonstrating no damaging effect on POLE protein function or splicing, with appropriate controls, is unavailable.
• Independent replication or clinical diagnostic-laboratory validation is unavailable.

Sources

Reasoning

No affected family members have been identified and no family genotyping or phenotype assessment is documented for NM_006231.4:c.1662C>A (p.Ser554Arg). Therefore, lack of segregation in affected members cannot be demonstrated; the BS4 phenocopy caveat also cannot be evaluated without family-level clinical information.

Rule

Lack of segregation in affected members of a family.

Evidence considered

• The available case evidence contains no affected relatives, family genotypes, segregation analysis, or family-level phenotype information for NM_006231.4:c.1662C>A.
• No evidence supports applying BS4, and the supplied phenocopy and multiple-pathogenic-variant caveats cannot be assessed from the available family data.

Still missing

• Affected family members with reliable disease diagnoses
• Variant testing results in affected relatives
• Phenotype concordance and assessment for phenocopies
• Family structure and potential second pathogenic variants

Sources

Reasoning

The reviewed materials do not establish that POLE disease is caused primarily by truncating variants. Instead, the governing POLE paper focuses on pathogenic somatic missense mutations in the exonuclease domain, while its supplementary table mixes missense and truncating observations without providing a gene-level disease-mechanism comparison. This is insufficient to apply BP1.

Rule

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

Evidence considered

• PATH-250-323.pdf states that pathogenic somatic missense mutations within the POLE exonuclease domain define the POLE-ultramutated endometrial-carcinoma subtype; it does not establish a primarily truncating disease mechanism.
• PATH-250-323-s002.xlsx lists recurrent POLE variants in somatic COSMIC/TCGA cohorts, including both missense and truncating variants, but does not establish that truncating variants are the primary disease mechanism.

Still missing

• A gene-level disease-mechanism review demonstrating that POLE disease is primarily caused by truncating variants is unavailable.
• The somatic POLE paper and recurrence table do not provide the required germline variant-spectrum comparison.

Sources

Reasoning

BP2 cannot be assessed because the available case evidence documents no observation of NM_006231.4:c.1662C>A (p.Ser554Arg) in trans with a pathogenic variant for a fully penetrant dominant disorder and no observation in cis with a pathogenic variant. No affected-proband, parental, family, or haplotype data establish either allelic configuration.

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 available case evidence contains no affected-proband allelic observation, parental testing, family segregation, haplotype analysis, or other phase evidence for NM_006231.4:c.1662C>A.
• ClinVar records the variant as uncertain significance and does not document a pathogenic allelic partner or phase; this classification was not used as evidence for BP2.

Still missing

• A documented pathogenic allelic partner
• Phase or haplotype testing establishing cis or trans configuration
• Relevant affected-proband or family observation

Reasoning

No evidence was available that this exact variant occurred in a case with an alternate molecular basis for the disease. The available ClinVar and literature records do not document an alternate molecular diagnosis for a clinically characterized case.

Rule

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

Still missing

• No case report or clinical record documenting an alternate molecular basis for disease was available.