CCDC3
protein-codingcoiled-coil domain containing 3
Gene summary
Involved in negative regulation of lipid metabolic process; negative regulation of tumor necrosis factor-mediated signaling pathway; and signal transduction. Located in endoplasmic reticulum and extracellular region. [provided by Alliance of Genome Resources, Jul 2025]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~203.0 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to CCDC3 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_031455.4. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 60 | 3 | 63 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 1 | 1 | ||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 60 | 3 | 1 | 64 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_113643.1 | 3 | MANE Select | |
| Ensembl | ENSP00000368102.3 | 3 | MANE Select | |
| RefSeq | NP_001269587.1 | 2 | Standard | |
| Ensembl | ENSP00000368116.1 | 2 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- negative regulation of tumor necrosis factor-mediated signaling pathway
- positive regulation of fat cell differentiation
- positive regulation of lipid biosynthetic process
Cellular Component
- extracellular region
- endoplasmic reticulum
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000378825
- Coding exons
- 3
- Length
- 203026
- Individuals with no LoFs
- 125654
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 94
- Defined
- 125748
- p
- 0.000374
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.849 | 175 | 146 | 1.20 | 0.00000905 | 1718 |
| Missense (PolyPhen) | 62 | 51.047 | 1.2146 | 600 | ||
| Synonymous | -0.0494 | 66 | 65.5 | 1.01 | 0.00000400 | 538 |
| Loss of Function | 1.39 | 5 | 9.66 | 0.517 | 4.98e-7 | 107 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.0015 | 0.0015 | notable |
| Latino/Admixed American | 0.00033 | 0.00032 | rare |
| Ashkenazi Jewish | 0.000099 | 0.000099 | rare |
| East Asian | 0.00011 | 0.00011 | rare |
| Finnish | 0.000046 | 0.000046 | rare |
| European (Non-Finnish) | 0.000035 | 0.000035 | rare |
| South Asian | 0.0016 | 0.0016 | notable |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Negatively regulates TNF-alpha-induced pro-inflammatory response in endothelial cells (ECs) via inhibition of TNF-alpha- induced NF-kappaB activation in ECs (PubMed:25193116). Positively regulates lipid accumulation in adipose cells (By similarity). {ECO:0000250|UniProtKB:Q9D6Y1, ECO:0000269|PubMed:25193116}.;
Recessive Scores
- pRec
- 0.110
Intolerance Scores
- LoFtool
- 0.313
- RVIS EVS
- -0.27
- RVIS percentile EVS
- 34.32
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.0543
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |