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Ccdc39 Gene Detail
Summary
  • Symbol
    Ccdc39
  • Name
    coiled-coil domain containing 39
  • Synonyms
    4921507O14Rik, b2b1304Clo, b2b1735Clo, b2b2025.1Clo, D3Ertd789e, prh
  • Feature Type
    protein coding gene
  • IDs
    MGI:1289263
    NCBI Gene: 51938
  • Alliance
    genome feature page
  • Transcription Start Sites
    3 TSS
Location &
Maps
more
  • Sequence Map
    Chr3:33866511-33898459 bp, - strand
    From Ensembl annotation of GRCm39
  • View this region in JBrowse
  • Genome Browsers
    Ensembl | UCSC | NCBI
  • Genetic Map
    Chromosome 3, 16.32 cM
  • Mapping Data
    3 experiments
Strain
Comparison
more
  • SNPs within 2kb
    930 from dbSNP Build 142
  • Strain Annotations
    19
For selected strains:
Strain Gene Model ID Feature Type Coordinates Select Strains
C57BL/6J MGI_C57BL6J_1289263
 protein coding gene Chr3:33864906-33898473 (-)
129S1/SvImJ ENSMUSG00200005944
 protein coding gene Chr3:30603919-30636248 (-)
A/J ENSMUSG00195001409
 protein coding gene Chr3:30602844-30634333 (-)
AKR/J ENSMUSG00220000558
 protein coding gene Chr3:30636191-30668148 (-)
BALB/cJ ENSMUSG00180002358
 protein coding gene Chr3:30717889-30749829 (-)
C3H/HeJ ENSMUSG00175003246
 protein coding gene Chr3:30633180-30664668 (-)
C57BL/6NJ ENSMUSG00215001349
 protein coding gene Chr3:30991970-31023910 (-)
CAROLI/EiJ MGP_CAROLIEiJ_G0024926
 protein coding gene Chr3:28751495-28784048 (-)
CAST/EiJ ENSTCUG00005024885
 protein coding gene Chr3:30493217-30529979 (-)
CBA/J ENSMUSG00210001056
 protein coding gene Chr3:30681468-30712954 (-)
DBA/2J ENSMUSG00185000931
 protein coding gene Chr3:30922226-30954182 (-)
FVB/NJ ENSMUSG00205007918
 protein coding gene Chr3:30089614-30121930 (-)
JF1/MsJ ENSUMUG00000004108
 protein coding gene Chr3:30363095-30394534 (-)
LP/J ENSMUSG00230018319
 protein coding gene Chr3:32846975-32879303 (-)
NOD/ShiLtJ ENSMUSG00190001396
 protein coding gene Chr3:30908639-30940968 (-)
NZO/HlLtJ ENSMUSG00225006678
 protein coding gene Chr3:35464945-35497273 (-)
PWK/PhJ ENSLUMG00010032329
 protein coding gene Chr3:30413039-30444537 (-)
SPRET/EiJ ENSMSPG00010000440
 protein coding gene Chr3:30801797-30835203 (-)
WSB/EiJ ENSIUOG00005013245
 protein coding gene Chr3:30914686-30946137 (-)



Homology
more
  • Human Ortholog
    CCDC39, coiled-coil domain 39 molecular ruler complex subunit
  • Vertebrate Orthologs
    3
Vertebrate Orthology Source
Alliance of Genome Resources
  • Human Ortholog
    CCDC39, coiled-coil domain 39 molecular ruler complex subunit
  • Synonyms
    CFAP59, CILD14, FAP59
  • Links
    NCBI Gene ID: 339829
    UniProt: Q9UFE4

  • Chr Location
    3q26.33; chr3:180602858-180684942 (-)  GRCh38
Human Diseases
more
  • Diseases
    4 with Ccdc39 mouse models; 1 with human CCDC39 associations

Human Disease Mouse Models
      
IDs
 View 3 models
      
IDs
 View 1 model
IDs
 View 2 models
IDs
 View 3 models
Click on a disease name to see all genes associated with that disease.

  • Mutations/Alleles
    4 with disease annotations
  • References
    3 with disease annotations
Mutations,
Alleles, and
Phenotypes
less
  • Phenotype Summary
    49 phenotypes from 6 alleles in 6 genetic backgrounds
    43 images
    16 phenotype references
Phenotype Overview

adipose tissue
behavior/neurological
cardiovascular system
cellular
craniofacial
digestive/alimentary system
embryo
endocrine/exocrine glands
growth/size/body
hearing/vestibular/ear
hematopoietic system
homeostasis/metabolism
integument
immune system
limbs/digits/tail
liver/biliary system
mortality/aging
muscle
nervous system
pigmentation
renal/urinary system
reproductive system
respiratory system
skeleton
taste/olfaction
neoplasm
vision/eye

Click cells to view annotations.
ENU induced mutations result in situs inversus totalis with dextrocardia, double outlet right ventricle and atrial septal defects, renal anomalies including cysts and hydronephrosis, and immotile tracheal airway cilia. One ENU induced mutation causes ependymal motile cilia defects and hydrocephalus.
Gene Ontology
(GO)
Classifications
less
  • All GO Annotations
    67
  • GO References
    13
Molecular Function

No experimental evidence to support Molecular Function annotation, following literature review. See J:73796.
Biological Process

carbohydrate derivative metabolism
cell differentiation
cell population proliferation
cellular component organization
DNA-templated transcription
establishment of localization
homeostatic process
immune system process
lipid metabolic process
programmed cell death
protein metabolic process
response to stimulus
signaling
system development
Cellular Component

cell projection
cytoplasmic vesicle
cytoskeleton
cytosol
endoplasmic reticulum
endosome
extracellular region
Golgi apparatus
mitochondrion
membraneless organelle
nucleus
organelle envelope
organelle lumen
plasma membrane
protein-containing complex
synapse
vacuole
Click cells to view annotations.
Expression
less
Expression Overview

early conceptus
embryo ectoderm
embryo endoderm
embryo mesoderm
embryo mesenchyme
extraembryonic component
alimentary system
auditory system
branchial arches
cardiovascular system
connective tissue
endocrine system
exocrine system
hemolymphoid system
integumental system
limbs
liver and biliary system
musculoskeletal system
nervous system
olfactory system
reproductive system
respiratory system
urinary system
visual system
Click cells to view annotations.


  • Assay Results
    681
  • Tissues
    32
  • cDNA Data
    17
  • Literature Summary
    4
  • Comparison Matrix
    Gene Expression + Phenotype
    • Sequences &
    Gene Models
    less
    Representative SequencesLengthStrain/SpeciesFlank
    genomic ENSMUSG00000027676 Ensembl Gene Model | MGI Sequence Detail 31949 C57BL/6J ±  kb
    transcript ENSMUST00000029222 Ensembl | MGI Sequence Detail 3606 Not Applicable  
    polypeptide ENSMUSP00000029222 Ensembl | MGI Sequence Detail 937 Not Applicable  
    For the selected sequence
    Protein
    Information
    less
    Molecular
    Reagents
    less
    • All nucleic 23
      cDNA 19
      Primer pair 3
      Other 1
      Antibodies 1

      Microarray probesets 9
    Other
    Accession IDs
    less
    MGI:1914785, MGI:2139706, MGI:2139809, MGI:5056360, MGI:5316773, MGI:5438051, MGI:5554524
    References
    more
    • Summaries
      All 53
      Developmental Gene Expression 4
      Diseases 3
      Gene Ontology 13
      Phenotypes 16
    • Earliest
      J:60984 Ko MS, et al., Large-scale cDNA analysis reveals phased gene expression patterns during preimplantation mouse development. Development. 2000 Apr;127(8):1737-49
    • Latest
      J:369747 Lin S, et al., Rbpms2 prevents major cardiac defects in cardiomyocyte-specific Rbpms-deficient mice. Dev Cell. 2025 Jun 24;
    Contributing Projects:
    Mouse Genome Database (MGD), Gene Expression Database (GXD), Mouse Models of Human Cancer database (MMHCdb) (formerly Mouse Tumor Biology (MTB)), Gene Ontology (GO)
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    Funding Information
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    Send questions and comments to User Support.     		last database update
    09/08/2026
    MGI 6.24     		The Jackson Laboratory