ALG3 c.*5C>T
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000254%, 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 -0.34 | GERP -3.2 |
| Non-coding constraint | Z 0.87 | 1 kb window · o/e 0.94 · regional · uncalibrated |
| Overall | ||
| CADD | 3.659 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000254%
European (non-Finnish) · 3/1,179,384 alleles
Filtering AF
6.8e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.9e-05%
Overall
0.000186%
3/1,612,466 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.*5C>T
- MANE Select
- NM_005787
- dbSNP
- rs757011568
- Type
- single nucleotide variant
- Location
- chr3:184242509 (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 p.Gln5= 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
- 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-c-star-5c-t (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown