POLE c.857C>G, p.Pro286Arg

Reasoning

NM_006231.4:c.857C>G produces p.Pro286Arg (p.P286R). The governing POLE paper identifies P286R as one of five common POLE mutations whose pathogenicity, defined there as causal for tumour ultramutation, has been confirmed; the same amino-acid change is therefore established as pathogenic in the available evidence. SpliceAI max delta is 0.002, so the result is not being attributed to a splice effect. The governing rule is applied to the protein-level change, not merely to the nucleotide substitution.

Rule

Same amino acid change as a previously established pathogenic variant regardless of nucleotide change. ... Example: Val->Leu caused by either G>C or G>T in the same codon. ... Caveat: Beware of changes that impact splicing rather than at the amino acid/protein level.

Evidence considered

• León-Castillo et al. 2020, PATH-250-323.pdf: the paper lists P286R among the five most common POLE mutations whose pathogenicity has been confirmed.
• León-Castillo et al. 2020, PATH-250-323-s002.xlsx, Supplementary Table S1, row p.P286R/c.857C>G: COSMIC 160, TCGA 21, total 181.
• Billingsley et al. 2015 (PMID:25224212): p.Pro286Arg is explicitly reported in endometrial tumors as a POLE exonuclease-domain mutation.
• Kane and Shcherbakova 2014 (PMID:24525744): the exact somatic c.857C>G/P286R substitution is reported and functionally characterized.
• SpliceAI result for NM_006231.4:c.857C>G: max delta score 0.002.

Sources

Reasoning

PS3 is met at Supporting strength for NM_006231.4:c.857C>G (NP_006222.2:p.(Pro286Arg), P286R). The exact P286R substitution was tested in a purified human POLE 3′–5′ exonuclease assay and caused a substantial reduction in exonuclease activity, with wild-type and comparator controls, and it produced a strand-specific replication-error phenotype in a cell-free DNA-synthesis assay (PMID:25228659; Results section, Figure 3A and Figure 3C). Independent functional work characterized the corresponding conserved yeast pol2-P301R allele: mutation rates increased 150-fold, 44-fold, and 370-fold in CanR, Lys+, and His+ assays, respectively, versus wild type; the heterozygous allele also increased mutation rates 27-fold and 29-fold (PMID:24525744; Tables 1–2). These orthogonal biochemical, replication-error, and mutator assays consistently support a damaging effect on POLE proofreading/fidelity. Supporting rather than Strong is appropriate because the studies are research assays rather than validated, reproducible functional testing in a clinical diagnostic laboratory setting.

Rule

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

Evidence considered

• Shinbrot et al. (PMID:25228659), Results section ‘Mutation of POLE-exo impairs 3′-5′ exonuclease activity,’ Figure 3A and Figure 3C: exact human POLE P286R substantially reduced 3′-5′ exonuclease activity and showed a strand-specific replication-error phenotype in a cell-free DNA-synthesis assay.
• Kane and Shcherbakova (PMID:24525744), Results/Discussion and Tables 1–2: the corresponding yeast pol2-P301R allele increased CanR, Lys+, and His+ mutation rates 150-fold, 44-fold, and 370-fold versus wild type; heterozygous pol2-P301R/+ increased CanR and His+ rates 27-fold and 29-fold.
• The assays provide orthogonal evidence of impaired proofreading and fidelity, but the studies were research assays rather than validated functional testing in a clinical diagnostic laboratory, limiting PS3 to Supporting strength.

Sources

Reasoning

PS4_Supporting is met under the León-Castillo et al. 2020 custom POLE framework. The governing rule requires the exact POLE missense variant to recur in both COSMIC and TCGA endometrial carcinoma cohorts, have a combined EC count >=10, and belong to the established/pathogenic set. Supplementary Table S1 lists p.P286R/c.857C>G in 160 COSMIC and 21 TCGA endometrial carcinomas, for 181 combined cases; the main paper identifies P286R as one of the five established pathogenic exonuclease-domain hotspot mutations. The direct case-count evidence is somatic recurrence rather than germline case-control evidence, so the framework caps this at Supporting. The paper also reports P286R in 2 of 74 colorectal cancers and in 10 of 535 endometrioid endometrial tumors, but those reports do not provide a matched unaffected-control comparison for this exact variant; no odds ratio or confidence interval was therefore calculated from those studies.

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 POLE framework: PS4_Supporting applies when the exact missense variant recurs in both COSMIC and TCGA endometrial carcinoma cohorts, has combined EC count >=10, and belongs to the established/pathogenic set; the framework caps this somatic-recurrence evidence at Supporting.
• PATH-250-323-s002.xlsx, Supplementary Table S1, row p.P286R / c.857C>G: COSMIC endometrial carcinoma count 160; TCGA count 21; combined count 181.
• PATH-250-323.pdf, León-Castillo et al. 2020: P286R is identified among the five established pathogenic POLE exonuclease-domain hotspot mutations.
• Briggs et al. 2013 (PMID:23447401): exact p.Pro286Arg was reported in 2 of 74 colorectal cancers and described as particularly frequent among POLE-mutant endometrial cancers; this is recurrence evidence without matched unaffected controls.
• The paper's reported affected-case counts were reviewed for case-control analysis; because no unaffected-control counts were reported for exact P286R, no odds ratio or 95% confidence interval was computed from those reports.

Still missing

• PATH-250-323-s001.tif was unavailable as searchable text and was not used; the PDF and Supplementary Table S1 supplied the governing evidence.
• The reviewed exact-variant cancer reports did not provide unaffected-control counts, so no variant-specific odds ratio or 95% confidence interval could be calculated from those papers.

Sources

Reasoning

The local León-Castillo et al. 2020 POLE framework specifies PM1_Strong for the exact five established exonuclease-domain hotspot substitutions, including p.P286R. The variant is p.Pro286Arg at residue 286 and is explicitly listed in the governing paper and Supplementary Table S1; the framework's exact-variant rule is satisfied. vcep_materials.json has no domain_tables entry for POLE, so there is no separate authoritative domain list to apply.

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.

Evidence considered

• vcep_materials.json PM1 rule: Apply PM1_Strong to the five established POLE exonuclease-domain hotspot missense variants, explicitly including p.P286R.
• León-Castillo et al. 2020, PATH-250-323.pdf, Table 1 and text: P286R is listed as a recurrent exonuclease-domain hotspot and among the five mutations whose pathogenicity has been confirmed.
• León-Castillo et al. 2020, PATH-250-323-s002.xlsx, Supplementary Table S1, row p.P286R/c.857C>G: COSMIC 160, TCGA 21, total 181.
• vcep_materials.json domain_tables is an empty object for POLE; no additional domain-boundary route was available.

Still missing

• PATH-250-323-s001.tif has no converted full text and could not be searched; this does not prevent application because the PDF and Supplementary Table S1 contain the exact variant and governing hotspot rule.

Sources

Reasoning

PM2 is met at supporting strength. The variant is absent from gnomAD v2.1 and gnomAD v4.1, and the available non-cancer records for gnomAD v2.1 and v3.1 also report absence. This satisfies the supplied generic PM2 supporting threshold of allele frequency <=0.0001; complete absence is below that threshold. No VCEP-specific population source rule governs PM2 in this case.

Rule

Absent from controls (or at extremely low frequency if recessive) in Exome Sequencing Project, 1000 Genomes or Exome Aggregation Consortium.

Evidence considered

• gnomAD v2.1 all-comers: variant absent.
• gnomAD v4.1 all-comers: variant absent.
• The available gnomAD v2.1 non-cancer and v3.1 non-cancer records also report the variant absent.
• The supplied generic PM2 calibration is allele frequency <=0.0001 for supporting strength, with PMID:25741868 identified in the governing prompt.

Sources

Reasoning

The variant is the missense substitution NM_006231.4:c.857C>G, p.Pro286Arg/p.P286R. The governing León-Castillo et al. 2020 custom POLE PP3 rule applies when the exact missense variant appears in Supplementary Table S2 or S3, the REVEL class is likely disease causing (including spelling variants), and the number of benign in-silico results is <=1. Supplementary Table S2 contains the exact row P286R: SIFT Deleterious, PANTHER probably damaging, SNAP2 effect, PolyPhen2 Probably damaging, PROVEAN Deleterious, REVEL class likely disease causing, and number of benign results 0. Therefore PP3 is met at Supporting strength. The missense-path rule uses the table-assigned protein-impact evidence; the available SpliceAI result is not additionally counted for PP3.

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.

Evidence considered

• León-Castillo et al. 2020 Supplementary Table S2, row P286R: SIFT=Deleterious; PANTHER=probably damaging; SNAP2=effect; PolyPhen2=Probably damaging; PROVEAN=Deleterious; REVEL class=likely disease causing; number of benign results=0.
• The case normalization identifies NM_006231.4:c.857C>G as a missense variant producing NP_006222.2:p.(Pro286Arg)/p.(P286R); the governing custom rule therefore follows its missense path and does not require a combined protein-impact and splice prediction.
• PATH-250-323-s004.xlsx, Supplementary Table S3, was searched for c.857C>G, p.Pro286Arg, and p.P286R; no exact entry was found.

Still missing

• The exact variant was not found in PATH-250-323-s004.xlsx, Supplementary Table S3; it is present in PATH-250-323-s003.xlsx, Supplementary Table S2.

Sources

Reasoning

The variant is a missense substitution at Pro286, but the searched governing POLE materials do not establish a different missense substitution at residue 286 as pathogenic. PATH-250-323-s002.xlsx contains alternate P286 substitutions in somatic recurrence entries, including p.P286(R^S), but that table does not establish p.P286S or another alternate residue-286 missense change as pathogenic, and the paper's established hotspot rule specifically identifies p.P286R rather than all substitutions at codon 286. Therefore the generic PM5 requirement is not met.

Rule

Novel missense change at an amino acid residue where a different missense change determined to be pathogenic has been seen before. ... Example: Arg156His is pathogenic; now you observe Arg156Cys. ... Caveat: Beware of changes that impact splicing rather than at the amino acid/protein level.

Evidence considered

• PATH-250-323-s002.xlsx, Supplementary Table S1: p.P286(R^S) appears as a somatic recurrence entry, but the table does not label p.P286S as pathogenic.
• PATH-250-323.pdf: the established pathogenic hotspot list names the exact p.P286R substitution, not every alternate substitution at residue 286.

Still missing

• No pathogenic alternate Pro286 missense comparator was found in PATH-250-323.pdf.
• No pathogenic alternate Pro286 missense comparator was found in PATH-250-323-s002.xlsx.

Sources

Reasoning

PP5 is not met. The exact-variant ClinVar record has no expert-panel submission and instead contains conflicting non-expert laboratory classifications, including one single-submitter Likely pathogenic classification. Under the required generic PP5 safeguard, ordinary laboratory submissions, aggregate labels, and non-expert assertions cannot trigger PP5; no qualifying exact-variant ClinVar 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

• ClinVar exact-variant record NM_006231.4(POLE):c.857C>G (p.Pro286Arg), Variation ID 376500: expert-panel submissions = 0; classifications include one single-submitter Likely pathogenic, one Uncertain significance, drug response, and Established risk allele.
• The reviewed León-Castillo paper and supplementary table are evidence available for independent evaluation, not a qualifying PP5 source under the required rule.

Sources

Reasoning

BA1 is not met. The variant is absent from gnomAD v2.1 and gnomAD v4.1, so there is no observed allele frequency at or above the generic stand-alone threshold of 0.05 (5%). The available non-cancer entries are also reported absent; no ancestry-specific elevated frequency is present.

