Is DAO p.Ala49= (c.147C>T) pathogenic?

DAO p.Ala49= (c.147C>T) is classified Likely benign in DAO (ClinVar, No assertion criteria, 1 submitter; last evaluated 2022-12-09). Rare (popmax 0.305%, sas); Associated with DAO-related disorder.

What condition is associated with DAO p.Ala49= (c.147C>T)?

DAO p.Ala49= (c.147C>T) is associated with DAO-related disorder (ClinVar).

How common is DAO p.Ala49= (c.147C>T) in the general population?

DAO p.Ala49= (c.147C>T) is rare (popmax 0.305%, sas) (gnomAD).

DAO p.Ala49=

c.147C>T · rs531749171 · VCV3046863

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

rare (popmax 0.305%, sas)

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 -20	GERP -4.7
Overall
CADD	0.061	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.305% South Asian · 278/91,074 alleles

Filtering AF 0.276% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.264%

Overall 0.0201% 324/1,613,372 alleles · rare exomes 294/1,461,094 · genomes 30/152,278 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.305%	328
East Asian	0.0379%	2,638
Remaining individualsnot grpmax-eligible	0.0176%	5,680
European (non-Finnish)	0.00144%	69,382
African / African-American	0.00133%	75,032

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.Ala49=
Coding: c.147C>T
MANE Select: NM_001917
dbSNP: rs531749171
Type: single nucleotide variant
Location: chr12:108885153 (GRCh38)
Gene constraint: LOEUF 1.222 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 96.26 · 22 PDB
Residue 49: a binding site

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-ala49 (accessed [today's date]).

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