Is ARX p.Arg384fs (c.1151_1152del) pathogenic?

ARX p.Arg384fs (c.11511152del) is classified Pathogenic in ARX (ClinVar, Single submitter, 1 submitter; last evaluated 2013-01-21). Absent from gnomAD.

How common is ARX p.Arg384fs (c.1151_1152del) in the general population?

ARX p.Arg384fs (c.1151_1152del) is absent from gnomAD (gnomAD).

ARX p.Arg384fs

c.1151_1152del · rs398124506 · VCV96448

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

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 4 of 5
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 7.7	GERP 2.1, 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: ARX
Protein: p.Arg384fs
Coding: c.1151_1152del
MANE Select: NM_139058
dbSNP: rs398124506
Type: Microsatellite
Location: chrX:25007407 (GRCh38)
Structure: AlphaFold pLDDT 56.51
Residue 384: a DNA-binding region

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

Similar variants

ARX p.Arg384Cys Pathogenic/Likely pathogenic ★★ same residue
ARX p.Arg384His Conflicting classifications of pathogenicity ★ ⚠ same residue
ARX p.Arg384Leu Pathogenic same residue
ARX p.Ala108_Ala115dup Pathogenic ★★ same type
ARX p.Leu410fs Pathogenic ★★ same type
ARX p.220GT[3] Uncertain significance ★★ same type
ARX p.Ala111_Ala115dup Uncertain significance ★★ same type
ARX p.Ala113_Ala115dup 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/arx-p-arg384fs (accessed [today's date]).

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