# NM_006164.5(NFE2L2):c.879C>T (p.Pro293=)

https://sugi.bio/variant/nfe2l2-p-pro293

## Summary

**NFE2L2 p.Pro293= (c.879C>T)** is classified **Likely benign** in NFE2L2 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-10-07). Very rare (popmax 8.47e-05%, nfe).

**At a glance:** Likely benign · review: Single submitter · rsID rs2105453587 · 1 submitter · very rare (popmax 8.47e-05%, nfe)

## For patients & families {#patients}

This is a change in the NFE2L2 gene that is classified as likely benign — not considered disease-causing, submitted by 1 submitter.

*Reference information, not medical advice, and not a prediction for any individual. A genetic counselor or clinician can interpret what it means for you and your family.*

**Support & next steps:** [Find a genetic counselor (NSGC)](https://findageneticcounselor.nsgc.org/).

## Identity {#identity}

| Field | Value |
| --- | --- |
| Gene | [NFE2L2](https://sugi.bio/atlas/gene/NFE2L2/) |
| Protein change (HGVS p.) | p.Pro293= |
| Coding change (HGVS c.) | c.879C>T |
| MANE Select transcript | [NM_006164](https://www.ncbi.nlm.nih.gov/nuccore/NM_006164) |
| dbSNP | [rs2105453587](https://www.ncbi.nlm.nih.gov/snp/rs2105453587/) |
| Variant type | single nucleotide variant |
| Location | chr2:177231724-177231724 (GRCh38) |
| ClinVar | [VCV2034487](https://www.ncbi.nlm.nih.gov/clinvar/variation/2034487/) |

**All HGVS expressions:** `NC_000002.11:g.178096452G>A`, `NC_000002.12:g.177231724G>A`, `NM_001145412.3:c.831C>T`, `NM_001145413.3:c.810C>T`, `NM_001313900.1:c.831C>T`, `NM_001313901.1:c.831C>T`, `NM_001313902.2:c.789C>T`, `NM_001313903.2:c.660C>T`, `NM_001313904.1:c.579C>T`, `NM_006164.5:c.879C>T`

## Computational & population evidence {#evidence}

**Concordance:** Mixed / partial computational evidence (see below).

- **Missense predictors (AlphaMissense/REVEL/SaProt) do not apply** to this variant type — they score amino-acid substitutions only. For non-missense variants the computational signal comes from conservation (below), not from a missing predictor score.
- Conservation: phyloP 2.293, GERP -4, phastCons 0.985 — highly conserved position (PP3-type support)
- CADD: **PHRED 2.416**. No single ClinGen-calibrated threshold exists and the expert panels that use CADD disagree — GUCY2D/AIPL1 require ≥ 20.0 for an untranslated-region variant, ABCA4 ≥ 28.1 for a synonymous or indel variant, the Pulmonary Hypertension panel imports Pejaver 2022's missense-calibrated numbers, and the Antibody Deficiencies panel declines CADD entirely for PIK3CD. CADD v1.7 also incorporates Zoonomia phyloP, so it partly re-expresses the conservation above. *Descriptive; no threshold applied.*
- SpliceAI: **not assessed** — no allele at this position is in our SpliceAI release, either because it lies outside the scored MANE transcript scope or because every allele is below Δ0.2. We cannot tell which, so this claims neither; absence is not evidence against a splicing effect.
- Population frequency (gnomAD v4.1): grpmax **8.47e-05%** (nfe) · 1/1,180,022 in the highest group · 1/1,614,184 alleles overall — very rare (popmax 8.47e-05%, nfe).

*Computational predictors are not independent (ClinGen Variant Classification guidance): AlphaMissense (Cheng et al. 2023) carries the ACMG weight for missense and conservation (phyloP/GERP/phastCons) for non-missense; REVEL (Pejaver-2022 calibrated strength bands) and SaProt (Su et al. 2023, structure-aware, ClinVar-independent protein language model, raw LLR) are shown as orthogonal agreement signals, not additive. For frequency, the gnomAD v4.1 grpmax filtering allele frequency (FAF95) is ClinGen's designated BA1/BS1 input (gnomAD v4 guidance v3.0, June 2025); BA1/BS1 thresholds are disease-specific, not a blanket 5%. Predictions, not a clinical determination.*

## Gene constraint & dosage {#gene-context}

**NFE2L2** population constraint: LOEUF 0.575, pLI 0.5022, missense-Z 2.2152. *Lower LOEUF and higher pLI indicate a gene that tolerates loss-of-function poorly; ClinGen dosage is the curated haploinsufficiency call.*

Curated gene–disease validity (ClinGen):

- **immunodeficiency, developmental delay, and hypohomocysteinemia** — Limited (AD)

## Protein context {#protein}


AlphaFold model confidence (whole protein): pLDDT 61.72, 22% of residues very-high.

**23 experimental structure(s)** (PDB): [2FLU](https://www.rcsb.org/structure/2FLU), [2LZ1](https://www.rcsb.org/structure/2LZ1), [3ZGC](https://www.rcsb.org/structure/3ZGC), [4IFL](https://www.rcsb.org/structure/4IFL), [5WFV](https://www.rcsb.org/structure/5WFV), [6T7V](https://www.rcsb.org/structure/6T7V).

## What this gene does {#gene-function}

*Describes the biological roles of NFE2L2 (the gene this variant disrupts) — not effects measured for this specific variant. A damaging variant is expected to affect these functions and pathways; the degree depends on the variant.*

**How this variant is thought to act:** NFE2L2's established molecular role includes transcription cis-regulatory region binding. In Reactome, NFE2L2 is annotated in disease pathway(s) including **Potential therapeutics for SARS**.

**Disease mechanism (Reactome):** NFE2L2 loss or alteration is curated in [Potential therapeutics for SARS](https://reactome.org/content/detail/R-HSA-9679191).

### Pathways affected {#pathways}

NFE2L2 participates in **17 Reactome pathways** (⚕ = disease pathway):

| Pathway (Reactome) | Evidence |
| --- | --- |
| ⚕ [Potential therapeutics for SARS](https://reactome.org/content/detail/R-HSA-9679191) | curated |
| [GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2](https://reactome.org/content/detail/R-HSA-9762114) | curated |
| [Heme signaling](https://reactome.org/content/detail/R-HSA-9707616) | curated |
| [NFE2L2 regulates pentose phosphate pathway genes](https://reactome.org/content/detail/R-HSA-9818028) | curated |
| [NFE2L2 regulating ER-stress associated genes](https://reactome.org/content/detail/R-HSA-9818035) | curated |
| [NFE2L2 regulating MDR associated enzymes](https://reactome.org/content/detail/R-HSA-9818032) | curated |
| [NFE2L2 regulating TCA cycle genes](https://reactome.org/content/detail/R-HSA-9818025) | curated |
| [NFE2L2 regulating inflammation associated genes](https://reactome.org/content/detail/R-HSA-9818026) | curated |
| [NFE2L2 regulating tumorigenic genes](https://reactome.org/content/detail/R-HSA-9818030) | curated |
| [Neddylation](https://reactome.org/content/detail/R-HSA-8951664) | curated |
| [Nuclear events mediated by NFE2L2](https://reactome.org/content/detail/R-HSA-9759194) | curated |
| [Regulation of HMOX1 expression and activity](https://reactome.org/content/detail/R-HSA-9707587) | curated |
| [Regulation of PD-L1(CD274) transcription](https://reactome.org/content/detail/R-HSA-9909649) | curated |
| [CHD6, CHD7, CHD8, CHD9 subfamily](https://reactome.org/content/detail/R-HSA-9943962) | electronic |
| [KEAP1-NFE2L2 pathway](https://reactome.org/content/detail/R-HSA-9755511) | electronic |
| [NFE2L2 regulating anti-oxidant/detoxification enzymes](https://reactome.org/content/detail/R-HSA-9818027) | electronic |
| [Regulation of NFE2L2 gene expression](https://reactome.org/content/detail/R-HSA-9818749) | electronic |

### Molecular function & processes (GO — experimentally supported) {#go}

**Molecular function:** transcription cis-regulatory region binding, DNA-binding transcription activator activity, RNA polymerase II-specific, DNA binding, DNA-binding transcription factor activity, protein domain specific binding, ubiquitin protein ligase binding.

**Biological process:** response to oxidative stress, proteasomal ubiquitin-independent protein catabolic process, positive regulation of gene expression, protein ubiquitination, cellular response to oxidative stress, proteasome-mediated ubiquitin-dependent protein catabolic process.

## Clinical significance {#significance}

**Likely benign** — review status Single submitter *(criteria provided, single submitter)*, last evaluated 2022-10-07.

**Submitter consensus:** unanimous (1/1 Likely benign).

### Submitter classifications {#submitters}

| Submitter | Classification | Review | Method | Date |
| --- | --- | --- | --- | --- |
| Labcorp Genetics (formerly Invitae), Labcorp | Likely benign | criteria provided, single submitter | clinical testing | 2022-10-07 |

**Reported phenotype names (ClinVar):** not provided, none provided.

## Similar variants {#similar}

Related NFE2L2 variant pages (same residue, condition, or type): [NFE2L2 p.Ala249Ser](/variant/nfe2l2-p-ala249ser), [NFE2L2 p.Ala496Gly](/variant/nfe2l2-p-ala496gly), [NFE2L2 p.Arg34Gln](/variant/nfe2l2-p-arg34gln), [NFE2L2 p.Arg449Cys](/variant/nfe2l2-p-arg449cys), [NFE2L2 p.Arg569Cys](/variant/nfe2l2-p-arg569cys), [NFE2L2 p.Asn101Ser](/variant/nfe2l2-p-asn101ser), [NFE2L2 p.Asn225Ser](/variant/nfe2l2-p-asn225ser), [NFE2L2 p.Asn278Ser](/variant/nfe2l2-p-asn278ser).

### Data sources & attribution {#sources}

ClinVar (NCBI — public domain, built 2026-10-14); gnomAD v4.1 (Broad Institute, built 2026-10-14); AlphaMissense (Cheng et al. 2023, © Google DeepMind — CC BY 4.0, built 2026-01-27); REVEL (Ioannidis et al. 2016 — ODbL, built 2026-07-13); SaProt (Su et al. 2023 — MIT, built 2026-10-14); SpliceAI (Illumina — free for non-commercial use, built 2026-10-13); CADD (Rentzsch et al. 2019, University of Washington — free for non-commercial use, built 2026-10-10); Conservation (phyloP/phastCons/GERP) (UCSC hg38 470-way mammal (Hiller Lab) + Ensembl Compara, built 2026-07-12); gnomAD Non-coding Constraint (Gnocchi) (Chen et al. 2024, Broad Institute — CC0, built 2026-10-11); gnomAD Regional Missense Constraint (Broad Institute — CC0, built 2026-10-13); Pangolin (Zeng & Li 2022 — CC BY 4.0, built 2026-10-11); Repeat regions (UCSC — RepeatMasker, TRF, segmental duplications, built 2026-10-11); ClinGen (ClinGen, built 2026-09-22); UniProt (CC BY 4.0); Reactome / GO (CC BY 4.0, built 2026-09-23); MaveDB (per-record license, built 2026-10-11); CIViC (CC0, built 2026-09-22); Orphanet (Orphanet, built 2026-06-12)

*Primary record: NCBI ClinVar (variation 2034487). Classifications reflect these databases as of the page's build date and may change. Free reference use — not medical advice; consult the primary submitters and a clinician.*