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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
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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

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

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
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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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