Is CCDC39 p.Phe514fs (c.1540_1544del) pathogenic?

CCDC39 p.Phe514fs (c.15401544del) is classified Pathogenic/Likely pathogenic in CCDC39 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2024-04-06). Absent from gnomAD; Associated with primary ciliary dyskinesia.

What condition is associated with CCDC39 p.Phe514fs (c.1540_1544del)?

CCDC39 p.Phe514fs (c.1540_1544del) is associated with primary ciliary dyskinesia, primary ciliary dyskinesia 14 (ClinVar).

How common is CCDC39 p.Phe514fs (c.1540_1544del) in the general population?

CCDC39 p.Phe514fs (c.1540_1544del) 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.

CCDC39 p.Phe514fs

c.1540_1544del · rs2108420039 · VCV1371704

Pathogenic/Likely pathogenic Multiple submitters

Classification

Pathogenic/Likely pathogenic

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

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 12 of 20
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 1.6	GERP 0.12, phastCons 1

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: CCDC39
Protein: p.Phe514fs
Coding: c.1540_1544del
MANE Select: NM_181426
dbSNP: rs2108420039
Type: Microsatellite
Location: chr3:180644241 (GRCh38)
Gene constraint: LOEUF 1.226 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 79.23 · 1 PDB

Full CCDC39 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

Also linked: primary ciliary dyskinesia 14

For Primary ciliary dyskinesia (Orphanet):

Inheritance: Autosomal dominant, Autosomal recessive, X-linked recessive
Onset: Neonatal
Prevalence: 1-5 / 10 000 (Pakistan)

Similar variants

CCDC39 p.Asn473fs Pathogenic ★★ same condition
CCDC39 p.Leu176fs Pathogenic ★★ same condition
CCDC39 p.Met831fs Pathogenic/Likely pathogenic ★★ same condition
CCDC39 p.Thr277fs Pathogenic/Likely pathogenic ★★ same condition
CCDC39 p.Glu23del Uncertain significance ★★ same condition
CCDC39 c.2409_2410del Likely pathogenic ★ same condition
CCDC39 p.Arg282fs Pathogenic ★ same condition
CCDC39 p.Arg38fs 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/ccdc39-p-phe514fs (accessed [today's date]).

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