STK11 c.658C>T, p.(Gln220Ter)

Reasoning

No STK11-specific VCEP or CSPEC specification was available, so the generic ClinGen SVI PVS1 framework (PMC6185798) applies. NM_000455.4:c.658C>T is a nonsense variant producing NP_000446.1:p.(Gln220Ter) in the RefSeq-selected STK11 transcript, and VariantValidator places it in exon 5 of the nine-exon transcript. The premature termination codon is well upstream of the final exon-exon junction, making escape from nonsense-mediated decay unlikely under the generic framework. It truncates the 434-residue protein at residue 220, within the functionally important central kinase-region context rather than a distal terminal tail, and there is no evidence that this exon is non-critical or enriched for benign loss-of-function variation. The variant is directly reported as c.658C>T/p.Q220X in a Peutz-Jeghers syndrome cohort and as a Gln-to-stop change compromising the LKB1 open reading frame in another germline study. Therefore, no named downgrade rule is triggered and PVS1 is met at full strength.

Rule

generic ClinGen SVI PVS1 framework (PMC6185798)

Evidence considered

• The generic ClinGen SVI PVS1 framework in PMC6185798 was used because no STK11-specific VCEP or CSPEC specification was available.
• VariantValidator identifies NM_000455.4:c.658C>T as a nonsense variant producing NP_000446.1:p.(Gln220Ter) in exon 5 of the RefSeq-selected nine-exon STK11 transcript; the stop is well upstream of the final exon-exon junction, supporting NMD rather than escape.
• The predicted protein consequence terminates STK11 at residue 220 of 434, within the central functional region and not in a distal terminal tail; no evidence in the case data indicates a non-critical exon or benign loss-of-function-enriched repeat region.
• PMID:17026623 reports c.658C>T:p.Q220X in a patient with Peutz-Jeghers syndrome, and PMID:9887330 reports the corresponding C658→T Gln-to-stop change as compromising the LKB1 open reading frame and producing a truncated protein.

Sources

Reasoning

Generic ACMG/ClinGen SVI guidance is applicable because no STK11-specific VCEP or gene framework was available. PM2 at supporting strength is satisfied when a variant is absent or sufficiently rare in population databases, using the supplied generic threshold of allele frequency <=0.0001. The variant was absent from gnomAD v2.1 and from the reported gnomAD v2.1 non-cancer and gnomAD v3.1 non-cancer datasets; gnomAD v4.1 also showed 0/1,608,534 alleles and 0 homozygotes. These data support PM2 at supporting strength.

Evidence considered

• gnomAD v2.1 reported the variant as absent.
• The gnomAD v2.1 non-cancer exome-only dataset reported the variant as absent.
• The gnomAD v3.1 non-cancer genome-only dataset reported the variant as absent.
• gnomAD v4.1 reported 0 alternate alleles among 1,608,534 total alleles, 0 homozygotes, and total allele frequency 0.
• Generic PM2 supporting calibration supplied for this review: allele frequency <=0.0001 (ClinGen SVI recommendation, PMID:25741868).

Sources

Reasoning

No applicable STK11-specific VCEP framework was identified, so generic ACMG/AMP PP4 applies. The exact variant c.658C>T (p.Gln220Ter) was reported in a patient diagnosed with Peutz–Jeghers syndrome at age 3 who had buccal freckling. Peutz–Jeghers syndrome is the relevant STK11-associated phenotype, and this characteristic phenotype in an exact-variant carrier supports PP4 at supporting strength. A second exact-variant report documents Peutz–Jeghers syndrome but gives the patient's family history and pigmentation status as unknown.

Rule

Generic ACMG/AMP PP4 supporting: the patient's phenotype or family history is highly specific for a disease with a single gene etiology; no STK11-specific VCEP threshold was available.

Evidence considered

• PMID:17026623 Table 1 reports c.658C>T:p.Q220X in patient 4, a female diagnosed with Peutz–Jeghers syndrome at age 3 with buccal freckling.
• Peutz–Jeghers syndrome with mucocutaneous pigmentation is the characteristic phenotype associated with germline STK11 disease.
• PMID:9887330 independently reports C658→T in a Peutz–Jeghers syndrome patient, although that patient's family history, pigmentation, and cancer history were unknown.

Sources

Reasoning

Generic ACMG/AMP is applicable because no STK11-specific VCEP or gene framework was available. BA1 requires an allele frequency of at least 0.05. The variant was absent from gnomAD v2.1 and had allele frequency 0 (0/1,608,534 alleles; 0 homozygotes) in gnomAD v4.1, with the highest reported ancestry-specific frequency also 0 (0/74,952 African/African American alleles). Therefore, the stand-alone benign frequency threshold is not met.

Evidence considered

• gnomAD v2.1 reported the variant as absent.
• gnomAD v4.1 reported 0 alternate alleles among 1,608,534 total alleles, 0 homozygotes, and an ancestry-specific maximum frequency of 0 among 74,952 African/African American alleles.
• Generic ACMG/AMP BA1 calibration: allele frequency >=0.05 is required (ACMG/AMP 2015, PMID:25741868).

Sources

Reasoning

Generic ACMG/AMP is applicable because no STK11-specific VCEP or gene framework was available. BS1 requires an allele frequency greater than or equal to 0.01 under the supplied generic default. The variant was absent from gnomAD v2.1 and had allele frequency 0 (0/1,608,534 alleles; 0 homozygotes) in gnomAD v4.1, including frequency 0 in the highest-observed ancestry group. Thus, the population frequency does not meet BS1.

Evidence considered

• gnomAD v2.1 reported the variant as absent.
• gnomAD v4.1 reported 0 alternate alleles among 1,608,534 total alleles, 0 homozygotes, and frequency 0 in every reported ancestry group.
• Generic BS1 calibration supplied for this review: allele frequency >=0.01 (Whiffin et al., PMID:28518168).

Sources

Reasoning

BS2 requires observation of the variant in healthy adults, typically including healthy homozygotes when relevant. The available population data show no alternate alleles and no homozygotes: gnomAD v2.1 reported absence, and gnomAD v4.1 reported 0/1,608,534 alleles and 0 homozygotes. No healthy-adult carrier or homozygote observation is documented, so BS2 is not met.

Evidence considered

• gnomAD v2.1 reported the variant as absent.
• gnomAD v4.1 reported 0 alternate alleles among 1,608,534 total alleles and 0 homozygotes; therefore it provides no healthy-population observation supporting BS2.

Sources

Reasoning

No case-level evidence establishes that NM_000455.4:c.658C>T (p.Gln220Ter) arose de novo. The variant is reported in a Peutz–Jeghers syndrome proband, but parental testing and confirmed unaffected parental carrier status are not reported; therefore neither confirmed de novo evidence nor a PS2 likelihood-based assessment is available.

Rule

Generic ACMG/AMP PS2: apply only when de novo status is established by parental testing and the phenotype is consistent; no applicable STK11-specific specification was found.

Evidence considered

• PMID:17026623 reports c.658C>T (p.Q220X) in a female Peutz–Jeghers syndrome patient diagnosed at age 3 with buccal freckling, but does not report parental testing or de novo status.
• PMID:9887330 reports the C658→T germline variant in patient P12, while the patient's family history and pigmentation status were unknown; parental testing is not reported.
• Under generic ACMG/AMP PS2, confirmed de novo occurrence requires appropriate parental testing and relevant clinical documentation; those data are unavailable here.

Still missing

• Parental testing results for the proband are not reported.
• The clinical status and genotype of both biological parents are not documented.
• No validated de novo likelihood calculation is available.

Sources

Reasoning

No validated functional assay directly evaluating NM_000455.4:c.658C>T (p.Gln220Ter) was identified. PMID:9887330 reports the variant in patient P12 and describes it as a Gln-to-stop change predicted to truncate the LKB1 protein, but explicitly indicates that functional assays were performed on other LKB1 alleles rather than C658>T. The available variant-specific evidence is therefore clinical observation and predicted consequence, not direct assay evidence of abnormal function, so PS3 cannot be applied.

