ATRX p.Arg1739=
c.5217A>C · rs1557099248 · VCV1642156
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000897%, nfe)
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. | ||
| REVEL | 0.046 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -0.35 | GERP -2.4, phastCons 0.3 |
| Overall | ||
| CADD | 6.714 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000897%
European (non-Finnish) · 8/891,910 alleles
Filtering AF
0.000386%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000279%
Overall
0.000663%
8/1,206,153 alleles · very rare
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.Arg1739=
- Coding
- c.5217A>C
- MANE Select
- NM_000489
- dbSNP
- rs1557099248
- Type
- single nucleotide variant
- Location
- chrX:77620450 (GRCh38)
- Structure
- AlphaFold pLDDT 52.40 · 13 PDB
- Residue 1739
- the helicase atp-binding domain
Similar variants
- ATRX p.Arg1739Gln Uncertain significance ⚠ same residue
- ATRX p.Arg1739Ter Likely pathogenic ★ 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
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-arg1739 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown