Is ALG9 c.*323A>G pathogenic?

ALG9 c.323A>G is classified Likely benign in ALG9 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2024-07-23). Rare (popmax 0.436%, afr); Associated with ALG9-related disorder.

What condition is associated with ALG9 c.*323A>G?

ALG9 c.*323A>G is associated with ALG9-related disorder (ClinVar).

How common is ALG9 c.*323A>G in the general population?

ALG9 c.*323A>G is rare (popmax 0.436%, afr) (gnomAD).

ALG9 c.*323A>G

VCV3354837

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

rare (popmax 0.436%, afr)

Conditions

ALG9-related disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -1.5	GERP -5
Non-coding constraint	Z 1.82	1 kb window · o/e 0.86 · regional · uncalibrated
Overall
CADD	4.802	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.436% African / African-American · 220/50,492 alleles

Filtering AF 0.389% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.37%

Overall 0.0496% 230/463,666 alleles · rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.436%	230
Admixed American	0.0164%	6,113
Remaining individualsnot grpmax-eligible	0.00594%	16,840
European (non-Finnish)	0.000863%	115,916

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: ALG9
Coding: c.*323A>G
MANE Select: NM_024740
Type: single nucleotide variant
Location: chr11:111786074 (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-related disorder

Similar variants

ALG9 p.Tyr287Cys Pathogenic/Likely pathogenic ★★ same condition
ALG9 p.Ala389Glu Uncertain significance ★ ⚠ same condition
ALG9 p.Arg247Ser Conflicting classifications of pathogenicity ★ ⚠ same condition
ALG9 c.131+6T>A Uncertain significance same condition
ALG9 p.Gly58Arg Uncertain significance ⚠ same condition
ALG9 p.Val471Ala Uncertain significance ⚠ same condition
ALG9 c.*4C>T Likely benign same condition
ALG9 p.Arg34= Likely benign 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-star-323a-g (accessed [today's date]).

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