ALG3 p.Arg8=
c.24C>T · rs746428888 · VCV390417
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0244%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.373 | indeterminate |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 0.85 | GERP 0.47, phastCons 0.99 |
| Overall | ||
| CADD | 13.28 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0244%
Admixed American · 14/57,332 alleles
Filtering AF
0.0147%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0118%
Overall
0.00126%
20/1,589,948 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0244% | 4,095 |
| Remaining individualsnot grpmax-eligible | 0.00487% | 20,515 |
| European (non-Finnish) | 0.000257% | 389,687 |
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.Arg8=
- Coding
- c.24C>T
- MANE Select
- NM_005787
- dbSNP
- rs746428888
- Type
- single nucleotide variant
- Location
- chr3:184248917 (GRCh38)
- Gene constraint
- LOEUF 0.972 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 89.05
Similar variants
- ALG3 p.Glu8= Likely benign ★★ same residue
- 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
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-arg8 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown