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] See more...

Aliases for CCDC39 Gene

Aliases for CCDC39 Gene

  • Coiled-Coil Domain Containing 39 2 3 5
  • Coiled-Coil Domain-Containing Protein 39 3 4
  • CILD14 3
  • FAP59 3

External Ids for CCDC39 Gene

Previous GeneCards Identifiers for CCDC39 Gene

  • GC03M181815
  • GC03M180320
  • GC03M177736
  • GC03M180614

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 Summary 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 , Rfam classification 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
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH03J180684 Enhancer 0.3 Ensembl 500.7 -0.1 -59 0.4 TBP CCDC39 CCDC39-AS1 lnc-TTC14-4
GH03J180870 Promoter/Enhancer 1.1 Ensembl ENCODE 7.5 -186.0 -186021 3.5 POLR2A ZNF316 POLR2G NFE2 E2F6 TAF1 L3MBTL2 MAX ZNF680 EZH2 ENSG00000285336 LOC101928882 piR-35581 CCDC39 ENSG00000242068 FXR1 LOC105374240 lnc-TTC14-3
GH03J180910 Promoter/Enhancer 2 EPDnew Ensembl ENCODE CraniofacialAtlas 4 -228.2 -228198 4.5 ZNF217 CTCF SIN3A NRF1 USF1 POLR2G GTF2E2 PHF8 TEAD4 ZFX NONHSAG036778.2 FXR1 DNAJC19 ENSG00000242068 CCDC39 HSALNG0031025
GH03J180929 Enhancer 0.5 Ensembl 6.5 -246.0 -245959 4.6 ZNF316 MAFF MAFK HIC1 ZBTB33 PRDM1 EMSY CCDC39 ENSG00000242068 NONHSAG036778.2 HSALNG0031025 FXR1
GH03J180630 Enhancer 0.5 Ensembl 4.9 +54.2 54241 1.4 CTCF FOS ZNF18 GATA2 JUN NFIL3 HLF RAD21 ETV6 lnc-CCDC39-3 CCDC39 RF00994-708
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around CCDC39 on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for CCDC39

Top Transcription factor binding sites by QIAGEN in the CCDC39 gene promoter:
  • aMEF-2
  • MEF-2A
  • NF-AT
  • NF-AT1
  • NF-AT2
  • NF-AT3
  • NF-AT4
  • S8
  • SRF
  • SRF (504 AA)

Genomic Locations for CCDC39 Gene

Genomic Locations for CCDC39 Gene
chr3:180,602,858-180,684,942
(GRCh38/hg38)
Size:
82,085 bases
Orientation:
Minus strand
chr3:180,320,646-180,588,793
(GRCh37/hg19)
Size:
268,148 bases
Orientation:
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:
    Q9UFE4-CCD39_HUMAN
    Recommended name:
    Coiled-coil domain-containing protein 39
    Protein Accession:
    Q9UFE4
    Secondary Accessions:
    • B4E2H1

    Protein attributes for CCDC39 Gene

    Size:
    941 amino acids
    Molecular mass:
    109901 Da
    Quaternary structure:
    No Data Available
    Miscellaneous:
    • [Isoform 2]: May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay.

    Alternative splice isoforms for CCDC39 Gene

    UniProtKB/Swiss-Prot:

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):
  • Predicted intracellular proteins
  • Disease related genes

Protein Domains for CCDC39 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for CCDC39 Gene

GenScript: Design optimal peptide antigens:
  • Coiled-coil domain-containing protein 39 (CCD39_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q9UFE4

UniProtKB/Swiss-Prot:

CCD39_HUMAN :
  • Belongs to the CCDC39 family.
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:
  • Ccdc39 Ccdc39<tm1a(KOMP)Wtsi>
  • Ccdc39 Ccdc39<tm2b(KOMP)Wtsi>

Animal Model Products

CRISPR 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

COMPARTMENTS
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
extracellular 3
cytosol 3
nucleus 2
plasma membrane 1
mitochondrion 0

Gene Ontology (GO) - Cellular Components for CCDC39 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region IEA --
GO:0005737 cytoplasm IEA --
GO:0005829 cytosol IEA --
GO:0005856 cytoskeleton IEA --
GO:0005929 cilium IEA,IDA 27120127
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

PathCards logo

SuperPathways for CCDC39 Gene

No Data Available

Interacting Proteins for CCDC39 Gene

Selected Interacting proteins: Q9UFE4-CCD39_HUMAN for CCDC39 Gene via IID

;

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:0003351 epithelial cilium movement IEA --
GO:0003356 regulation of cilium beat frequency IMP 23255504
GO:0007368 determination of left/right symmetry 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

1 REFSEQ mRNAs :
4 NCBI additional mRNA sequence :
11 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

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
CCDC39

Expression for CCDC39 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and 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



Transcriptomic regulation report from SPP (The Signaling Pathways Project) for CCDC39

SOURCE GeneReport for Unigene cluster for CCDC39 Gene:

Hs.712820

mRNA Expression by UniProt/SwissProt for CCDC39 Gene:

Q9UFE4-CCD39_HUMAN
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
Systems:
  • cardiovascular
  • digestive
  • endocrine
  • immune
  • integumentary
  • lymphatic
  • nervous
  • reproductive
  • respiratory
  • skeleton
  • urinary
Regions:
Head and neck:
  • brain
  • cranial nerve
  • ear
  • epiglottis
  • eye
  • head
  • larynx
  • meninges
  • middle ear
  • mouth
  • neck
  • nose
  • olfactory bulb
  • outer ear
  • pharynx
  • sinus
  • skull
Thorax:
  • bronchus
  • lung
  • trachea
Abdomen:
  • spleen
Pelvis:
  • ovary
  • testicle
General:
  • 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
chimpanzee
(Pan troglodytes)
Mammalia CCDC39 30
  • 99.57 (n)
dog
(Canis familiaris)
Mammalia CCDC39 30
  • 89.05 (n)
cow
(Bos Taurus)
Mammalia CCDC39 30
  • 89.01 (n)
rat
(Rattus norvegicus)
Mammalia Ccdc39 30
  • 80.15 (n)
mouse
(Mus musculus)
Mammalia Ccdc39 17 30
  • 79.15 (n)
chicken
(Gallus gallus)
Aves CCDC39 30
  • 67.2 (n)
tropical clawed frog
(Silurana tropicalis)
Amphibia ccdc39 30
  • 63.24 (n)
zebrafish
(Danio rerio)
Actinopterygii ccdc39 30
  • 58.28 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP001293 30
  • 40.88 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG17387 30
  • 39.45 (n)
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)
  • lizard (Anolis carolinensis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • oppossum (Monodelphis domestica)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (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 CCDC39 Gene

ENSEMBL:
Gene Tree for CCDC39 (if available)
TreeFam:
Gene Tree for CCDC39 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for CCDC39: view image

Paralogs for CCDC39 Gene

No data available for Paralogs for CCDC39 Gene

Variants for CCDC39 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for CCDC39 Gene

SNP ID Clinical significance and condition Chr 03 pos Variation AA Info Type
638904 Uncertain Significance: Primary ciliary dyskinesia 180,648,305(-) C/T MISSENSE_VARIANT
639710 Uncertain Significance: Primary ciliary dyskinesia 180,660,662(-) C/T MISSENSE_VARIANT
644244 Uncertain Significance: Primary ciliary dyskinesia 180,661,863(-) CTTT/C INFRAME_DELETION
646035 Uncertain Significance: Primary ciliary dyskinesia 180,614,944(-) T/TAAC INFRAME_INSERTION,INTRON_VARIANT
646484 Uncertain Significance: Primary ciliary dyskinesia 180,661,921(-) A/C MISSENSE_VARIANT

Additional dbSNP identifiers (rs#s) for CCDC39 Gene

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)
CCDC39
SNPedia medical, phenotypic, and genealogical associations of SNPs for
CCDC39

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

Disorders for CCDC39 Gene

MalaCards: The human disease database

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

- elite association - COSMIC cancer census association via MalaCards

UniProtKB/Swiss-Prot

CCD39_HUMAN
  • 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
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
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 54
  2. Mutations in GAS8, a Gene Encoding a Nexin-Dynein Regulatory Complex Subunit, Cause Primary Ciliary Dyskinesia with Axonemal Disorganization. (PMID: 27120127) Jeanson L … Legendre M (Human mutation 2016) 3 4 54
  3. 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 54
  4. 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 54
  5. 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 54

Products for CCDC39 Gene

  • Biorbyt antibodies for CCDC39

Sources for CCDC39 Gene