NFE2L2 p.Asp3=
c.9C>T · rs2468352610 · VCV2106189
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 8.84e-05%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 2.9 | GERP -0.16, phastCons 1 |
| Overall | ||
| CADD | 15.98 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
8.84e-05%
European (non-Finnish) · 1/1,131,538 alleles
Overall
6.59e-05%
1/1,517,234 alleles · very rare
exomes 1/1,365,022 · genomes 0/152,212 · joint denominator
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- NFE2L2
- Protein
- p.Asp3=
- Coding
- c.9C>T
- MANE Select
- NM_006164
- dbSNP
- rs2468352610
- Type
- single nucleotide variant
- Location
- chr2:177264568 (GRCh38)
- Gene constraint
- LOEUF 0.575 · pLI 0.50 (gnomAD)
- Structure
- AlphaFold pLDDT 61.72 · 23 PDB
Similar variants
- NFE2L2 p.Ala249Ser Uncertain significance ★★ ⚠ same type
- NFE2L2 p.Ala496Gly Uncertain significance ★★ ⚠ same type
- NFE2L2 p.Arg34Gln Uncertain significance ★★ ⚠ same type
- NFE2L2 p.Arg449Cys Uncertain significance ★★ ⚠ same type
- NFE2L2 p.Arg569Cys Uncertain significance ★★ ⚠ same type
- NFE2L2 p.Asn101Ser Uncertain significance ★★ ⚠ same type
- NFE2L2 p.Asn225Ser Uncertain significance ★★ ⚠ same type
- NFE2L2 p.Asn278Ser Uncertain significance ★★ ⚠ same type
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/nfe2l2-p-asp3 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown