Is ODAD2 p.Arg130= (c.390A>G) pathogenic?

ODAD2 p.Arg130= (c.390A>G) is classified Likely benign in ODAD2 (ClinVar, Multiple submitters, 6 submitters; last evaluated 2026-01-18). Rare (popmax 0.317%, nfe); Associated with primary ciliary dyskinesia 23.

What condition is associated with ODAD2 p.Arg130= (c.390A>G)?

ODAD2 p.Arg130= (c.390A>G) is associated with primary ciliary dyskinesia 23, primary ciliary dyskinesia (ClinVar).

How common is ODAD2 p.Arg130= (c.390A>G) in the general population?

ODAD2 p.Arg130= (c.390A>G) is rare (popmax 0.317%, nfe) (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.Arg130=

c.390A>G · rs12777433 · VCV417181

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 6 submitters

gnomAD v4.1

Rare

rare (popmax 0.317%, nfe)

Conditions

primary ciliary dyskinesia 23

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal.
Splicing
SpliceAI	Δ0.21	acceptor gain · deltas
Constraint at this position
Conservation	phyloP 4	GERP 0.91, phastCons 1
Overall
CADD	10.63	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.317% European (non-Finnish) · 3,598/1,136,598 alleles

Filtering AF 0.308% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.304%

Overall 0.258% 3,897/1,510,956 alleles · rare exomes 3,631/1,361,606 · genomes 266/149,350 · joint denominator

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.317%	316
Remaining individualsnot grpmax-eligible	0.255%	392
Admixed American	0.223%	449
African / African-American	0.053%	1,887
Finnishnot grpmax-eligible	0.0409%	2,447

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.Arg130=
Coding: c.390A>G
MANE Select: NM_018076
dbSNP: rs12777433
Type: single nucleotide variant
Location: chr10:27985204 (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-arg130 (accessed [today's date]).

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