CCDC39

Chr 3AR

coiled-coil domain 39 molecular ruler complex subunit

Also known as: CFAP59, CILD14, FAP59

NCBI Gene: 339829ENSG00000284862UniProt: Q9UFE4OMIM: 613798

The protein is required for assembly of dynein regulatory and inner dynein arm complexes that regulate ciliary beat, playing a central role in cilia and flagella motility. Mutations cause primary ciliary dyskinesia type 14, an autosomal recessive disorder affecting the respiratory system, fertility, and other ciliated organs. This gene is not highly constrained against loss-of-function variants.

OMIMResearchSummary from RefSeq, OMIM, UniProt
LOFmechanismARLOEUF 0.751 OMIM phenotype
Clinical Summary— CCDC39
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Gene-Disease Validity (ClinGen)
primary ciliary dyskinesia 14 · ARDefinitive

Definitive — sufficient evidence for diagnostic panels

⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
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ClinVar Variants
90 unique Pathogenic / Likely Pathogenic· 91 VUS of 400 total submissions
Explore recent and relevant literature in Research Assistant →

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint
0.75LOEUF
pLI 0.000
Z-score 2.93
OE 0.54 (0.40–0.75)
Tolerant

Typical tolerance to LoF variation

Missense Constraint
0.36Z-score
OE missense 0.95 (0.88–1.03)
402 obs / 423.0 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios
LoF OE0.54 (0.40–0.75)
0≤0.351.4
Missense OE0.95 (0.88–1.03)
0≤0.61.4
Synonymous OE0.98
0≤1.21.6
LoF obs/exp: 26 / 47.8Missense obs/exp: 402 / 423.0Syn Z: 0.23
Curated Mechanism (G2P)Gene2Phenotype (DDG2P) ↗
definitiveCCDC39-related primary ciliary dyskinesiaLOFAR

Predictions shown for reference only — model trained on dominant genes, not applicable to AR conditions.

DN
0.85top 5%
GOF
0.6737th %ile
LOF
0.1796th %ile

The Badonyi & Marsh prediction model was trained exclusively on dominant disease genes. Predictions are not reliable for genes with autosomal recessive inheritance and are shown at reduced opacity for reference only.

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312.

ClinVar Variant Classifications

400 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic65
Likely Pathogenic25
VUS91
Likely Benign214
Benign3
Conflicting2
65
Pathogenic
25
Likely Pathogenic
91
VUS
214
Likely Benign
3
Benign
2
Conflicting

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
52
0
13
0
65
Likely Pathogenic
23
1
1
0
25
VUS
1
81
7
2
91
Likely Benign
0
0
104
110
214
Benign
0
0
3
0
3
Conflicting
—2
Total7682128112400

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

Protein Context — Lollipop Plot

CCDC39 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

3D Protein StructureAlphaFold

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →
Clinical Literature
Open Research Assistant →
Full-Text Mentions
NLP-detected gene mentions in article bodies · via PubTator3
PubTator3
Top 5 full-text resultsSearch PubTator3 ↗
Key Publications
Landmark & review papers · by relevance
PubMed
Top 5 results · since 2015Search PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Top 5 resultsSearch Europe PMC ↗

External Resources

Links to major genomics databases and tools

Franklin by Genoox
AI-powered variant curation and clinical analysis
DECIPHER
Genomic variants and phenotypes in rare disease patients