NR2F2 p.Cys79=
c.237C>T · rs369494475 · VCV2038653
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000935%, nfe)
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 0.26 | GERP 1.7, phastCons 0.99 |
| Overall | ||
| CADD | 12.9 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000935%
European (non-Finnish) · 11/1,176,570 alleles
Filtering AF
0.000502%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000367%
Overall
0.000685%
11/1,606,592 alleles · very rare
exomes 9/1,454,464 · genomes 2/152,128 · 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.Cys79=
- Coding
- c.237C>T
- MANE Select
- NM_021005
- dbSNP
- rs369494475
- Type
- single nucleotide variant
- Location
- chr15:96332342 (GRCh38)
- Gene constraint
- LOEUF 0.197 · pLI 1.00 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 77.94 · 1 PDB
- Residue 79
- a DNA-binding region
Similar variants
- 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
- NR2F2 p.Thr358Met 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-cys79 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown