Is ALG13 p.Glu69del (c.204AGA[1]) pathogenic?

ALG13 p.Glu69del (c.204AGA[1]) is classified Likely pathogenic in ALG13 (ClinVar, No assertion criteria, 1 submitter). No gnomAD frequency available for this variant; Associated with congenital disorder of glycosylation.

What condition is associated with ALG13 p.Glu69del (c.204AGA[1])?

ALG13 p.Glu69del (c.204AGA[1]) is associated with congenital disorder of glycosylation (ClinVar).

How common is ALG13 p.Glu69del (c.204AGA[1]) in the general population?

ALG13 p.Glu69del (c.204AGA[1]) is no gnomAD frequency available for this variant (gnomAD).

ALG13 p.Glu69del

c.204AGA[1] · rs2147626590 · VCV1184824

Likely pathogenic No assertion criteria

Classification

Likely pathogenic

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

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 0.97	GERP -0.34, phastCons 0.99

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: ALG13
Protein: p.Glu69del
Coding: c.204AGA[1]
MANE Select: NM_001099922
dbSNP: rs2147626590
Type: Microsatellite
Location: chrX:111682253 (GRCh38)
Structure: AlphaFold pLDDT 54.42
Residue 69: the 'glycosyltransferase activity' region

Full ALG13 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

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

Similar variants

ALG13 p.Glu69Asp Conflicting classifications of pathogenicity ★ ⚠ same residue
ALG13 p.Arg791Gln Uncertain significance ★★ ⚠ same condition
ALG13 p.Leu611Phe Likely benign ★★ same condition
ALG13 p.Ile17Asn Likely pathogenic ★ same condition
ALG13 p.Gly972Val Uncertain significance ★ ⚠ same condition
ALG13 c.2457+15_2457+17del Benign/Likely benign ★★ same type
ALG13 c.751-8_751-6del Benign/Likely benign ★★ same type
ALG13 p.Glu795del Benign/Likely benign ★★ same type

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/alg13-p-glu69del (accessed [today's date]).

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