ALG3 p.Gln331Ter
c.991C>T · rs1553827968 · VCV521583
Pathogenic
Single submitter
Classification
Pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
Consequence
nonsense (stop-gain)
predicted LoF
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
2
Inborn genetic diseases
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | nonsense (stop-gain) | predicted loss-of-function |
|---|---|---|
| NMD | predicted | premature termination codon in exon 7 of 9 |
| REVEL | 0.396 | indeterminate |
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 9.9 | GERP 1.7, phastCons 1 |
| Overall | ||
| CADD | 45.0 | PHRED · no single calibrated threshold — expert panels disagree |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- ALG3
- Protein
- p.Gln331Ter
- Coding
- c.991C>T
- MANE Select
- NM_005787
- dbSNP
- rs1553827968
- Type
- single nucleotide variant
- Location
- chr3:184243572 (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 condition
- ALG3 p.Arg171Gln Pathogenic/Likely pathogenic ★★ same condition
- ALG3 p.Arg266Cys Pathogenic ★★ same condition
- ALG3 p.Arg354Cys Likely pathogenic ★★ same condition
- ALG3 p.Arg354His Pathogenic/Likely pathogenic ★★ same condition
- ALG3 p.Asn174Ser Likely pathogenic ★★ ⚠ same condition
- ALG3 p.Gly55= Pathogenic/Likely pathogenic ★★ same condition
- ALG3 p.Ile69Thr Likely pathogenic ★★ same condition
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-gln331ter (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown