ALG3 p.Gln5=
c.15G>A · rs779358679 · VCV3050161
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00424%, nfe)
Conditions
1
ALG3-related disorder
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 0.21 | GERP -3.3 |
| Overall | ||
| CADD | 8.034 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00424%
European (non-Finnish) · 50/1,179,254 alleles
Filtering AF
0.00326%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00294%
Overall
0.00323%
52/1,612,108 alleles · very rare
exomes 52/1,459,778 · genomes 0/152,330 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00424% | 23,585 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,430 |
| South Asian | 0.00111% | 90,478 |
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- ALG3
- Protein
- p.Gln5=
- Coding
- c.15G>A
- MANE Select
- NM_005787 · reported on NM_001006941
- dbSNP
- rs779358679
- Type
- single nucleotide variant
- Location
- chr3:184249263 (GRCh38)
- Gene constraint
- LOEUF 0.972 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 89.05
Disease context
ALG3-related disorder
Similar variants
- ALG3 p.Leu5Val Uncertain significance ★★ ⚠ same residue
- ALG3 p.Leu5Pro Uncertain significance ★ ⚠ same residue
- ALG3 c.1154+5C>T Likely benign same condition
- ALG3 c.*5C>T Likely benign same condition
- ALG3 p.Glu18= Likely benign same condition
- ALG3 p.His62= Likely benign same condition
- ALG3 p.Val180= Likely benign same condition
- ALG3 c.444+1G>T Likely pathogenic ★★ same type
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-gln5 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown