Seroatlas · Human Serome Atlas

CCDC39

Coiled-coil domain-containing protein 39

Also known as: CCD39_HUMAN, CFAP59, CILD14, DKFZp434A128, FAP59

Cross-references: UniProt · Ensembl · Human Protein Atlas · GeneCards · NCBI Gene

Protein identityUniProt · HPA

UniProt accession: Q9UFE4
Gene: CCDC39
Ensembl: ENSG00000284862
Chromosome: 3
Canonical length: 941 aa
Protein class: Disease related genes, Human disease related genes, Predicted intracellular proteins
Subcellular location: Nucleoplasm,Centrosome,Basal body,Acrosome

OverviewNCBI Gene

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 primary ciliary dyskinesia type 14 (CILD14). [provided by RefSeq, Jul 2011]

Canonical amino-acid sequenceUniProt

941 residues, UniProt reviewed canonical sequence.

>Q9UFE4|CCDC39
     1  MSSEFLAELH WEDGFAIPVA NEENKLLEDQ LSKLKDERAS LQDELREYEE RINSMTSHFK
    61  NVKQELSITQ SLCKARERET ESEEHFKAIA QRELGRVKDE IQRLENEMAS ILEKKSDKEN
   121  GIFKATQKLD GLKCQMNWDQ QALEAWLEES AHKDSDALTL QKYAQQDDNK IRALTLQLER
   181  LTLECNQKRK ILDNELTETI SAQLELDKAA QDFRKIHNER QELIKQWENT IEQMQKRDGD
   241  IDNCALELAR IKQETREKEN LVKEKIKFLE SEIGNNTEFE KRISVADRKL LKCRTAYQDH
   301  ETSRIQLKGE LDSLKATVNR TSSDLEALRK NISKIKKDIH EETARLQKTK NHNEIIQTKL
   361  KEITEKTMSV EEKATNLEDM LKEEEKDVKE VDVQLNLIKG VLFKKAQELQ TETMKEKAVL
   421  SEIEGTRSSL KHLNHQLQKL DFETLKQQEI MYSQDFHIQQ VERRMSRLKG EINSEEKQAL
   481  EAKIVELRKS LEEKKSTCGL LETQIKKLHN DLYFIKKAHS KNSDEKQSLM TKINELNLFI
   541  DRSEKELDKA KGFKQDLMIE DNLLKLEVKR TREMLHSKAE EVLSLEKRKQ QLYTAMEERT
   601  EEIKVHKTML ASQIRYVDQE RENISTEFRE RLSKIEKLKN RYEILTVVML PPEGEEEKTQ
   661  AYYVIKAAQE KEELQREGDC LDAKINKAEK EIYALENTLQ VLNSCNNNYK QSFKKVTPSS
   721  DEYELKIQLE EQKRAVDEKY RYKQRQIREL QEDIQSMENT LDVIEHLANN VKEKLSEKQA
   781  YSFQLSKETE EQKPKLERVT KQCAKLTKEI RLLKDTKDET MEEQDIKLRE MKQFHKVIDE
   841  MLVDIIEENT EIRIILQTYF QQSGLELPTA STKGSRQSSR SPSHTSLSAR SSRSTSTSTS
   901  QSSIKVLELK FPASSSLVGS PSRPSSASSS SSNVKSKKSS K

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against CCDC39 can act on the native protein depends on physical access: surface and secreted proteins are reachable by circulating antibodies, intracellular proteins usually are not.

Antibody reachability: Intracellular
Secreted: No
Transmembrane segments: 0
Mean surface accessibility (rSASA): 0.5
Highest tissue expression: 20 nTPM

Expression across tissuesHPA

Tissue

lymph node: 20 nTPM
retina: 20 nTPM
skin: 19 nTPM
fallopian tube: 11 nTPM
spleen: 10 nTPM
appendix: 8.8 nTPM

Single-cell type

cardiomyocytes: 283 nCPM
epicardial cells: 223 nCPM
adipocytes: 114 nCPM
ependymal cells: 42 nCPM
respiratory ciliated cells: 33 nCPM
fallopian tube ciliated cells: 30 nCPM

Immune cell

gdT-cell: 0.1 nTPM
MAIT T-cell: 0.1 nTPM
memory B-cell: 0.1 nTPM
naive CD4 T-cell: 0.1 nTPM
T-reg: 0.1 nTPM
basophil: 0 nTPM

Brain region

choroid plexus: 21 nTPM
medulla oblongata: 17 nTPM
cerebral cortex: 15 nTPM
midbrain: 15 nTPM
white matter: 14 nTPM
spinal cord: 14 nTPM

DiseaseUniProt · ClinVar · IEDB · PubMed

Four sources answering four different questions about CCDC39.

Disease | AllUniProt

Conditions CCDC39 is implicated in, by any mechanism.

Ciliary dyskinesia, primary, 14 (CILD14) MIM:613807

Disease | GeneticClinVar

177 pathogenic / likely-pathogenic of 973 ClinVar records.

Conditions with pathogenic or likely-pathogenic variants.

Primary ciliary dyskinesia
Primary ciliary dyskinesia 14
CCDC39-related disorder
Respiratory ciliopathies including non-CF bronchiectasis
Infertility disorder

Genetic constraint and essentialitygnomAD · DepMap

Does the body need this protein intact? Low LOEUF or a strong DepMap dependency means loss or blockade of the protein is likely to be felt.

gnomAD LOEUF (loss-of-function intolerance): 0.75
gnomAD pLI: 0
gnomAD missense Z: 0.36
DepMap mean gene effect: 0.01
DepMap dependency class: selective

Cancer expressionTCGA

Across TCGA tumor cohorts, this protein is over-expressed in roughly 4% of surveyed tumor types (aggregate summary; per-cohort expression, alteration, and survival load in the interactive view).

OntologyGO

Biological processes

Cellular components

Protein domainsUniProt · Pfam · InterPro

Coiled-coil domain-containing protein 39
Coiled-coil domain-containing protein 39

KeywordsUniProt

Antibody and autoantibody relevanceSeroatlas analysis

Seroatlas reads CCDC39 as an antibody target. Whether an autoantibody or antibody against CCDC39 could matter depends on whether native CCDC39 is physically reachable, whether the body needs it intact, and whether it acts in a disease-relevant tissue.

CCDC39 is annotated as predominantly intracellular. Intracellular proteins are common autoantibody markers, becoming visible to the immune system after cell injury or altered processing, but are usually markers of disease rather than direct drivers.

Annotation status

The present source text does not explicitly label CCDC39 as an autoantigen. Seroatlas presents hypothesis context only and does not manufacture a known-serology claim.

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