GLA p.Cys90fs
c.267_268dup · rs2520914004 · VCV2440471
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 2 of 7 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 7.6 | GERP 2.5, phastCons 1 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Population frequency
No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.
Variant & gene context
- Gene
- GLA
- Protein
- p.Cys90fs
- Coding
- c.267_268dup
- MANE Select
- NM_000169
- dbSNP
- rs2520914004
- Type
- Microsatellite
- Location
- chrX:101403911 (GRCh38)
- Structure
- AlphaFold pLDDT 94.45 · 31 PDB
- Residue 90
- a β-strand
Similar variants
- GLA p.Cys90Tyr Pathogenic ★★ ⚠ same residue
- GLA p.Cys90Gly Likely pathogenic ★ ⚠ same residue
- GLA p.Cys90Phe Likely pathogenic ★ ⚠ same residue
- GLA p.Cys90Ter Pathogenic ★ same residue
- GLA p.Cys90Trp Pathogenic ★ ⚠ same residue
- GLA p.Cys90Arg Conflicting classifications of pathogenicity ★ ⚠ same residue
- GLA p.Ala121fs Pathogenic ★★ same type
- GLA p.Arg17fs Pathogenic ★★ 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/gla-p-cys90fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown