Starting
Initialising…
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KEAP1
Final classification
VUS
KEAP1 c.542_543insT · p.Ser182GlnfsTer11
KEAP1

PVS1 (very strong) is met: NM_012289.4:c.542_543insT is a frameshift insertion in exon 2 of 6 creating a premature termination codon at position 192 (NP_036421.2:p.(Ser182GlnfsTer11)), predicted to trigger nonsense-mediated decay. KEAP1 loss of function is an established germline disease mechanism, supported by published pathogenic frameshift variants causing familial multinodular goiter (PMID:39373520).

Gene
KEAP1
Transcript
NM_012289.4
HGVS · transcript:coding
NM_012289.4:c.542_543insT
Consequence
N/A
GRCh38
chr19:10499491 G>GA
GRCh37
chr19:10610167 G>GA
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 supporting; combination = 1 very strong + 1 supporting, which maps to VUS.
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 supporting; combination = 1 very strong + 1 supporting, which maps to VUS.
Classification rationale
PVS1PM2 VUS
KEAP1 c.542_543insT

PVS1 (very strong) is met: NM_012289.4:c.542_543insT is a frameshift insertion in exon 2 of 6 creating a premature termination codon at position 192 (NP_036421.2:p.(Ser182GlnfsTer11)), predicted to trigger nonsense-mediated decay. KEAP1 loss of function is an established germline disease mechanism, supported by published pathogenic frameshift variants causing familial multinodular goiter (PMID:39373520).1 PM2 (supporting) is met: the variant is completely absent from gnomAD v2.1 and v4.1 population databases, consistent with a rare pathogenic variant.2 No additional pathogenic criteria are met. The variant has not been reported in affected individuals (PS4 not met), no functional studies are available for this exact variant (PS3 not assessed), no de novo observations exist (PS2/PM6 not met), and no segregation or case-level data is available (PP1/PP4 not met). No benign criteria are met. The variant is absent from population databases (BA1/BS1 not met), and no functional or clinical evidence supports a benign interpretation.3 Under generic ACMG/AMP 2015 combination rules (PMID:25741868), PVS1 (very strong) + PM2 (supporting) does not reach a Likely Pathogenic or Pathogenic threshold. The minimum requirement for Likely Pathogenic with PVS1 is one additional moderate criterion, which is not met. The classification is therefore Variant of Uncertain Significance (VUS).4

PVS1 + PM2 VUS
1 pvs1_generic_framework ↗pvs1_gene_contextpvs1_variant_assessment
4 generic_acmg_combination_rules
Gene diagram · NM_012289.4 · variants mapped to exon structure
KEAP1 NM_012289.4
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
      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
      This variant is absent from gnomAD-Canada.
      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 = 0.00).
      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.
      Literature · how each cited paper was used
      1papers cited
      Each card is an audit: what was searched, what was found, whether it names the variant, which criteria it fed, and why. 3 further PMIDs triaged but not cited — see Sources & References.
      PMID 39373520
      Found
      Frameshift insertion (c.542_543insT) creating premature termination codon at position 192 of 625 amino acids NMD predicted (PTC in exon 2 of 6 well upstream of the last exon-exon junction) KEAP1 germline loss-of-function mechanism supported by published pathogenic frameshift variants (PMID:39373520: p.V411fs in familial multinodular goiter)
      Applied to
      PVS1 supports · met
      Sources & reference links
      7Sources
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      SpliceAI
      OncoKB
      COSMIC
      Cancer hotspots
      Triaged references · 3 PMIDs not cited in assessment
      17020408 ↗ Dysfunctional KEAP1-NRF2 interaction in non-small-cell lung cancer. ONCOKB
      24142871 ↗ The emerging role of the Nrf2-Keap1 signaling pathway in cancer. ONCOKB
      24322982 ↗ Cancer-derived mutations in KEAP1 impair NRF2 degradation but not ubiquitination. ONCOKB