CCDC169

Chr 13

coiled-coil domain containing 169

Also known as: C13orf38

NCBI Gene: 728591ENSG00000242715UniProt: A6NNP5

This gene encodes a coiled-coil domain containing protein of unknown function. Mutations cause autosomal recessive primary ciliary dyskinesia, a disorder affecting ciliary structure and function that leads to chronic respiratory infections, bronchiectasis, and often situs inversus. The gene shows minimal constraint against loss-of-function variants in population databases.

Research
MultiplemechanismLOEUF 1.25
Clinical Summary— CCDC169
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
49 unique Pathogenic / Likely Pathogenic· 22 VUS of 72 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
1.25LOEUF
pLI 0.000
Z-score 0.91
OE 0.73 (0.45–1.25)
Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint
0.33Z-score
OE missense 0.91 (0.78–1.07)
102 obs / 111.9 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios
LoF OE0.73 (0.45–1.25)
0≤0.351.4
Missense OE0.91 (0.78–1.07)
0≤0.61.4
Synonymous OE0.85
0≤1.21.6
LoF obs/exp: 10 / 13.6Missense obs/exp: 102 / 111.9Syn Z: 0.72
DN
0.82top 10%
GOF
0.6931th %ile
LOF
0.2582th %ile

This gene has evidence for multiple mechanisms of pathogenicity (dominant-negative and gain-of-function). Both the Badonyi & Marsh prediction and the broader genomic evidence point to dominant-negative as the predominant mechanism. Different variants in this gene may act through different mechanisms — interpret in context of the specific variant.

DNprediction above median
GOFprediction above median

Note: In-silico variant effect predictors (SIFT, PolyPhen, REVEL, CADD) may underestimate pathogenicity of missense variants in genes with GOF or DN mechanisms. Consider functional evidence and clinical context.

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

ClinVar Variant Classifications

72 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic49
VUS22
Likely Benign1
49
Pathogenic
22
VUS
1
Likely Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
49
0
49
Likely Pathogenic
0
0
0
0
0
VUS
0
20
2
0
22
Likely Benign
0
1
0
0
1
Benign
0
0
0
0
0
Total02151072

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

View in ClinVar →

Protein Context — Lollipop Plot

CCDC169 · 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 ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC

No open access results found

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