ATRX p.Phe2135=
c.6405C>T · rs148659669 · VCV196162
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 8 submitters
gnomAD v4.1
Rare
rare (popmax 0.27%, amr)
Conditions
2
Inborn genetic diseases
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 1.2 | GERP -4.2, phastCons 1 |
| Overall | ||
| CADD | 5.452 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.27%
Admixed American · 123/45,602 alleles
Filtering AF
0.231%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.216%
Overall
0.0137%
165/1,200,502 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.27% | 371 |
| East Asian | 0.0327% | 3,060 |
| Middle Eastern | 0.0231% | 4,326 |
| African / African-American | 0.0228% | 4,383 |
| Remaining individualsnot grpmax-eligible | 0.0106% | 9,466 |
| South Asian | 0.00884% | 11,314 |
| Finnishnot grpmax-eligible | 0.00215% | 46,467 |
| European (non-Finnish) | 0.000677% | 147,819 |
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.Phe2135=
- Coding
- c.6405C>T
- MANE Select
- NM_000489
- dbSNP
- rs148659669
- Type
- single nucleotide variant
- Location
- chrX:77558768 (GRCh38)
- Structure
- AlphaFold pLDDT 52.40 · 13 PDB
- Residue 2135
- the 'interaction with mecp2' region; the helicase c-terminal domain
Similar variants
- 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
- ATRX p.Arg2386Ter 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-phe2135 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown