Is ALG1 p.Asp289= (c.867C>T) pathogenic?

ALG1 p.Asp289= (c.867C>T) is classified Likely benign in ALG1 (ClinVar, Multiple submitters, 4 submitters; last evaluated 2026-01-26). Rare (popmax 0.818%, afr); Associated with ALG1-congenital disorder of glycosylation.

What condition is associated with ALG1 p.Asp289= (c.867C>T)?

ALG1 p.Asp289= (c.867C>T) is associated with ALG1-congenital disorder of glycosylation (ClinVar).

How common is ALG1 p.Asp289= (c.867C>T) in the general population?

ALG1 p.Asp289= (c.867C>T) is rare (popmax 0.818%, afr) (gnomAD).

How is ALG1-CDG inherited?

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

ALG1 p.Asp289=

c.867C>T · rs144029725 · VCV382580

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 4 submitters

gnomAD v4.1

Rare

rare (popmax 0.818%, afr)

Conditions

ALG1-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 -7.2	GERP -3
Overall
CADD	6.961	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.818% African / African-American · 613/74,972 alleles

Filtering AF 0.764% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.743%

Overall 0.0497% 796/1,600,082 alleles · rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.818%	122
Remaining individualsnot grpmax-eligible	0.0611%	1,638
Admixed American	0.0567%	1,764
European (non-Finnish)	0.0089%	11,235
South Asian	0.0066%	15,156

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: ALG1
Protein: p.Asp289=
Coding: c.867C>T
MANE Select: NM_019109
dbSNP: rs144029725
Type: single nucleotide variant
Location: chr16:5079068 (GRCh38)
Gene constraint: LOEUF 1.419 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 93.24
Residue 289: a UniProt-annotated variant site (in cdg1k; decreased function in protein glycosylation as shown by rescue assays in an alg1-deficient yeast strain)

Full ALG1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

ALG1-congenital disorder of glycosylation — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For ALG1-CDG (Orphanet):

Inheritance: Autosomal recessive
Onset: Infancy, Neonatal

Similar variants

ALG1 p.Asp289Gly Likely pathogenic ★★ same residue
ALG1 c.1187+1G>A Pathogenic/Likely pathogenic ★★ same condition
ALG1 c.1187+2T>C Pathogenic ★★ same condition
ALG1 c.1188-2A>G Pathogenic/Likely pathogenic ★★ same condition
ALG1 c.209-2A>G Likely pathogenic ★★ same condition
ALG1 c.539+1G>A Pathogenic/Likely pathogenic ★★ same condition
ALG1 c.630-2A>G Likely pathogenic ★★ same condition
ALG1 c.863-2A>G 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/alg1-p-asp289 (accessed [today's date]).

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