NM_006164.4:c.101G>A

NFE2L2 · NP_006155.2:p.(Arg34Gln) · NM_006164.4

GRCh37: chr2:178098944 C>T · GRCh38: chr2:177234216 C>T

Gene: NFE2L2 Transcript: NM_006164.4

Final call

VUS

PS3 supporting PM1 moderate PM2 moderate BP4 supporting benign

Variant details

Gene

NFE2L2

Transcript

NM_006164.4

Protein

NP_006155.2:p.(Arg34Gln)

gnomAD AF

ClinVar

Uncertain significance

OncoKB

Likely Oncogenic

Classification rationale

Interpretation summary

Generated evidence synthesis

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).

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.

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.

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.

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.

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.

Final determination: Generic ACMG/AMP 2015 fallback rules do not meet benign, likely benign, likely pathogenic, or pathogenic combination thresholds, so the variant is classified as Variant of Uncertain Significance.

Criteria assessment

ACMG/AMP criteria review

Criteria shown when status is available

All criteria require review: For research and educational purposes only.

Criterion	Status	Rationale	Evidence used
PVS1	N/A	NM_006164.4:c.101G>A is a missense variant (p.Arg34Gln). PVS1 applies only to null variants (nonsense, frameshift, canonical splice ±1,2); this variant falls into the 'other' bucket per ClinGen SVI PVS1 recommendations (PMC6185798).	pvs1_generic_framework pvs1_variant_assessment
PS1	Not met	No alternative nucleotide change at codon 34 encoding the same amino acid (Arg34Gln) has been established as pathogenic. The only confirmed Arg34Gln change is c.101G>A; other codon 34 changes (c.100C>G p.Arg34Gly, c.101G>C p.Arg34Pro, c.101G>T p.Arg34Leu) have not been classified as pathogenic in ClinVar or the literature.	PMID:30150714 clinvar
PS2	Not met	No confirmed de novo observation of NM_006164.4:c.101G>A has been reported in any published family or cohort. NFE2L2 germline de novo events have not been documented.
PS3	Met	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.	PMID:30150714
PS4	Not met	No case-control study has compared the prevalence of NM_006164.4:c.101G>A in affected individuals versus controls. The variant is recurrent in somatic cancers (COSMIC, n=46) but germline case enrichment has not been demonstrated.	gnomad_v2 gnomad_v4
PS5	Not assessed	Insufficient data to determine whether affected individuals with this variant have an alternative molecular cause for their phenotype. No clinical phenotype data are available for the reported ClinVar cases.
PM1	Met	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.	PMID:30150714
PM2	Met	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.	gnomad_v2 gnomad_v4 gnomad_canada
PM5	Not met	No pathogenic missense variant at Arg34 with a different amino acid change has been established through ClinVar or the literature. While other R34 mutations (R34G, R34P, R34L) are documented in somatic cancer datasets, none are classified as pathogenic in a germline context.	pm5_candidates PMID:30150714
PM6	Not assessed	No de novo paternity-confirmed cases of NM_006164.4:c.101G>A have been reported. NFE2L2 germline de novo events are not documented in the literature or ClinVar.
PP1	Not met	No cosegregation data are available for NM_006164.4:c.101G>A. No family studies with NFE2L2 germline variants have been published.
PP2	Not met	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. The HCI prior score is unavailable for NFE2L2. The known disease mechanism is somatic gain-of-function in cancer, not germline Mendelian disease.
PP3	Not met	Multiple in silico prediction tools do not support a deleterious effect. REVEL score is 0.412 (below 0.5 threshold), BayesDel score is 0.146 (low), and SpliceAI maximum delta score is 0.00 (no predicted splice impact). These scores collectively argue against computational evidence of pathogenicity.	revel bayesdel spliceai
PP4	Not met	No specific phenotype or family history data are available for individuals carrying this variant. ClinVar submissions report 'Not Provided' or unspecified conditions, and no detailed clinical phenotypes have been published.	clinvar
PP5	Not met	No reputable source has classified NM_006164.4:c.101G>A as pathogenic. ClinVar reports Uncertain significance from two clinical laboratories (GeneDx, Labcorp). The ClinVar-cited PMID (28492532) is a methods paper on classification criteria and does not discuss this specific variant.	clinvar PMID:28492532
BA1	Not met	The variant is absent from gnomAD v2.1, v4.1, and gnomAD-Canada. Population allele frequency is 0.00, far below the BA1 threshold of >1%.	gnomad_v2 gnomad_v4 gnomad_canada
BS1	Not met	The variant is absent from all population databases (gnomAD v2.1, v4.1, gnomAD-Canada). Allele frequency is 0.00, which is below the BS1 threshold of >0.3%.	gnomad_v2 gnomad_v4 gnomad_canada
BS2	Not met	The variant has not been observed in healthy adults. It is absent from gnomAD, which precludes observation in presumed healthy population controls. No published reports document this variant in unaffected individuals with full penetrance expected.	gnomad_v2 gnomad_v4
BS3	Not met	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. This is evidence of a damaging effect, not evidence of no damaging effect as required for BS3.	PMID:30150714
BS4	Not met	No segregation data are available to assess whether this variant segregates with disease in families. No studies have examined cosegregation of NFE2L2 variants with a specific phenotype.
BP1	Not met	BP1 applies to missense variants in genes where truncating variants are the primary disease mechanism. For NFE2L2, the established disease mechanism in cancer is gain-of-function through missense mutations in the Neh2 domain that disrupt KEAP1 binding, not loss-of-function through truncation.	PMID:30150714
BP2	Not met	No observation of NM_006164.4:c.101G>A in trans with a known pathogenic NFE2L2 variant has been reported. Given that NFE2L2-associated phenotypes follow a dominant gain-of-function mechanism, BP2 is unlikely to be applicable.
BP3	N/A	NM_006164.4:c.101G>A is a single-nucleotide missense substitution, not an in-frame insertion/deletion in a repetitive region.
BP4	Met	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 bayesdel spliceai
BP5	Not assessed	Insufficient data to determine whether affected individuals carrying this variant have an alternative molecular explanation for their phenotype. Clinical phenotype data are not available.
BP6	Not met	No reputable source has classified NM_006164.4:c.101G>A as benign. ClinVar reports Uncertain significance from two clinical laboratories.	clinvar
BP7	N/A	NM_006164.4:c.101G>A is a missense variant (p.Arg34Gln), not a synonymous variant. BP7 applies only to synonymous variants with no predicted splice impact.
PM3	N/A	NFE2L2-associated phenotypes follow a dominant gain-of-function mechanism; biallelic observations are not expected. No homozygous or compound heterozygous reports exist, nor are they applicable to this gene.
PM4	N/A	NM_006164.4:c.101G>A is a single-nucleotide missense substitution, not a non-frameshift deletion/insertion or stop-loss variant.

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