Is ALG9 p.His366Arg (c.1097A>G) pathogenic?

ALG9 p.His366Arg (c.1097A>G) is classified Likely pathogenic in ALG9 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-01-07). AlphaMissense: likely pathogenic (0.9198); Absent from gnomAD v4.1; Associated with Gillessen-Kaesbach-Nishimura syndrome.

What condition is associated with ALG9 p.His366Arg (c.1097A>G)?

ALG9 p.His366Arg (c.1097A>G) is associated with Gillessen-Kaesbach-Nishimura syndrome (ClinVar).

How common is ALG9 p.His366Arg (c.1097A>G) in the general population?

ALG9 p.His366Arg (c.1097A>G) is absent from gnomAD v4.1 (gnomAD).

How is ALG9-CDG inherited?

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

What do computational predictors say about ALG9 p.His366Arg (c.1097A>G)?

AlphaMissense predicts likely pathogenic (score 0.9198) — an in-silico prediction, not a clinical call.

ALG9 p.His366Arg

c.1097A>G · VCV4813467

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.9198 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

3/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Gillessen-Kaesbach-Nishimura syndrome

Computational evidence

Protein change
AlphaMissense	0.9198	likely pathogenic ✓ concordant with ClinVar
REVEL	0.956	strongly pathogenic-leaning
SaProt	LLR -13.72	damaging
⇒ AlphaMissense, REVEL and SaProt all call this damaging.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.9	GERP 1.9, phastCons 1
Regional constraint	o/e 0.40	unconstrained · MANE · 3,925 bp · p 1.5e-05 · regional, not allelic
Overall
CADD	26.7	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: ALG9
Protein: p.His366Arg
Coding: c.1097A>G
MANE Select: NM_024740
Type: single nucleotide variant
Location: chr11:111840731 (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

Gillessen-Kaesbach-Nishimura syndrome — 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.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
ALG9 p.Tyr287Cys Pathogenic/Likely pathogenic ★★ same condition
ALG9 p.Ala389Val Uncertain significance ★★ ⚠ same condition
ALG9 p.Ala585Thr Uncertain significance ★★ ⚠ same condition
ALG9 p.Arg607Gln Uncertain significance ★★ ⚠ 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-his366arg (accessed [today's date]).

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