Is DAO p.Asp58Val (c.173A>T) pathogenic?

DAO p.Asp58Val (c.173A>T) is classified Uncertain significance in DAO (ClinVar, Single submitter, 1 submitter; last evaluated 2022-01-27). AlphaMissense: likely benign (0.1422); Very rare (popmax 0.000137%); Associated with Inborn genetic diseases.

What condition is associated with DAO p.Asp58Val (c.173A>T)?

DAO p.Asp58Val (c.173A>T) is associated with Inborn genetic diseases (ClinVar).

How common is DAO p.Asp58Val (c.173A>T) in the general population?

DAO p.Asp58Val (c.173A>T) is very rare (popmax 0.000137%) (gnomAD).

What do computational predictors say about DAO p.Asp58Val (c.173A>T)?

AlphaMissense predicts likely benign (score 0.1422) — an in-silico prediction, not a clinical call.

DAO p.Asp58Val

c.173A>T · rs1207752179 · VCV2274437

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1422 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.000137%)

Missense predictors

0/2 damaging

AlphaMissense, SaProt · REVEL no call

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.1422	likely benign
REVEL	0.411	indeterminate
SaProt	LLR -3.72	tolerated
⇒ AlphaMissense and SaProt both call this tolerated; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 4.5	GERP -1.9, phastCons 0.37
Regional constraint	o/e 0.99	unconstrained · MANE · 16 kb · p 0.87 · regional, not allelic
Overall
CADD	18.66	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

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

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.000137%

Overall 0.000137% 2/1,460,984 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.Asp58Val
Coding: c.173A>T
MANE Select: NM_001917
dbSNP: rs1207752179
Type: single nucleotide variant
Location: chr12:108885179 (GRCh38)
Gene constraint: LOEUF 1.222 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 96.26 · 22 PDB

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

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

DAO p.Ile318Ser Uncertain significance ★★ ⚠ same condition
DAO p.Ala175Thr Uncertain significance ★ ⚠ same condition
DAO p.Arg115Gln Uncertain significance ★ ⚠ same condition
DAO p.Arg286His Uncertain significance ★ ⚠ same condition
DAO p.Arg297Cys Uncertain significance ★ ⚠ same condition
DAO p.Arg2Cys Uncertain significance ★ ⚠ same condition
DAO p.Asn180Ser Uncertain significance ★ ⚠ same condition
DAO p.Asn246Ser 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-asp58val (accessed [today's date]).

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