Is DUOX2 p.Pro1069Arg (c.3206C>G) pathogenic?

DUOX2 p.Pro1069Arg (c.3206C>G) is classified Uncertain significance in DUOX2 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-06-25). AlphaMissense: likely benign (0.088); Ultra-rare (popmax 0.0133%, afr); Associated with Inborn genetic diseases.

What condition is associated with DUOX2 p.Pro1069Arg (c.3206C>G)?

DUOX2 p.Pro1069Arg (c.3206C>G) is associated with Inborn genetic diseases (ClinVar).

How common is DUOX2 p.Pro1069Arg (c.3206C>G) in the general population?

DUOX2 p.Pro1069Arg (c.3206C>G) is ultra-rare (popmax 0.0133%, afr) (gnomAD).

What do computational predictors say about DUOX2 p.Pro1069Arg (c.3206C>G)?

AlphaMissense predicts likely benign (score 0.088) — an in-silico prediction, not a clinical call.

DUOX2 p.Pro1069Arg

c.3206C>G · VCV3505744

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.088 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0133%, afr)

Missense predictors

0/2 damaging

AlphaMissense, REVEL · SaProt no call

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.088	likely benign
REVEL	0.128	moderately benign-leaning
SaProt	—	withheld · numbering disagrees past residue 25 · why
⇒ AlphaMissense and REVEL both call this tolerated; SaProt makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 4.3	GERP -0.58, phastCons 1
Regional constraint	o/e 1.01	unconstrained · MANE · 17 kb · p 0.63 · regional, not allelic
Overall
CADD	20.2	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 is an independent agreement signal.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0133% African / African-American · 10/75,052 alleles

Filtering AF 0.00722% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00549%

Overall 0.00062% 10/1,614,092 alleles · ultra-rare exomes 5/1,461,796 · genomes 5/152,296 · 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: DUOX2
Protein: p.Pro1069Arg
Coding: c.3206C>G
MANE Select: NM_001363711
Type: single nucleotide variant
Location: chr15:45099871 (GRCh38)
Gene constraint: LOEUF 1.165 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 84.37
Residue 1069: the 'interaction with txndc11' region

Full DUOX2 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

DUOX2 c.513+1G>C Pathogenic/Likely pathogenic ★★ same condition
DUOX2 p.Arg434Ter Pathogenic ★★ same condition
DUOX2 p.Arg625Ter Pathogenic/Likely pathogenic ★★ same condition
DUOX2 c.3693+5G>C Uncertain significance ★★ same condition
DUOX2 p.Ala1133Pro Uncertain significance ★★ ⚠ same condition
DUOX2 p.Ala1138Thr Uncertain significance ★★ ⚠ same condition
DUOX2 p.Ala1230Ser Uncertain significance ★★ ⚠ same condition
DUOX2 p.Ala1306Thr 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/duox2-p-pro1069arg (accessed [today's date]).

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