Is NR2F2 p.Val299fs (c.896_903del) pathogenic?

NR2F2 p.Val299fs (c.896903del) is classified Pathogenic in NR2F2 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-03-28). Associated with Congenital heart disease (variable).

What condition is associated with NR2F2 p.Val299fs (c.896_903del)?

NR2F2 p.Val299fs (c.896_903del) is associated with Congenital heart disease (variable) (ClinVar).

NR2F2 p.Val299fs

c.896_903del · VCV3895676

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Rare

Conditions

Congenital heart disease (variable)

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 2 of 3
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 7.6	GERP 2.7, phastCons 1

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Variant & gene context

Gene: NR2F2
Protein: p.Val299fs
Coding: c.896_903del
MANE Select: NM_021005
Type: Deletion
Location: chr15:96334526 (GRCh38)
Gene constraint: LOEUF 0.197 · pLI 1.00 · ClinGen HI 0/3 (gnomAD)
Structure: AlphaFold pLDDT 77.94 · 1 PDB
Residue 299: the nr lbd domain; an α-helix; the 'interaction with zfpm2' region

Full NR2F2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Congenital heart disease (variable) — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

NR2F2 p.Gly35fs Pathogenic/Likely pathogenic ★★ same type
NR2F2 p.Asn120fs Pathogenic ★ same type
NR2F2 p.Asn229fs Likely pathogenic ★ same type
NR2F2 p.Cys200fs Likely pathogenic ★ same type
NR2F2 p.Cys343fs Pathogenic ★ same type
NR2F2 p.Glu214fs Pathogenic ★ same type
NR2F2 p.Lys340fs Likely pathogenic ★ same type
NR2F2 p.Pro33fs 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/nr2f2-p-val299fs (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown