Is ODAD3 p.Arg133= (c.399C>T) pathogenic?

ODAD3 p.Arg133= (c.399C>T) is classified Likely benign in ODAD3 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-07-01). Ultra-rare (popmax 0.0374%, afr); Associated with primary ciliary dyskinesia 30.

What condition is associated with ODAD3 p.Arg133= (c.399C>T)?

ODAD3 p.Arg133= (c.399C>T) is associated with primary ciliary dyskinesia 30 (ClinVar).

How common is ODAD3 p.Arg133= (c.399C>T) in the general population?

ODAD3 p.Arg133= (c.399C>T) is ultra-rare (popmax 0.0374%, afr) (gnomAD).

How is Primary ciliary dyskinesia inherited?

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

ODAD3 p.Arg133=

c.399C>T · rs370372097 · VCV2057782

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0374%, afr)

Conditions

primary ciliary dyskinesia 30

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 -1.5	GERP -4.2
Overall
CADD	1.682	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0374% African / African-American · 28/74,828 alleles

Filtering AF 0.0266% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0229%

Overall 0.00409% 66/1,613,796 alleles · ultra-rare exomes 53/1,461,868 · genomes 13/151,928 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.0374%	2,672
Middle Eastern	0.0164%	6,084
Remaining individualsnot grpmax-eligible	0.008%	12,496
South Asian	0.00329%	30,359
European (non-Finnish)	0.00237%	42,143
Admixed American	0.00167%	59,930

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: ODAD3
Protein: p.Arg133=
Coding: c.399C>T
MANE Select: NM_145045
dbSNP: rs370372097
Type: single nucleotide variant
Location: chr19:11430744 (GRCh38)
Gene constraint: LOEUF 1.019 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 77.97 · 1 PDB

Full ODAD3 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

primary ciliary dyskinesia 30 — 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

ODAD3 p.Arg133Cys Uncertain significance ★★ ⚠ same residue
ODAD3 p.Arg133His Likely benign ★★ same residue
ODAD3 c.964-1G>A Likely pathogenic ★★ same condition
ODAD3 p.Gln354Ter Pathogenic ★★ same condition
ODAD3 c.1435-5C>A Uncertain significance ★★ same condition
ODAD3 p.Ala203Pro Uncertain significance ★★ ⚠ same condition
ODAD3 p.Ala220Val Uncertain significance ★★ ⚠ same condition
ODAD3 p.Ala308Thr 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/odad3-p-arg133 (accessed [today's date]).

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