Is ARX p.Gly197= (c.591C>T) pathogenic?

ARX p.Gly197= (c.591C>T) is classified Likely benign in ARX (ClinVar, Multiple submitters, 3 submitters; last evaluated 2024-10-04). Very rare (popmax 0.00224%, nfe); Associated with intellectual disability, X-linked, with or without seizures, ARX-related.

How common is ARX p.Gly197= (c.591C>T) in the general population?

ARX p.Gly197= (c.591C>T) is very rare (popmax 0.00224%, nfe) (gnomAD).

ARX p.Gly197=

Q: What condition is associated with ARX p.Gly197= (c.591C>T)?

ARX p.Gly197= (c.591C>T) is associated with intellectual disability, X-linked, with or without seizures, ARX-related, developmental and epileptic encephalopathy, 1 (ClinVar).

c.591C>T · rs1200326478 · VCV1208287

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Rare

very rare (popmax 0.00224%, nfe)

Conditions

intellectual disability, X-linked, with or without seizures, ARX-related

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 2.1	GERP -3.1, phastCons 1
Overall
CADD	12.34	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00224% European (non-Finnish) · 18/804,223 alleles

Filtering AF 0.0014% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00115%

Overall 0.00189% 19/1,007,643 alleles · very rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.00224%	44,679
African / African-American	0.00205%	48,818

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: ARX
Protein: p.Gly197=
Coding: c.591C>T
MANE Select: NM_139058
dbSNP: rs1200326478
Type: single nucleotide variant
Location: chrX:25013404 (GRCh38)
Structure: AlphaFold pLDDT 56.51
Residue 197: the 'disordered' region

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

Disease context

intellectual disability, X-linked, with or without seizures, ARX-related — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: developmental and epileptic encephalopathy, 1

Similar variants

ARX p.Gly197Asp Conflicting classifications of pathogenicity ★ ⚠ same residue
ARX p.Gly197Val Uncertain significance ★ same residue
ARX p.Arg330His Likely pathogenic ★★ same condition
ARX p.Arg332Gly Pathogenic/Likely pathogenic ★★ same condition
ARX p.Arg332His Pathogenic ★★ same condition
ARX p.Arg371Gln Likely pathogenic ★★ same condition
ARX p.Arg371Ter Pathogenic ★★ same condition
ARX p.Arg384Cys 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/arx-p-gly197 (accessed [today's date]).

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