Gene Gene information from NCBI Gene database.
Entrez ID 339829
Gene name Coiled-coil domain 39 molecular ruler complex subunit
Gene symbol CCDC39
Synonyms (NCBI Gene)
CFAP59CILD14FAP59
Chromosome 3
Chromosome location 3q26.33
Summary 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 pri
SNPs SNP information provided by dbSNP.
39
SNP ID Visualize variation Clinical significance Consequence
rs140505857 G>A Conflicting-interpretations-of-pathogenicity, uncertain-significance Missense variant, coding sequence variant
rs200089274 A>G,T Conflicting-interpretations-of-pathogenicity, likely-benign Intron variant
rs201780665 G>A,T Pathogenic, uncertain-significance Coding sequence variant, synonymous variant, stop gained
rs376782159 G>A,T Conflicting-interpretations-of-pathogenicity Coding sequence variant, stop gained, synonymous variant
rs397515392 C>G Pathogenic Splice donor variant
miRNA miRNA information provided by mirtarbase database.
380
miRTarBase ID miRNA Experiments Reference
MIRT023078 hsa-miR-124-3p Microarray 18668037
MIRT712571 hsa-miR-4709-5p HITS-CLIP 19536157
MIRT712570 hsa-miR-4742-3p HITS-CLIP 19536157
MIRT712569 hsa-miR-421 HITS-CLIP 19536157
MIRT712568 hsa-miR-335-3p HITS-CLIP 19536157
Gene ontology (GO) Gene Ontology (GO) annotations describing the biological processes, molecular functions, and cellular components associated with a gene.
46
GO ID Ontology Definition Evidence Reference
GO:0001947 Process Heart looping IMP 22693285
GO:0003341 Process Cilium movement IEA
GO:0003341 Process Cilium movement IMP 22499950
GO:0003351 Process Epithelial cilium movement involved in extracellular fluid movement IEA
GO:0003356 Process Regulation of cilium beat frequency IMP 23255504
Other IDs Other IDs provides unique identifiers for this gene in OMIM, HGNC, and Ensembl databases.
MIM HGNC e!Ensembl
613798 25244 ENSG00000284862
Protein Protein information from UniProt database.
UniProt ID Unique identifier for the protein in the UniProt database. Click to view detailed protein information.
Q9UFE4
Protein name Coiled-coil domain-containing protein 39
Protein 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 t
PDB 8J07
Family and domains
Tissue specificity TISSUE SPECIFICITY: Mainly expressed in nasal brushings and, to a lesser extent, in lungs and testis. {ECO:0000269|PubMed:21131972}.
Sequence
MSSEFLAELHWEDGFAIPVANEENKLLEDQLSKLKDERASLQDELREYEERINSMTSHFK
NVKQELSITQSLCKARERETESEEHFKAIAQRELGRVKDEIQRLENEMASILEKKSDKEN
GIFKATQKLDGLKCQMNWDQQALEAWLEESAHKDSDALTLQKYAQQDDNKIRALTLQLER
LTLECNQKRKILDNELTETISAQLELDKAAQDFRKIHNERQELIKQWENTIEQMQKRDGD
IDNCALELARIKQETREKENLVKEKIKFLESEIGNNTEFEKRISVADRKLLKCRTAYQDH
ETSRIQLKGELDSLKATVNRTSSDLEALRKNISKIKKDIHEETARLQKTKNHNEIIQTKL
KEITEKTMSVEEKATNLEDMLKEEEKDVKEVDVQLNLIKGVLFKKAQELQTETMKEKAVL
SEIEGTRSSLKHLNHQLQKLDFETLKQQEIMYSQDFHIQQVERRMSRLKGEINSEEKQAL
EAKIVELRKSLEEKKSTCGLLETQIKKLHNDLYFIKKAHSKNSDEKQSLMTKINELNLFI
DRSEKELDKAKGFKQDLMIEDNLLKLEVKRTREMLHSKAEEVLSLEKRKQQLYTAMEERT
EEIKVHKTMLASQIRYVDQERENISTEFRERLSKIEKLKNRYEILTVVMLPPEGEEEKTQ
AYYVIKAAQEKEELQREGDCLDAKINKAEKEIYALENTLQVLNSCNNNYKQSFKKVTPSS
DEYELKIQLEEQKRAVDEKYRYKQRQIRELQEDIQSMENTLDVIEHLANNVKEKLSEKQA
YSFQLSKETEEQKPKLERVTKQCAKLTKEIRLLKDTKDETMEEQDIKLREMKQFHKVIDE
MLVDIIEENTEIRIILQTYFQQSGLELPTASTKGSRQSSRSPSHTSLSARSSRSTSTSTS
QSSIKVLELKFPASSSLVGSPSRPSSASSSSSNVKSKKSSK
Sequence length 941
Interactions View interactions
Associated diseases Disease associations from ClinVar (causal & non-causal) and other databases (OMIM, Orphanet, GWAS, etc.).
17
Evidence Score: ★☆☆☆☆  Gene-disease association found in Text Mining only ★★☆☆☆  Found in Text Mining and Unknown/Other Associations ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Phenotype Name Clinical Significance dbSNP ID RCV Accession Evidence Score
CCDC39-related disorder Pathogenic; Likely pathogenic rs878855279, rs397515392, rs1415346246, rs1560086701 RCV004755823
RCV003914861
RCV004755993
RCV003420209
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Heterotaxy Pathogenic rs1560086701 RCV001731885
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Infertility disorder Pathogenic rs397515392 RCV001327942
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Primary ciliary dyskinesia Pathogenic; Likely pathogenic rs1174553107, rs751239231, rs1717267418, rs1717695462, rs2108418891, rs2108421980, rs1399517463, rs375839864, rs2108429507, rs2108404522, rs2108420039, rs750086296, rs762287443, rs2473806213, rs1717963637
View all (111 more)
RCV003382515
RCV001849603
RCV001380089
RCV001382031
RCV001382042
View all (124 more)
★★★★★
ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
Phenotype Name Clinical Significance Source Evidence Score
AUTISM SPECTRUM DISORDER CTD
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
AUTISM SPECTRUM DISORDERS Disgenet
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
CILIARY DYSKINESIA, PRIMARY, 14 CTD, Disgenet, HPO
CTD, Disgenet, HPO
CTD, Disgenet, HPO
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
CILIARY MOTILITY DISORDERS Disgenet
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Associations from Text Mining Disease associations identified through text mining
Disease Name Disease (Merged) Source PMID Relationship Type Evidence Score
Asthenozoospermia Asthenozoospermia HPO_DG
★☆☆☆☆
Found in Text Mining only
Asthma Asthma HPO_DG
★☆☆☆☆
Found in Text Mining only
Bronchiectasis Bronchiectasis GENOMICS_ENGLAND_DG
★☆☆☆☆
Found in Text Mining only
Bronchiectasis Bronchiectasis HPO_DG
★☆☆☆☆
Found in Text Mining only
Bronchitis, Chronic Gastric Cancer HPO_DG
★☆☆☆☆
Found in Text Mining only
Chronic otitis media Otitis media HPO_DG
★☆☆☆☆
Found in Text Mining only
Chronic sinusitis Sinusitis HPO_DG
★☆☆☆☆
Found in Text Mining only
CILIARY DYSKINESIA, PRIMARY, 14 Ciliary dyskinesia GENOMICS_ENGLAND_DG 21131972, 23255504, 24896178
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
CILIARY DYSKINESIA, PRIMARY, 14 Ciliary dyskinesia UNIPROT_DG 21131972, 22693285, 23255504, 25186273
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
CILIARY DYSKINESIA, PRIMARY, 14 Ciliary dyskinesia CLINVAR_DG 23255504, 23891469, 24498942
★★☆☆☆
Found in Text Mining + Unknown/Other Associations