Is ALG12 p.Leu158= (c.474G>C) pathogenic?

ALG12 p.Leu158= (c.474G>C) is classified Likely benign in ALG12 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-06-23). Very rare (popmax 0.00225%, eas); Associated with ALG12-congenital disorder of glycosylation.

What condition is associated with ALG12 p.Leu158= (c.474G>C)?

ALG12 p.Leu158= (c.474G>C) is associated with ALG12-congenital disorder of glycosylation (ClinVar).

How common is ALG12 p.Leu158= (c.474G>C) in the general population?

ALG12 p.Leu158= (c.474G>C) is very rare (popmax 0.00225%, eas) (gnomAD).

How is ALG12-CDG inherited?

Typically Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

ALG12 p.Leu158=

c.474G>C · rs1400445262 · VCV2725442

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00225%, eas)

Conditions

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 -0.29	GERP -1.2, phastCons 0.15
Overall
CADD	6.833	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00225% East Asian · 1/44,532 alleles

Overall 6.88e-05% 1/1,453,946 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: ALG12
Protein: p.Leu158=
Coding: c.474G>C
MANE Select: NM_024105
dbSNP: rs1400445262
Type: single nucleotide variant
Location: chr22:49910084 (GRCh38)
Gene constraint: LOEUF 0.965 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 93.26
Residue 158: a UniProt-annotated variant site (in cdg1g; loss of dolichyl-p-man:man7glcnac2-pp-dolichyl mannosyltransferase activity)

Full ALG12 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

ALG12-congenital disorder of glycosylation — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For ALG12-CDG (Orphanet):

Inheritance: Autosomal recessive
Onset: Infancy, Neonatal

Similar variants

ALG12 p.Leu158Val Uncertain significance ★ ⚠ same residue
ALG12 p.Leu158Pro Pathogenic 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-leu158 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown