Is ODAD3 p.Pro4Ser (c.10C>T) pathogenic?

ODAD3 p.Pro4Ser (c.10C>T) is classified Uncertain significance in ODAD3 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2022-11-17). AlphaMissense: likely benign (0.2411); Ultra-rare (popmax 0.0406%, sas); Associated with primary ciliary dyskinesia 30.

What condition is associated with ODAD3 p.Pro4Ser (c.10C>T)?

ODAD3 p.Pro4Ser (c.10C>T) is associated with primary ciliary dyskinesia 30 (ClinVar).

How common is ODAD3 p.Pro4Ser (c.10C>T) in the general population?

ODAD3 p.Pro4Ser (c.10C>T) is ultra-rare (popmax 0.0406%, sas) (gnomAD).

How is Primary ciliary dyskinesia inherited?

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

What do computational predictors say about ODAD3 p.Pro4Ser (c.10C>T)?

AlphaMissense predicts likely benign (score 0.2411) — an in-silico prediction, not a clinical call.

ODAD3 p.Pro4Ser

c.10C>T · rs546113125 · VCV1682800

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

AlphaMissense

likely benign

0.2411 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0406%, sas)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

primary ciliary dyskinesia 30

Computational evidence

Protein change
AlphaMissense	0.2411	likely benign
REVEL	0.064	moderately benign-leaning
SaProt	LLR -5.83	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.7	GERP 0.066, phastCons 1
Regional constraint	o/e 1.04	unconstrained · MANE · 14 kb · p 0.23 · regional, not allelic
Overall
CADD	23.9	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0406% South Asian · 37/91,066 alleles

Filtering AF 0.0303% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0267%

Overall 0.00366% 59/1,610,964 alleles · ultra-rare exomes 49/1,458,584 · genomes 10/152,380 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.0406%	2,461
African / African-American	0.0107%	9,381
East Asian	0.00891%	11,218
Remaining individualsnot grpmax-eligible	0.0016%	62,460
European (non-Finnish)	0.000763%	131,074

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.Pro4Ser
Coding: c.10C>T
MANE Select: NM_145045
dbSNP: rs546113125
Type: single nucleotide variant
Location: chr19:11435007 (GRCh38)
Gene constraint: LOEUF 1.019 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 77.97 · 1 PDB
Residue 4: the 'disordered' region

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 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
ODAD3 p.Ala341Ser Uncertain significance ★★ ⚠ same condition
ODAD3 p.Ala432Thr 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-pro4ser (accessed [today's date]).

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