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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 applied · 19 assessed
Applied · 4
Strength Supporting Moderate Strong Very strong
PS3 supporting review Pathogenic
Functional studies in HEK293T cells demonstrate that NRF2-R34Q partially escapes KEAP1-mediated repression (luciferase activity retained at ~60% vs <10% for wild-type upon KEAP1 co-expression). Cycloheximide chase assays show extended protein half-life (31-49 min vs 15 min wild-type), and ubiquitylation is reduced. These findings support a gain-of-function effect consistent with the known NFE2L2 oncogenic mechanism.
Luciferase reporter assay: KEAP1 co-expression reduced NRF2-R34Q activity to ~60% vs <10% for WT. Cycloheximide chase: R34Q half-life 31-49 min vs WT 15 min. Reduced ubiquitylation confirmed. All data from a single comprehensive study (Kerins & Ooi 2018).
PM1 moderate Pathogenic
Arg34 is located in the Neh2 domain (residues 1-98), the KEAP1-binding domain critical for NRF2 regulation. Arg34 is the most frequently mutated NRF2 residue across cancer types (14.2% of all NRF2 mutations in TCGA, per PMID:30150714) and falls within a statistically significant mutational hotspot.
Neh2 domain is a critical functional domain for KEAP1 binding. Arg34 is the most frequently mutated NRF2 residue (14.2% of NRF2 mutationsp<0.05). Cancer Hotspots confirms residue-level statistical significance.
PM2 moderate Pathogenic
NM_006164.4:c.101G>A is absent from gnomAD v2.1 (exomes), gnomAD v4.1 (exomes+genomes), and gnomAD-Canada v1.0 (HostSeq genomes). Population allele frequency = 0.00, which is well below the <0.1% threshold for PM2 in non-VCEP ACMG/AMP.
Absent from gnomAD v2.1 (AF=null)gnomAD v4.1 (AF=null)and gnomAD-Canada v1.0 (AF=0.0). No homozygotes observed.
BP4 supporting Benign
Multiple in silico prediction tools do not predict a deleterious effect. REVEL score is 0.412 (below the 0.5 pathogenic threshold), BayesDel score is 0.146 (low), and SpliceAI maximum delta score is 0.00 (no predicted splice impact). The concordance of benign predictions across multiple algorithm types supports BP4 at supporting level.
REVEL=0.412 (benign range)BayesDel=0.145684 (low impact)SpliceAI max delta=0.00 (no splice effect). Three independent algorithm classes concur on benign prediction.
Assessed · not applied
Pathogenic
PS1 No alternative nucleotide change at codon 34 encoding the same amino acid (Arg34Gln) has been established as pathogenic.
PS2 No confirmed de novo observation of NM_006164.4:c.101G>A has been reported in any published family or cohort.
PS4 No case-control study has compared the prevalence of NM_006164.4:c.101G>A in affected individuals versus controls.
PM5 No pathogenic missense variant at Arg34 with a different amino acid change has been established through ClinVar or the literature.
PM6 No de novo paternity-confirmed cases of NM_006164.4:c.101G>A have been reported.
PP1 No cosegregation data are available for NM_006164.4:c.101G>A.
PP2 NFE2L2 is not established as a germline disease gene with a low rate of benign missense variation where missense variants are a common disease mechanism.
PP3 Multiple in silico prediction tools do not support a deleterious effect.
PP4 No specific phenotype or family history data are available for individuals carrying this variant.
PP5 No reputable source has classified NM_006164.4:c.101G>A as pathogenic.
Benign
BA1 The variant is absent from gnomAD v2.1, v4.1, and gnomAD-Canada.
BS1 The variant is absent from all population databases (gnomAD v2.1, v4.1, gnomAD-Canada).
BS2 The variant has not been observed in healthy adults.
BS3 Well-validated functional studies in PMID:30150714 demonstrate that NRF2-R34Q has a gain-of-function effect (partial escape from KEAP1-mediated repression, extended protein half-life, reduced ubiquitylation), consistent with the known oncogenic mechanism of NFE2L2.
BS4 No segregation data are available to assess whether this variant segregates with disease in families.
BP1 BP1 applies to missense variants in genes where truncating variants are the primary disease mechanism.
BP2 No observation of NM_006164.4:c.101G>A in trans with a known pathogenic NFE2L2 variant has been reported.
BP5 Insufficient data to determine whether affected individuals carrying this variant have an alternative molecular explanation for their phenotype.
BP6 No reputable source has classified NM_006164.4:c.101G>A as benign.
N/A · 5 PVS1 · PM3 · PM4 · BP3 · BP7
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