Is ALG9 p.Ala23fs (c.65_66insTC) pathogenic?

ALG9 p.Ala23fs (c.6566insTC) is classified Likely pathogenic in ALG9 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-02-08). Absent from gnomAD; Associated with ALG9-congenital disorder of glycosylation.

What condition is associated with ALG9 p.Ala23fs (c.65_66insTC)?

ALG9 p.Ala23fs (c.65_66insTC) is associated with ALG9-congenital disorder of glycosylation (ClinVar).

How common is ALG9 p.Ala23fs (c.65_66insTC) in the general population?

ALG9 p.Ala23fs (c.65_66insTC) is absent from gnomAD (gnomAD).

How is ALG9-CDG inherited?

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

ALG9 p.Ala23fs

c.65_66insTC · rs2497784482 · VCV3066316

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

ALG9-congenital disorder of glycosylation

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function
NMD	predicted	premature termination codon in exon 1 of 15
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP -3.4	GERP -4.7

Predicted loss-of-function is descriptive, not an applied PVS1 code.

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: ALG9
Protein: p.Ala23fs
Coding: c.65_66insTC
MANE Select: NM_024740
dbSNP: rs2497784482
Type: Insertion
Location: chr11:111871417 (GRCh38)
Gene constraint: LOEUF 0.853 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 88.35 · 2 PDB
Residue 23: the 'disordered' region

Full ALG9 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

ALG9-congenital disorder of glycosylation — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For ALG9-CDG (Orphanet):

Inheritance: Autosomal recessive
Onset: Antenatal, Infancy, Neonatal

Similar variants

ALG9 c.132-13_132-12insTG Benign/Likely benign ★★ same condition
ALG9 c.132-13_132-12insTTG Likely benign ★ same condition
ALG9 c.132-13_132-12insTTTTG Likely benign ★ same condition
ALG9 c.132-13_132-12insTTTTTTTTG Likely benign ★ same condition
ALG9 c.566-1G>A Pathogenic/Likely pathogenic ★★ same condition
ALG9 c.896-2A>G Likely pathogenic ★★ same condition
ALG9 p.Arg143Ter Pathogenic/Likely pathogenic ★★ same condition
ALG9 p.Trp248Ter 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/alg9-p-ala23fs (accessed [today's date]).

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