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    CCDC40 coiled-coil domain 40 molecular ruler complex subunit [ Homo sapiens (human) ]

    Gene ID: 55036, updated on 5-Mar-2024

    Summary

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    Official Symbol
    CCDC40provided by HGNC
    Official Full Name
    coiled-coil domain 40 molecular ruler complex subunitprovided by HGNC
    Primary source
    HGNC:HGNC:26090
    See related
    Ensembl:ENSG00000141519 MIM:613799; AllianceGenome:HGNC:26090
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    CILD15; FAP172; CFAP172
    Summary
    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]
    Expression
    Broad expression in testis (RPKM 4.5), lung (RPKM 1.1) and 14 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    17q25.3
    Exon count:
    22
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (80036642..80100613)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (80935298..81001052)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (78010441..78074412)

    Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene TBC1 domain family member 16 Neighboring gene uncharacterized LOC124904073 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:77961646-77962517 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9097 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr17:77966696-77967895 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:77975818-77976678 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:77987013-77987179 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:77996703-77997568 Neighboring gene uncharacterized LOC124904072 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:78003463-78004332 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_47575 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9098 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12927 Neighboring gene Sharpr-MPRA regulatory region 13982 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:78018463-78018964 Neighboring gene uncharacterized LOC124904074 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:78039691-78040515 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:78056255-78056756 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:78064021-78064580 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9099 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12928 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:78083610-78084585 Neighboring gene microRNA 1268b Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:78086615-78087127 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:78091523-78092024 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:78097302-78097924 Neighboring gene alpha glucosidase Neighboring gene ReSE screen-validated silencer GRCh37_chr17:78107357-78107522 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:78120154-78120868 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:78120869-78121581 Neighboring gene eukaryotic translation initiation factor 4A3

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

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    Related articles in PubMed

    1. CCDC40 mutation as a cause of infertility in a Chinese family with primary ciliary dyskinesia. Liu L, et al. Medicine (Baltimore), 2021 Dec 23. PMID 34941110, Free PMC Article
    2. CCDC40 mutation as a cause of primary ciliary dyskinesia: a case report and review of literature. Sui W, et al. Clin Respir J, 2016 Sep. PMID 25619595
    3. Clinical and genetic spectrum in 33 Egyptian families with suspected primary ciliary dyskinesia. Fassad MR, et al. Clin Genet, 2020 Mar. PMID 31650533
    4. Clinical features of childhood primary ciliary dyskinesia by genotype and ultrastructural phenotype. Davis SD, et al. Am J Respir Crit Care Med, 2015 Feb 1. PMID 25493340, Free PMC Article
    5. MCM3AP, a novel HBV integration site in hepatocellular carcinoma and its implication in hepatocarcinogenesis. Wang J, et al. J Huazhong Univ Sci Technolog Med Sci, 2010 Aug. PMID 20714864

    See all (24) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. CCDC40 mutation as a cause of infertility in a Chinese family with primary ciliary dyskinesia.
      Title: CCDC40 mutation as a cause of infertility in a Chinese family with primary ciliary dyskinesia.
    2. Clinical and genetic spectrum in 33 Egyptian families with suspected primary ciliary dyskinesia.
      Title: Clinical and genetic spectrum in 33 Egyptian families with suspected primary ciliary dyskinesia.
    3. A novel mutation causing primary ciliary dyskinesia was found in Japanese patients.
      Title: A targeted next-generation sequencing panel reveals novel mutations in Japanese patients with primary ciliary dyskinesia.
    4. Results identified a novel mutant alleles in CCDC40 gene, which altered the protein sequence and resulted in the ultrastructural defects in the microtubule structure of cilia suggesting that CCDC40 mutation may be a cause for ciliary dyskinesia.
      Title: CCDC40 mutation as a cause of primary ciliary dyskinesia: a case report and review of literature.
    5. Lung disease was worse in those with IDA/CA/MTD ultrastructural defects, most of whom had biallelic mutations in ccdc40.
      Title: Clinical features of childhood primary ciliary dyskinesia by genotype and ultrastructural phenotype.
    6. This study shows that CCDC39 and CCDC40 mutations are the major cause of Primary ciliary dyskinesia in patients with the previously termed "radial spoke defect".
      Title: Mutations in CCDC39 and CCDC40 are the major cause of primary ciliary dyskinesia with axonemal disorganization and absent inner dynein arms.
    7. Aiming to delineate the CCDC39/CCDC40 mutation spectrum and associated phenotypes, a large cohort of patients with IDA defects were screened. Biallelic CCDC39 or CCDC40 mutations were identified in 30/34 unrelated families with IDA defects.
      Title: Delineation of CCDC39/CCDC40 mutation spectrum and associated phenotypes in primary ciliary dyskinesia.
    8. CCDC40 mutations in humans result in a variant of primary ciliary dyskinesia characterized by misplacement of the central pair of microtubules and defective assembly of inner dynein arms and dynein regulatory complexes.
      Title: The coiled-coil domain containing protein CCDC40 is essential for motile cilia function and left-right axis formation.
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Associated conditions

    Description Tests
    Primary ciliary dyskinesia 15
    MedGen: C3151137 OMIM: 613808 GeneReviews: Primary Ciliary Dyskinesia
    		Compare labs

    EBI GWAS Catalog

    Description
    Loci associated with N-glycosylation of human immunoglobulin G show pleiotropy with autoimmune diseases and haematological cancers.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ20753, FLJ32021, KIAA1640

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables molecular_function ND
    No biological Data available
    more info
    		  
    Process Evidence Code Pubs
    involved_in axonemal dynein complex assembly IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in axoneme assembly IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within cilium movement IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in determination of digestive tract left/right asymmetry IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in determination of liver left/right asymmetry IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in determination of pancreatic left/right asymmetry IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in epithelial cilium movement involved in determination of left/right asymmetry IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in epithelial cilium movement involved in determination of left/right asymmetry IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in epithelial cilium movement involved in extracellular fluid movement IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within flagellated sperm motility IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in heart looping IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in heart looping IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within inner dynein arm assembly IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in lung development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within motile cilium assembly IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within regulation of cilium beat frequency IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in regulation of cilium beat frequency IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in axoneme IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in cilium IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cilium IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cilium ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytoplasm ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in extracellular region IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    coiled-coil domain-containing protein 40
    Names
    coiled-coil domain containing 40

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    Genomic

    1. NG_029761.1 RefSeqGene

      Range
      5011..68982
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001243342.2 → NP_001230271.1  coiled-coil domain-containing protein 40 isoform 2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 3' coding region and 3' UTR, compared to variant 1. The encoded isoform (2) has a distinct and shorter C-terminus, compared to isoform 1.
      Source sequence(s)
      AB046860, AC087741, BC035251, BQ009577, DA842356, DB230102
      Consensus CDS
      CCDS58604.1
      UniProtKB/Swiss-Prot
      Q4G0X9
      Related
      ENSP00000364011.3, ENST00000374877.7
      Conserved Domains (2) summary
      TIGR02168
      Location:239 → 934
      SMC_prok_B; chromosome segregation protein SMC, common bacterial type
      pfam08647
      Location:780 → 878
      BRE1; BRE1 E3 ubiquitin ligase

    2. NM_001330508.2 → NP_001317437.1  coiled-coil domain-containing protein 40 isoform 3

      Status: REVIEWED

      Source sequence(s)
      AC116025
      Consensus CDS
      CCDS82212.1
      UniProtKB/Swiss-Prot
      Q4G0X9
      Related
      ENSP00000269318.5, ENST00000269318.9

    3. NM_017950.4 → NP_060420.2  coiled-coil domain-containing protein 40 isoform 1

      See identical proteins and their annotated locations for NP_060420.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1). There are no publicly available full-length transcripts representing this variant, but it is supported by partial transcript alignments and by data in PMID:21131974.
      Source sequence(s)
      AB046860, AW300891, BC035251, DA842356, DB230102
      Consensus CDS
      CCDS42395.1
      UniProtKB/Swiss-Prot
      A8MTD2, C9JTI9, C9JTJ0, C9JXW1, J3QSY2, Q4G0X9, Q6PE47, Q9HCD2, Q9NWL5
      Related
      ENSP00000380679.4, ENST00000397545.9
      Conserved Domains (2) summary
      COG1196
      Location:295 → 1129
      Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
      pfam08647
      Location:780 → 878
      BRE1; BRE1 E3 ubiquitin ligase

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000017.11 Reference GRCh38.p14 Primary Assembly

      Range
      80036642..80100613
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCh38.p14 PATCHES

    Genomic

    1. NW_025791802.1 Reference GRCh38.p14 PATCHES

      Range
      59553..125319
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060941.1 Alternate T2T-CHM13v2.0

      Range
      80935298..81001052
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q4G0X9.2 GenPept UniProtKB/Swiss-Prot:Q4G0X9

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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