Evidence considered

• PMID:9887330 reports C658>T (p.Gln220Ter) in patient P12 and describes disruption of the LKB1 open reading frame with a predicted truncated protein.
• PMID:9887330 states that the reported functional assays were performed on other LKB1 mutant alleles; no C658>T-specific functional assay was reported.

Still missing

• A validated assay directly testing p.Gln220Ter, with appropriate wild-type and loss-of-function controls and a biologically relevant readout, is not available.

Sources

Reasoning

No applicable STK11-specific VCEP framework was identified, so generic ACMG/AMP PS4 applies. The exact variant is reported in individual Peutz–Jeghers syndrome cases, but the available publications provide no affected-case versus control counts, case-control p-value, odds ratio, confidence interval, or validated enrichment likelihood ratio. Individual case observations do not establish the required statistically significant prevalence increase; PS4 cannot be assessed.

Rule

Generic ACMG/AMP PS4: prevalence is significantly increased in affected individuals compared with controls; no STK11-specific VCEP threshold was available.

Evidence considered

• Generic ACMG/AMP PS4 requires a statistically significant increase in variant prevalence among affected individuals compared with controls.
• PMID:17026623 reports the exact variant in one Peutz–Jeghers syndrome patient but does not provide a case-control enrichment analysis for this variant.
• PMID:9887330 reports the exact C658→T variant in one Peutz–Jeghers syndrome patient, with no case-control prevalence analysis for the variant.

Still missing

• Exact-variant affected-case and control counts or a validated case-control enrichment statistic with its governing threshold are unavailable.

Sources

Reasoning

The available reports do not establish presumed de novo occurrence of NM_000455.4:c.658C>T (p.Gln220Ter). Although the variant is described in affected Peutz–Jeghers syndrome patients, no report documents absent parental testing with sufficient family and phenotype information to support presumed de novo evidence.

Rule

Generic ACMG/AMP PM6: apply only for presumed de novo occurrence with adequate phenotype and family information when parental testing is unavailable; no applicable STK11-specific specification was found.

Evidence considered

• PMID:17026623 identifies the target variant in one affected patient but provides no parental genotype or presumed de novo conclusion.
• PMID:9887330 identifies the target variant in patient P12 but states that family history was unknown, so presumed de novo status cannot be inferred.
• Under generic ACMG/AMP PM6, presumed de novo evidence requires adequate clinical and family information even when parental testing is unavailable; that information is insufficient here.

Still missing

• No report documents parental genotypes or a reliable family history for this variant.
• No evidence establishes presumed de novo status when direct parental testing is unavailable.

Sources

Reasoning

The available case reports identify NM_000455.4:c.658C>T (p.Gln220Ter) in affected individuals, but provide no informative relatives with documented genotype and phenotype across one or more meioses. The reported family information is absent or unknown, so variant–disease co-segregation cannot be assessed and no PP1 strength can be assigned.

Rule

Generic ACMG/AMP PP1: use only for demonstrated co-segregation of the variant with disease in multiple affected family members; no applicable STK11-specific specification was found.

Evidence considered

• PMID:17026623 reports the target variant in one Peutz–Jeghers syndrome patient with buccal freckling, but does not report segregation in relatives.
• PMID:9887330 reports the target variant in patient P12, with family history unknown and no variant-specific segregation analysis.
• PMID:9850045 was screened as a segregation-focused STK11/PJS publication, but the available case evidence does not establish segregation of this target variant.
• Generic ACMG/AMP PP1 requires co-segregation in affected family members; informative meioses and corresponding genotype–phenotype data are not available.

Still missing

• No pedigree with affected and unaffected relatives is available.
• No relative-level genotype and phenotype data or meiosis count is reported.
• No validated gene-specific or calibrated segregation threshold is available.

Sources

Reasoning

No validated functional assay directly demonstrating preserved STK11 function for NM_000455.4:c.658C>T (p.Gln220Ter) was identified. The available variant-specific publications describe the premature stop consequence and clinical occurrence, while the functional experiments in PMID:9887330 concerned other LKB1 alleles. Because there is no appropriately controlled benign functional result for this variant, BS3 cannot be applied.

Evidence considered

• PMID:9887330 identifies C658>T as a Gln-to-stop variant predicted to produce a truncated LKB1 protein but does not provide a benign functional result for this variant.
• PMID:9887330 reports functional assays for other LKB1 mutant alleles, not for C658>T.

Still missing

• A validated, biologically relevant assay demonstrating preserved function for p.Gln220Ter, with adequate positive and negative controls, is not available.

Sources

Reasoning

No informative unaffected relatives are reported to carry NM_000455.4:c.658C>T (p.Gln220Ter), and no pedigree-level non-segregation analysis is available. The absence of documented parental or relative genotypes is insufficient to establish BS4 rather than treating the criterion as unassessed.

Rule

Generic ACMG/AMP BS4: apply only when the variant is shown not to segregate with disease in an informative family or is present in an adequately evaluated unaffected adult; no applicable STK11-specific specification was found.

Evidence considered

• PMID:17026623 reports one affected patient with the target variant but does not provide unaffected carrier relatives or non-segregation data.
• PMID:9887330 states that family history and pigmentation status were unknown for the patient carrying the target variant, so unaffected carrier evidence is unavailable.
• Generic ACMG/AMP BS4 requires lack of segregation in affected families or presence of the variant in unaffected adults when penetrance and evaluation are informative; those data are not reported.

Still missing

• No unaffected relatives with both phenotype assessment and genotype are reported.
• No pedigree-based non-segregation analysis is available.
• No information establishes that an unaffected carrier had reached an informative age or received adequate clinical evaluation.

Sources

Reasoning

No applicable STK11-specific VCEP specification was identified, so generic ACMG/AMP logic applies. BP2 would require observation of the target variant in trans with a pathogenic variant in a dominant disorder, or in cis with a pathogenic variant in a recessive disorder. The case evidence identifies c.658C>T (p.Gln220Ter) in affected Peutz-Jeghers syndrome probands, but it contains no additional pathogenic variant, parental genotypes, genotype-level phase result, or cis/trans observation for the same proband. Because the needed allelic observation is absent, BP2 cannot be assessed; absence of documentation is not evidence that BP2 is unmet.

Rule

BP2 requires the target variant to be observed in trans with a pathogenic variant for a dominant disorder or in cis with a pathogenic variant for a recessive disorder.

Evidence considered

• PMID:17026623 identifies the target variant in an affected Peutz-Jeghers syndrome patient but reports no second pathogenic variant or phase information.
• PMID:9887330 identifies the target variant in patient P12 and states that family history was unknown; it provides no cis/trans result or second-variant observation.
• The available case materials do not document parental testing, a second pathogenic allele, or molecular phase for this proband.

Still missing

• A second pathogenic or likely pathogenic variant and its cis/trans relationship to NM_000455.4:c.658C>T are not documented.
• Parental or family genotypes sufficient to establish phase are not available.

Sources

Reasoning

No applicable STK11-specific VCEP framework or BP5-specific numeric threshold was identified. The available evidence reports the exact variant in Peutz–Jeghers syndrome and does not document a convincing alternate molecular basis for the patient's disease or a likelihood-ratio-style BP5 result. BP5 therefore cannot be assessed.

Rule

Generic ACMG/AMP BP5: the variant is found in a patient with an alternate molecular basis for disease; no STK11-specific VCEP threshold was available.

Evidence considered

• Generic ACMG/AMP BP5 concerns a variant found in a case with an alternate molecular basis for disease.
• The exact-variant publications report Peutz–Jeghers syndrome cases but do not identify an alternate molecular etiology or provide a BP5 likelihood-ratio measurement.
• No BP5 numeric threshold was available from a governing STK11-specific specification or the supplied published calibration data; no numeric comparison was performed.

Still missing

• Evidence for an alternate molecular basis of the relevant disease, or a governing BP5 rule with an exact-variant benign likelihood ratio, is unavailable.

Sources