NR2F2 p.Pro409=
c.1227G>A · VCV4926754
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00223%, eas)
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 -1.7 | GERP -5.6 |
| Overall | ||
| CADD | 4.511 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00223%
East Asian · 1/44,860 alleles
Filtering AF
6.8e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.9e-05%
Overall
0.000372%
6/1,612,540 alleles · very rare
exomes 5/1,460,344 · genomes 1/152,196 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00223% | 44,860 |
| African / African-American | 0.00133% | 74,944 |
| South Asian | 0.0011% | 90,986 |
| European (non-Finnish) | 0.000254% | 392,957 |
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
- NR2F2
- Protein
- p.Pro409=
- Coding
- c.1227G>A
- MANE Select
- NM_021005
- Type
- single nucleotide variant
- Location
- chr15:96337604 (GRCh38)
- Gene constraint
- LOEUF 0.197 · pLI 1.00 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 77.94 · 1 PDB
- Residue 409
- the 'interaction with zfpm2' region; the 'important for dimerization' region
Similar variants
- NR2F2 p.Ser341Tyr Pathogenic/Likely pathogenic ★★ same type
- NR2F2 p.Trp249Ter Pathogenic/Likely pathogenic ★★ same type
- NR2F2 p.Ala2Ser Uncertain significance ★★ ⚠ same type
- NR2F2 p.Gly180Arg Uncertain significance ★★ ⚠ same type
- NR2F2 p.Gly361Arg Uncertain significance ★★ ⚠ same type
- NR2F2 p.His90Arg Uncertain significance ★★ ⚠ same type
- NR2F2 p.Lys137Arg Uncertain significance ★★ ⚠ same type
- NR2F2 p.Pro32Arg 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/nr2f2-p-pro409 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown