Is ODAD1 p.Ser554= (c.1662C>T) pathogenic?

ODAD1 p.Ser554= (c.1662C>T) is classified Likely benign in ODAD1 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-04-19). Ultra-rare (popmax 0.0151%, amr); Associated with primary ciliary dyskinesia.

What condition is associated with ODAD1 p.Ser554= (c.1662C>T)?

ODAD1 p.Ser554= (c.1662C>T) is associated with primary ciliary dyskinesia (ClinVar).

How common is ODAD1 p.Ser554= (c.1662C>T) in the general population?

ODAD1 p.Ser554= (c.1662C>T) is ultra-rare (popmax 0.0151%, 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.Ser554=

c.1662C>T · rs771346177 · VCV2421639

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0151%, 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 0.004	GERP 0.11
Overall
CADD	1.705	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0151% Admixed American · 9/59,740 alleles

Filtering AF 0.00776% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00581%

Overall 0.00225% 36/1,603,306 alleles · ultra-rare exomes 28/1,451,060 · genomes 8/152,246 · joint denominator

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.0151%	6,638
African / African-American	0.00267%	37,472
East Asian	0.00223%	44,822
European (non-Finnish)	0.00204%	49,114

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.Ser554=
Coding: c.1662C>T
MANE Select: NM_001364171
dbSNP: rs771346177
Type: single nucleotide variant
Location: chr19:48297438 (GRCh38)
Gene constraint: LOEUF 0.904 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 73.25 · 1 PDB
Residue 554: the 'disordered' region

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 p.Ser554Thr Uncertain significance ★ ⚠ same residue
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

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-ser554 (accessed [today's date]).

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