Is ODAD1 p.Pro275= (c.825C>T) pathogenic?

ODAD1 p.Pro275= (c.825C>T) is classified Benign/Likely benign in ODAD1 (ClinVar, Multiple submitters, 5 submitters; last evaluated 2026-02-01). Low-frequency (popmax 3.25%, afr); Associated with primary ciliary dyskinesia.

What condition is associated with ODAD1 p.Pro275= (c.825C>T)?

ODAD1 p.Pro275= (c.825C>T) is associated with primary ciliary dyskinesia (ClinVar).

How common is ODAD1 p.Pro275= (c.825C>T) in the general population?

ODAD1 p.Pro275= (c.825C>T) is low-frequency (popmax 3.25%, afr) (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.Pro275=

c.825C>T · rs34628933 · VCV241880

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 5 submitters

gnomAD v4.1

Rare

low-frequency (popmax 3.25%, afr)

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 -5	GERP -2.1
Overall
CADD	0.582	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 3.25% African / African-American · 2,443/75,058 alleles

Filtering AF 3.15% ClinGen BA1/BS1 input FAF95, joint · FAF99 3.1%

Overall 0.533% 8,611/1,614,142 alleles · low-frequency

Ancestry group	Frequency	1 in
African / African-Americangrpmax	3.25%	31
South Asian	0.951%	105
Middle Eastern	0.808%	124
Remaining individualsnot grpmax-eligible	0.558%	179
European (non-Finnish)	0.391%	255
Admixed American	0.293%	341
Ashkenazi Jewishnot grpmax-eligible	0.26%	384
Finnishnot grpmax-eligible	0.0469%	2,134
East Asian	0.00446%	22,441

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.Pro275=
Coding: c.825C>T
MANE Select: NM_001364171
dbSNP: rs34628933
Type: single nucleotide variant
Location: chr19:48303981 (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 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
ODAD1 p.Ala105Val 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/odad1-p-pro275 (accessed [today's date]).

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