Is ALG9 c.1602+14del pathogenic?

ALG9 c.1602+14del is classified Likely benign in ALG9 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-07-19). Associated with ALG9-congenital disorder of glycosylation.

What condition is associated with ALG9 c.1602+14del?

ALG9 c.1602+14del is associated with ALG9-congenital disorder of glycosylation (ClinVar).

How is ALG9-CDG inherited?

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

ALG9 c.1602+14del

VCV3730397

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

Conditions

ALG9-congenital disorder of glycosylation

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
Splice region	donor +14	near-intronic (+14 nt from the splice site)
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 1.9	GERP -0.8, phastCons 1
Non-coding constraint	Z 1.72	1 kb window · o/e 0.87 · regional · uncalibrated

Variant & gene context

Gene: ALG9
Coding: c.1602+14del
MANE Select: NM_024740
Type: Deletion
Location: chr11:111836151 (GRCh38)
Gene constraint: LOEUF 0.853 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 88.35 · 2 PDB

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.1605_1608del Likely pathogenic ★ same condition
ALG9 p.Leu235fs Likely pathogenic ★ same condition
ALG9 p.Met331fs Pathogenic ★ same condition
ALG9 p.Thr43fs Pathogenic ★ same condition
ALG9 c.132-13del Benign ★ same condition
ALG9 c.1734-17del Benign ★ same condition
ALG9 c.702-9_702-8del Likely benign ★ same condition
ALG9 c.566-1G>A 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-c-1602-plus-14del (accessed [today's date]).

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