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STK11
Final classification
Likely Pathogenic
STK11 c.129_141del · p.Lys44SerfsTer3
STK11

NM_000455.5(STK11):c.129_141del is a 13bp frameshift deletion in exon 1 producing p.(Lys44SerfsTer3), predicted to trigger nonsense-mediated decay and complete loss of STK11 protein expression. STK11 loss of function is a well-established mechanism for Peutz-Jeghers syndrome (autosomal dominant).

Gene
STK11
Transcript
NM_000455.5
HGVS · transcript:coding
NM_000455.5:c.129_141del
Consequence
N/A
GRCh38
chr19:1207038 GGGCCAAGCTCATC>G
GRCh37
chr19:1207037 GGGCCAAGCTCATC>G
Basis gene-specific framework lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: PVS1 very strong, PM2 moderate; combination = 1 very strong + 1 moderate, which maps to Likely Pathogenic.
gene-specific framework lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: PVS1 very strong, PM2 moderate; combination = 1 very strong + 1 moderate, which maps to Likely Pathogenic.
Classification rationale
PVS1PM2 Likely Pathogenic
STK11 c.129_141del

NM_000455.5(STK11):c.129_141del is a 13bp frameshift deletion in exon 1 producing p.(Lys44SerfsTer3), predicted to trigger nonsense-mediated decay and complete loss of STK11 protein expression. STK11 loss of function is a well-established mechanism for Peutz-Jeghers syndrome (autosomal dominant).1 This variant is absent from gnomAD v2.1 and v4.1 population databases, consistent with a rare pathogenic variant.2 The variant has not been reported in ClinVar, COSMIC, or any published patient cohort evaluated in this assessment.3 No variant-specific functional studies, segregation data, or de novo observations were identified in the literature. Five OncoKB-curated STK11 publications were reviewed; none mention this variant.4 Applying generic ACMG/AMP 2015 classification rules (PMID:25741868): PVS1 (very_strong) + PM2 (moderate) meets the Likely Pathogenic combination threshold (1 Very Strong + 1 Moderate).5

PVS1 + PM2 Likely Pathogenic
1 pvs1_generic_framework ↗pvs1_gene_context
5 generic_acmg_combination_rules
Gene diagram · NM_000455.5 · variants mapped to exon structure
STK11 NM_000455.5
Fetching transcript structure from UCSC…
Applied criteria · 2 met · select any tile
Met
Not met
Not assessed
N/A
Strength very strong supporting
Pathogenic evidence
PVS
PS
PM
PP
Benign evidence
BA
BS
BP
Rationale
Select a criterion.
Sources
Evidence used
    Gaps remaining
      Rule
      Research & evidence
      Population frequency · supports pathogenic
      gnomAD v4.1 screenshot
      gnomAD v4.1
      gnomAD v2.1 screenshot
      gnomAD v2.1
      v4.1
      Absent from gnomAD v4.1.
      v2.1
      Absent from gnomAD v2.1.
      🇨🇦 CA
      Absent from gnomAD-Canada v1.0.
      Allele frequency by ancestry
      three datasets · side by side
      gnomAD v4.1
      Absent · 0 / ?
      0 hom
      Not observed in any ancestry group.
      gnomAD v2.1
      Absent · 0 / ?
      0 hom
      Not observed in any ancestry group.
      gnomAD Canada 🇨🇦
      Absent · 0 / ?
      0 hom
      Not observed in any ancestry group.
      ClinVar screenshot
      ClinVar
      This variant is absent from ClinVar.
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.02).
      Functional / OncoKB screenshot
      Functional Likely Oncogenic
      OncoKB identified variant-specific curated literature and context relevant to functional review; biological-effect context: Likely Loss-of-function; curated oncogenicity label: Likely Oncogenic.
      OncoKB ↗
      COSMIC screenshot
      COSMIC
      Cancer hotspots screenshot
      Cancer hotspots
      Somatic evidence Not in COSMIC / hotspots
      COSMIC
      This variant does not lie in a statistically significant hotspot. This variant has not previously been reported in somatic cancers (COSMIC).
      Hotspots
      This variant does not lie in a statistically significant hotspot.
      Sources & reference links
      8Sources
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      gnomAD-Canada
      SpliceAI
      OncoKB
      COSMIC
      Cancer hotspots
      Triaged references · 5 PMIDs not cited in assessment
      19340305 ↗ Somatic LKB1 mutations promote cervical cancer progression. ONCOKB
      19892943 ↗ Structure of the LKB1-STRAD-MO25 complex reveals an allosteric mechanism of kinase activation. ONCOKB
      21516316 ↗ The role of LKB1 in lung cancer. ONCOKB
      24652667 ↗ STK11 domain XI mutations: candidate genetic drivers leading to the development of dysplastic polyps in Peutz-Jeghers syndrome. ONCOKB
      25079552 ↗ Comprehensive molecular profiling of lung adenocarcinoma. ONCOKB