Rule

Allele frequency is above 5% in Exome Sequencing Project, 1000 Genomes or Exome Aggregation Consortium.

Evidence considered

• gnomAD v2.1 all-comers: variant absent.
• gnomAD v4.1 all-comers: variant absent.
• The available gnomAD v2.1 non-cancer and v3.1 non-cancer records also report the variant absent; no population frequency approaches 0.05.

Sources

Reasoning

BS1 is not met. The variant is absent from gnomAD v2.1 and gnomAD v4.1, so no allele frequency greater than expected for the disorder is observed. Because there is no elevated frequency, a maximum-credible-allele-frequency calculation using prevalence, penetrance, and allelic heterogeneity is not triggered; the generic 1% default is not exceeded.

Rule

Allele frequency is greater than expected for disorder.

Evidence considered

• gnomAD v2.1 all-comers: variant absent.
• gnomAD v4.1 all-comers: variant absent.
• The available gnomAD v2.1 non-cancer and v3.1 non-cancer records also report the variant absent.
• Whiffin et al. 2017 (PMID:28518168) is the supplied reference for considering maximum credible allele frequency from disorder prevalence, penetrance, and allelic heterogeneity; no calculation is needed because no elevated allele frequency was observed.

Sources

Reasoning

BS3 is not met. No well-established assay in the reviewed evidence shows that POLE P286R has no damaging effect on protein function or splicing. Instead, the exact human P286R substitution reduced 3′–5′ exonuclease activity and independent work showed strong mutator effects for the corresponding conserved yeast allele (PMID:25228659; PMID:24525744).

Rule

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

Evidence considered

• Shinbrot et al. (PMID:25228659), Results section ‘Mutation of POLE-exo impairs 3′-5′ exonuclease activity,’ Figure 3A: exact human POLE P286R reduced exonuclease activity rather than showing preserved function.
• Kane and Shcherbakova (PMID:24525744), Tables 1–2: corresponding yeast pol2-P301R showed markedly increased mutation rates relative to wild type, providing evidence against a no-damaging-effect interpretation.

Sources

Reasoning

BP1 is not supported because the governing POLE materials identify recurrent pathogenic missense substitutions in the exonuclease domain, including p.P286R, and describe missense exonuclease-domain mutations as causally associated with the ultramutated phenotype. This is inconsistent with a gene for which primarily truncating variants are known to cause disease.

Rule

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

Evidence considered

• León-Castillo et al. 2020, PATH-250-323.pdf: five recurrent POLE exonuclease-domain missense mutations are treated as established pathogenic hotspot mutations.
• León-Castillo et al. 2020, PATH-250-323-s002.xlsx, Supplementary Table S1, row p.P286R/c.857C>G: 181 recurrent endometrial carcinoma observations across COSMIC and TCGA.
• Palles et al. 2013 (PMID:23263490): the paper discusses germline proofreading-domain variants in POLE and separately reports somatic P286R exonuclease-domain mutations.

Sources

Reasoning

The variant is a missense substitution and the exact P286R row is present in governing Supplementary Table S2. The León-Castillo et al. 2020 custom POLE BP4 rule requires the exact missense variant in Supplementary Table S2 or S3, REVEL class Likely benign or Likely-benign, and >=4 benign in-silico results. The P286R row instead reports REVEL class likely disease causing and 0 benign results. Thus the explicit BP4 requirements are not satisfied. The SpliceAI max delta of 0.002 is not used to create BP4 because the governing missense rule assigns this situation to the protein-impact table path, and predictions must not be double-counted across PP3/BP4.

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.

