Aliases for CCDC3 Gene

Aliases for CCDC3 Gene

  • Coiled-Coil Domain Containing 3 2 3 5
  • Favine 2 3 4
  • Coiled-Coil Domain-Containing Protein 3 3 4
  • Fat/Vessel-Derived Secretory Protein 3 4
  • DKFZp761F241 2
  • CCDC3 5

External Ids for CCDC3 Gene

Previous GeneCards Identifiers for CCDC3 Gene

  • GC10M012943
  • GC10M012978
  • GC10M012938

Summaries for CCDC3 Gene

GeneCards Summary for CCDC3 Gene

CCDC3 (Coiled-Coil Domain Containing 3) is a Protein Coding gene.

UniProtKB/Swiss-Prot Summary for CCDC3 Gene

  • 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).

Gene Wiki entry for CCDC3 Gene

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for CCDC3 Gene

Genomics for CCDC3 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for CCDC3 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH10J013098 Promoter/Enhancer 2.2 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas 250.7 -1.1 -1103 4.4 CEBPA CTCF THAP11 SIN3A ZNF740 ZNF511 ZNF639 VEZF1 TRIM22 SMAD4 CCDC3 OPTN lnc-CCDC3-1 ENSG00000239665 lnc-CCDC3-2 MCM10
GH10J013001 Promoter 1.5 EPDnew Ensembl CraniofacialAtlas 260.1 +99.1 99088 3 ZIC2 ZNF2 ZBTB48 ATF2 GLIS1 EGR1 ZBTB8A KLF10 EZH2 ZFX CCDC3 OPTN piR-40110-038 piR-57856-001 CAMK1D
GH10J013160 Promoter/Enhancer 2 EPDnew Ensembl ENCODE CraniofacialAtlas 10.6 -61.6 -61612 2.4 TBP SP1 MXD4 FEZF1 SIX5 MNT DEK IKZF1 SMAD5 ETS1 HSALNG0076260 MCM10 RPL36AP36 lnc-CCDC3-6 SEPHS1 OPTN CCDC3 HSALNG0076261 UCMA
GH10J012959 Enhancer 0.9 Ensembl ENCODE dbSUPER 19 +139.6 139586 4 RXRA FOXA2 JUND HNF4A MAX SP1 NFIA NR2F2 CCDC3 OPTN piR-57856-001 piR-40110-038 ENSG00000285520 CAMK1D
GH10J012705 Enhancer 1.3 FANTOM5 ENCODE CraniofacialAtlas 10.7 +391.3 391311 6.3 FEZF1 CTCF ZIC2 CEBPB ZNF513 REST ZNF395 NBN IRF4 TRIM22 CAMK1D CCDC3 OPTN ENSG00000239665 MIR548Q piR-50444-037
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around CCDC3 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for CCDC3

Top Transcription factor binding sites by QIAGEN in the CCDC3 gene promoter:
  • AML1a
  • AREB6
  • En-1
  • MyoD
  • NCX
  • Pax-3
  • POU2F1
  • POU2F1a
  • STAT5A
  • YY1

Genomic Locations for CCDC3 Gene

Latest Assembly
203,365 bases
Minus strand

Previous Assembly
(GRCh37/hg19 by Entrez Gene)
203,365 bases
Minus strand

(GRCh37/hg19 by Ensembl)
203,026 bases
Minus strand

Genomic View for CCDC3 Gene

Genes around CCDC3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CCDC3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CCDC3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CCDC3 Gene

Proteins for CCDC3 Gene

  • Protein details for CCDC3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Coiled-coil domain-containing protein 3
    Protein Accession:
    Secondary Accessions:
    • Q5VYV8
    • Q5VYV9

    Protein attributes for CCDC3 Gene

    270 amino acids
    Molecular mass:
    30731 Da
    Quaternary structure:
    • Homodimer.

    Alternative splice isoforms for CCDC3 Gene


neXtProt entry for CCDC3 Gene

Post-translational modifications for CCDC3 Gene

  • Glycosylation at Asn100
  • Modification sites at PhosphoSitePlus

Other Protein References for CCDC3 Gene

No data available for DME Specific Peptides for CCDC3 Gene

Domains & Families for CCDC3 Gene

Gene Families for CCDC3 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins
  • Predicted secreted proteins

Protein Domains for CCDC3 Gene


Suggested Antigen Peptide Sequences for CCDC3 Gene

GenScript: Design optimal peptide antigens:
  • Fat/vessel-derived secretory protein (CCDC3_HUMAN)
genes like me logo Genes that share domains with CCDC3: view

No data available for Graphical View of Domain Structure and UniProtKB/Swiss-Prot for CCDC3 Gene

Function for CCDC3 Gene

Molecular function for CCDC3 Gene

UniProtKB/Swiss-Prot 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).
UniProtKB/Swiss-Prot Induction:
Up-regulated by pioglitazone and down-regulated by TNF in HUVEC.

Phenotypes From GWAS Catalog for CCDC3 Gene

genes like me logo Genes that share phenotypes with CCDC3: view

Animal Models for CCDC3 Gene

MGI Knock Outs for CCDC3:

miRNA for CCDC3 Gene

miRTarBase miRNAs that target CCDC3

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CCDC3

No data available for Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for CCDC3 Gene

Localization for CCDC3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for CCDC3 Gene


Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for CCDC3 gene
Compartment Confidence
extracellular 5
endoplasmic reticulum 4
plasma membrane 1
cytoskeleton 1
mitochondrion 1
nucleus 1
cytosol 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (2)
  • Nucleoplasm (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for CCDC3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region IDA 28827783
GO:0005783 endoplasmic reticulum IDA --
genes like me logo Genes that share ontologies with CCDC3: view

Pathways & Interactions for CCDC3 Gene

PathCards logo

SuperPathways for CCDC3 Gene

No Data Available

Interacting Proteins for CCDC3 Gene

Gene Ontology (GO) - Biological Process for CCDC3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0010629 negative regulation of gene expression IDA 28827783
GO:0010804 negative regulation of tumor necrosis factor-mediated signaling pathway IMP 25193116
GO:0045600 positive regulation of fat cell differentiation IEA --
GO:0045833 negative regulation of lipid metabolic process IDA 28827783
GO:0046889 positive regulation of lipid biosynthetic process IEA --
genes like me logo Genes that share ontologies with CCDC3: view

No data available for Pathways by source and SIGNOR curated interactions for CCDC3 Gene

Drugs & Compounds for CCDC3 Gene

No Compound Related Data Available

Transcripts for CCDC3 Gene

mRNA/cDNA for CCDC3 Gene

12 NCBI additional mRNA sequence :
2 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CCDC3

Alternative Splicing Database (ASD) splice patterns (SP) for CCDC3 Gene

No ASD Table

Relevant External Links for CCDC3 Gene

GeneLoc Exon Structure for

Expression for CCDC3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for CCDC3 Gene

mRNA differential expression in normal tissues according to GTEx for CCDC3 Gene

This gene is overexpressed in Artery - Coronary (x9.3), Artery - Tibial (x6.0), and Artery - Aorta (x5.0).

Protein differential expression in normal tissues from HIPED for CCDC3 Gene

This gene is overexpressed in Gallbladder (68.8).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for CCDC3 Gene

Protein tissue co-expression partners for CCDC3 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for CCDC3

SOURCE GeneReport for Unigene cluster for CCDC3 Gene:


mRNA Expression by UniProt/SwissProt for CCDC3 Gene:

Tissue specificity: Expressed in umbilical vein endothelial cells (HUVEC), and at lower levels in aortic smooth muscle cells (HASMC).

Evidence on tissue expression from TISSUES for CCDC3 Gene

  • Nervous system(4.5)
  • Spleen(4.5)
  • Muscle(2.6)
  • Heart(2.6)
  • Skin(2.4)
  • Lung(2.3)
  • Kidney(2.3)
genes like me logo Genes that share expression patterns with CCDC3: view

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for CCDC3 Gene

Orthologs for CCDC3 Gene

This gene was present in the common ancestor of chordates.

Orthologs for CCDC3 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia CCDC3 30 31
  • 98.64 (n)
(Bos Taurus)
Mammalia CCDC3 30 31
  • 90.34 (n)
-- 31
  • 76 (a)
-- 31
  • 75 (a)
-- 31
  • 71 (a)
(Canis familiaris)
Mammalia CCDC3 30 31
  • 89.63 (n)
(Mus musculus)
Mammalia Ccdc3 30 17 31
  • 88.37 (n)
(Rattus norvegicus)
Mammalia Ccdc3 30
  • 87.71 (n)
(Ornithorhynchus anatinus)
Mammalia CCDC3 31
  • 76 (a)
(Monodelphis domestica)
Mammalia CCDC3 31
  • 68 (a)
(Gallus gallus)
Aves CCDC3 30 31
  • 77.55 (n)
(Anolis carolinensis)
Reptilia CCDC3 31
  • 76 (a)
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia ccdc3 30
  • 71.37 (n)
Str.19636 30
(Danio rerio)
Actinopterygii ccdc3 30 31
  • 68.68 (n)
Species where no ortholog for CCDC3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Baker's yeast (Saccharomyces cerevisiae)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Fruit Fly (Drosophila melanogaster)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Squirt (Ciona savignyi)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)
  • Worm (Caenorhabditis elegans)

Evolution for CCDC3 Gene

Gene Tree for CCDC3 (if available)
Gene Tree for CCDC3 (if available)
Evolutionary constrained regions (ECRs) for CCDC3: view image

Paralogs for CCDC3 Gene

No data available for Paralogs for CCDC3 Gene

Variants for CCDC3 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for CCDC3 Gene

SNP ID Clinical significance and condition Chr 10 pos Variation AA Info Type
157153 Not Provided: Small for gestational age 13,014,586(-) ACGGGAACTGAAATGT
157154 Not Provided: Normal pregnancy 13,014,586(-) ACGGGAACTGAAATGT
rs4748011 Association Not Found: Lip and oral cavity carcinoma 12,899,157(-) T/C
rs556171792 Benign: not provided 12,898,429(-) TA/T
NM_031455.4(CCDC3):c.799del (p.Tyr267fs)

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for CCDC3 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for CCDC3 Gene

Variant ID Type Subtype PubMed ID
dgv176e212 CNV loss 25503493
dgv367n106 OTHER inversion 24896259
dgv957n54 CNV loss 21841781
dgv958n54 CNV loss 21841781
dgv959n54 CNV loss 21841781
esv1638252 OTHER inversion 17803354
esv1974400 CNV deletion 18987734
esv24014 CNV loss 19812545
esv2439266 OTHER inversion 19546169
esv2661464 CNV deletion 23128226
esv2668184 CNV deletion 23128226
esv2677992 CNV deletion 23128226
esv2733295 CNV deletion 23290073
esv2733306 CNV deletion 23290073
esv2759733 CNV loss 17122850
esv2762844 CNV loss 21179565
esv2762845 CNV loss 21179565
esv2764257 CNV loss 21179565
esv2863457 CNV insertion 24192839
esv3302488 CNV tandem duplication 20981092
esv3352556 CNV duplication 20981092
esv3386766 OTHER inversion 20981092
esv3545918 CNV deletion 23714750
esv3578643 CNV loss 25503493
esv3622390 CNV loss 21293372
esv3622392 CNV loss 21293372
esv3622393 CNV loss 21293372
esv3622394 CNV loss 21293372
esv3622395 CNV loss 21293372
esv3622397 CNV loss 21293372
esv3622398 OTHER inversion 21293372
esv3622399 CNV loss 21293372
esv3766 OTHER inversion 18987735
esv8188 OTHER inversion 19470904
nsv1035341 CNV loss 25217958
nsv1045253 CNV loss 25217958
nsv1051704 CNV loss 25217958
nsv1053098 CNV gain 25217958
nsv1074181 CNV deletion 25765185
nsv1125330 OTHER inversion 24896259
nsv1127089 CNV deletion 24896259
nsv442570 CNV loss 18776908
nsv473053 CNV novel sequence insertion 20440878
nsv473780 CNV novel sequence insertion 20440878
nsv514543 CNV loss 21397061
nsv516198 CNV loss 19592680
nsv521491 CNV gain 19592680
nsv549979 CNV loss 21841781
nsv5831 CNV insertion 18451855
nsv818747 CNV loss 17921354
nsv818748 CNV loss 17921354
nsv8604 CNV loss 18304495
nsv947739 CNV duplication 23825009
nsv971901 CNV duplication 23825009

Variation tolerance for CCDC3 Gene

Residual Variation Intolerance Score: 51.1% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.78; 47.30% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for CCDC3 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CCDC3 Gene

Disorders for CCDC3 Gene

Additional Disease Information for CCDC3

Genetic Association Database
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform

No disorders were found for CCDC3 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for CCDC3 Gene

Publications for CCDC3 Gene

  1. Identification of a new secretory factor, CCDC3/Favine, in adipocytes and endothelial cells. (PMID: 20043878) Kobayashi S … Shimomura I (Biochemical and biophysical research communications 2010) 2 3 4
  2. Coiled-coil domain containing 3 (CCDC3) represses tumor necrosis factor-α/nuclear factor κB-induced endothelial inflammation. (PMID: 25193116) Azad AK … Fu Y (Cellular signalling 2014) 3 4
  3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4
  4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4
  5. Toward a catalog of human genes and proteins: sequencing and analysis of 500 novel complete protein coding human cDNAs. (PMID: 11230166) Wiemann S … Poustka A (Genome research 2001) 3 4

Products for CCDC3 Gene

Sources for CCDC3 Gene