Is ALG3 p.Ala17= (c.51A>G) pathogenic?

ALG3 p.Ala17= (c.51A>G) is classified Conflicting classifications of pathogenicity in ALG3 (ClinVar, Conflicting submitters, 3 submitters; last evaluated 2025-09-03). Rare (popmax 0.143%, amr); Associated with ALG3-congenital disorder of glycosylation.

What condition is associated with ALG3 p.Ala17= (c.51A>G)?

ALG3 p.Ala17= (c.51A>G) is associated with ALG3-congenital disorder of glycosylation (ClinVar).

How common is ALG3 p.Ala17= (c.51A>G) in the general population?

ALG3 p.Ala17= (c.51A>G) is rare (popmax 0.143%, amr) (gnomAD).

How is ALG3-CDG inherited?

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

ALG3 p.Ala17=

c.51A>G · rs763727038 · VCV344361

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 3 submitters

gnomAD v4.1

Rare

rare (popmax 0.143%, amr)

Conditions

ALG3-congenital disorder of glycosylation

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.01	strongly benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -4.7	GERP -2.8
Overall
CADD	6.622	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.143% Admixed American · 84/58,890 alleles

Filtering AF 0.118% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.109%

Overall 0.00561% 90/1,603,340 alleles · rare

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.143%	701
East Asian	0.00449%	22,252
Remaining individualsnot grpmax-eligible	0.00323%	30,986
European (non-Finnish)	0.00017%	587,772

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
Protein: p.Ala17=
Coding: c.51A>G
MANE Select: NM_005787
dbSNP: rs763727038
Type: single nucleotide variant
Location: chr3:184248890 (GRCh38)
Gene constraint: LOEUF 0.972 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 89.05

Full ALG3 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

ALG3-congenital disorder of glycosylation — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For ALG3-CDG (Orphanet):

Inheritance: Autosomal recessive
Onset: Infancy, Neonatal

Similar variants

ALG3 p.Ala17Val Uncertain significance ★★ ⚠ same residue
ALG3 p.Ala17Gly Uncertain significance ★ ⚠ same residue
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

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-ala17 (accessed [today's date]).

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