Is ALG9 p.Arg69= (c.207G>A) pathogenic?

ALG9 p.Arg69= (c.207G>A) is classified Likely benign in ALG9 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2024-08-17). Very rare (popmax 0.00269%, afr); Associated with ALG9-related disorder.

What condition is associated with ALG9 p.Arg69= (c.207G>A)?

ALG9 p.Arg69= (c.207G>A) is associated with ALG9-related disorder (ClinVar).

How common is ALG9 p.Arg69= (c.207G>A) in the general population?

ALG9 p.Arg69= (c.207G>A) is very rare (popmax 0.00269%, afr) (gnomAD).

ALG9 p.Arg69=

c.207G>A · VCV3355995

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00269%, 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 -1.2	GERP -5
Overall
CADD	10.72	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00269% African / African-American · 2/74,368 alleles

Filtering AF 0.000446% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000167%

Overall 0.000124% 2/1,611,146 alleles · very rare exomes 0/1,460,474 · genomes 2/150,672 · joint denominator

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
Protein: p.Arg69=
Coding: c.207G>A
MANE Select: NM_024740
Type: single nucleotide variant
Location: chr11:111870295 (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.*323A>G Likely benign same condition
ALG9 c.*4C>T 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-p-arg69 (accessed [today's date]).

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