Is CCNO p.Pro309fs (c.926del) pathogenic?

CCNO p.Pro309fs (c.926del) is classified Pathogenic in CCNO (ClinVar, No assertion criteria, 1 submitter; last evaluated 2014-06-01). Absent from gnomAD; Associated with primary ciliary dyskinesia 29.

What condition is associated with CCNO p.Pro309fs (c.926del)?

CCNO p.Pro309fs (c.926del) is associated with primary ciliary dyskinesia 29 (ClinVar).

How common is CCNO p.Pro309fs (c.926del) in the general population?

CCNO p.Pro309fs (c.926del) is absent from gnomAD (gnomAD).

How is Primary ciliary dyskinesia inherited?

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

CCNO p.Pro309fs

c.926del · rs587777500 · VCV139601

Pathogenic No assertion criteria

Classification

Pathogenic

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

primary ciliary dyskinesia 29

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function
NMD	escapes	premature termination codon in the last exon (3 of 3) — the truncated protein is likely expressed. PVS1 input, not an applied code
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP -11	GERP -3.8

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: CCNO
Protein: p.Pro309fs
Coding: c.926del
MANE Select: NM_021147
dbSNP: rs587777500
Type: Deletion
Location: chr5:55231502 (GRCh38)
Gene constraint: LOEUF 1.698 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 79.06

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

Disease context

primary ciliary dyskinesia 29 — 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

CCNO p.Cys5fs Likely pathogenic ★ same condition
CCNO p.Ile219fs Likely pathogenic ★ same condition
CCNO p.Leu303fs Pathogenic ★ same condition
CCNO p.Pro142fs Pathogenic ★ same condition
CCNO p.Leu322fs Likely pathogenic same condition
CCNO p.Gln103Ter Pathogenic ★★ same condition
CCNO p.Gln88fs Pathogenic ★★ same condition
CCNO p.Gly85fs 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/ccno-p-pro309fs (accessed [today's date]).

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