NR2F1 p.Pro61=
c.183C>T · rs1054029785 · VCV373470
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
very rare (popmax 0.0042%, 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 0.081 | GERP 1.4, phastCons 0.95 |
| Overall | ||
| CADD | 14.58 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0042%
European (non-Finnish) · 48/1,143,614 alleles
Filtering AF
0.00325%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00287%
Overall
0.00331%
51/1,540,314 alleles · very rare
exomes 47/1,389,700 · genomes 4/150,614 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0042% | 23,825 |
| African / African-American | 0.00275% | 36,306 |
| Remaining individualsnot grpmax-eligible | 0.00167% | 59,738 |
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.Pro61=
- Coding
- c.183C>T
- MANE Select
- NM_005654
- dbSNP
- rs1054029785
- Type
- single nucleotide variant
- Location
- chr5:93585206 (GRCh38)
- Gene constraint
- LOEUF 0.133 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 76.81 · 1 PDB
- Residue 61
- the 'disordered' region
Similar variants
- 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
- NR2F1 p.Gly105Ser 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-pro61 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown