NR2F2 p.Thr55fs
c.139_155dup · VCV4722378
Pathogenic
Single submitter
Classification
Pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
frameshift
predicted LoF
gnomAD v4.1
Rare
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. | ||
| Consequence | frameshift | predicted loss-of-function in a LoF-intolerant gene |
|---|---|---|
| NMD | predicted | premature termination codon in exon 1 of 3 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 5.9 | GERP 0.25, phastCons 1 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Variant & gene context
- Gene
- NR2F2
- Protein
- p.Thr55fs
- Coding
- c.139_155dup
- MANE Select
- NM_021005
- Type
- Duplication
- Location
- chr15:96332243 (GRCh38)
- Gene constraint
- LOEUF 0.197 · pLI 1.00 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 77.94 · 1 PDB
- Residue 55
- the 'disordered' region
Similar variants
- NR2F2 p.Arg187fs Likely pathogenic ★ same condition
- NR2F2 p.Val286fs Pathogenic ★ same condition
- NR2F2 p.Val29fs Likely pathogenic ★ same condition
- NR2F2 c.970+12_970+16dup Benign ★ same condition
- 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
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-thr55fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown