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Aliases for CCDC39 Gene

Aliases for CCDC39 Gene

  • Coiled-Coil Domain Containing 39 2 3 5
  • Coiled-Coil Domain-Containing Protein 39 3
  • CILD14 3
  • FAP59 3

External Ids for CCDC39 Gene

Previous GeneCards Identifiers for CCDC39 Gene

  • GC03M181815
  • GC03M180320
  • GC03M177736

Summaries for CCDC39 Gene

Entrez Gene Summary for CCDC39 Gene

  • The protein encoded by this gene is involved in the motility of cilia and flagella. The encoded protein is essential for the assembly of dynein regulatory and inner dynein arm complexes, which regulate ciliary beat. Defects in this gene are a cause of primary ciliary dyskinesia type 14 (CILD14). [provided by RefSeq, Jul 2011]

GeneCards Summary for CCDC39 Gene

CCDC39 (Coiled-Coil Domain Containing 39) is a Protein Coding gene. Diseases associated with CCDC39 include Ciliary Dyskinesia, Primary, 14 and Primary Ciliary Dyskinesia. Gene Ontology (GO) annotations related to this gene include nucleotide binding.

UniProtKB/Swiss-Prot for CCDC39 Gene

  • Required for assembly of dynein regulatory complex (DRC) and inner dynein arm (IDA) complexes, which are responsible for ciliary beat regulation, thereby playing a central role in motility in cilia and flagella (PubMed:21131972). Probably acts together with CCDC40 to form a molecular ruler that determines the 96 nanometer (nm) repeat length and arrangements of components in cilia and flagella (By similarity). Not required for outer dynein arm complexes assembly (PubMed:21131972).

Additional gene information for CCDC39 Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for CCDC39 Gene

Genomics for CCDC39 Gene

GeneHancer (GH) Regulatory Elements for CCDC39 Gene

Promoters and enhancers for CCDC39 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
GH03I180678 Promoter/Enhancer 1.9 EPDnew Ensembl ENCODE 550.1 +191.3 191338 1.5 ELF3 ARID4B MZF1 SIN3A BMI1 RAD21 ZNF2 ZNF48 ZBTB40 ZNF335 CCDC39-AS1 CCDC39 GC03M180608
GH03I180870 Promoter/Enhancer 1.1 Ensembl ENCODE 558.2 -0.4 -358 2.7 ZNF680 L3MBTL2 MAX E2F1 ZNF316 NFE2 EMSY EZH2 MGA CCDC39 LOC101928882 PIR58626 LOC647253 LOC105374240 FXR1 RPL32P10
GH03I180718 Enhancer 1 VISTA UCNEbase 10.6 +151.6 151600 1.5 MAFF MAFK CCDC39-AS1 CCDC39 LOC647253 RN7SL229P LOC101928882
GH03I180910 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 4.2 -41.8 -41764 3.8 HDGF PKNOX1 FOXA2 ARID4B SIN3A DMAP1 ZBTB7B YY1 POLR2B ZNF766 FXR1 DNAJC19 LOC647253 CCDC39 RPL32P10 GC03P180962
GH03I180708 Enhancer 0.3 ENCODE 10.8 +162.9 162877 0.2 POLR2A CCDC39-AS1 CCDC39 RN7SL229P LOC101928882
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around CCDC39 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the CCDC39 gene promoter:

Genomic Locations for CCDC39 Gene

Genomic Locations for CCDC39 Gene
268,148 bases
Minus strand

Genomic View for CCDC39 Gene

Genes around CCDC39 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CCDC39 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CCDC39 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CCDC39 Gene

Proteins for CCDC39 Gene

  • Protein details for CCDC39 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Coiled-coil domain-containing protein 39
    Protein Accession:
    Secondary Accessions:
    • B4E2H1

    Protein attributes for CCDC39 Gene

    941 amino acids
    Molecular mass:
    109901 Da
    Quaternary structure:
    No Data Available

    Alternative splice isoforms for CCDC39 Gene


neXtProt entry for CCDC39 Gene

Post-translational modifications for CCDC39 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for CCDC39 Gene

No data available for DME Specific Peptides for CCDC39 Gene

Domains & Families for CCDC39 Gene

Gene Families for CCDC39 Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • Predicted intracellular proteins

Protein Domains for CCDC39 Gene


Suggested Antigen Peptide Sequences for CCDC39 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the CCDC39 family.
  • Belongs to the CCDC39 family.
genes like me logo Genes that share domains with CCDC39: view

Function for CCDC39 Gene

Molecular function for CCDC39 Gene

UniProtKB/Swiss-Prot Function:
Required for assembly of dynein regulatory complex (DRC) and inner dynein arm (IDA) complexes, which are responsible for ciliary beat regulation, thereby playing a central role in motility in cilia and flagella (PubMed:21131972). Probably acts together with CCDC40 to form a molecular ruler that determines the 96 nanometer (nm) repeat length and arrangements of components in cilia and flagella (By similarity). Not required for outer dynein arm complexes assembly (PubMed:21131972).

