NR2F2 p.Val29=
c.87G>A · VCV4715705
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00209%, sas)
Conditions
1
congenital heart defects, multiple types, 4
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 6.4 | GERP 0.31, phastCons 1 |
| Overall | ||
| CADD | 14.66 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00209%
South Asian · 1/47,846 alleles
Overall
7.5e-05%
1/1,334,036 alleles · very rare
exomes 1/1,182,498 · genomes 0/151,538 · 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
- NR2F2
- Protein
- p.Val29=
- Coding
- c.87G>A
- MANE Select
- NM_021005
- Type
- single nucleotide variant
- Location
- chr15:96332192 (GRCh38)
- Gene constraint
- LOEUF 0.197 · pLI 1.00 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 77.94 · 1 PDB
- Residue 29
- the 'disordered' region
Similar variants
- NR2F2 p.Val29fs Likely pathogenic ★ same residue
- NR2F2 p.Ser341Tyr Pathogenic/Likely pathogenic ★★ same condition
- NR2F2 p.Trp249Ter Pathogenic/Likely pathogenic ★★ same condition
- NR2F2 p.Ala2Ser Uncertain significance ★★ ⚠ same condition
- NR2F2 p.Gly180Arg Uncertain significance ★★ ⚠ same condition
- NR2F2 p.Gly361Arg Uncertain significance ★★ ⚠ same condition
- NR2F2 p.His90Arg Uncertain significance ★★ ⚠ same condition
- NR2F2 p.Pro32Arg Uncertain significance ★★ ⚠ same condition
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-val29 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown