GNE p.Pro382=
c.1146A>T · rs2133041945 · VCV1573271
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
2
GNE myopathy
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 1.1 | GERP 0.55, phastCons 1 |
| Overall | ||
| CADD | 10.59 | 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
- GNE
- Protein
- p.Pro382=
- Coding
- c.1146A>T
- MANE Select
- NM_005476
- dbSNP
- rs2133041945
- Type
- single nucleotide variant
- Location
- chr9:36227383 (GRCh38)
- Gene constraint
- LOEUF 0.821 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 92.96 · 5 PDB
Disease context
GNE myopathy — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsAlso linked: sialuria
For GNE myopathy (Orphanet):
- Inheritance
- Autosomal dominant, Autosomal recessive
- Onset
- Adolescent, Adult
- Prevalence
- 1-9 / 100 000 (Worldwide)
Similar variants
- GNE c.1816+2T>C Pathogenic/Likely pathogenic ★★ same condition
- GNE c.1816+5G>A Pathogenic ★★ same condition
- GNE c.617-1G>A Likely pathogenic ★★ same condition
- GNE c.617-2A>G Pathogenic/Likely pathogenic ★★ same condition
- GNE c.982+2T>A Likely pathogenic ★★ same condition
- GNE p.Ala524Val Pathogenic/Likely pathogenic ★★ same condition
- GNE p.Ala630Thr Pathogenic/Likely pathogenic ★★ same condition
- GNE p.Ala631Thr 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/gne-p-pro382 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown