This gene encodes a protein that is necessary for motile cilia function. It functions in correct left-right axis formation by regulating the assembly of the inner dynein arm and the dynein regulatory complexes, which control ciliary beat. Mutations in this gene cause ciliary dyskinesia type 15, a disorder due to defects in cilia motility. Alternative splicing results in multipl... See more...

Aliases for CCDC40 Gene

Aliases for CCDC40 Gene

  • Coiled-Coil Domain Containing 40 2 3 5
  • Coiled-Coil Domain-Containing Protein 40 3 4
  • KIAA1640 4
  • CILD15 3
  • FAP172 3

External Ids for CCDC40 Gene

Previous GeneCards Identifiers for CCDC40 Gene

  • GC17P075637
  • GC17P078010
  • GC17P073449

Summaries for CCDC40 Gene

Entrez Gene Summary for CCDC40 Gene

  • This gene encodes a protein that is necessary for motile cilia function. It functions in correct left-right axis formation by regulating the assembly of the inner dynein arm and the dynein regulatory complexes, which control ciliary beat. Mutations in this gene cause ciliary dyskinesia type 15, a disorder due to defects in cilia motility. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2011]

GeneCards Summary for CCDC40 Gene

CCDC40 (Coiled-Coil Domain Containing 40) is a Protein Coding gene. Diseases associated with CCDC40 include Ciliary Dyskinesia, Primary, 15 and Kartagener Syndrome.

UniProtKB/Swiss-Prot Summary for CCDC40 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:21131974). Probably acts together with CCDC39 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. Required for axonemal recruitment of CCDC39 (PubMed:21131974).

Additional gene information for CCDC40 Gene

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for CCDC40 Gene

Genomics for CCDC40 Gene

GeneHancer (GH) Regulatory Elements for CCDC40 Gene

Promoters and enhancers for CCDC40 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
GH17J080034 Promoter/Enhancer 2.2 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas 790.5 -0.6 -631 3.6 ZNF785 RBPJ POLR2A NFYC L3MBTL2 RAD21 MNT NKRF ELF3 CSDE1 CCDC40 TBC1D16 EIF4A3 CHMP6 ENSG00000262768 SGSH ENGASE ENSG00000260369 ENDOV GAA
GH17J079984 Promoter/Enhancer 2.2 FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 46.4 -46.6 -46639 11.2 ZNF785 CTCF ZBTB6 FOXA1 LCORL MLX RBPJ TCF7L2 CTBP1 USF2 CCDC40 EIF4A3 ENSG00000262768 ENGASE CBX2 TBC1D16 RNF213-AS1 ENDOV SGSH CANT1
GH17J079836 Promoter/Enhancer 2.6 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 27.9 -195.7 -195717 12.2 ZNF785 SIN3A ZBTB40 CTCF ZBTB6 LCORL MLX RBPJ SMARCE1 POLR2A CBX4 USP36 ENDOV CCDC40 EIF4A3 RNF213-AS1 CBX8 RF00017-2579
GH17J080022 Promoter/Enhancer 1.6 Ensembl ENCODE CraniofacialAtlas dbSUPER 33.8 -11.7 -11660 4.2 LCORL RBPJ MIXL1 NFIB ZNF652 RERE POLR2A AHR SP1 TFE3 ENSG00000261978 CCDC40 EIF4A3 GAA TBC1D16
GH17J080028 Enhancer 0.9 ENCODE dbSUPER 37.6 -6.7 -6720 3.5 CTCF FOXA1 RBPJ MYC HLF RAD21 MNT SP1 PPARG CREB1 CCDC40 EIF4A3 TBC1D16 GAA ENSG00000262580 ENSG00000261978
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around CCDC40 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the CCDC40 gene promoter:
  • AP-2alpha
  • AP-2alphaA
  • AP-2beta
  • AP-2gamma
  • GATA-1
  • MRF-2
  • RORalpha1
  • SREBP-1a
  • SREBP-1b
  • SREBP-1c

Genomic Locations for CCDC40 Gene

Genomic Locations for CCDC40 Gene
chr17:80,036,632-80,100,613
(GRCh38/hg38)
Size:
63,982 bases
Orientation:
Plus strand
chr17:78,010,435-78,074,412
(GRCh37/hg19)
Size:
63,978 bases
Orientation:
Plus strand

Genomic View for CCDC40 Gene

Genes around CCDC40 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CCDC40 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CCDC40 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CCDC40 Gene

Proteins for CCDC40 Gene

  • Protein details for CCDC40 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q4G0X9-CCD40_HUMAN
    Recommended name:
    Coiled-coil domain-containing protein 40
    Protein Accession:
    Q4G0X9
    Secondary Accessions:
    • A8MTD2
    • C9JTI9
    • C9JTJ0
    • C9JXW1
    • J3QSY2
    • Q6PE47
    • Q9HCD2
    • Q9NWL5

    Protein attributes for CCDC40 Gene

    Size:
    1142 amino acids
    Molecular mass:
    130113 Da
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=BAB13466.1; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305};

    Alternative splice isoforms for CCDC40 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for CCDC40 Gene

Post-translational modifications for CCDC40 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for CCDC40 Gene

Domains & Families for CCDC40 Gene

Gene Families for CCDC40 Gene

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

Protein Domains for CCDC40 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for CCDC40 Gene

GenScript: Design optimal peptide antigens:
  • Coiled-coil domain-containing protein 40 (CCD40_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q4G0X9

UniProtKB/Swiss-Prot:

CCD40_HUMAN :
  • Belongs to the CCDC40 family.
Family:
  • Belongs to the CCDC40 family.
genes like me logo Genes that share domains with CCDC40: view

Function for CCDC40 Gene

Molecular function for CCDC40 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:21131974). Probably acts together with CCDC39 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. Required for axonemal recruitment of CCDC39 (PubMed:21131974).

Phenotypes From GWAS Catalog for CCDC40 Gene

Gene Ontology (GO) - Molecular Function for CCDC40 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003674 molecular_function ND --
genes like me logo Genes that share ontologies with CCDC40: view
genes like me logo Genes that share phenotypes with CCDC40: view

Human Phenotype Ontology for CCDC40 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

CRISPR Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for CCDC40 Gene

Localization for CCDC40 Gene

Subcellular locations from UniProtKB/Swiss-Prot for CCDC40 Gene

Cytoplasm. Cell projection, cilium. Note=Localizes to cytoplasm and motile cilium. {ECO:0000250 UniProtKB:Q8BI79}.

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 CCDC40 gene
Compartment Confidence
cytoskeleton 5
extracellular 2
nucleus 2

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for CCDC40 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region IEA --
GO:0005737 cytoplasm ISS --
GO:0005929 cilium ISS --
GO:0005930 axoneme IDA 23255504
GO:0042995 cell projection IEA --
genes like me logo Genes that share ontologies with CCDC40: view

Pathways & Interactions for CCDC40 Gene

PathCards logo

SuperPathways for CCDC40 Gene

No Data Available

Gene Ontology (GO) - Biological Process for CCDC40 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001947 heart looping IMP 22693285
GO:0003341 cilium movement IMP 22499950
GO:0003351 epithelial cilium movement IMP 21131974
GO:0003356 regulation of cilium beat frequency IMP 21131974
GO:0030317 flagellated sperm motility IMP 23255504
genes like me logo Genes that share ontologies with CCDC40: view

No data available for Pathways by source and SIGNOR curated interactions for CCDC40 Gene

Drugs & Compounds for CCDC40 Gene

No Compound Related Data Available

Transcripts for CCDC40 Gene

CRISPR Products

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for CCDC40 Gene

ExUns: 1a · 1b · 1c ^ 2 ^ 3 ^ 4a · 4b · 4c · 4d · 4e · 4f ^ 5a · 5b · 5c ^ 6a · 6b ^ 7 ^ 8a · 8b ^ 9a · 9b ^ 10a · 10b ^ 11 ^ 12 ^ 13a ·
SP1: - - - - - - - -
SP2: - - - -
SP3: - - - - - - - -
SP4:
SP5:
SP6: - - - - - - -
SP7: -
SP8: -
SP9:
SP10:
SP11:
SP12: - -

ExUns: 13b · 13c ^ 14 ^ 15 ^ 16 ^ 17a · 17b ^ 18 ^ 19 ^ 20 ^ 21a · 21b ^ 22a · 22b
SP1: -
SP2: - -
SP3:
SP4: - -
SP5:
SP6:
SP7:
SP8:
SP9:
SP10:
SP11:
SP12:

Relevant External Links for CCDC40 Gene

GeneLoc Exon Structure for
CCDC40
ECgene alternative splicing isoforms for
CCDC40

Expression for CCDC40 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for CCDC40 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for CCDC40 Gene

This gene is overexpressed in Testis (x4.6).

Protein differential expression in normal tissues from HIPED for CCDC40 Gene

This gene is overexpressed in Bone (24.7), Urinary Bladder (24.5), and Synovial fluid (16.2).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for CCDC40 Gene



NURSA nuclear receptor signaling pathways regulating expression of CCDC40 Gene:

CCDC40

SOURCE GeneReport for Unigene cluster for CCDC40 Gene:

Hs.202542

Evidence on tissue expression from TISSUES for CCDC40 Gene

  • Nervous system(4.2)

Phenotype-based relationships between genes and organs from Gene ORGANizer for CCDC40 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 CCDC40: view

No data available for Protein tissue co-expression partners and mRNA Expression by UniProt/SwissProt for CCDC40 Gene

Orthologs for CCDC40 Gene

This gene was present in the common ancestor of animals.

Orthologs for CCDC40 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia CCDC40 33 32
  • 98.57 (n)
OneToOne
cow
(Bos Taurus)
Mammalia CCDC40 33 32
  • 78.12 (n)
OneToOne
dog
(Canis familiaris)
Mammalia CCDC40 33 32
  • 76.79 (n)
OneToOne
rat
(Rattus norvegicus)
Mammalia Ccdc40 32
  • 76.04 (n)
mouse
(Mus musculus)
Mammalia Ccdc40 17 33 32
  • 73.25 (n)
oppossum
(Monodelphis domestica)
Mammalia CCDC40 33
  • 52 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia CCDC40 33
  • 46 (a)
OneToOne
chicken
(Gallus gallus)
Aves CCDC40 33 32
  • 61.91 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia CCDC40 33
  • 52 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia LOC100486955 32
  • 59.16 (n)
Str.11059 32
zebrafish
(Danio rerio)
Actinopterygii ccdc40 33 32
  • 50.95 (n)
OneToOne
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.6406 32
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP009129 32
  • 46.01 (n)
fruit fly
(Drosophila melanogaster)
Insecta l(2)41Ab 33 32
  • 40.45 (n)
OneToOne
sea squirt
(Ciona savignyi)
Ascidiacea -- 33
  • 44 (a)
OneToOne
Species where no ortholog for CCDC40 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)
  • 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 CCDC40 Gene

ENSEMBL:
Gene Tree for CCDC40 (if available)
TreeFam:
Gene Tree for CCDC40 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for CCDC40: view image

Paralogs for CCDC40 Gene

No data available for Paralogs for CCDC40 Gene

Variants for CCDC40 Gene

Sequence variations from dbSNP and Humsavar for CCDC40 Gene

SNP ID Clin Chr 17 pos Variation AA Info Type
rs1028095921 likely-benign, Ciliary dyskinesia 80,097,370(+) C/T coding_sequence_variant, genic_downstream_transcript_variant, non_coding_transcript_variant, synonymous_variant
rs1060501718 uncertain-significance, Ciliary dyskinesia 80,039,831(+) A/G coding_sequence_variant, genic_upstream_transcript_variant, missense_variant, non_coding_transcript_variant
rs1060501719 pathogenic, Ciliary dyskinesia 80,087,748(+) CA/ACCG coding_sequence_variant, frameshift, genic_downstream_transcript_variant, non_coding_transcript_variant
rs1060501720 uncertain-significance, Ciliary dyskinesia 80,058,593(+) A/G coding_sequence_variant, missense_variant, non_coding_transcript_variant
rs1060501721 uncertain-significance, Ciliary dyskinesia 80,099,623(+) C/G coding_sequence_variant, genic_downstream_transcript_variant, missense_variant, non_coding_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for CCDC40 Gene

Variant ID Type Subtype PubMed ID
esv1580229 CNV insertion 17803354
esv1736428 CNV deletion 17803354
esv2673221 CNV deletion 23128226
esv2716356 CNV deletion 23290073
esv2716357 CNV deletion 23290073
esv2716358 CNV deletion 23290073
esv3307674 CNV mobile element insertion 20981092
esv3309706 CNV mobile element insertion 20981092
esv3397033 CNV duplication 20981092
esv3401938 CNV insertion 20981092
esv3403530 CNV insertion 20981092
esv3641360 CNV loss 21293372
esv3641362 CNV loss 21293372
esv3641363 CNV gain 21293372
esv990091 CNV deletion 20482838
nsv1066606 CNV gain 25217958
nsv1113893 CNV deletion 24896259
nsv1142231 CNV tandem duplication 24896259
nsv469591 CNV loss 16826518
nsv476494 CNV novel sequence insertion 20440878
nsv478261 CNV novel sequence insertion 20440878
nsv480137 CNV novel sequence insertion 20440878
nsv828122 CNV loss 20364138
nsv833561 CNV loss 17160897

Variation tolerance for CCDC40 Gene

Residual Variation Intolerance Score: 94.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 7.21; 80.98% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for CCDC40 Gene

Human Gene Mutation Database (HGMD)
CCDC40
SNPedia medical, phenotypic, and genealogical associations of SNPs for
CCDC40

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CCDC40 Gene

Disorders for CCDC40 Gene

MalaCards: The human disease database

(6) MalaCards diseases for CCDC40 Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
ciliary dyskinesia, primary, 15
  • cild15
kartagener syndrome
  • kartagener's syndrome
primary ciliary dyskinesia
  • pcd
ciliary dyskinesia, primary, 1
  • pcd
situs inversus
  • situs inversus viscerum
- elite association - COSMIC cancer census association via MalaCards

UniProtKB/Swiss-Prot

CCD40_HUMAN
  • Ciliary dyskinesia, primary, 15 (CILD15) [MIM:613808]: 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:21131974, ECO:0000269 PubMed:22693285, ECO:0000269 PubMed:23255504, ECO:0000269 PubMed:23402890, 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 CCDC40

genes like me logo Genes that share disorders with CCDC40: view

No data available for Genatlas for CCDC40 Gene

Publications for CCDC40 Gene

  1. 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) 2 3 4 56
  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 56
  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 56
  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 56
  5. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 56

Products for CCDC40 Gene

  • Biorbyt antibodies for CCDC40

Sources for CCDC40 Gene