ATRX p.Asp1014=
c.3042T>C · rs140476563 · VCV774375
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 5 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0457%, mid)
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 | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 4.1 | GERP 0.083, phastCons 1 |
| Overall | ||
| CADD | 4.695 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0457%
Middle Eastern · 2/4,372 alleles
Filtering AF
0.00809%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00339%
Overall
0.00397%
48/1,208,847 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0457% | 2,186 |
| Remaining individualsnot grpmax-eligible | 0.0126% | 7,928 |
| Admixed American | 0.00438% | 22,852 |
| European (non-Finnish) | 0.00425% | 23,537 |
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.Asp1014=
- Coding
- c.3042T>C
- MANE Select
- NM_000489
- dbSNP
- rs140476563
- Type
- single nucleotide variant
- Location
- chrX:77682214 (GRCh38)
- Structure
- AlphaFold pLDDT 52.40 · 13 PDB
- Residue 1014
- the 'disordered' region
Similar variants
- ATRX p.Asp1014Asn Benign ★ ⚠ 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-asp1014 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown