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CCDC40 coiled-coil domain containing 40 [ Homo sapiens (human) ]

Gene ID: 55036, updated on 5-Aug-2022

Summary

Official Symbol
CCDC40provided by HGNC
Official Full Name
coiled-coil domain containing 40provided 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

See CCDC40 in Genome Data Viewer
Location:
17q25.3
Exon count:
22
Annotation release Status Assembly Chr Location
110 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (80036642..80100613)
110 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 uncharacterized LOC124904072 Neighboring gene Sharpr-MPRA regulatory region 13982 Neighboring gene uncharacterized LOC124904074 Neighboring gene microRNA 1268b Neighboring gene alpha glucosidase Neighboring gene eukaryotic translation initiation factor 4A3

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

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

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

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
PubMed 
involved_in 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
PubMed 
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 
involved_in flagellated sperm motility IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in heart looping IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in heart looping IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in inner dynein arm assembly IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in lung development IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in motile cilium assembly 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
PubMed 
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
PubMed 
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

Preferred Names
coiled-coil domain-containing protein 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_001243342.2NP_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:239934
    SMC_prok_B; chromosome segregation protein SMC, common bacterial type
    pfam08647
    Location:780878
    BRE1; BRE1 E3 ubiquitin ligase
  2. NM_001330508.2NP_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_017950.4NP_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
    Q4G0X9, Q9NWL5
    Related
    ENSP00000380679.4, ENST00000397545.9
    Conserved Domains (2) summary
    COG1196
    Location:2951129
    Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
    pfam08647
    Location:780878
    BRE1; BRE1 E3 ubiquitin ligase

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 110 details...Open this link in a new tab

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)