Is PAOX p.Thr482= (c.1446G>A) pathogenic?

PAOX p.Thr482= (c.1446G>A) is classified Likely benign in PAOX (ClinVar, Single submitter, 1 submitter; last evaluated 2024-04-20). Very rare (popmax 0.00933%, afr).

How common is PAOX p.Thr482= (c.1446G>A) in the general population?

PAOX p.Thr482= (c.1446G>A) is very rare (popmax 0.00933%, afr) (gnomAD).

PAOX p.Thr482=

c.1446G>A · VCV3304212

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00933%, afr)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.115	moderately benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -5.3
Overall
CADD	0.282	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00933% African / African-American · 7/75,032 alleles

Filtering AF 0.00437% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00308%

Overall 0.00192% 31/1,613,500 alleles · very rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.00933%	10,719
South Asian	0.00329%	30,361
European (non-Finnish)	0.00178%	56,192

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: PAOX
Protein: p.Thr482=
Coding: c.1446G>A
MANE Select: NM_152911
Type: single nucleotide variant
Location: chr10:133391365 (GRCh38)
Gene constraint: LOEUF 1.292 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 92.77
Residue 482: a binding site

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

Similar variants

PAOX p.Thr482Met Uncertain significance ★ same residue
PAOX p.Glu329Asp Uncertain significance ★★ ⚠ same type
PAOX p.Ala116Ser Uncertain significance ★ ⚠ same type
PAOX p.Ala128Val Uncertain significance ★ ⚠ same type
PAOX p.Ala131Gly Uncertain significance ★ ⚠ same type
PAOX p.Ala235Thr Uncertain significance ★ ⚠ same type
PAOX p.Arg277Trp Uncertain significance ★ ⚠ same type
PAOX p.Arg415Trp Uncertain significance ★ ⚠ same type

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/paox-p-thr482 (accessed [today's date]).

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