GLA p.Asn34=
c.102T>C · rs2520945054 · VCV1770904
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
Cardiovascular phenotype
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.65 | GERP 1.1, phastCons 0.2 |
| Overall | ||
| CADD | 7.001 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- GLA
- Protein
- p.Asn34=
- Coding
- c.102T>C
- MANE Select
- NM_000169
- dbSNP
- rs2520945054
- Type
- single nucleotide variant
- Location
- chrX:101407802 (GRCh38)
- Structure
- AlphaFold pLDDT 94.45 · 31 PDB
- Residue 34
- a UniProt-annotated variant site (in fabryd)
Similar variants
- GLA p.Asn34Ser Pathogenic ★★ ⚠ same residue
- GLA p.Asn34His Likely pathogenic ★ same residue
- GLA p.Asn34Lys Likely pathogenic ★ same residue
- GLA p.Asn34Thr Likely pathogenic ★ ⚠ same residue
- GLA p.Asn34Asp Conflicting classifications of pathogenicity ★ ⚠ 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
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-asn34 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown