ALG3 p.Leu181=
c.541C>T · VCV3619433
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
ALG3-congenital disorder of glycosylation
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.088 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · G>T here scores Δ0.40 · evaluated, not missing |
| Constraint at this position | ||
| Conservation | phyloP 2.5 | GERP 0.47, phastCons 1 |
| Overall | ||
| CADD | 7.839 | 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
- ALG3
- Protein
- p.Leu181=
- Coding
- c.541C>T
- MANE Select
- NM_005787
- Type
- single nucleotide variant
- Location
- chr3:184245262 (GRCh38)
- Gene constraint
- LOEUF 0.972 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 89.05
Disease context
ALG3-congenital disorder of glycosylation — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor ALG3-CDG (Orphanet):
- Inheritance
- Autosomal recessive
- Onset
- Infancy, Neonatal
Similar variants
- ALG3 c.444+1G>T Likely pathogenic ★★ same condition
- ALG3 p.Arg171Gln Pathogenic/Likely pathogenic ★★ same condition
- ALG3 p.Arg266Cys Pathogenic ★★ same condition
- ALG3 p.Arg354Cys Likely pathogenic ★★ same condition
- ALG3 p.Arg354His Pathogenic/Likely pathogenic ★★ same condition
- ALG3 p.Asn174Ser Likely pathogenic ★★ ⚠ same condition
- ALG3 p.Gly55= Pathogenic/Likely pathogenic ★★ same condition
- ALG3 p.Ile69Thr 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/alg3-p-leu181 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown