NR2F1 p.Pro64=
c.192C>T · rs747522225 · VCV388391
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0796%, afr)
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 0.01 | GERP -4.6, phastCons 0.68 |
| Overall | ||
| CADD | 15.72 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0796%
African / African-American · 58/72,822 alleles
Filtering AF
0.0632%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0573%
Overall
0.0044%
68/1,544,244 alleles · ultra-rare
exomes 32/1,393,334 · genomes 36/150,910 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0796% | 1,256 |
| Remaining individualsnot grpmax-eligible | 0.00668% | 14,973 |
| South Asian | 0.00119% | 84,094 |
| European (non-Finnish) | 0.000437% | 228,985 |
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
- NR2F1
- Protein
- p.Pro64=
- Coding
- c.192C>T
- MANE Select
- NM_005654
- dbSNP
- rs747522225
- Type
- single nucleotide variant
- Location
- chr5:93585215 (GRCh38)
- Gene constraint
- LOEUF 0.133 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 76.81 · 1 PDB
- Residue 64
- the 'disordered' region
Similar variants
- NR2F1 p.Pro64Leu Uncertain significance ★ ⚠ same residue
- NR2F1 c.463+1G>A Likely pathogenic ★★ same type
- NR2F1 p.Arg366Cys Likely pathogenic ★★ same type
- NR2F1 p.Cys106Tyr Pathogenic/Likely pathogenic ★★ same type
- NR2F1 p.Cys122Tyr Likely pathogenic ★★ same type
- NR2F1 p.Cys128Arg Likely pathogenic ★★ same type
- NR2F1 p.Cys146Tyr Pathogenic/Likely pathogenic ★★ same type
- NR2F1 p.Cys86Arg Pathogenic/Likely pathogenic ★★ 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/nr2f1-p-pro64 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown