CCDC42

Chr 17

coiled-coil domain containing 42

Also known as: CCDC42A

NCBI Gene: 146849ENSG00000161973UniProt: Q96M95

CCDC42 encodes a protein essential for male fertility and required for sperm development, with predicted roles in centrosome cycle and cilium assembly. Mutations cause autosomal recessive male infertility due to multiple morphological abnormalities of the flagella (MMAF), affecting sperm motility and structure. The gene shows no evidence of constraint against loss-of-function variants in the general population.

ResearchSummary from RefSeq, UniProt
MultiplemechanismLOEUF 1.07
Clinical Summary— CCDC42
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
11 unique Pathogenic / Likely Pathogenic· 49 VUS of 65 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
1.07LOEUF
pLI 0.000
Z-score 1.36
OE 0.64 (0.40–1.07)
Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint
0.66Z-score
OE missense 0.87 (0.77–0.98)
176 obs / 202.5 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios
LoF OE0.64 (0.40–1.07)
0≤0.351.4
Missense OE0.87 (0.77–0.98)
0≤0.61.4
Synonymous OE0.88
0≤1.21.6
LoF obs/exp: 11 / 17.1Missense obs/exp: 176 / 202.5Syn Z: 0.80
DN
0.85top 5%
GOF
0.7028th %ile
LOF
0.1598th %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

65 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic11
VUS49
Likely Benign3
11
Pathogenic
49
VUS
3
Likely Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
11
0
11
Likely Pathogenic
0
0
0
0
0
VUS
0
45
4
0
49
Likely Benign
0
3
0
0
3
Benign
0
0
0
0
0
Total04815063

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

View in ClinVar →

Protein Context — Lollipop Plot

CCDC42 · 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 1 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