Is CCNO p.Ser65fs (c.192del) pathogenic?

CCNO p.Ser65fs (c.192del) is classified Pathogenic in CCNO (ClinVar, Single submitter, 1 submitter; last evaluated 2023-05-05). Very rare (popmax 8.49e-05%, nfe); Associated with primary ciliary dyskinesia.

What condition is associated with CCNO p.Ser65fs (c.192del)?

CCNO p.Ser65fs (c.192del) is associated with primary ciliary dyskinesia (ClinVar).

How common is CCNO p.Ser65fs (c.192del) in the general population?

CCNO p.Ser65fs (c.192del) is very rare (popmax 8.49e-05%, nfe) (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.Ser65fs

c.192del · rs752106293 · VCV2963070

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Rare

very rare (popmax 8.49e-05%, nfe)

Conditions

primary ciliary dyskinesia

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function
NMD	predicted	premature termination codon in exon 1 of 3
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 0.22	GERP -2.4, phastCons 0.14

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

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 8.49e-05% European (non-Finnish) · 1/1,177,282 alleles

Overall 6.23e-05% 1/1,605,622 alleles · very rare exomes 1/1,453,398 · genomes 0/152,224 · joint denominator

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: CCNO
Protein: p.Ser65fs
Coding: c.192del
MANE Select: NM_021147
dbSNP: rs752106293
Type: Deletion
Location: chr5:55233332 (GRCh38)
Gene constraint: LOEUF 1.698 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 79.06
Residue 65: the 'disordered' region

Full CCNO 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

CCNO p.Asn159fs Pathogenic ★ same condition
CCNO p.Asp292fs Pathogenic ★ same condition
CCNO p.Gln249fs Pathogenic ★ same condition
CCNO p.Gly56fs Pathogenic ★ same condition
CCNO p.Ile185fs Likely pathogenic ★ same condition
CCNO c.568-16del Likely benign ★ same condition
CCNO p.Gln103Ter Pathogenic ★★ same condition
CCNO p.Gln88fs 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-ser65fs (accessed [today's date]).

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