Is DAO p.Gly239= (c.717A>G) pathogenic?

DAO p.Gly239= (c.717A>G) is classified Likely benign in DAO (ClinVar, No assertion criteria, 1 submitter; last evaluated 2023-09-05). Very rare (popmax 8.48e-05%, nfe); Associated with DAO-related disorder.

What condition is associated with DAO p.Gly239= (c.717A>G)?

DAO p.Gly239= (c.717A>G) is associated with DAO-related disorder (ClinVar).

How common is DAO p.Gly239= (c.717A>G) in the general population?

DAO p.Gly239= (c.717A>G) is very rare (popmax 8.48e-05%, nfe) (gnomAD).

DAO p.Gly239=

c.717A>G · VCV3348720

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 8.48e-05%, nfe)

Conditions

DAO-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 -3.1
Overall
CADD	2.604	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 8.48e-05% European (non-Finnish) · 1/1,179,116 alleles

Overall 6.85e-05% 1/1,460,872 alleles · very rare

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: DAO
Protein: p.Gly239=
Coding: c.717A>G
MANE Select: NM_001917
Type: single nucleotide variant
Location: chr12:108898700 (GRCh38)
Gene constraint: LOEUF 1.222 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 96.26 · 22 PDB
Residue 239: a β-strand

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

Disease context

DAO-related disorder

Similar variants

DAO p.Arg290Gln Uncertain significance ★ ⚠ same condition
DAO p.Arg297His Uncertain significance ★ ⚠ same condition
DAO p.Arg2Ser Uncertain significance ★ ⚠ same condition
DAO p.Arg38His Uncertain significance ★ ⚠ same condition
DAO p.Gly131Cys Uncertain significance ★ ⚠ same condition
DAO p.Pro103= Uncertain significance ★ same condition
DAO p.Thr235Ile Uncertain significance ★ ⚠ same condition
DAO p.Arg286Cys 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/dao-p-gly239 (accessed [today's date]).

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