Phenotypes From GWAS Catalog for CCDC39 Gene

genes like me logo Genes that share phenotypes with CCDC39: view

Human Phenotype Ontology for CCDC39 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for CCDC39 Gene

MGI Knock Outs for CCDC39:

Animal Model Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , Transcription Factor Targets and HOMER Transcription for CCDC39 Gene

Localization for CCDC39 Gene

Subcellular locations from UniProtKB/Swiss-Prot for CCDC39 Gene

Cytoplasm, cytoskeleton, cilium axoneme. Note=CCDC40 is required for localization to axonemes. {ECO:0000269 PubMed:21131974}.

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 CCDC39 gene
Compartment Confidence
cytoskeleton 5
nucleus 3
cytosol 2
extracellular 1
mitochondrion 1

Gene Ontology (GO) - Cellular Components for CCDC39 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IEA --
GO:0005856 cytoskeleton IEA --
GO:0005929 cilium IEA --
GO:0005930 axoneme IDA,IEA 21131972
GO:0042995 cell projection IEA --
genes like me logo Genes that share ontologies with CCDC39: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for CCDC39 Gene

Pathways & Interactions for CCDC39 Gene

SuperPathways for CCDC39 Gene

No Data Available

Interacting Proteins for CCDC39 Gene

STRING Interaction Network Preview (showing 1 interactants - click image to see details)
Selected Interacting proteins: Q9UFE4-CCD39_HUMAN ENSP00000405708 for CCDC39 Gene via IID STRING

Gene Ontology (GO) - Biological Process for CCDC39 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001947 heart looping IMP 22693285
GO:0003341 cilium movement IEA,IMP 22499950
GO:0003356 regulation of cilium beat frequency IMP 23255504
GO:0007368 determination of left/right symmetry IEA --
GO:0007507 heart development IEA --
genes like me logo Genes that share ontologies with CCDC39: view

No data available for Pathways by source and SIGNOR curated interactions for CCDC39 Gene

Drugs & Compounds for CCDC39 Gene

No Compound Related Data Available

Transcripts for CCDC39 Gene

mRNA/cDNA for CCDC39 Gene

Unigene Clusters for CCDC39 Gene

Coiled-coil domain containing 39:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for CCDC39 Gene

No ASD Table

Relevant External Links for CCDC39 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for CCDC39 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for CCDC39 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for CCDC39 Gene

This gene is overexpressed in Stomach (60.9).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for CCDC39 Gene

NURSA nuclear receptor signaling pathways regulating expression of CCDC39 Gene:


SOURCE GeneReport for Unigene cluster for CCDC39 Gene:


mRNA Expression by UniProt/SwissProt for CCDC39 Gene:

Tissue specificity: Mainly expressed in nasal brushings and, to a lesser extent, in lungs and testis.

Evidence on tissue expression from TISSUES for CCDC39 Gene

  • Nervous system(4.1)
  • Lung(3.9)
  • Skin(3.6)
  • Intestine(3.2)
  • Heart(2.9)
  • Pancreas(2.5)
  • Kidney(2.1)

Phenotype-based relationships between genes and organs from Gene ORGANizer for CCDC39 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
  • cardiovascular
  • digestive
  • endocrine
  • immune
  • integumentary
  • lymphatic
  • nervous
  • reproductive
  • respiratory
  • skeleton
  • urinary
Head and neck:
  • brain
  • cranial nerve
  • ear
  • epiglottis
  • eye
  • head
  • larynx
  • meninges
  • middle ear
  • mouth
  • neck
  • nose
  • olfactory bulb
  • outer ear
  • pharynx
  • sinus
  • skull
  • bronchus
  • lung
  • trachea
  • spleen
  • ovary
  • testicle
  • blood
  • blood vessel
  • peripheral nervous system
  • white blood cell
genes like me logo Genes that share expression patterns with CCDC39: view

No data available for mRNA differential expression in normal tissues and Protein tissue co-expression partners for CCDC39 Gene

Orthologs for CCDC39 Gene

This gene was present in the common ancestor of animals.

Orthologs for CCDC39 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia CCDC39 33 34
  • 99.57 (n)
(Canis familiaris)
Mammalia CCDC39 33 34
  • 89.05 (n)
(Bos Taurus)
Mammalia CCDC39 33 34
  • 89.01 (n)
(Rattus norvegicus)
Mammalia Ccdc39 33
  • 80.15 (n)
(Mus musculus)
Mammalia Ccdc39 33 16 34
  • 79.15 (n)
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 77 (a)
-- 34
  • 72 (a)
-- 34
  • 69 (a)
-- 34
  • 69 (a)
-- 34
  • 60 (a)
(Monodelphis domestica)
Mammalia CCDC39 34
  • 65 (a)
(Gallus gallus)
Aves CCDC39 33 34
  • 67.2 (n)
(Anolis carolinensis)
Reptilia CCDC39 34
  • 52 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia ccdc39 33
  • 63.24 (n)
(Danio rerio)
Actinopterygii ccdc39 33
  • 58.28 (n)
CCDC39 34
  • 49 (a)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP001293 33
  • 40.88 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG17387 33 34
  • 39.45 (n)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 50 (a)
Species where no ortholog for CCDC39 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • 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)
  • 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 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 CCDC39 Gene

Gene Tree for CCDC39 (if available)
Gene Tree for CCDC39 (if available)

Paralogs for CCDC39 Gene

No data available for Paralogs for CCDC39 Gene

Variants for CCDC39 Gene

Sequence variations from dbSNP and Humsavar for CCDC39 Gene

SNP ID Clin Chr 03 pos Variation AA Info Type
rs1007345781 pathogenic, Primary ciliary dyskinesia 180,616,604(-) TGT/T coding_sequence_variant, frameshift
rs1030308648 likely-benign, Primary ciliary dyskinesia 180,631,532(-) C/A coding_sequence_variant, synonymous_variant
rs1060502867 uncertain-significance, Primary ciliary dyskinesia 180,616,948(-) C/T coding_sequence_variant, missense_variant
rs1060502868 uncertain-significance, Primary ciliary dyskinesia 180,642,170(-) A/G coding_sequence_variant, missense_variant
rs112738198 benign, not specified, Primary ciliary dyskinesia 180,659,741(-) G/C/T coding_sequence_variant, missense_variant

Structural Variations from Database of Genomic Variants (DGV) for CCDC39 Gene

Variant ID Type Subtype PubMed ID
esv2244500 CNV deletion 18987734
esv2484281 CNV deletion 19546169
nsv472530 CNV novel sequence insertion 20440878
nsv509869 OTHER sequence alteration 20534489

Variation tolerance for CCDC39 Gene

Residual Variation Intolerance Score: 84.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 5.71; 73.14% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for CCDC39 Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CCDC39 Gene

Disorders for CCDC39 Gene

MalaCards: The human disease database

(7) MalaCards diseases for CCDC39 Gene - From: HGMD, OMIM, ClinVar, GTR, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
ciliary dyskinesia, primary, 14
  • cild14
primary ciliary dyskinesia
  • ciliary motility disorder
ciliary dyskinesia, primary, 1
  • pcd
skin papilloma
  • cutaneous papilloma
situs inversus
  • situs inversus viscerum
- elite association - COSMIC cancer census association via MalaCards


  • Ciliary dyskinesia, primary, 14 (CILD14) [MIM:613807]: A disorder characterized by abnormalities of motile cilia. Respiratory infections leading to chronic inflammation and bronchiectasis are recurrent, due to defects in the respiratory cilia; reduced fertility is often observed in male patients due to abnormalities of sperm tails. Half of the patients exhibit randomization of left-right body asymmetry and situs inversus, due to dysfunction of monocilia at the embryonic node. Primary ciliary dyskinesia associated with situs inversus is referred to as Kartagener syndrome. {ECO:0000269 PubMed:21131972, ECO:0000269 PubMed:22693285, ECO:0000269 PubMed:23255504, ECO:0000269 PubMed:25186273}. Note=The disease is caused by mutations affecting the gene represented in this entry. The disease is characterized by primary ciliary dyskinesia with inner dynein arm (IDA) defects and axonemal dizorganisation: defects in CCDC39 and CCDC40 constitute the major cause of this phenotype. {ECO:0000269 PubMed:22693285, ECO:0000269 PubMed:23255504}.

Additional Disease Information for CCDC39

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with CCDC39: view

No data available for Genatlas for CCDC39 Gene

Publications for CCDC39 Gene

  1. CCDC39 is required for assembly of inner dynein arms and the dynein regulatory complex and for normal ciliary motility in humans and dogs. (PMID: 21131972) Merveille AC … Amselem S (Nature genetics 2011) 2 3 4 58
  2. Mutations in CCDC39 and CCDC40 are the major cause of primary ciliary dyskinesia with axonemal disorganization and absent inner dynein arms. (PMID: 23255504) Antony D … Mitchison HM (Human mutation 2013) 3 4 58
  3. Delineation of CCDC39/CCDC40 mutation spectrum and associated phenotypes in primary ciliary dyskinesia. (PMID: 22693285) Blanchon S … Amselem S (Journal of medical genetics 2012) 3 4 58
  4. The coiled-coil domain containing protein CCDC40 is essential for motile cilia function and left-right axis formation. (PMID: 21131974) Becker-Heck A … Burdine RD (Nature genetics 2011) 3 4 58
  5. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 44 58

Products for CCDC39 Gene

Sources for CCDC39 Gene

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