ALG3 c.-49G>A
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00195%, amr)
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 -0.28 | GERP -0.64 |
| Non-coding constraint | Z 0.64 | 1 kb window · o/e 0.96 · regional · uncalibrated |
| Overall | ||
| CADD | 8.348 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00195%
Admixed American · 1/51,270 alleles
Overall
7.18e-05%
1/1,392,970 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
- Coding
- c.-49G>A
- MANE Select
- NM_005787
- Type
- single nucleotide variant
- Location
- chr3:184248989 (GRCh38)
- Gene constraint
- LOEUF 0.972 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 89.05
Similar variants
- ALG3 c.444+1G>T Likely pathogenic ★★ same type
- ALG3 p.Arg171Gln Pathogenic/Likely pathogenic ★★ same type
- ALG3 p.Arg266Cys Pathogenic ★★ same type
- ALG3 p.Arg354Cys Likely pathogenic ★★ same type
- ALG3 p.Arg354His Pathogenic/Likely pathogenic ★★ same type
- ALG3 p.Asn174Ser Likely pathogenic ★★ ⚠ same type
- ALG3 p.Gly55= Pathogenic/Likely pathogenic ★★ same type
- ALG3 p.Ile69Thr 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-c-minus-49g-a (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown