POLE c.4519_4520del, p.(Gln1507AlafsTer37)

Reasoning

No POLE-specific VCEP CSPEC or local gene-specific framework was found for PVS1 (cspec.found = false; the only local POLE package, Leon-Castillo et al. 2020, addresses somatic missense hotspots in endometrial carcinoma and explicitly is not a germline ACMG/AMP rule specification). Fell back to the generic ClinGen SVI PVS1 recommendations (PMC6185798) per pvs1_variant_assessment, which flags this transcript as eligible for the generic PVS1 decision tree. NM_006231.4:c.4519_4520del is a 2-bp frameshift deletion (variant_class/consequence_class = frameshift) predicted to produce NP_006222.2:p.(Gln1507AlafsTer37) on the MANE Select transcript (mane_select=true). The variant lies in coding exon 35 of 49 total exons (c.4445-4551 exon boundary; well upstream of the terminal exon and not within the last 50 bp of the penultimate exon), so the resulting premature termination codon is predicted to trigger nonsense-mediated decay rather than escape it. Even assuming residual translation, the predicted truncated protein (1543 aa) removes roughly a third of the 2287-aa POLE1 protein, including the C-terminal zinc-finger/CysA-CysB domains required for POLE4/POLE2 subunit interactions and holoenzyme assembly, downstream of the N-terminal polymerase/exonuclease catalytic domains. Germline loss-of-function is an established POLE disease mechanism: PMID:30503519 (Logan et al.) reports 15 individuals from 12 families with biallelic POLE LoF variants (nonsense, frameshift, essential splice-site) causing an IMAGe-syndrome-overlapping phenotype with immunodeficiency, confirming markedly reduced POLE1 protein levels (5-11% of control) on immunoblot in LoF-variant carriers, directly demonstrating that POLE truncating/LoF variants produce a loss-of-function/haploinsufficiency-compatible molecular phenotype in humans. PMID:23230001 (FILS syndrome) and the targeted germline literature search in pvs1_gene_context (lof_mechanism_supported=true, pvs1_gene_gate=eligible) corroborate that POLE loss-of-function is an accepted germline disease mechanism, satisfying the gene-level PVS1 eligibility gate. None of the downgrade_considerations in pvs1_variant_assessment apply: transcript relevance is confirmed (MANE Select), NMD is predicted to occur (not escaped), the truncation removes essential C-terminal protein sequence rather than affecting only a non-critical distal region, and the exon is not reported as enriched for population LoF variation. PVS1 is therefore applied at full (very strong) strength under the generic PMC6185798 framework.

Rule

PVS1 (generic PMC6185798 framework, frameshift variant predicted to undergo NMD in a gene with an established germline loss-of-function disease mechanism)

Evidence considered

• pvs1_variant_assessment.json: consequence_class='frameshift', variant_bucket='frameshift', protein_1l='NP_006222.2:p.(Q1507Afs*37)', apply_generic_pvs1_framework=true, suggested_default_strength='PVS1', framework_source=PMC6185798.
• pvs1_gene_context.json: germline_disease_context_found=true, lof_mechanism_supported=true, pvs1_gene_gate='eligible'; no official CSPEC/VCEP POLE PVS1 framework exists so generic fallback per PMC6185798 was used.
• prefetch.json VariantValidator exon/CDS map: variant falls in coding exon 35 of 49 total exons (c.4445-4551), far from the terminal exon/penultimate-exon 50bp NMD-escape boundary, supporting NMD.
• prefetch.json protein prediction: position_last_original=2287 aa (wild-type POLE1 length) vs position_last_predicted=1543 aa for the frameshifted product, a substantial truncation removing C-terminal protein sequence.
• PMID:30503519 (Logan et al., DNA Polymerase Epsilon Deficiency Causes IMAGe Syndrome...): reports biallelic POLE loss-of-function variants (nonsense/frameshift/splice) in 15 individuals; immunoblot in subject fibroblasts confirmed markedly reduced POLE1 protein (5% and 11% of control levels), directly evidencing that POLE truncating variants produce a loss-of-function molecular phenotype in humans.
• PMID:23230001 (FILS syndrome, Pachlopnik Schmid et al.): establishes POLE loss-of-function/hypomorphic alleles as a germline human disease mechanism, supporting gene-level PVS1 eligibility.
• index_guidance/vcep_materials: the only local POLE VCEP-style package (Leon-Castillo et al. 2020, PATH-250-323) addresses somatic missense hotspots for PM1/PS4/PP3/BP4 only and explicitly states it is not a germline ACMG/AMP rule specification, confirming no gene-specific PVS1 override exists.

