Is ARX p.Pro184Arg (c.551C>G) pathogenic?

ARX p.Pro184Arg (c.551C>G) is classified Likely benign in ARX (ClinVar, Single submitter, 1 submitter; last evaluated 2017-12-18). AlphaMissense: likely benign (0.1066); Absent from gnomAD v4.1.

How common is ARX p.Pro184Arg (c.551C>G) in the general population?

ARX p.Pro184Arg (c.551C>G) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about ARX p.Pro184Arg (c.551C>G)?

AlphaMissense predicts likely benign (score 0.1066) — an in-silico prediction, not a clinical call.

ARX p.Pro184Arg

c.551C>G · rs1131691410 · VCV429491

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1066 · ACMG-weighted

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 932,600)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1066	likely benign
REVEL	0.257	benign-leaning
SaProt	LLR -7.42	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 8.6	GERP 0.46, phastCons 1
Regional constraint	o/e 0.87	unconstrained · MANE · 2,633 bp · p 0.032 · regional, not allelic
Overall
CADD	22.1	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 932,600). 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.Pro184Arg
Coding: c.551C>G
MANE Select: NM_139058
dbSNP: rs1131691410
Type: single nucleotide variant
Location: chrX:25013444 (GRCh38)
Structure: AlphaFold pLDDT 56.51
Residue 184: the 'disordered' region

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

Similar variants

ARX p.Pro184Ala Uncertain significance ★ ⚠ same residue
ARX p.Pro184= Likely benign ★ same residue
ARX p.Arg330His Likely pathogenic ★★ same type
ARX p.Arg332Cys Pathogenic/Likely pathogenic ★★ same type
ARX p.Arg332Gly Pathogenic/Likely pathogenic ★★ same type
ARX p.Arg332His Pathogenic ★★ same type
ARX p.Arg371Gln Likely pathogenic ★★ same type
ARX p.Arg371Ter 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/arx-p-pro184arg (accessed [today's date]).

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