ATRX p.Ser48fs
c.142_143del · VCV3337976
Likely pathogenic
Single submitter
Classification
Likely pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
frameshift
predicted LoF
gnomAD v4.1
Rare
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | frameshift | predicted loss-of-function in a haploinsufficient gene (ClinGen) |
|---|---|---|
| NMD | predicted | premature termination codon in exon 3 of 35 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 5.7 | phastCons 1 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Variant & gene context
- Gene
- ATRX
- Protein
- p.Ser48fs
- Coding
- c.142_143del
- MANE Select
- NM_000489
- Type
- Deletion
- Location
- chrX:77698620 (GRCh38)
- Structure
- AlphaFold pLDDT 52.40 · 13 PDB
- Residue 48
- the 'disordered' region
Similar variants
- ATRX p.Ser48Cys Likely benign ★ ⚠ same residue
- ATRX p.Ser48Gly Likely benign ★ ⚠ same residue
- ATRX p.Lys1030fs Pathogenic ★★ same type
- ATRX p.Arg1089_Lys1091del Uncertain significance ★★ same type
- ATRX p.Asn1165_Lys1166del Uncertain significance ★★ same type
- ATRX p.Asp635_Leu639del Uncertain significance ★★ same type
- ATRX p.Leu821_Glu822del Uncertain significance ★★ same type
- ATRX p.Lys1449_Glu1453del Uncertain significance ★★ 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/atrx-p-ser48fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown