ALG3 p.Val180=
c.540G>A · rs369032582 · VCV3047306
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00134%, afr)
Conditions
1
ALG3-related disorder
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| REVEL | 0.03 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | Δ0.82 | donor gain · deltas |
| Pangolin | Δ0.45 | gain · loss 0.00 · agrees with SpliceAI · independent |
| Constraint at this position | ||
| Conservation | phyloP -9 | GERP -3.1 |
| Overall | ||
| CADD | 16.49 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00134%
African / African-American · 1/74,902 alleles
Overall
0.000657%
1/152,172 alleles · very rare
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.Val180=
- Coding
- c.540G>A
- MANE Select
- NM_005787
- dbSNP
- rs369032582
- Type
- single nucleotide variant
- Location
- chr3:184245263 (GRCh38)
- Gene constraint
- LOEUF 0.972 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 89.05
Disease context
ALG3-related disorder
Similar variants
- ALG3 c.1154+5C>T Likely benign same condition
- ALG3 c.*5C>T Likely benign same condition
- ALG3 p.Gln5= Likely benign same condition
- ALG3 p.Glu18= Likely benign same condition
- ALG3 p.His62= Likely benign same condition
- ALG3 c.444+1G>T Likely pathogenic ★★ same type
- ALG3 p.Arg171Gln Pathogenic/Likely pathogenic ★★ same type
- ALG3 p.Arg266Cys 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-val180 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown