POLE c.2413C>T, p.(Gln805Ter)

Reasoning

NM_006231.4 is the MANE Select transcript for POLE (RefSeq Select; CCDS9278.1) and c.2413C>T is a single-nucleotide substitution creating a premature termination codon p.(Gln805Ter) in exon 21 of 49 (exon c.2320-2468 per Mutalyzer selector data; CDS 1-6861), i.e., a nonsense null variant (variant bucket 'nonsense' in pvs1_variant_assessment; not a canonical splice-site change). The PTC sits ~4.3 kb upstream of the final exon-exon junction (exon 49 starts at c.6748), far beyond the 50-55 nt NMD boundary, so the transcript is predicted to undergo nonsense-mediated decay; if translated, the allele would delete 1,481 of 2,286 residues (~65% of POLE1), truncating C-terminal to the exonuclease domain (the framework's exonuclease-domain hotspot set ends at p.S459F) within the polymerase/catalytic region and removing all downstream sequence. Germline loss of function is an established mechanism of POLE disease: biallelic LoF alleles cause autosomal recessive FILS syndrome (PMID:23230001, PMID:25948378) and IMAGe syndrome/primordial dwarfism (PMID:30503519), with severely depleted POLE1 protein in patient cells; heterozygous carriers of these null alleles are reported asymptomatic. No official ClinGen CSPEC or local VCEP specification for POLE exists, and the local Leon-Castillo custom framework customizes only PM1/PS4/PP3/BP4 (all missense/hotspot rules), explicitly falling back to generic ACMG/AMP outside that scope; accordingly the ClinGen SVI PVS1 recommendations (PMC6185798, pvs1_generic_framework) govern this criterion. Under that decision tree, a nonsense null variant in a gene with an established LoF mechanism that is NOT in the last exon and NOT within 50 nt of the last exon-exon junction is assigned PVS1_VeryStrong with no NMD-escape downgrade. Exon 21 is a constitutive coding exon of the MANE Select transcript (no evidence of alternative-splicing rescue), and the position shows no population LoF-enrichment signal (variant absent from gnomAD-Canada v1.0; gnomAD v2.1/v4.1 frequencies unavailable due to retrieval timeout). Caveat recorded for downstream steps: the LoF-associated POLE phenotypes are autosomal recessive, whereas the dominant cancer-predisposition phenotype is caused by exonuclease-domain missense variants (a distinct mechanism), so PVS1_VeryStrong is applied here on the gene-level LoF mechanism; confirm the testing indication before final classification.

Rule

Generic fallback (no POLE CSPEC; Leon-Castillo custom framework does not cover PVS1): ClinGen SVI PVS1 recommendations (PMC6185798) - null (nonsense) variant in a gene with established loss-of-function mechanism, PTC not in last exon and >50-55 nt upstream of the final exon-exon junction (NMD predicted) -> PVS1_VeryStrong

Evidence considered

• Mutalyzer/VariantValidator normalization (prefetch.json, summarized in pvs1_variant_assessment): NM_006231.4 is the MANE Select transcript for POLE (NP_006222.2, 2,286 aa; CDS 1-6861 across 49 exons); c.2413C>T is a nonsense substitution predicting p.(Gln805Ter) with consequence class 'nonsense', located in exon 21 (c.2320-2468 exon block; VariantValidator start/end exon 21).
• PTC position analysis: codon 805 lies in exon 21, with the final exon-exon junction (exon 49 start, c.6748) ~4.3 kb downstream; a PTC this far upstream is predicted to undergo nonsense-mediated decay (50-55 nt rule). If the transcript escaped NMD, translation would terminate at residue 804, deleting ~65% of POLE1 (residues 805-2286) C-terminal to the exonuclease domain.
• ClinGen SVI PVS1 recommendations (pvs1_generic_framework, PMC6185798): for a null (nonsense) variant in a gene with an established LoF mechanism, PVS1_VeryStrong applies when the PTC is not in the last exon and not within 50 nt of the final exon-exon junction; no NMD-escape or distal-critical-region downgrade applies at this position, and exon 21 is a constitutive MANE Select coding exon.
• pvs1_gene_context.json gene gate: germline LoF mechanism flagged as supported and PVS1 generic assessment eligible for POLE, with the caveat that the automated supporting-source list is unreliable (see warnings); the gate conclusion is corroborated directly by the fetched full-text papers below.
• PMID:23230001 (FILS syndrome, first POLE1 germline disease report): homozygous splice variant c.4444+3A>G in a consanguineous French kindred causes exon 34 skipping with frameshift PTC p.(Ser1483Valfs*79) and severe reduction of full-length Pol-epsilon-1 (~10% residual, haploinsufficiency), establishing biallelic POLE1 LoF as a germline disease mechanism; heterozygous parents asymptomatic. The exact c.2413C>T p.(Gln805Ter) variant is not mentioned.
• PMID:25948378 (POLE1 deficiency): a second family with homozygous c.4444+3A>G; the variant confers abnormal splicing with exon 34 deletion and significant decrease of the POLE1 subunit, with proliferation defect and impaired cell-cycle progression in patient T-lymphocytes. The exact c.2413C>T p.(Gln805Ter) variant is not mentioned.
• PMID:30503519 (IMAGe syndrome): biallelic POLE LoF alleles (nonsense/frameshift/essential-splice) in trans with a recurrent hypomorphic intronic variant cause IMAGe syndrome/primordial dwarfism; POLE LoF variants enriched vs gnomAD controls (p=5.1e-5), POLE1 protein 5-11% of control in patient fibroblasts. The exact c.2413C>T p.(Gln805Ter) variant is not mentioned.
• Framework scope: the local Leon-Castillo custom POLE framework (vcep_path_250_323) customizes only PM1, PS4, PP3 and BP4 (missense/hotspot/in-silico rules) and directs generic ACMG/AMP fallback outside that scope; it provides no POLE-specific specification for PVS1, PM4 or BP3, so generic ACMG/AMP 2015 with the SVI PVS1 decision tree governs these criteria.
• Population context: the variant is absent from gnomAD-Canada v1.0 (gnomad_canada); ClinVar submission SCV002125552 likewise notes absence from gnomAD, consistent with no population-based LoF-tolerance signal at this position.

Still missing

• Clinical indication/phenotype not specified in the case material (ClinVar condition 'not provided'); PVS1_VeryStrong rests on the gene-level LoF mechanism that is autosomal recessive (FILS/IMAGe syndromes; heterozygous null carriers reported asymptomatic). If the tested phenotype is the autosomal dominant cancer-predisposition phenotype (exonuclease-domain missense mechanism), PVS1 applicability should be re-confirmed against that indication.
• NMD is predicted bioinformatically from the PTC position (~4.3 kb 5' of the final exon-exon junction); no RNA/cDNA assay of this allele was available to confirm NMD or residual protein.
• gnomAD v2.1 and v4.1 population frequencies were not retrieved (timeout), so the population-based check against LoF-enriched regions at this position relies only on absence from gnomAD-Canada v1.0.

Sources

Reasoning

PM2 (pathogenic moderate, ACMG/AMP 2015, PMID 25741868) is met when the variant is absent from population databases, or at extremely low frequency if the disorder is recessive. c.2413C>T (p.Gln805Ter) is a protein-truncating allele in POLE, a gene in which biallelic loss of function causes the ultra-rare autosomal-recessive FILS and IMAGe syndromes (PMID 23230001, PMID 30503519). The variant is absent from every population source reporting data: the direct gnomAD-Canada v1.0 (HostSeq genomes, GRCh38) query returned 'absent' (zero alleles), and the single ClinVar clinical submission (SCV002125552, Labcorp) states the variant is 'not present in population databases (gnomad no frequency)', which was independently flagged as a PM2 criterion lead by the ClinVar submission audit. None of the fetched POLE papers report the allele in any cohort. Absence/effective AF of 0 in all reporting population datasets supports extreme rarity, consistent with a recessive-disease truncating allele. Caveats: (1) gnomAD v2.1 and v4.1 (the two largest reference datasets) could not be queried directly due to lookup timeouts, so AF = 0 in the global gnomAD exome/genome sets is asserted only via the submitter's statement and the smaller Canadian dataset - this warrants a confirmatory gnomAD browser check; (2) under the generic ACMG/AMP 2015 fallback that governs this case (the custom POLE framework specifies only PM1/PS4/PP3/BP4), PM2 retains its 2015 default strength of Moderate; if the lab applies the later ClinGen SVI-recalibrated PM2_supporting convention, strength should be downgraded accordingly at combination time.

Rule

PM2 (ACMG/AMP 2015, PMID 25741868): absent from population databases, or at extremely low frequency if the disorder is recessive (pathogenic moderate).

Evidence considered

• gnomAD-Canada v1.0 (HostSeq genomes, GRCh38) direct query for 12-132665357-G-A returned search_status 'absent' (found: false) - zero alleles observed; evidence sentence 'Absent from gnomAD-Canada v1.0.'
• ClinVar submission SCV002125552 (Labcorp, single submitter, criteria provided) states 'this variant is not present in population databases (gnomad no frequency)'; the ClinVar submission audit extracted this as a PM2 evidence signal (confidence 0.8). Used as a population-absence data statement, not as adoption of the submitter's overall Pathogenic classification.
• Under ACMG/AMP 2015 (PMID 25741868), PM2 is 'absent in controls (or at extremely low frequency if recessive)'; POLE germline LoF disease is recessive and ultra-rare (FILS syndrome, PMID 23230001; IMAGe syndrome, PMID 30503519), so effective AF of 0 across reporting population datasets meets the criterion.
• gnomAD v2.1 and v4.1 lookups timed out in this case and returned no allele-frequency data, so global-dataset absence rests on the submitter statement and the Canadian dataset rather than a directly retrieved gnomAD count.

Still missing

• gnomAD v2.1 (exomes) and gnomAD v4.1 (exomes/genomes) allele frequencies could not be retrieved (lookup timeout); confirm AF = 0 in the global gnomAD datasets by direct query to fully verify PM2 at the proposed strength.
• Strength of PM2 is Moderate per ACMG/AMP 2015 default because no VCEP/CSPEC or local framework rule specifying PM2 strength was available for POLE; confirm whether the lab's convention caps PM2 at supporting before final combination.

Sources

Reasoning

Governing framework: no ClinGen CSPEC exists for POLE, so the local custom Leon-Castillo et al. 2020 POLE framework (precedence rank 2) applies. Its PS4 rule is a somatic-recurrence adaptation whose literal text is: '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 Leon-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.' The variant under review, c.2413C>T (p.(Gln805Ter)/p.Q805*), is a nonsense variant in exon 21, not a missense exonuclease-domain variant, and is not among the PS4-eligible variants enumerated by the package; it is also absent from the recurrence evidence (COSMIC search for 'POLE c.2413C>T' returned no record). Because the rule's first precondition (exact missense variant recurrent in both COSMIC and TCGA in Supp Table S1) fails, the numeric element of the rule (combined EC count >=10) is never reached, so no threshold-direction comparison is engaged for the custom rule. Outside the paper-derived rules the framework falls back to generic ACMG/AMP, where PS4 requires the prevalence of the variant in affected individuals to be significantly increased versus controls (case-control enrichment); no germline case-control or cohort prevalence data exist for this exact variant. The three ClinVar-linked publications (PMID:23230001, PMID:25948378, PMID:30503519) were checked in paper_extracts as potential case-level/enrichment sources: all report different POLE variants (e.g., c.4444+3A>G) and never mention c.2413C>T/p.Q805* (variant_mentioned=false), so they contribute no PS4 support. The ClinVar Pathogenic assertion for variation 1358933 is a single 1-star clinical-laboratory submission (Labcorp/Invitae, 'criteria provided, single submitter'); per policy a laboratory classification is not case-control prevalence data and no criterion is inferred from another source's final classification. PS4 is therefore not met.

Evidence considered

• Governing custom POLE framework (Leon-Castillo et al. 2020): PS4_Supporting is restricted to exact missense variants recurrent in both COSMIC and TCGA endometrial-carcinoma cohorts (Supplementary Table S1) with combined EC count >=10 that belong to the established/pathogenic set; under the current package this supports only p.P286R, p.V411L, p.A456P, and p.S297F, capped at Supporting because it is somatic-recurrence context rather than germline case-control evidence.
• c.2413C>T is a nonsense variant (p.(Gln805Ter)/p.Q805*, exon 21) and is not in the framework's PS4-eligible set, so the rule's >=10 combined-EC-count threshold is never engaged (no numeric comparison is reached for the custom rule).
• COSMIC search for 'POLE c.2413C>T' returned no record (variant not previously reported in somatic cancers), consistent with absence of recurrence evidence.
• Generic ACMG/AMP PS4 fallback requires the variant's prevalence in affected individuals to be significantly increased versus controls; no case-control or cohort enrichment data exist for c.2413C>T in any consulted source.
• PMID:23230001, PMID:25948378, and PMID:30503519 were checked via paper_extracts for case-level reports of c.2413C>T: all three describe other POLE variants (e.g., c.4444+3A>G) and never mention c.2413C>T/p.Q805* (variant_mentioned=false), providing no enrichment or case-count evidence.
• ClinVar variation 1358933 carries a single clinical-laboratory submission (SCV002125552, Labcorp/Invitae; review status 'criteria provided, single submitter', 1 star) classifying the variant Pathogenic; a laboratory classification is not case-control prevalence data and is not used to infer PS4.

Still missing

• No germline case-control or cohort prevalence study exists for c.2413C>T (p.Gln805Ter); PS4 could only be revisited if such enrichment data are published.
• The variant is not represented in the Leon-Castillo recurrence tables (Supplementary Table S1), so the somatic-recurrence-based PS4_Supporting rule cannot apply to it under any scenario.

Sources

Reasoning

The governing framework (León-Castillo et al. 2020 custom POLE framework, custom_internal, not an official ClinGen VCEP specification) restricts PM1 to its enumerated exact exonuclease-domain missense substitutions: PM1_Strong p.P286R, p.V411L, p.S297F, p.A456P, p.S459F; PM1_Moderate p.F367S, p.L424I, p.M295R, p.P436R, p.M444K, p.D368Y; PM1_Supporting p.A465V, p.L424V, p.T278M, p.A428T - with the explicit instruction to use these only for the exact substitutions, not for all substitutions at the same codon. p.(Gln805Ter) is none of these substitutions and is not even a missense change; residue 805 lies roughly 340 residues C-terminal of the framework's most C-terminal exonuclease-domain variant (p.A465V), i.e., outside the exonuclease-domain hotspot region (approximately residues 278-465) that the framework's PM1 rules cover. The VCEP materials for this case contain no approved domain table (the domain_tables key is empty), so there is no authoritative VCEP entry placing residue 805 in a critical functional domain. Independently, CancerHotspots reports no statistically significant hotspot at POLE Q805 ('This variant does not lie in a statistically significant hotspot') and COSMIC has no record for POLE c.2413C>T, providing no hotspot or somatic-recurrence support. Under the generic ACMG/AMP 2015 fallback, PM1 likewise requires a mutational hotspot and/or critical well-established functional domain, which the case evidence does not establish for residue 805; moreover, PM1 is a location criterion designed around missense-style perturbation of a critical region, whereas the pathogenic effect of this truncating allele is scored under PVS1. PM1 is therefore not met.

Rule

Custom POLE framework (León-Castillo et al. 2020) PM1: apply PM1_Strong to p.P286R, p.V411L, p.S297F, p.A456P, p.S459F; PM1_Moderate to p.F367S, p.L424I, p.M295R, p.P436R, p.M444K, p.D368Y; PM1_Supporting to p.A465V, p.L424V, p.T278M, p.A428T - only for these exact substitutions, not all substitutions at the same codon; generic ACMG/AMP 2015 PM1 (mutational hotspot and/or critical well-established functional domain) otherwise

Evidence considered

• Governing framework (final_classification_framework: 'León-Castillo et al. 2020 custom POLE framework', framework_mode custom_internal, precedence_rank 2, not an official ClinGen VCEP) PM1 rules apply only to exact exonuclease-domain missense substitutions: PM1_Strong p.P286R, p.V411L, p.S297F, p.A456P, p.S459F; PM1_Moderate p.F367S, p.L424I, p.M295R, p.P436R, p.M444K, p.D368Y; PM1_Supporting p.A465V, p.L424V, p.T278M, p.A428T - 'Use this only for these exact substitutions, not all substitutions at the same codon.'
• p.(Gln805Ter) is not any framework-listed substitution; residue 805 is ~340 residues C-terminal of the framework's most C-terminal exonuclease-domain variant (p.A465V), outside the exonuclease-domain hotspot region (approx. residues 278-465) the PM1 rules cover.
• vcep_materials.json domain_tables is empty for POLE: no authoritative VCEP-approved critical-functional-domain table exists in the case evidence to place residue 805 in a domain.
• CancerHotspots query 'POLE Q805' returned no result ('This variant does not lie in a statistically significant hotspot') and COSMIC has no record for POLE c.2413C>T - no hotspot or somatic-recurrence support for PM1.
• PM1 in the generic ACMG/AMP 2015 fallback also requires a mutational hotspot and/or critical well-established functional domain; no evidence in this case places residue 805 in such a region, and the variant is a truncating nonsense change whose effect is evaluated under PVS1 rather than as a missense-type domain perturbation.

Still missing

• vcep_materials.json domain_tables is empty for POLE and no other in-case annotation defines POLE domain boundaries beyond the framework's exonuclease-domain hotspot region (approx. residues 278-465); if an authoritative full-length POLE functional-domain annotation (e.g., polymerase-domain boundaries) becomes available, residue 805's location relative to other critical domains should be re-checked for PM1.

Sources

Reasoning

Policy for this group: PP5 is applied (at supporting strength) only for an exact-variant ClinVar expert-panel classification of Pathogenic or Likely pathogenic; ordinary laboratory submissions, aggregate ClinVar labels, and non-expert assertions must never trigger PP5. ClinVar variation 1358933 (NM_006231.4(POLE):c.2413C>T (p.Gln805Ter)) contains exactly one submission - SCV002125552 from Labcorp Genetics (formerly Invitae), review status 'criteria provided, single submitter' (1 star). The submission audit records expert_panel_submissions = 0, and the ClinVar API shows no expert-panel classifications for this variant. No exact-variant expert-panel Pathogenic/Likely pathogenic classification exists, so the PP5 trigger condition is not met.

Evidence considered

• ClinVar variation 1358933 has exactly one submission (SCV002125552, Labcorp Genetics (formerly Invitae)) with review status 'criteria provided, single submitter' (1 star); expert_panel_submissions = 0; no expert-panel classification exists for the exact variant.
• Per the expert-panel-only policy, an ordinary clinical-laboratory submission (even one classifying the variant Pathogenic) must never trigger PP5; the criterion is therefore not met.

Still missing

• No ClinVar expert-panel (3-star) classification exists for c.2413C>T; PP5 could only be triggered if an expert-panel Pathogenic/Likely pathogenic classification is submitted in the future.

Sources

Reasoning

BA1 (stand-alone benign) requires an allele frequency above the reference-population threshold (ACMG/AMP 2015, PMID 25741868, specifies >5% in large reference datasets such as ExAC/1000G/ESP). No population dataset consulted reports any allele for NM_006231.4:c.2413C>T (p.Gln805Ter): the direct gnomAD-Canada v1.0 (HostSeq genomes, GRCh38) query returned 'absent', and the single ClinVar clinical submission (SCV002125552, Labcorp) states the variant is not present in population databases ('gnomad no frequency'). The observed allele frequency is therefore effectively 0 in every dataset that returned data, which is orders of magnitude below any plausible BA1 frequency threshold. The two largest reference datasets (gnomAD v2.1 exomes and v4.1 exomes/genomes) could not be queried directly in this case (lookup timeout), so a formally verified global AF of 0 is not available; however, nothing in any source suggests the variant is anything but rare, and absence/rarity is the opposite of what BA1 requires. Verdict: not met.

Rule

BA1 (ACMG/AMP 2015, PMID 25741868): allele frequency >5% in a large reference population dataset (ExAC/gnomAD/1000 Genomes/ESP) would constitute stand-alone benign evidence.

Evidence considered

• gnomAD-Canada v1.0 (HostSeq genomes, GRCh38) direct variant query for 12-132665357-G-A returned search_status 'absent' (found: false), i.e., zero alleles observed; evidence sentence: 'Absent from gnomAD-Canada v1.0.'
• ClinVar submission SCV002125552 (Labcorp, single clinical laboratory, criteria provided) contains the assertion 'this variant is not present in population databases (gnomad no frequency)'; treated only as a population-frequency data statement corroborating absence, not as adoption of the submitter's Pathogenic classification (ClinVar record VCV001358933, variation ID 1358933).
• No BA1-triggering allele frequency (per ACMG/AMP 2015, PMID 25741868) exists in any reporting dataset; observed frequency is 0.

Still missing

• gnomAD v2.1 and gnomAD v4.1 allele frequency/allele count could not be retrieved (lookup timeout); confirm global AF = 0 via a direct gnomAD browser query before any stand-alone-benign consideration is fully closed out.

Sources

Reasoning

BS1 (benign strong) requires an allele frequency greater than expected for the disorder in question. POLE germline loss-of-function alleles cause extremely rare autosomal-recessive syndromes (FILS syndrome, PMID 23230001; IMAGe syndrome/primordial dwarfism, PMID 30503519), so the disease-expected allele frequency is very low and any benign-triggering frequency would be far higher than observed. For c.2413C>T (p.Gln805Ter), the observed allele frequency is 0 in every dataset that returned data: absent from gnomAD-Canada v1.0 (HostSeq genomes) by direct query, and reported absent from gnomAD ('no frequency') in the single ClinVar clinical submission (SCV002125552). No dataset shows an allele count approaching a BS1 range, and the variant is a protein-truncating allele of the type expected to be selected against rather than common. Direct gnomAD v2.1/v4.1 frequencies were unavailable (lookup timeout), but the consistent absence across all reporting sources means BS1 is not met.

Rule

BS1 (ACMG/AMP 2015, PMID 25741868): allele frequency greater than expected for the disorder (benign strong).

Evidence considered

• gnomAD-Canada v1.0 (HostSeq genomes) reports the variant absent (search_status 'absent'), i.e., no alleles observed in that population cohort.
• ClinVar submission SCV002125552 (single laboratory) states the variant is 'not present in population databases (gnomad no frequency)', corroborating that no population allele count exists.
• Disease context (PMID 23230001, PMID 30503519): biallelic POLE loss-of-function causes the ultra-rare recessive FILS and IMAGe syndromes, so a benign-consistent allele frequency for such alleles would need to exceed the expected (very low) disease-allele frequency - not observed here.

Still missing

• gnomAD v2.1 and v4.1 allele frequencies not retrievable (lookup timeout); a direct population-frequency check in the global gnomAD datasets would formally quantify how far AF is from any BS1 range.

Sources

Reasoning

BS2 (benign strong) requires the variant to be observed in a healthy adult individual - for a recessive disorder, in the homozygous state (or in the compound-heterozygous/heterozygous state where disease is recessive the healthy-carrier state alone does not trigger BS2). c.2413C>T (p.Gln805Ter) has not been observed in any healthy adult: the gnomAD-Canada v1.0 query returned no alleles (hence no homozygotes or heterozygotes), and the ClinVar clinical submission reports no population-database frequency for the variant. None of the fetched full-text papers (PMID 23230001, 25948378, 30503519) report this exact variant in affected individuals or healthy carriers - they describe other POLE loss-of-function alleles (e.g., c.4444+3A>G) whose heterozygous carrier parents were unaffected, which is gene-level mechanism context only and cannot substitute for observation of this specific allele in healthy individuals. The disease (FILS/IMAGe syndromes) is extremely rare and recessive, so the absence of any healthy-adult observation is expected for a pathogenic allele and provides no benign evidence. Verdict: not met.

Rule

BS2 (ACMG/AMP 2015, PMID 25741868): observed in a healthy adult individual - homozygous for a recessive disorder, heterozygous for a dominant disorder, or hemizygous for an X-linked disorder (benign strong).

Evidence considered

• gnomAD-Canada v1.0 (HostSeq genomes) returned no alleles for 12-132665357-G-A (search_status 'absent'), meaning no homozygous or heterozygous healthy-adult observations in that population cohort.
• ClinVar submission SCV002125552 reports the variant is not present in population databases (no gnomAD frequency), consistent with the absence of any control observation.
• PMID 23230001, PMID 25948378, and PMID 30503519 do not mention c.2413C>T (p.Gln805Ter) at all (variant_mentioned: false in paper_extracts.json); they describe different POLE LoF alleles (e.g., homozygous c.4444+3A>G causing FILS syndrome with asymptomatic heterozygous parents), which is not variant-level BS2 evidence.

Still missing

• No case-level or cohort observation of c.2413C>T in healthy adults exists in the retrieved sources; BS2 would only become relevant if population or case-control data showed the variant in healthy individuals (homozygotes for this recessive phenotype).

Sources

Reasoning

Policy for this group: BP6 is applied (at supporting strength) only for an exact-variant ClinVar expert-panel classification of Benign or Likely benign; ordinary laboratory submissions, aggregate ClinVar labels, and non-expert assertions must never trigger BP6. ClinVar variation 1358933 contains no expert-panel submission and no benign or likely-benign assertion of any kind: the sole entry is SCV002125552 (Labcorp Genetics (formerly Invitae)), a clinical-laboratory Pathogenic submission with review status 'criteria provided, single submitter' (1 star). The required expert-panel benign/likely-benign classification does not exist, so the BP6 trigger condition is not met. (The single laboratory Pathogenic assertion points away from benignity in any case, but per policy no criterion is inferred from another source's classification.)

Evidence considered

• ClinVar variation 1358933 contains no expert-panel submission and no benign/likely-benign assertion; the only entry is a 1-star clinical-laboratory Pathogenic submission (SCV002125552, Labcorp/Invitae).
• Per the expert-panel-only policy, ordinary laboratory submissions and non-expert assertions must never trigger BP6; the criterion is therefore not met.

Still missing

• No ClinVar expert-panel benign/likely-benign classification exists for c.2413C>T; BP6 could only be triggered if an expert-panel benign assertion is submitted in the future.

Sources

Reasoning

No de novo evidence exists for c.2413C>T (p.Gln805Ter). The governing rules for PS2 fall back to generic ACMG/AMP 2015 (Richards et al., PMID:25741868) because the local POLE custom framework (León-Castillo et al. 2020) customizes only PM1, PS4, PP3, and BP4, and no official ClinGen CSPEC for POLE is available (cspec found=false). PS2 requires a de novo occurrence with confirmed maternity and paternity in a proband, but no proband-parent trio, parental genotyping result, or de novo annotation for this exact variant appears in any source: all three full-text papers (PMID:23230001, PMID:25948378, PMID:30503519) report different POLE alleles (e.g., homozygous c.4444+3A>G in FILS syndrome; assorted biallelic LoF alleles in IMAGe syndrome) and none mentions c.2413C>T (pre-computed full-text extraction: variant_mentioned=false for all three), and the single ClinVar germline submission (variation 1358933, Labcorp, Pathogenic, SCV002125552, condition not provided) contains no parental-testing or de novo annotation and discloses no submitted criteria codes. In addition, the germline POLE loss-of-function phenotypes documented in the retrieved literature (FILS and IMAGe syndromes) are autosomal recessive, so a de novo dominant occurrence would be mechanistically unexpected unless a dominant presentation is the queried context. Paternity/maternity-confirmed de novo status of p.Gln805Ter is therefore unevaluated.

Rule

Generic ACMG/AMP 2015 (PMID:25741868) PS2: de novo variant with confirmed maternity and paternity (Strong). No POLE VCEP/custom rule governs PS2 (custom framework covers only PM1/PS4/PP3/BP4).

Evidence considered

• PS2/PM6/PP1/BS4 are governed by generic ACMG/AMP 2015 (Richards et al., PMID:25741868): the León-Castillo 2020 custom POLE framework (precedence_rank 2, official_clingen=false) customizes only PM1, PS4, PP3, and BP4, and no ClinGen CSPEC was found for POLE.
• Pre-computed full-text extraction reports variant_mentioned=false for c.2413C>T (p.Gln805Ter) in PMID:23230001, PMID:25948378, and PMID:30503519; the exact-variant strings searched in each paper included c.2413C>T and p.(Q805*).
• ClinVar variation 1358933 (SCV002125552, Labcorp, germline, Pathogenic, single submitter, condition 'not provided', last evaluated 2022-05-12) provides no de novo, parental-testing, or segregation annotation and no submitted criteria codes.
• No proband-parent trio or parental genotyping result for this exact variant exists anywhere in the case evidence, so paternity/maternity-confirmed de novo status (PS2) cannot be evaluated.

Still missing

• No proband-parent trio or parental genotyping result for c.2413C>T (p.Gln805Ter) in any published case or in the ClinVar submission; confirmed de novo status is unknown.
• The POLE germline LoF phenotypes described in the retrieved papers (FILS, IMAGe) are autosomal recessive; applicability of de novo criteria depends on the unstated clinical context of this germline heterozygous submission.

Sources

Reasoning

PS3 was evaluated against the generic ACMG/AMP 2015 definition (Richards et al., PMID 25741868), because no ClinGen CSPEC/VCEP specification exists for POLE and the local custom POLE framework (Leon-Castillo et al. 2020) defines rules only for PM1/PS4/PP3/BP4 (all missense-specific), explicitly deferring all other criteria to generic ACMG/AMP. No well-established functional study of this exact variant, c.2413C>T p.(Gln805Ter), was identified. OncoKB lists no variant-specific reviewed functional evidence ('Unknown Oncogenic Effect', no supporting PMIDs); COSMIC has no record for the variant and Cancer Hotspots has no Q805 entry. All three ClinVar-linked full-text papers were reviewed (PMID:23230001 FILS syndrome kindred; PMID:25948378 POLE1-deficiency patient; PMID:30503519 IMAGe syndrome/primordial dwarfism) and none mentions p.Q805*; their functional assays (exon-34 skipping with severely decreased POLE1 subunit for the c.4444+3A>G FILS allele; POLE1 protein depleted to ~5-11% of control with delayed S-phase for biallelic LoF alleles in IMAGe) test other POLE alleles and support only a gene-level loss-of-function mechanism. The predicted truncation (nonsense at residue 805 of the 2,286-residue protein) is a variant-consequence consideration evaluated under the SVI PVS1 framework, not an observed assay result, and cannot substitute for PS3. PS3 is therefore not assessed: it could only be applied if a validated, calibrated POLE functional assay (per ClinGen SVI PS3/BS3 guidance, Brnich et al., Genome Medicine 2020) were performed on this exact allele and demonstrated a damaging effect.

Rule

Generic ACMG/AMP 2015 (Richards et al., PMID 25741868): PS3 - well-established functional studies show a damaging effect on the gene or gene product.

Evidence considered

• Governing framework: no ClinGen CSPEC/VCEP for POLE was retrieved; the local custom framework (Leon-Castillo et al. 2020) customizes only PM1/PS4/PP3/BP4 for missense variants, so PS3/BS3 fall back to generic ACMG/AMP 2015 (Richards et al., PMID 25741868), where PS3 requires well-established functional studies showing a damaging effect on the gene or gene product.
• OncoKB (oncokb) reports no variant-specific reviewed functional evidence for POLE p.Q805* and classifies it 'Unknown Oncogenic Effect'; no supporting PMIDs are provided, so no assay result backs a damaging-effect call.
• COSMIC has no somatic record and Cancer Hotspots has no statistically significant hotspot at residue Q805, providing no functional or recurrence context for this allele.
• Full-text review of PMID:23230001 (FILS syndrome): the paper's functional work (aberrant splicing deleting exon 34, ~90% abnormal transcript, severely decreased full-length POLE1 with no truncated protein detected, impaired proliferation/cell cycle rescued by WT POLE1 complementation) was performed for the homozygous c.4444+3A>G allele in a consanguineous kindred; c.2413C>T p.Q805* is not mentioned, so this is gene/mechanism-level evidence only.
• Full-text review of PMID:25948378 (POLE1 deficiency): reports the same c.4444+3A>G splice variant in a second family with abnormal splicing, exon 34 deletion, significant decrease in POLE1 subunit, and T-lymphocyte proliferation/cell-cycle defects; p.Q805* is not mentioned.
• Full-text review of PMID:30503519 (IMAGe syndrome): biallelic POLE LoF (nonsense/frameshift/splice) alleles in trans with hypomorphic c.1686+32C>G cause POLE1 depletion (5-11% of control in patient fibroblasts) and delayed S-phase; c.2413C>T p.Q805* is not mentioned and no variant-level assay of it was performed.
• p.Gln805Ter is a nonsense change; predicted loss of function is a PVS1-type variant-consequence inference evaluated under the SVI PVS1 framework (pvs1_generic_framework), not a functional-assay observation, and must not be double-counted as PS3.

Still missing

• No variant-specific (or same-residue) functional assay for p.Q805* was identified in OncoKB, COSMIC, Cancer Hotspots, or the fetched literature; a validated POLE functional assay (e.g., replication-fidelity/complementation or POLE1 protein-expression assay, calibrated per ClinGen SVI PS3/BS3 guidance, Brnich et al., Genome Medicine 2020) applied to this exact allele would be required before PS3 can be met at any strength.
• Gene-level loss-of-function evidence from biallelic POLE LoF disorders (FILS/IMAGe) concerns other truncating/splice alleles and was not performed on p.Q805*; it documents disease mechanism (relevant to PVS1) but is not variant-level functional evidence for PS3.

Sources

Reasoning

PM3 (generic ACMG/AMP 2015, PMID 25741868) applies to recessive disorders when the variant is detected in trans with a pathogenic/likely pathogenic variant. No ClinGen CSPEC exists for POLE, and the governing local framework (León-Castillo et al. 2020 custom POLE) customizes only PM1, PS4, PP3 and BP4, all missense-focused rules; PM3 therefore falls back to the generic rule. The criterion is applicable in principle: germline POLE truncating/loss-of-function alleles cause autosomal recessive FILS syndrome / POLE1 deficiency / IMAGe-like primordial dwarfism, so a nonsense allele such as p.Gln805Ter could in theory be observed in trans with a second pathogenic POLE allele in an affected proband. However, no such observation exists in any consulted source. The only clinical record, ClinVar VCV001358933 (submission SCV002125552, Labcorp Genetics, Pathogenic, criteria provided/single submitter, germline, evaluated 2022-05-12), reports no condition, no second POLE allele, no zygosity and no phase information; its only stated criterion signal is absence from population databases (PM2). All three full-text papers retrieved for this case (PMID:23230001 FILS syndrome, PMID:25948378 POLE1 deficiency, PMID:30503519 IMAGe syndrome) document biallelic POLE loss-of-function disease caused by other variants (e.g., homozygous c.4444+3A>G) and never mention c.2413C>T / p.Gln805Ter (variant_mentioned = false for each). Because trans phase with a pathogenic POLE allele cannot be established from any available data, PM3 cannot be scored; evidence is insufficient rather than contradictory, so the criterion is returned as not_assessed with the specific data gap noted.

Rule

PM3 (generic ACMG/AMP 2015, PMID 25741868): for recessive disorders, apply when the variant is detected in trans with a pathogenic/likely pathogenic variant. Not customized by the local León-Castillo POLE framework, which specifies only PM1/PS4/PP3/BP4.

Evidence considered

• Generic ACMG/AMP 2015 rules (source_pmid 25741868) define PM3 for recessive disorders as detection in trans with a pathogenic/likely pathogenic variant; the local León-Castillo POLE framework does not customize PM3, so the generic rule governs.
• ClinVar VCV001358933 (SCV002125552, Labcorp Genetics, Pathogenic, single submitter, germline, 2022-05-12) reports NM_006231.4:c.2413C>T (p.Gln805Ter) but lists no condition, no second POLE allele, no zygosity and no phase; the stated criterion signal is limited to absence from population databases.
• PMID:23230001 (Pachlopnik Schmid et al., FILS syndrome): biallelic POLE1 loss-of-function causes an autosomal recessive syndrome in a consanguineous kindred, but the causal variant was a different homozygous splice-site change (g.G4444+3A>G / c.4444+3A>G); c.2413C>T (p.Q805*) is not mentioned (variant_mentioned = false).
• PMID:25948378 (Thiffault et al., POLE1 deficiency): a second family with autosomal recessive POLE1 deficiency carried a different homozygous splice variant (c.4444+3A>G) inherited from unaffected heterozygous parents; c.2413C>T is not mentioned (variant_mentioned = false).
• PMID:30503519 (Logan et al., IMAGe syndrome): biallelic POLE loss-of-function alleles (nonsense/frameshift/essential-splice) observed in trans with a recurrent hypomorphic intronic allele cause IMAGe syndrome/primordial dwarfism; c.2413C>T is not mentioned (variant_mentioned = false).

Still missing

• No affected-proband observation of c.2413C>T together with a second pathogenic POLE allele; parental/phase (trans vs cis) testing results are not available in the ClinVar record (SCV002125552) or in any consulted publication.
• No zygosity or segregation data for c.2413C>T; a homozygous or compound-heterozygous observation in an affected individual would be required to apply PM3.

Sources

Reasoning

No assumed-de novo evidence is available for c.2413C>T (p.Gln805Ter). PM6 (generic ACMG/AMP 2015, PMID:25741868) is applied when a de novo occurrence is assumed but maternity/paternity have not been confirmed; here there is not even an unconfirmed de novo observation, because no proband with this variant and no parental genotyping results are reported in any source. The three full-text papers (PMID:23230001, PMID:25948378, PMID:30503519) never mention p.Gln805Ter (variant_mentioned=false in the pre-computed extractions; they describe other POLE alleles: homozygous c.4444+3A>G in FILS families and assorted biallelic LoF/hypomorphic allele combinations in IMAGe families), and the ClinVar record (variation 1358933) is a single germline Pathogenic submission with no family-based annotation or disclosed criteria. PM6 therefore cannot be assessed; the gap is the complete absence of proband and parental genotype data for this exact variant.

Rule

Generic ACMG/AMP 2015 (PMID:25741868) PM6: assumed de novo variant without confirmation of maternity and paternity. No POLE VCEP/custom rule governs PM6.

Evidence considered

• PM6 (generic ACMG/AMP 2015, PMID:25741868) requires an assumed de novo occurrence without confirmed parentage; the POLE custom framework provides no PM6 specification.
• All three full-text papers (PMID:23230001, PMID:25948378, PMID:30503519) were checked for c.2413C>T / p.(Q805*) and none mentions the variant (variant_mentioned=false), so no proband-level de novo report exists in the literature reviewed.
• ClinVar variation 1358933 contains a single germline Pathogenic submission with no de novo/parental-testing annotation or criteria codes, so no assumed de novo event is recorded there either.

Still missing

• No proband observation of c.2413C>T with parental testing results, so even an unconfirmed (assumed) de novo event cannot be documented.
• No phenotype/inheritance context is attached to this germline variant submission, precluding assessment of whether a de novo mechanism is clinically plausible.

Sources

Reasoning

No segregation evidence exists for c.2413C>T (p.Gln805Ter). PP1 (generic ACMG/AMP 2015, PMID:25741868; no POLE-specific specification, as the custom framework customizes only PM1/PS4/PP3/BP4) requires cosegregation of the variant with disease in affected family members, but no family in which p.Gln805Ter segregates is reported in any source. The segregation data present in the three full-text papers concern different alleles: PMID:23230001 and PMID:25948378 report homozygous c.4444+3A>G segregating with FILS syndrome in consanguineous families with heterozygous asymptomatic parents, and PMID:30503519 reports biallelic combinations of various POLE LoF alleles with the hypomorphic c.1686+32C>G in IMAGe/primordial dwarfism families; none involves c.2413C>T, and per the pre-computed full-text extraction all three have variant_mentioned=false for this variant. Segregation of other POLE alleles does not count toward PP1 for this exact variant. The number of informative meioses for p.Gln805Ter is zero.

Rule

Generic ACMG/AMP 2015 (PMID:25741868) PP1: cosegregation with disease in multiple affected family members in a gene definitively known to cause the disease (Supporting). No POLE VCEP/custom rule governs PP1.

Evidence considered

• PP1 (generic ACMG/AMP 2015, PMID:25741868) requires cosegregation with disease in affected relatives; the local POLE custom framework defines no PP1 rule.
• PMID:23230001 describes 14 affected individuals homozygous for c.4444+3A>G with heterozygous asymptomatic parents, and PMID:25948378 a second family with the same splice variant inherited from heterozygous carriers; these are segregation data for c.4444+3A>G, not for c.2413C>T.
• PMID:30503519 reports biallelic POLE LoF variants (nonsense/frameshift/splice) in trans with the hypomorphic c.1686+32C>G in IMAGe syndrome; c.2413C>T is not among the alleles.
• Pre-computed full-text extraction confirms c.2413C>T / p.(Q805*) is not mentioned in any of the three papers (variant_mentioned=false), so no affected relative carrying this variant is documented.
• ClinVar variation 1358933 reports no family or segregation observations for c.2413C>T.

Still missing

• No reported family in which c.2413C>T (p.Gln805Ter) cosegregates with a POLE-related phenotype; informative meioses for this exact variant = 0.
• Segregation data in the retrieved papers (homozygous c.4444+3A>G in FILS; biallelic LoF plus c.1686+32C>G in IMAGe) involve different alleles and cannot be transferred to p.Gln805Ter.

Sources

Reasoning

Generic ACMG/AMP PP4 requires a phenotype or family history highly specific for a disease with a single genetic etiology. POLE germline loss-of-function is associated with autosomal-recessive FILS syndrome (facial dysmorphism, immunodeficiency, livedo, short stature; PMID:23230001), POLE1 deficiency overlapping DNA breakage/instability syndromes (PMID:25948378), and IMAGe syndrome/microcephalic primordial dwarfism with variable immunodeficiency (PMID:30503519) - phenotypes clinically distinct from the dominant exonuclease-domain cancer predisposition caused by POLE missense hotspots. However, the case materials contain no proband phenotype description, family history, zygosity, or phase information (monoallelic versus biallelic context) for c.2413C>T; the ClinVar submission itself lists condition as 'not provided'. Without the proband's phenotype, it cannot be determined whether the presentation is highly specific for a POLE-related disorder, so PP4 cannot be evaluated. Not assessed; a human reviewer with access to the clinical requisition is required.

Evidence considered

• POLE biallelic loss-of-function phenotypes documented in the literature: FILS syndrome (facial dysmorphism, immunodeficiency, livedo, short stature; PMID:23230001), POLE1 deficiency overlapping DNA breakage/instability syndromes (PMID:25948378), and IMAGe syndrome/microcephalic primordial dwarfism with variable immunodeficiency (PMID:30503519).
• The ClinVar submission for c.2413C>T (SCV002125552) lists the condition as 'not provided', and no proband phenotype or family history is documented anywhere in the case materials.
• Because PP4 requires the proband's phenotype/family history to be highly specific for a single-etiology disease, and that clinical information is absent, the criterion is not assessed and requires human review with the clinical requisition.

Still missing

• Proband phenotype, family history, zygosity, and monoallelic/biallelic context are absent from the case materials - all required to evaluate PP4.
• ClinVar submission lists condition as 'not provided', so no clinical indication is available from that source either.

Sources

Reasoning

BS3 was evaluated against the generic ACMG/AMP 2015 definition (Richards et al., PMID 25741868): well-established functional studies showing the variant has no damaging effect on gene/protein function. No functional data of any kind exist for c.2413C>T p.(Gln805Ter): OncoKB provides no reviewed functional evidence for the allele, COSMIC is negative (no somatic report), and none of the three full-text papers linked to the ClinVar record (PMID:23230001, PMID:25948378, PMID:30503519) mentions the variant or reports any assay showing preserved POLE function. The single-submitter ClinVar Pathogenic assertion is a final classification, not functional evidence, and was not used to refute BS3. Absence of damaging-effect data is not evidence of no damaging effect. BS3 is therefore not assessed: applying it would require a validated functional assay demonstrating normal (or near-normal) polymerase function for this exact allele, which is not available.

Rule

Generic ACMG/AMP 2015 (Richards et al., PMID 25741868): BS3 - well-established functional studies show no damaging effect on the gene or gene product.

Evidence considered

• Governing framework: no ClinGen CSPEC/VCEP for POLE was retrieved; the local custom framework (Leon-Castillo et al. 2020) customizes only PM1/PS4/PP3/BP4 for missense variants, so PS3/BS3 fall back to generic ACMG/AMP 2015 (Richards et al., PMID 25741868), where BS3 requires well-established functional studies showing no damaging effect on the gene or gene product.
• No source provides assay evidence of preserved POLE function for p.Q805*: OncoKB (oncokb) lists no variant-specific functional data ('Unknown Oncogenic Effect'); COSMIC has no record; Cancer Hotspots has no Q805 entry.
• All three full-text papers (PMID:23230001, PMID:25948378, PMID:30503519) were checked for the variant and none mentions c.2413C>T p.Q805* or reports any experiment bearing on its function; their data concern other POLE alleles and a gene-level LoF mechanism, none of which supports a no-damaging-effect conclusion for this allele.
• The ClinVar Pathogenic submission (SCV002125552, single submitter, 1-star review status) is a final classification and was not used as evidence for or against BS3, consistent with the rule that criteria are never inferred from another source's classification.

Still missing

• No functional study of p.Q805* demonstrating absence of a damaging effect (e.g., normal polymerase activity, successful complementation, or normal POLE1 protein level in a validated assay) was identified in OncoKB, COSMIC, or the fetched literature; BS3 cannot be applied without such an assay.
• The variant is a nonsense allele, a class in which 'no damaging effect' would be an unexpected and high-bar conclusion; any future benign-functional claim would need a calibrated assay and careful reconciliation with the recessive LoF disease mechanism.

Sources

Reasoning

No non-segregation evidence can be evaluated for c.2413C>T (p.Gln805Ter). BS4 (generic ACMG/AMP 2015, PMID:25741868; no POLE-specific rule exists since the custom framework customizes only PM1/PS4/PP3/BP4) is met when the variant is absent in affected family members despite segregation studies; conversely it is not met when segregation is observed. Neither situation is documented for this variant: no affected family members have been genotyped for p.Gln805Ter in any source. The family observations in the three full-text papers (PMID:23230001, PMID:25948378: homozygous c.4444+3A>G in affected FILS patients with heterozygous carrier parents; PMID:30503519: biallelic LoF plus c.1686+32C>G in IMAGe families) concern different POLE alleles and do not test c.2413C>T in any affected individual (variant_mentioned=false in all three pre-computed extractions). The ClinVar record (variation 1358933) contains no segregation observations. BS4 is therefore not_assessed, not met: there is no positive segregation against the variant, but equally no genotyped affected-relative data to affirm absence of segregation.

Rule

Generic ACMG/AMP 2015 (PMID:25741868) BS4: lack of segregation in affected family members (Strong, benign direction). No POLE VCEP/custom rule governs BS4.

Evidence considered

• BS4 (generic ACMG/AMP 2015, PMID:25741868) requires absence of the variant in affected family members; the POLE custom framework provides no BS4 specification.
• None of the three full-text papers (PMID:23230001, PMID:25948378, PMID:30503519) mentions c.2413C>T (variant_mentioned=false), so no affected individual has been genotyped for this variant in the reviewed literature.
• ClinVar variation 1358933 (single germline Pathogenic submission) contains no affected-relative testing or segregation observations for c.2413C>T.
• Documented family observations in PMID:23230001/PMID:25948378 (c.4444+3A>G homozygosity in affected patients) and PMID:30503519 (biallelic LoF/hypomorphic combinations) are allele-specific and cannot support or refute BS4 for p.Gln805Ter.

Still missing

• No affected family members tested for c.2413C>T (p.Gln805Ter), so non-segregation cannot be affirmed; conversely no segregation has been observed either.
• Family studies reported in the retrieved literature test other POLE alleles only and are uninformative for this variant.

Sources

Reasoning

BP2 (generic ACMG/AMP 2015, PMID 25741868) applies when a variant is observed in trans with a pathogenic variant for a fully dominant disease/gene, or in cis with a pathogenic variant in any inheritance pattern. The local León-Castillo POLE framework does not customize BP2, so the generic rule governs. Regarding the first (dominant-trans) arm: the germline disease caused by POLE truncating/loss-of-function alleles is autosomal recessive (FILS syndrome, POLE1 deficiency, IMAGe-like primordial dwarfism), and in all three full-text papers heterozygous carriers of truncating alleles (parents) are unaffected, indicating POLE loss-of-function phenotypes are not fully dominant; the dominant-trans arm of BP2 is therefore not the operative scenario for this nonsense allele. Regarding the second (cis) arm: no source reports c.2413C>T in cis with any pathogenic POLE variant. The only clinical observation, ClinVar VCV001358933 (SCV002125552, Labcorp Genetics, Pathogenic, single submitter, germline), contains no information about a second POLE allele, phase, or familial genotypes, and none of the full-text papers (PMID:23230001, PMID:25948378, PMID:30503519) mentions the variant at all. Because no cis or trans configuration with a pathogenic variant is documented, BP2 cannot be scored from the available evidence and is returned as not_assessed with the data gap noted.

Rule

BP2 (generic ACMG/AMP 2015, PMID 25741868): observed in trans with a pathogenic variant for a fully dominant disease/gene, or observed in cis with a pathogenic variant in any inheritance pattern. Not customized by the local León-Castillo POLE framework.

Evidence considered

• Generic ACMG/AMP 2015 rules (source_pmid 25741868) define BP2 as observation in trans with a pathogenic variant for a fully dominant disease/gene, or in cis with a pathogenic variant in any inheritance pattern; the local León-Castillo POLE framework does not customize BP2.
• ClinVar VCV001358933 (SCV002125552, Labcorp Genetics, Pathogenic, single submitter, germline) is the only clinical observation of c.2413C>T and reports no second POLE variant, phase, or familial genotypes, so no cis or trans configuration with a pathogenic variant can be established.
• PMID:23230001, PMID:25948378 and PMID:30503519 all describe autosomal recessive disease from biallelic POLE truncating/LoF alleles, with heterozygous carrier parents unaffected; this indicates POLE loss-of-function phenotypes are not fully dominant, removing the dominant-trans arm of BP2 from consideration for this nonsense allele.
• None of the three full-text publications (PMID:23230001, PMID:25948378, PMID:30503519) mentions c.2413C>T / p.Q805* (variant_mentioned = false for each), so no cis-observation of this variant with a pathogenic POLE variant is reported anywhere.

Still missing

• No familial genotyping data establishing the configuration of c.2413C>T relative to any pathogenic POLE variant (cis vs trans); the single ClinVar submission reports no second allele.
• No evidence of a proband carrying c.2413C>T together with another POLE variant in cis on the same allele.

Sources

Reasoning

Generic ACMG/AMP BP5 is met when a variant is found in a case with an alternate molecular basis for disease. The governing POLE custom framework does not customize BP5 (its customized criteria are PM1, PS4, PP3, and BP4 only), and no ClinGen CSPEC or VCEP specification defining an alternative BP5 rule (e.g., a likelihood-ratio-style value where met requires value <= threshold) was retrieved for POLE; no numeric threshold is therefore engaged for this criterion. No proband-level molecular findings are documented in the case materials - there is no report of an alternate causative variant or alternative molecular diagnosis - so whether an alternate molecular basis exists cannot be determined. Not assessed; a human reviewer with the proband's molecular work-up is required.

Evidence considered

• Generic ACMG/AMP BP5 definition: variant found in a case with an alternate molecular basis for disease.
• The governing POLE custom framework does not define any alternative BP5 specification (customized criteria are limited to PM1, PS4, PP3, BP4), and no VCEP/CSpec with a numeric BP5 definition was retrieved, so no likelihood-ratio-style threshold comparison is applicable.
• No proband-level information about an alternate causative variant or molecular diagnosis exists in the case materials, so BP5 cannot be evaluated.

Still missing

• No proband molecular work-up results are available; whether the case has an alternate molecular basis (the BP5 requirement) cannot be determined without them.