Is NR4A2 p.Pro201fs (c.598_601dup) pathogenic?

NR4A2 p.Pro201fs (c.598601dup) is classified Likely pathogenic in NR4A2 (ClinVar, No assertion criteria, 1 submitter). No gnomAD frequency available for this variant; Associated with autism spectrum disorder.

What condition is associated with NR4A2 p.Pro201fs (c.598_601dup)?

NR4A2 p.Pro201fs (c.598_601dup) is associated with autism spectrum disorder (ClinVar).

How common is NR4A2 p.Pro201fs (c.598_601dup) in the general population?

NR4A2 p.Pro201fs (c.598_601dup) is no gnomAD frequency available for this variant (gnomAD).

NR4A2 p.Pro201fs

c.598_601dup · rs1686821540 · VCV996680

Likely pathogenic No assertion criteria

Classification

Likely pathogenic

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

autism spectrum disorder

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 haploinsufficient gene (ClinGen)
NMD	predicted	premature termination codon in exon 3 of 8
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 12	GERP 2.5, 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: NR4A2
Protein: p.Pro201fs
Coding: c.598_601dup
MANE Select: NM_006186
dbSNP: rs1686821540
Type: Duplication
Location: chr2:156329585 (GRCh38)
Gene constraint: LOEUF 0.093 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 66.39 · 8 PDB

Full NR4A2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

autism spectrum disorder — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

NR4A2 p.Pro201His Uncertain significance ★ ⚠ same residue
NR4A2 p.Pro201_Met202insTer Pathogenic same residue
NR4A2 p.Lys522Asn Likely benign ★ same condition
NR4A2 p.Ile500fs Likely pathogenic ★ same type
NR4A2 p.Ser59fs Pathogenic ★ same type
NR4A2 p.Asn294fs Conflicting classifications of pathogenicity ★ ⚠ same type
NR4A2 p.Pro183_Gly184insPro Uncertain significance ★ same type
NR4A2 p.Ser110fs Uncertain significance ★ 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/nr4a2-p-pro201fs (accessed [today's date]).

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