GLA p.Ile239del
c.716_718del · VCV4087113
Likely pathogenic
Single submitter
Classification
Likely pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
Conditions
1
Fabry disease
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 2.9 | GERP 3.2, phastCons 1 |
Variant & gene context
- Gene
- GLA
- Protein
- p.Ile239del
- Coding
- c.716_718del
- MANE Select
- NM_000169
- Type
- Deletion
- Location
- chrX:101398868 (GRCh38)
- Structure
- AlphaFold pLDDT 94.45 · 31 PDB
- Residue 239
- an α-helix
Disease context
Fabry disease — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor Fabry disease (Orphanet):
- Inheritance
- X-linked dominant, X-linked recessive
- Onset
- Adolescent, Adult, Childhood
- Prevalence
- 1-9 / 1 000 000 (Worldwide)
Similar variants
- GLA p.Ile239fs Pathogenic ★ same residue
- GLA p.Ile239Thr Likely pathogenic ★ same residue
- GLA p.Ile239Met Conflicting classifications of pathogenicity ★ ⚠ same residue
- GLA c.548del Pathogenic ★★ same condition
- GLA c.802-3_802-2del Pathogenic ★★ same condition
- GLA c.803_806del Pathogenic ★★ same condition
- GLA p.Ala190fs Pathogenic ★★ same condition
- GLA p.Ala288fs 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/gla-p-ile239del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown