ARX p.Pro409Arg
c.1226C>G · VCV3384963
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
AlphaMissense
likely pathogenic
0.8605 · ACMG-weighted
gnomAD v4.1
Absent
absent from gnomAD v4.1
Missense predictors
2/3 damaging
AlphaMissense, REVEL, SaProt
Computational evidence
| Protein change | ||
| AlphaMissense | 0.8605 | likely pathogenic |
|---|---|---|
| REVEL | 0.728 | pathogenic-leaning |
| SaProt | LLR -7.99 | tolerated |
| ⇒ AlphaMissense and REVEL call this damaging; SaProt does not. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 12 | GERP 1.9, phastCons 1 |
| Regional constraint | o/e 0.71 | unconstrained · MANE · 2,715 bp · p 0.00019 · regional, not allelic |
| Overall | ||
| CADD | 27.9 | 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
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- ARX
- Protein
- p.Pro409Arg
- Coding
- c.1226C>G
- MANE Select
- NM_139058
- Type
- single nucleotide variant
- Location
- chrX:25007333 (GRCh38)
- Structure
- AlphaFold pLDDT 56.51
Similar variants
- ARX p.Pro409Gln Uncertain significance ★ ⚠ 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
- ARX p.Arg384Cys Pathogenic/Likely 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-pro409arg (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown