GLA p.Arg404fs
c.1210dup · rs2520849107 · VCV1750330
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 | escapes | premature termination codon in the last exon (7 of 7) — the truncated protein is likely expressed. PVS1 input, not an applied code |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 3.5 | GERP 0.77, 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.Arg404fs
- Coding
- c.1210dup
- MANE Select
- NM_000169
- dbSNP
- rs2520849107
- Type
- Duplication
- Location
- chrX:101397888 (GRCh38)
- Structure
- AlphaFold pLDDT 94.45 · 31 PDB
- Residue 404
- a UniProt-annotated variant site (in fabryd; loss of enzyme activity); a β-strand
Similar variants
- GLA p.Arg404del Pathogenic/Likely pathogenic ★★ same residue
- GLA p.Gln99fs Pathogenic ★★ same condition
- GLA p.Arg404Lys Uncertain significance ★ ⚠ same residue
- GLA c.802-2A>T Pathogenic/Likely pathogenic ★★ same condition
- GLA p.Ala143Pro Pathogenic/Likely pathogenic ★★ same condition
- GLA p.Arg112His Pathogenic/Likely pathogenic ★★ ⚠ same condition
- GLA p.Arg112Leu Pathogenic/Likely pathogenic ★★ same condition
- GLA p.Arg301Gln 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-arg404fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown