GLDC p.Pro1003=
c.3009A>T · rs2489005985 · VCV2827666
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
glycine encephalopathy
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 -3.7 | GERP -3 |
| Overall | ||
| CADD | 2.672 | 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
- GLDC
- Protein
- p.Pro1003=
- Coding
- c.3009A>T
- MANE Select
- NM_000170
- dbSNP
- rs2489005985
- Type
- single nucleotide variant
- Location
- chr9:6533071 (GRCh38)
- Gene constraint
- LOEUF 1.09 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 94.50 · 3 PDB
- Residue 1003
- an α-helix
Disease context
glycine encephalopathy — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor Glycine encephalopathy (Orphanet):
- Inheritance
- Autosomal recessive
- Onset
- Infancy, Neonatal
- Prevalence
- 1-9 / 1 000 000 (Europe)
Similar variants
- GLDC p.Pro1003Ser Uncertain significance ★★ ⚠ same residue
- GLDC c.1401+1G>A Pathogenic/Likely pathogenic ★★ same condition
- GLDC c.1580+2T>G Pathogenic ★★ same condition
- GLDC c.1851-1G>A Pathogenic ★★ same condition
- GLDC c.2053-2A>G Likely pathogenic ★★ same condition
- GLDC c.2203-2A>G Pathogenic/Likely pathogenic ★★ same condition
- GLDC c.2315+2T>A Pathogenic/Likely pathogenic ★★ same condition
- GLDC c.2315+2T>G 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/gldc-p-pro1003 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown