Is ODAD1 p.Arg89Pro (c.266G>C) pathogenic?

ODAD1 p.Arg89Pro (c.266G>C) is classified Benign/Likely benign in ODAD1 (ClinVar, Multiple submitters, 6 submitters; last evaluated 2026-01-24). AlphaMissense: likely pathogenic (0.7532); Low-frequency (popmax 3.34%, eas); Associated with primary ciliary dyskinesia.

What condition is associated with ODAD1 p.Arg89Pro (c.266G>C)?

ODAD1 p.Arg89Pro (c.266G>C) is associated with primary ciliary dyskinesia, primary ciliary dyskinesia 20 (ClinVar).

How common is ODAD1 p.Arg89Pro (c.266G>C) in the general population?

ODAD1 p.Arg89Pro (c.266G>C) is low-frequency (popmax 3.34%, eas) (gnomAD).

How is Primary ciliary dyskinesia inherited?

Typically Autosomal dominant, Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

What do computational predictors say about ODAD1 p.Arg89Pro (c.266G>C)?

AlphaMissense predicts likely pathogenic (score 0.7532) — an in-silico prediction, not a clinical call.

ODAD1 p.Arg89Pro

c.266G>C · rs58966182 · VCV241874

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 6 submitters

AlphaMissense

likely pathogenic

0.7532 · ACMG-weighted

gnomAD v4.1

Rare

low-frequency (popmax 3.34%, eas)

Missense predictors

2/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

primary ciliary dyskinesia

Computational evidence

Protein change
AlphaMissense	0.7532	likely pathogenic · top 4% in ODAD1
REVEL	0.145	moderately benign-leaning
SaProt	LLR -10.21	damaging
⇒ AlphaMissense and SaProt call this damaging; REVEL does not.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -0.57	GERP 0.35
Regional constraint	o/e 0.94	unconstrained · MANE · 23 kb · p 0.066 · regional, not allelic
Overall
CADD	14.99	PHRED · no single calibrated threshold — expert panels disagree

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

⚠ Isoform check: AlphaMissense numbered on a different transcript (AM R52P vs ClinVar R89P) — verify the residue.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 3.34% East Asian · 1,368/40,910 alleles

Filtering AF 3.2% ClinGen BA1/BS1 input FAF95, joint · FAF99 3.14%

Overall 0.104% 1,621/1,551,646 alleles · low-frequency exomes 1,365/1,399,364 · genomes 256/152,282 · joint denominator

Ancestry group	Frequency	1 in
East Asiangrpmax	3.34%	30
Remaining individualsnot grpmax-eligible	0.221%	452
South Asian	0.0666%	1,501
Admixed American	0.0177%	5,665
African / African-American	0.0082%	12,192
European (non-Finnish)	0.00418%	23,896
Finnishnot grpmax-eligible	0.00167%	59,866

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: ODAD1
Protein: p.Arg89Pro
Coding: c.266G>C
MANE Select: NM_001364171
dbSNP: rs58966182
Type: single nucleotide variant
Location: chr19:48318481 (GRCh38)
Gene constraint: LOEUF 0.904 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 73.25 · 1 PDB

Full ODAD1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

primary ciliary dyskinesia — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: primary ciliary dyskinesia 20

For Primary ciliary dyskinesia (Orphanet):

Inheritance: Autosomal dominant, Autosomal recessive, X-linked recessive
Onset: Neonatal
Prevalence: 1-5 / 10 000 (Pakistan)

Similar variants

ODAD1 p.Arg89Gln Uncertain significance ★★ ⚠ same residue
ODAD1 p.Arg89Trp Uncertain significance ★★ ⚠ same residue
ODAD1 c.1502+5G>A Pathogenic/Likely pathogenic ★★ same condition
ODAD1 c.1503-2A>G Likely pathogenic ★★ same condition
ODAD1 c.597+1G>A Pathogenic/Likely pathogenic ★★ same condition
ODAD1 c.598-2A>G Pathogenic ★★ same condition
ODAD1 p.Ala285Thr Pathogenic/Likely pathogenic ★★ ⚠ same condition
ODAD1 p.Arg150Ter Pathogenic/Likely pathogenic ★★ 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/odad1-p-arg89pro (accessed [today's date]).

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