Is NR2F2 p.Pro33fs (c.97_103del) pathogenic?

NR2F2 p.Pro33fs (c.97103del) is classified Pathogenic in NR2F2 (ClinVar, Single submitter, 2 submitters; last evaluated 2025-04-22). Absent from gnomAD; Associated with congenital heart defects, multiple types, 4.

What condition is associated with NR2F2 p.Pro33fs (c.97_103del)?

NR2F2 p.Pro33fs (c.97_103del) is associated with congenital heart defects, multiple types, 4, 46,xx sex reversal 5 (ClinVar).

How common is NR2F2 p.Pro33fs (c.97_103del) in the general population?

NR2F2 p.Pro33fs (c.97_103del) is absent from gnomAD (gnomAD).

NR2F2 p.Pro33fs

c.97_103del · rs1899167019 · VCV916034

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 2 submitters

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

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 11	GERP 0.47, phastCons 1

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

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: NR2F2
Protein: p.Pro33fs
Coding: c.97_103del
MANE Select: NM_021005
dbSNP: rs1899167019
Type: Deletion
Location: chr15:96332197 (GRCh38)
Gene constraint: LOEUF 0.197 · pLI 1.00 · ClinGen HI 0/3 (gnomAD)
Structure: AlphaFold pLDDT 77.94 · 1 PDB
Residue 33: the 'disordered' region

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

Disease context

congenital heart defects, multiple types, 4 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: 46,xx sex reversal 5

Similar variants

NR2F2 p.Gly35fs Pathogenic/Likely pathogenic ★★ same condition
NR2F2 p.Asn120fs Pathogenic ★ same condition
NR2F2 p.Asn229fs Likely pathogenic ★ same condition
NR2F2 p.Glu214fs Pathogenic ★ same condition
NR2F2 p.Lys340fs Likely pathogenic ★ same condition
NR2F2 p.Thr193fs Pathogenic ★ same condition
NR2F2 p.Ser341Tyr Pathogenic/Likely pathogenic ★★ same condition
NR2F2 p.Trp249Ter Pathogenic/Likely pathogenic ★★ 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-pro33fs (accessed [today's date]).

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