ATRX p.Pro1334=
c.4002A>T · rs782625886 · VCV1129574
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00349%, afr)
Conditions
1
alpha thalassemia-X-linked intellectual disability syndrome
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -0.1 | GERP -2.6, phastCons 0.84 |
| Overall | ||
| CADD | 8.021 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00349%
African / African-American · 2/57,304 alleles
Filtering AF
0.000579%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000217%
Overall
0.000165%
2/1,209,620 alleles · very rare
exomes 1/1,097,284 · genomes 1/112,336 · joint denominator
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
- ATRX
- Protein
- p.Pro1334=
- Coding
- c.4002A>T
- MANE Select
- NM_000489
- dbSNP
- rs782625886
- Type
- single nucleotide variant
- Location
- chrX:77663500 (GRCh38)
- Structure
- AlphaFold pLDDT 52.40 · 13 PDB
- Residue 1334
- the 'disordered' region
Similar variants
- ATRX p.Pro1334Arg Uncertain significance ★ ⚠ same residue
- ATRX c.5449-7A>G Likely pathogenic ★★ same condition
- ATRX p.Arg1022Ter Pathogenic/Likely pathogenic ★★ same condition
- ATRX p.Arg1661Cys Likely pathogenic ★★ ⚠ same condition
- ATRX p.Arg2085Cys Pathogenic/Likely pathogenic ★★ same condition
- ATRX p.Arg2085His Pathogenic/Likely pathogenic ★★ same condition
- ATRX p.Arg2131Gln Pathogenic/Likely pathogenic ★★ same condition
- ATRX p.Arg2178Trp 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/atrx-p-pro1334 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown