ALG12 p.Leu187=
c.561G>A · rs1601823586 · VCV763997
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
ALG12-congenital disorder of glycosylation
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 0.065 | GERP -2.5, phastCons 0.003 |
| Overall | ||
| CADD | 5.048 | PHRED · no single calibrated threshold — expert panels disagree |
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
- ALG12
- Protein
- p.Leu187=
- Coding
- c.561G>A
- MANE Select
- NM_024105
- dbSNP
- rs1601823586
- Type
- single nucleotide variant
- Location
- chr22:49909997 (GRCh38)
- Gene constraint
- LOEUF 0.965 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 93.26
Disease context
ALG12-congenital disorder of glycosylation — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor ALG12-CDG (Orphanet):
- Inheritance
- Autosomal recessive
- Onset
- Infancy, Neonatal
Similar variants
- ALG12 p.Leu187Met Uncertain significance ★ ⚠ same residue
- ZBED4 p.Leu187Phe Uncertain significance ★ ⚠ same residue
- ALG12 c.295+1G>A Pathogenic/Likely pathogenic ★★ same condition
- ALG12 c.768+1G>A Likely pathogenic ★★ same condition
- ALG12 p.Arg146Gln Pathogenic/Likely pathogenic ★★ same condition
- ALG12 p.Arg202Ter Pathogenic/Likely pathogenic ★★ same condition
- ALG12 p.Gly101Arg Likely pathogenic ★★ same condition
- ALG12 p.Thr67Met Pathogenic/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/alg12-p-leu187 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown