Is ODAD2 p.Cys693= (c.2079C>T) pathogenic?

ODAD2 p.Cys693= (c.2079C>T) is classified Likely benign in ODAD2 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2022-06-20). Very rare (popmax 0.00938%, afr); Associated with primary ciliary dyskinesia 23.

What condition is associated with ODAD2 p.Cys693= (c.2079C>T)?

ODAD2 p.Cys693= (c.2079C>T) is associated with primary ciliary dyskinesia 23, primary ciliary dyskinesia (ClinVar).

How common is ODAD2 p.Cys693= (c.2079C>T) in the general population?

ODAD2 p.Cys693= (c.2079C>T) is very rare (popmax 0.00938%, afr) (gnomAD).

How is Primary ciliary dyskinesia inherited?

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

ODAD2 p.Cys693=

c.2079C>T · rs140338410 · VCV1088713

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

very rare (popmax 0.00938%, afr)

Conditions

primary ciliary dyskinesia 23

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 -6.9	GERP -3.9
Overall
CADD	0.333	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00938% African / African-American · 7/74,630 alleles

Filtering AF 0.00439% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0031%

Overall 0.00212% 34/1,606,926 alleles · very rare exomes 28/1,454,698 · genomes 6/152,228 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.00938%	10,661
Admixed American	0.0085%	11,764
East Asian	0.00226%	44,308
European (non-Finnish)	0.00161%	61,928
Remaining individualsnot grpmax-eligible	0.00161%	62,178
South Asian	0.00111%	90,050

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: ODAD2
Protein: p.Cys693=
Coding: c.2079C>T
MANE Select: NM_018076
dbSNP: rs140338410
Type: single nucleotide variant
Location: chr10:27939915 (GRCh38)
Gene constraint: LOEUF 0.977 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 80.63 · 1 PDB

Full ODAD2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

primary ciliary dyskinesia 23 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: primary ciliary dyskinesia

For Primary ciliary dyskinesia (Orphanet):

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

Similar variants

ODAD2 c.2097+1G>A Pathogenic/Likely pathogenic ★★ same condition
ODAD2 c.2097+1G>T Pathogenic/Likely pathogenic ★★ same condition
ODAD2 c.2495+1G>A Pathogenic ★★ same condition
ODAD2 c.2800-2A>G Pathogenic/Likely pathogenic ★★ same condition
ODAD2 c.383-1G>T Likely pathogenic ★★ same condition
ODAD2 c.576-2A>T Likely pathogenic ★★ same condition
ODAD2 p.Gln657Ter Pathogenic ★★ same condition
ODAD2 p.Glu335Ter 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/odad2-p-cys693 (accessed [today's date]).

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