Still missing

• No POLE-specific VCEP PVS1 exon-criticality or NMD-boundary table was available; the last-exon/50-bp-rule determination was made from generic exon coordinates rather than an official POLE PVS1 decision table.
• Exact zygosity of this variant in the tested individual is not documented in the bundle; the cited functional LoF evidence (PMID:30503519) derives from biallelic carriers, so the molecular consequence (frameshift, NMD, protein truncation) is used here rather than inheritance pattern.

Sources

Reasoning

PM2 is met at Moderate strength under the generic ACMG/AMP fallback. The variant is absent from gnomAD v2.1 and gnomAD-Canada v1.0 and occurs once in gnomAD v4.1 (overall AF 6.19631e-07; highest reported subset AF 1.75932e-06), with no homozygotes. These frequencies are far below the generic operational PM2 rarity threshold of <0.1% and are not near a threshold boundary.

Rule

{'framework': 'generic_acmg_fallback', 'strength': 'Moderate', 'threshold': '<0.1% allele frequency', 'interpretation': 'PM2 applies to a variant absent from controls or present only at a frequency far below the generic rare-variant threshold; no POLE-specific specification was available.'}

Evidence considered

• gnomAD v2.1 reports the variant as absent.
• gnomAD v4.1 reports one allele among 1,613,864 total alleles (overall AF 6.19631e-07; 0 homozygotes); highest reported frequency is 1/568,400 non-Finnish European XY alleles (AF 1.75932e-06).
• gnomAD-Canada v1.0 reports the variant as absent.
• The highest observed AF (0.000176%) is far below the generic operational PM2 threshold of <0.1%; a single observed allele does not preclude PM2 under this rarity rule.

Still missing

• No POLE-specific PM2 threshold or disease-specific maximum credible allele frequency was retrieved.

Sources

Reasoning

The applicable local POLE PS4 specification is limited to selected exact recurrent POLE missense hotspot variants in endometrial-carcinoma cohorts. This frameshift variant, p.(Gln1507AlafsTer37), is outside that defined set and has no reported somatic COSMIC record; therefore PS4 is not met.

Rule

Local POLE PS4 rule: apply PS4_Supporting only to the specified exact recurrent POLE missense variants with combined COSMIC and TCGA endometrial-carcinoma count >=10; do not exceed Supporting.

Evidence considered

• The local POLE framework permits PS4_Supporting only for specified exact recurrent POLE missense variants (P286R, V411L, A456P, and S297F) with combined endometrial-carcinoma cohort count at least 10; it is capped at Supporting because it represents somatic recurrence rather than germline case-control evidence.
• The queried variant is a frameshift, NM_006231.4:c.4519_4520del / p.(Gln1507AlafsTer37), not one of the framework's specified missense variants.
• OncoKB reports no variant-specific reviewed functional evidence for this variant, and the consolidated evidence bundle reports no COSMIC result for the exact variant.

Sources

Reasoning

ClinVar has no exact-variant expert-panel pathogenic or likely pathogenic assertion. The reported pathogenic submission is an ordinary single clinical-laboratory submission and is ineligible for PP5.

Rule

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

Evidence considered

• For exact ClinVar Variation ID 2443222, the submission audit reports zero expert-panel submissions. The pathogenic assertion is from Labcorp and has review status 'criteria provided, single submitter'; it is not an expert-panel assertion.

Sources

Reasoning

BA1 is not met. The highest observed frequency is 1/568,400 alleles in the gnomAD v4.1 non-Finnish European XY subset (AF 1.75932e-06; 0.000176%), with overall AF 6.19631e-07 (1/1,613,864). These frequencies are far below the generic BA1 threshold of >1%.

Rule

{'framework': 'generic_acmg_fallback', 'threshold': '>1% allele frequency', 'interpretation': 'BA1 requires a population frequency sufficiently common for a benign classification; the highest observed frequency is far below this threshold.'}

Evidence considered

• gnomAD v2.1 reports the variant as absent.
• gnomAD v4.1 reports one allele among 1,613,864 total alleles (AF 6.19631e-07; 0 homozygotes); the highest reported subset frequency is 1/568,400 non-Finnish European XY alleles (AF 1.75932e-06; 0 homozygotes).
• gnomAD-Canada v1.0 reports the variant as absent.
• No official ClinGen CSPEC/VCEP population specification was retrieved for POLE; the local POLE framework customizes only PM1, PS4, PP3, and BP4, so generic ACMG/AMP population thresholds apply.

Sources

Reasoning

BS1 is not met. The highest observed allele frequency is 1.75932e-06 (0.000176%) in the gnomAD v4.1 non-Finnish European XY subset, far below the generic operational BS1 threshold of >0.3%. The observation is a single allele in a large subset and does not create an ancestry-specific threshold artifact.

Rule

{'framework': 'generic_acmg_fallback', 'threshold': '>0.3% allele frequency', 'interpretation': 'BS1 requires an allele frequency greater than expected for the disorder; no POLE-specific maximum credible frequency was available, so the generic operational threshold was used.'}

Evidence considered

• gnomAD v2.1 reports the variant as absent.
• gnomAD v4.1 reports one allele among 1,613,864 total alleles (AF 6.19631e-07); the highest subset frequency is 1/568,400 non-Finnish European XY alleles (AF 1.75932e-06). No homozygotes are reported.
• gnomAD-Canada v1.0 reports the variant as absent.
• The highest observed AF is far below the generic BS1 operational threshold of >0.3%.

Still missing

• No POLE disease-specific prevalence, penetrance, or maximum credible allele-frequency threshold was retrieved.

Sources

Reasoning

BS2 is not met. gnomAD v4.1 reports zero homozygotes, and the bundle contains no phenotype- and age-documented unaffected homozygous individuals or other qualifying unaffected carrier observations. Absence of a qualifying observation cannot support BS2.

Rule

{'framework': 'generic_acmg_fallback', 'requirement': 'Observation in healthy adult individuals for a disorder expected to be fully penetrant at an early age', 'interpretation': 'No qualifying phenotype- and age-documented unaffected carrier observation is available.'}

Evidence considered

• gnomAD v2.1 and gnomAD-Canada v1.0 report the variant as absent.
• gnomAD v4.1 reports 0 homozygotes among 1,613,864 alleles and provides no individual-level phenotype or age data for its one heterozygous carrier.
• No official ClinGen CSPEC/VCEP BS2 specification was retrieved for POLE; generic ACMG/AMP BS2 requires qualifying observations in unaffected individuals.

Still missing

• No phenotype-annotated, adequately aged unaffected homozygous individuals or qualifying unaffected carrier cohort was identified.

Sources

Reasoning

ClinVar has no exact-variant expert-panel benign or likely benign assertion. The two uncertain-significance submissions are ordinary clinical-laboratory submissions and are ineligible for BP6.

Rule

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

Evidence considered

• For exact ClinVar Variation ID 2443222, the submission audit reports zero expert-panel submissions. The available non-expert submissions are two uncertain-significance assertions and one pathogenic assertion.

Sources

Reasoning

No confirmed de novo occurrence is documented for NM_006231.4:c.4519_4520del (p.Gln1507AlafsTer37). The bundle contains no proband phenotype, parental genotype, parentage confirmation, or parental mosaicism assessment.

Rule

Generic ACMG/AMP PS2: requires a de novo variant in a patient with the disease and no family history, with maternity and paternity confirmed; this evidence is not present.

Evidence considered

• No ClinGen CSPEC is available for POLE. The local POLE framework customizes PM1, PS4, PP3, and BP4 only; PS2 is therefore assessed using generic ACMG/AMP logic.
• The consolidated case-evidence bundle provides variant normalization and ClinVar/literature records but no case-level de novo or parental-testing observation for this variant.

Still missing

• Obtain the proband phenotype and indication for testing.
• Perform targeted testing of both biological parents for the variant, with parentage confirmation where feasible.
• Assess possible parental mosaicism if the variant is absent in routine parental blood testing.

Reasoning

No functional/experimental assay evidence (in vitro polymerase activity, exonuclease proofreading assay, complementation, cell-based, or minigene splicing assay) for NM_006231.4:c.4519_4520del is present anywhere in the case-evidence bundle. The local POLE custom framework (derived from Leon-Castillo et al. 2020) covers only PM1 (exonuclease-domain hotspot missense), PS4 (somatic EC cohort recurrence), PP3, and BP4 (in silico) for missense substitutions in the exonuclease domain; it contains no PS3 specification and is not applicable to this frameshift/truncating variant. No ClinGen POLE VCEP CSPEC was found (cspec.found=false in case_summary.json). The three functional-themed ClinVar-linked papers (PMID 23230001, 25948378, 30503519) describe clinical case series of patients with biallelic POLE hypomorphic missense/splice variants causing FILS/IMAGe-like syndromes; they report patient phenotypes and molecular findings for their own reported variants, not a validated functional assay of this exact variant (p.Gln1507Alafs*37), so they cannot be used to support PS3 without risking ungrounded citation.

Still missing

• No variant-specific functional/complementation/enzymatic assay data available for this variant
• No applicable VCEP or local gene-specific PS3 rule specification exists for this gene/variant type
• None of the retrieved ClinVar-linked publications report a functional assay of this exact variant

Reasoning

Not assessed. The POLE local framework does not specify PM3, so generic ACMG/AMP allelic-evidence logic applies; however, the bundle contains no affected-proband observation of NM_006231.4:c.4519_4520del with a second pathogenic/likely pathogenic POLE variant, no phase determination, and no segregation data establishing trans configuration.

Rule

Generic ACMG/AMP PM3 fallback: require the target variant to be observed in an affected individual in trans with a pathogenic/likely pathogenic variant for a recessive disease; no POLE-specific PM3 specification was retrieved.

Evidence considered

• No ClinGen CSPEC was retrieved for POLE. The governing local POLE framework customizes only PM1, PS4, PP3, and BP4 and directs generic ACMG/AMP fallback outside that scope.
• The normalized target is NM_006231.4:c.4519_4520del, predicted NP_006222.2:p.(Gln1507AlafsTer37). The case bundle contains no target-variant affected-proband genotype, co-occurring POLE variant, trans/cis phase result, or segregation result.
• ClinVar lists three germline submissions for the exact variant but the supplied record contains no co-occurrence or phase evidence; its submitter classifications were not used to infer PM3.

Still missing

• Affected-proband genotype data identifying any second POLE variant.
• Laboratory or family-based phase evidence showing that NM_006231.4:c.4519_4520del is in trans with a pathogenic/likely pathogenic POLE variant.
• Phenotype and inheritance information supporting a recessive POLE disease context for any potential biallelic observation.

Reasoning

No reported de novo occurrence without confirmed parentage is available for this variant. There is also no proband phenotype or parental testing record from which to evaluate a de novo assertion.

Rule

Generic ACMG/AMP PM6: a de novo occurrence may be considered when maternity and paternity are not confirmed; no such occurrence is documented here.

Evidence considered

• No ClinGen CSPEC is available for POLE, and the local POLE framework does not specify PM6; generic ACMG/AMP logic applies.
• The consolidated case-evidence bundle contains no case-level parental testing or de novo assertion for NM_006231.4:c.4519_4520del.

Still missing

• Obtain a documented de novo observation for the exact variant.
• If parentage cannot be confirmed, provide both parental targeted-test results and the proband phenotype/diagnosis.

Reasoning

No informative affected or unaffected relatives, genotypes, phenotypes, pedigrees, or meioses are reported for the exact variant. Segregation cannot be evaluated.

Rule

Generic ACMG/AMP PP1: requires co-segregation of the variant with disease in multiple affected family members; no segregation observations are available.

Evidence considered

• No ClinGen CSPEC is available for POLE, and the local POLE framework does not specify PP1; generic ACMG/AMP logic applies.
• The consolidated case-evidence bundle contains no family segregation dataset for NM_006231.4:c.4519_4520del.

Still missing

• Provide a pedigree with disease status and age/phenotype information for tested relatives.
• Provide targeted variant results for informative relatives and the number of independent informative meioses.

Reasoning

No proband phenotype, diagnosis, or phenotype-to-gene differential data are supplied for this case. Phenotypic specificity for a POLE-associated disorder cannot be evaluated.

Rule

Generic ACMG/AMP PP4: phenotype or family history must be highly specific for a disease with a single genetic etiology.

Evidence considered

• The consolidated case-evidence bundle contains variant-level, database, and literature-triage information but no affected individual's phenotype or diagnostic workup.

Still missing

• Clinical phenotype, indication for testing, and relevant differential diagnoses for the individual carrying the variant are required.

Reasoning

No functional assay evidence of normal/wild-type activity is present in the case-evidence bundle for this variant, and no applicable PS3/BS3 rule specification exists in the local POLE custom framework (which is limited to PM1/PS4/PP3/BP4 for exonuclease-domain missense variants) or from any official ClinGen POLE VCEP CSPEC (none found: cspec.found=false). No assay data of any kind (functional, complementation, or otherwise) contradicting a deleterious effect was identified for this frameshift/truncating variant.

Still missing

• No functional assay data of any kind (showing normal or abnormal activity) available for this variant
• No applicable VCEP or local gene-specific BS3 rule specification exists for this gene/variant type

Reasoning

No well-phenotyped affected non-carriers or clearly unaffected carriers are reported. Consequently, lack of segregation cannot be established.

Rule

Generic ACMG/AMP BS4: requires lack of segregation in affected family members; no informative family data are available.

Evidence considered

• No ClinGen CSPEC is available for POLE, and the local POLE framework does not specify BS4; generic ACMG/AMP logic applies.
• The consolidated case-evidence bundle contains no non-segregation evidence for NM_006231.4:c.4519_4520del.

Still missing

• Provide a pedigree and genotype/phenotype data for informative relatives.
• Document whether any affected relatives lack the variant, considering age-dependent penetrance and phenocopies where relevant.

Reasoning

Not assessed. The POLE local framework does not specify BP2, so generic ACMG/AMP allelic-evidence logic applies; the bundle contains no observation showing NM_006231.4:c.4519_4520del in cis with a pathogenic/likely pathogenic POLE variant, nor an observation of the relevant pair in an individual whose phenotype establishes that the cis combination is non-causative.

Rule

Generic ACMG/AMP BP2 fallback: require documented cis co-occurrence with a pathogenic/likely pathogenic variant, or another qualifying non-causative co-occurrence observation under the relevant inheritance model; no POLE-specific BP2 specification was retrieved.

Evidence considered

• No ClinGen CSPEC was retrieved for POLE. The governing local POLE framework customizes only PM1, PS4, PP3, and BP4 and directs generic ACMG/AMP fallback outside that scope.
• The case bundle contains no target-variant co-occurrence observation, no cis phase result, and no unaffected or phenotype-discordant carrier evidence relevant to BP2.
• ClinVar lists three germline submissions for the exact variant but the supplied record contains no co-occurrence or phase evidence; its submitter classifications were not used to infer BP2.

Still missing

• A documented co-occurring pathogenic/likely pathogenic POLE variant.
• Phase evidence establishing cis configuration with NM_006231.4:c.4519_4520del.
• Phenotype, inheritance, and genotype information demonstrating that the observed cis configuration is not causative for the relevant disease.

Reasoning

No individual-level phenotype, molecular diagnosis, or evidence for an alternative cause of the presenting condition is supplied. BP5 cannot be assessed.

Rule

Generic ACMG/AMP BP5: variant is found in a case with an alternate molecular basis for disease.

Evidence considered

• The consolidated case-evidence bundle provides no proband-level diagnostic or phenotype information.

Still missing

• A documented molecular diagnosis that fully explains the individual's phenotype, together with the phenotype and testing context, is required.