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NFE2L2
Final classification
VUS
NFE2L2 c.101G>A · p.Arg34Gln
NFE2L2

NM_006164.4:c.101G>A (p.Arg34Gln) in NFE2L2 is a missense variant absent from all population databases (gnomAD v2.1, v4.1, gnomAD-Canada).

Gene
NFE2L2
Transcript
NM_006164.4
HGVS · transcript:coding
NM_006164.4:c.101G>A
Consequence
N/A
GRCh38
chr2:177234216 C>T
GRCh37
chr2:178098944 C>T
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: PS3 supporting, PM1 moderate, PM2 moderate, BP4 supporting benign; combination = 2 moderate + 1 supporting + 1 supporting benign, 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: PS3 supporting, PM1 moderate, PM2 moderate, BP4 supporting benign; combination = 2 moderate + 1 supporting + 1 supporting benign, which maps to VUS.
Classification rationale
PS3PM1PM2 BP4 VUS
NFE2L2 c.101G>A

NM_006164.4:c.101G>A (p.Arg34Gln) in NFE2L2 is a missense variant absent from all population databases (gnomAD v2.1, v4.1, gnomAD-Canada).1 The variant is located at Arg34 in the Neh2 domain, the KEAP1-binding domain critical for NRF2 regulation. Arg34 is the most frequently mutated NRF2 residue across cancer types and lies within a statistically significant mutational hotspot.2 Functional studies in HEK293T cells demonstrate that NRF2-R34Q partially escapes KEAP1-mediated repression (luciferase activity retained at ~60% vs <10% for wild-type), has extended protein half-life, and shows reduced ubiquitylation, consistent with a gain-of-function effect.3 Multiple in silico prediction tools do not predict a deleterious effect: REVEL score 0.412, BayesDel score 0.146, and SpliceAI maximum delta score 0.00.4 This variant has been reported in ClinVar as Uncertain significance by two clinical laboratories (GeneDx, Labcorp). No de novo observations, cosegregation data, or case-control studies are available.5 Applying generic ACMG/AMP 2015 combination rules (PMID:25741868), the evidence profile includes two moderate pathogenic criteria (PM1, PM2), one supporting pathogenic criterion (PS3), and one supporting benign criterion (BP4), resulting in an overall classification of Uncertain significance.6

PS3 + PM1 + PM2 + BP4 VUS
Gene diagram · NM_006164.4 · variants mapped to exon structure
NFE2L2 NM_006164.4
Fetching transcript structure from UCSC…
Applied criteria · 4 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
      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 has been reported in ClinVar as Uncertain significance (2 clinical laboratories). (ClinVarID = 3360940)
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). REVEL score = 0.412. BayesDel score = 0.145684.
      Functional / OncoKB screenshot
      Functional Likely Oncogenic
      OncoKB identified variant-specific curated literature and context relevant to functional review; biological-effect context: Likely Gain-of-function; curated oncogenicity label: Likely Oncogenic.
      OncoKB ↗
      COSMIC screenshot
      COSMIC
      Cancer hotspots screenshot
      Cancer hotspots
      Somatic evidence Hotspot
      COSMIC
      This variant lies in a statistically significant hotspot. This variant has previously been reported in somatic cancers (COSMIC; COSV67960161, n = 46 times).
      Hotspots
      This variant lies 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. 2 further PMIDs triaged but not cited — see Sources & References.
      A catalogue of somatic NRF2 gain-of-function mutations in cancer.
      Found
      Structured finding pending for this record — see source link.
      Applied to
      PM1 supports · met PS3 supports · met
      Sources & reference links
      8Sources
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      gnomAD-Canada
      SpliceAI
      OncoKB
      COSMIC
      Cancer hotspots
      Triaged references · 2 PMIDs not cited in assessment
      20421815 ↗ NFE2L2 gene mutation in male Japanese squamous cell carcinoma of the lung. ONCOKB
      28492532 ↗ Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. CLINVAR