Evidence considered

• León-Castillo et al. 2020 Supplementary Table S2, row P286R: REVEL class=likely disease causing and number of benign results=0; these fail the BP4 requirements of Likely benign/Likely-benign and >=4 benign results.
• SpliceAI reports DS_AG=0.001, DS_AL=0.002, DS_DG=0.0, and DS_DL=0.002, with max delta score=0.002; this missense-variant splice result is not used as an additional BP4 path.
• PATH-250-323-s004.xlsx, Supplementary Table S3, was searched for c.857C>G, p.Pro286Arg, and p.P286R; no exact entry was found.

Still missing

• The exact variant was not found in PATH-250-323-s004.xlsx, Supplementary Table S3; it is present in PATH-250-323-s003.xlsx, Supplementary Table S2.

Sources

Reasoning

BP6 is not met. The exact-variant ClinVar record has no expert-panel submission and contains no qualifying expert-panel Benign or Likely benign classification. The record's non-expert classifications are conflicting and none is an exact-variant ClinVar expert-panel benign assertion.

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 NM_006231.4(POLE):c.857C>G (p.Pro286Arg), Variation ID 376500: expert-panel submissions = 0 and no Benign or Likely benign submission is listed.
• The available exact-variant ClinVar classifications are conflicting non-expert assertions, not a qualifying expert-panel benign classification.

Sources

Reasoning

PS2 cannot be assessed because there is no documented affected proband with a confirmed de novo NM_006231.4:c.857C>G result, no confirmation of both maternity and paternity, and no documented absence of family history. The available variant-specific literature describes somatic P286R observations; one extract explicitly states that no germline P286R carrier or segregation data were reported, which does not establish a de novo germline event.

Rule

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

Evidence considered

• PMID:23263490: the extracted report describes P286R in two hypermutated colorectal cancers as a somatic mutation and states that no germline P286R carrier or segregation data are reported.
• PMID:24525744: the extracted report describes a heterozygous P286R mutation in a colorectal tumor that was absent from matched normal tissue; this is somatic tumor evidence, not confirmed germline de novo evidence.

Still missing

• Proband clinical phenotype and disease diagnosis are not documented for this variant-level assessment.
• Parental testing results are unavailable.
• Maternity and paternity are not documented as confirmed.
• Family history is not documented.
• Germline origin of the variant is not established by the available evidence.

Sources

Reasoning

PM3 cannot be assessed because the available evidence does not document a second pathogenic variant, affected-proband biallelic status, parental or offspring testing, or phase demonstrating that NM_006231.4:c.857C>G (p.Pro286Arg) is in trans. The case evidence describes this variant in somatic tumor studies but provides no qualifying recessive-disease allelic observation.

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 case evidence identifies p.Pro286Arg in somatic POLE tumor studies, but contains no affected-proband report with a second pathogenic POLE allele or phase information.
• No parental, offspring, cis/trans, compound-heterozygous, or biallelic testing result is provided for NM_006231.4:c.857C>G.

Still missing

• Documented affected-proband observation with a second pathogenic variant is missing.
• Parental or offspring testing establishing phase is missing.
• The applicable recessive disorder and inheritance context are not established in the available evidence.

Reasoning

PM6 cannot be assessed because no germline de novo occurrence is documented in a patient with disease. The available variant-specific reports concern somatic tumors, and no parental testing, family history, or proband-level germline evidence is provided. Therefore, an assumed de novo event without parental confirmation cannot be established.

Rule

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

Evidence considered

• PMID:23263490: the extracted report identifies P286R in somatic colorectal cancer samples and reports no germline P286R carrier or segregation data.
• PMID:24525744: the extracted report identifies P286R in a tumor and its absence from matched normal tissue, without documenting a germline affected patient or de novo parental comparison.

Still missing

• A germline variant result from an affected patient is not documented.
• Parental testing results are unavailable.
• Family history is not documented.
• The variant's germline origin is not established.

Sources

Reasoning

PP1 cannot be assessed because no affected family members, variant-positive relatives, number of informative meioses, or co-segregation results are documented. The available literature extracts concern somatic tumor observations and do not provide a germline pedigree or segregation analysis for P286R.

Rule

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

Evidence considered

• PMID:23263490: the extracted report states that no segregation data are reported for P286R.
• PMID:24525744: the extracted report describes a somatic tumor study and provides no germline family segregation data.

Still missing

• Family pedigree and affected-relative diagnoses are unavailable.
• Variant testing results in relatives are unavailable.
• The number of informative meioses is unavailable.
• Germline co-segregation analysis is unavailable.

Sources

Reasoning

The available POLE materials document pathogenic missense hotspot biology and recurrent somatic missense variation, but they do not provide the gene-level benign missense rate or a governing threshold establishing that POLE has a low rate of benign missense variation while missense variants are a common disease mechanism under the generic PP2 rule. The required combined gene-level evidence is therefore insufficient.

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 consulted POLE paper and Supplementary Table S1 show recurrent/pathogenic somatic missense hotspots, but do not supply the gene-level benign missense rate required by PP2.

Still missing

• A validated gene-level benign missense constraint or low-benign-missense metric for POLE is unavailable in the consulted case evidence.
• A source establishing the generic PP2 gene-level applicability requirement for POLE is unavailable in the consulted case evidence.

Reasoning

PP4 cannot be assessed because the available case materials do not provide the patient's phenotype or family history, and the somatic endometrial-carcinoma phenotype associated with POLE P286R is not a patient-specific phenotype assessment for this criterion.

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 were not provided.

Reasoning

BS2 cannot be assessed from the available evidence. The population records report database absence, but do not identify healthy adult individuals carrying the variant or provide genotype-level observations demonstrating a heterozygous, homozygous, or hemizygous healthy adult. The required early-onset, fully penetrant disorder context and individual-level phenotype information are also not available.

Rule

BS2

Evidence considered

• gnomAD v2.1 and v4.1 report the variant absent and therefore do not provide a healthy adult carrier observation for BS2.
• No individual-level genotype, age, health status, zygosity, or penetrance information was available for this criterion.

Still missing

• Individual-level healthy adult carrier observations with genotype and phenotype details.
• Confirmation that the relevant disorder is expected to be fully penetrant and early onset.

Sources

Reasoning

BS4 cannot be assessed because no affected family members with negative variant testing are documented. There are no reported non-segregating relatives, informative meioses, or pedigree-level phenotype and genotype data. Somatic cancer observations do not constitute lack of segregation in an affected family.

Rule

Lack of segregation in affected members of a family.

Evidence considered

• PMID:23263490: the extracted report provides somatic tumor observations and no family non-segregation data.
• PMID:24525744: the extracted report provides tumor-versus-matched-normal testing, which is not evidence of lack of segregation among affected family members.

Still missing

• Affected relatives are not identified.
• Variant testing results for affected relatives are unavailable.
• Pedigree-level phenotype and genotype data are unavailable.
• Informative meioses are unavailable.

Sources

Reasoning

BP2 cannot be assessed because the available evidence does not document NM_006231.4:c.857C>G (p.Pro286Arg) with another pathogenic variant in trans in an affected individual with a fully penetrant dominant disorder, or with a pathogenic variant in cis. No phase-resolved allelic observation is reported.

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 case evidence contains no cis/trans result involving NM_006231.4:c.857C>G and another pathogenic variant.
• The available literature extracts concern somatic POLE tumor observations and functional studies, not phase-resolved allelic observations in a qualifying dominant disorder.

Still missing

• A phase-resolved observation with another pathogenic variant is missing.
• For the trans pathway, a fully penetrant dominant gene/disorder context is not established.

Reasoning

BP5 cannot be assessed because the available materials do not identify a patient case in which this variant was found alongside an alternate molecular basis for the disease. Somatic recurrence in endometrial or colorectal tumors is not, by itself, evidence that an alternate molecular basis explains a particular patient's disease.

Rule

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

Still missing

• No patient-level alternate molecular diagnosis or alternate molecular basis was provided.