GLA p.Cys202fs
c.606del · VCV4086982
Pathogenic
Single submitter
Classification
Pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
frameshift
predicted LoF
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. | ||
| Consequence | frameshift | predicted loss-of-function in a haploinsufficient gene (ClinGen) |
|---|---|---|
| NMD | predicted | premature termination codon in exon 4 of 7 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 7.7 | GERP 2.8, phastCons 1 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Variant & gene context
- Gene
- GLA
- Protein
- p.Cys202fs
- Coding
- c.606del
- MANE Select
- NM_000169
- Type
- Deletion
- Location
- chrX:101400699 (GRCh38)
- Structure
- AlphaFold pLDDT 94.45 · 31 PDB
- Residue 202
- a disulfide bond; a UniProt-annotated variant site (in fabryd); a UniProt-annotated variant site (in fabryd; loss of enzyme activity); a β-strand
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.Cys202Arg Pathogenic/Likely pathogenic ★★ same residue
- GLA p.Cys202Trp Pathogenic ★★ same residue
- GLA p.Cys202Tyr Pathogenic/Likely pathogenic ★★ same residue
- GLA p.Cys202_Glu203delinsTer Pathogenic ★ same residue
- GLA p.Cys202Ser Likely pathogenic ★ ⚠ same residue
- GLA p.Cys202Phe Uncertain significance ★ ⚠ same residue
- GLA c.548del Pathogenic ★★ same condition
- GLA c.802-3_802-2del 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-cys202fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown