Is ODAD1 p.Pro489= (c.1467G>A) pathogenic?

ODAD1 p.Pro489= (c.1467G>A) is classified Likely benign in ODAD1 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-10-17). Very rare (popmax 0.00446%, eas); Associated with primary ciliary dyskinesia.

What condition is associated with ODAD1 p.Pro489= (c.1467G>A)?

ODAD1 p.Pro489= (c.1467G>A) is associated with primary ciliary dyskinesia (ClinVar).

How common is ODAD1 p.Pro489= (c.1467G>A) in the general population?

ODAD1 p.Pro489= (c.1467G>A) is very rare (popmax 0.00446%, eas) (gnomAD).

How is Primary ciliary dyskinesia inherited?

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

ODAD1 p.Pro489=

c.1467G>A · rs201076998 · VCV2103172

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00446%, eas)

Conditions

primary ciliary dyskinesia

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 -7.6	GERP -2.5
Overall
CADD	0.923	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00446% East Asian · 2/44,872 alleles

Filtering AF 0.000763% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000605%

Overall 0.00118% 19/1,613,306 alleles · very rare exomes 13/1,461,190 · genomes 6/152,116 · joint denominator

Ancestry group	Frequency	1 in
East Asiangrpmax	0.00446%	22,436
Admixed American	0.00167%	59,740
African / African-American	0.00134%	74,866
European (non-Finnish)	0.00127%	78,657

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.Pro489=
Coding: c.1467G>A
MANE Select: NM_001364171
dbSNP: rs201076998
Type: single nucleotide variant
Location: chr19:48298035 (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

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.Pro489Leu 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
ODAD1 p.Gln120Ter 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-pro489 (accessed [today's date]).

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