Is ALG1 p.Glu405del (c.1210GAA[1]) pathogenic?

ALG1 p.Glu405del (c.1210GAA[1]) is classified Uncertain significance in ALG1 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-07-05). Absent from gnomAD; Associated with ALG1-congenital disorder of glycosylation.

What condition is associated with ALG1 p.Glu405del (c.1210GAA[1])?

ALG1 p.Glu405del (c.1210GAA[1]) is associated with ALG1-congenital disorder of glycosylation (ClinVar).

How common is ALG1 p.Glu405del (c.1210GAA[1]) in the general population?

ALG1 p.Glu405del (c.1210GAA[1]) is absent from gnomAD (gnomAD).

How is ALG1-CDG inherited?

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

ALG1 p.Glu405del

c.1210GAA[1] · rs1957058389 · VCV2181826

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

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 · substitutions only
Constraint at this position
Conservation	phyloP -12	GERP -2.7
Region caveats
Repeat context	seg dup	· reads may not map uniquely · confidence, not pathogenicity

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: ALG1
Protein: p.Glu405del
Coding: c.1210GAA[1]
MANE Select: NM_019109
dbSNP: rs1957058389
Type: Microsatellite
Location: chr16:5083704 (GRCh38)
Gene constraint: LOEUF 1.419 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 93.24

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.Leu366fs Pathogenic ★★ same condition
ALG1 p.Leu20dup Uncertain significance ★★ same condition
ALG1 c.1073-12_1073-11del Likely benign ★ same condition
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_539+1delinsTC 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-glu405del (accessed [today's date]).

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