Is ODAD1 p.Ser243= (c.729C>T) pathogenic?

ODAD1 p.Ser243= (c.729C>T) is classified Likely benign in ODAD1 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2025-12-16). Ultra-rare (popmax 0.0616%, amr); Associated with primary ciliary dyskinesia.

What condition is associated with ODAD1 p.Ser243= (c.729C>T)?

ODAD1 p.Ser243= (c.729C>T) is associated with primary ciliary dyskinesia (ClinVar).

How common is ODAD1 p.Ser243= (c.729C>T) in the general population?

ODAD1 p.Ser243= (c.729C>T) is ultra-rare (popmax 0.0616%, amr) (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.Ser243=

c.729C>T · rs547074727 · VCV700637

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0616%, amr)

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 -0.1	GERP -2.1
Overall
CADD	2.262	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0616% Admixed American · 37/60,022 alleles

Filtering AF 0.0459% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0405%

Overall 0.00378% 61/1,614,066 alleles · ultra-rare

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.0616%	1,622
African / African-American	0.00799%	12,510
Remaining individualsnot grpmax-eligible	0.0016%	62,512
European (non-Finnish)	0.00136%	73,748
South Asian	0.0011%	91,088

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.Ser243=
Coding: c.729C>T
MANE Select: NM_001364171
dbSNP: rs547074727
Type: single nucleotide variant
Location: chr19:48304077 (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-ser243 (accessed [today's date]).

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