CCDC93

gene
On this page

Also known as FLJ10996

Summary

CCDC93 (CCC complex scaffolding subunit CCDC93, HGNC:25611) is a protein-coding gene on chromosome 2q14.1, encoding Coiled-coil domain-containing protein 93 (Q567U6). Component of the commander complex that is essential for endosomal recycling of transmembrane cargos; the commander complex is composed of composed of the CCC subcomplex and the retriever subcomplex.

Involved in Golgi to plasma membrane transport and endocytic recycling. Located in intracellular membrane-bounded organelle.

Source: NCBI Gene 54520 — RefSeq curated summary.

At a glance

  • GWAS associations: 12
  • Clinical variants (ClinVar): 114 total
  • MANE Select transcript: NM_019044

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:25611
Approved symbolCCDC93
NameCCC complex scaffolding subunit CCDC93
Location2q14.1
Locus typegene with protein product
StatusApproved
AliasesFLJ10996
Ensembl geneENSG00000125633
Ensembl biotypeprotein_coding
OMIM620553
Entrez54520

Gene structure

Transcript identifiers

Ensembl transcripts: 18 — 11 protein_coding, 5 retained_intron, 1 nonsense_mediated_decay, 1 protein_coding_CDS_not_defined

ENST00000319432, ENST00000376300, ENST00000437999, ENST00000460781, ENST00000466171, ENST00000470650, ENST00000474006, ENST00000474546, ENST00000488908, ENST00000884938, ENST00000884939, ENST00000884940, ENST00000926449, ENST00000926450, ENST00000951763, ENST00000951764, ENST00000951765, ENST00000951766

RefSeq mRNA: 1 — MANE Select: NM_019044 NM_019044

CCDS: CCDS2121

Canonical transcript exons

ENST00000376300 — 24 exons

ExonStartEnd
ENSE00000857044117945529117945582
ENSE00000857045117946811117946882
ENSE00000857046117948105117948186
ENSE00000963694117958365117958481
ENSE00001130888118000821118000932
ENSE00001470257118006722118006816
ENSE00001470264118008545118008658
ENSE00003476726117936702117936739
ENSE00003501811117939029117939111
ENSE00003559509117977994117978030
ENSE00003582463117935495117935579
ENSE00003585356117995446117995502
ENSE00003597780117974850117974900
ENSE00003603950117931037117931150
ENSE00003609352117973908117973994
ENSE00003631214117985969117986069
ENSE00003639421117996264117996362
ENSE00003641937117949322117949395
ENSE00003644166117941189117941297
ENSE00003647395117952373117952435
ENSE00003655122117975188117975280
ENSE00003665483117944024117944086
ENSE00003843098117915481117920396
ENSE00003849439118013954118014070

Expression profiles

Bgee: expression breadth ubiquitous, 291 present calls, max score 96.60.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 23.0050 / max 228.4067, expressed in 1805 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter IDTPM avgSamples expressed
3036920.11551795
303702.40661263
303710.4829270

Top tissues by expression

295 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
sural nerveUBERON:001548896.60gold quality
calcaneal tendonUBERON:000370195.34gold quality
adrenal tissueUBERON:001830393.36gold quality
tendonUBERON:000004392.15gold quality
apex of heartUBERON:000209892.05gold quality
right testisUBERON:000453492.01gold quality
left testisUBERON:000453391.92gold quality
pituitary glandUBERON:000000791.55gold quality
cervix squamous epitheliumUBERON:000692291.43gold quality
right adrenal gland cortexUBERON:003582791.30gold quality
adenohypophysisUBERON:000219691.18gold quality
testisUBERON:000047390.95gold quality
right uterine tubeUBERON:000130290.74gold quality
dorsal motor nucleus of vagus nerveUBERON:000287090.68gold quality
tibial nerveUBERON:000132390.60gold quality
rectumUBERON:000105290.44gold quality
right adrenal glandUBERON:000123390.24gold quality
right hemisphere of cerebellumUBERON:001489090.24gold quality
left ovaryUBERON:000211989.96gold quality
adrenal cortexUBERON:000123589.89gold quality
parietal pleuraUBERON:000240089.79gold quality
body of pancreasUBERON:000115089.76gold quality
left adrenal glandUBERON:000123489.72gold quality
adrenal glandUBERON:000236989.72gold quality
colonic epitheliumUBERON:000039789.69gold quality
left ventricle myocardiumUBERON:000656689.68gold quality
mucosa of stomachUBERON:000119989.67gold quality
visceral pleuraUBERON:000240189.66gold quality
metanephros cortexUBERON:001053389.62gold quality
left adrenal gland cortexUBERON:003582589.62gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-ANND-3yes9.42

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

153 targeting CCDC93, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-6867-5P100.0082.213464
HSA-MIR-7110-3P100.0073.182486
HSA-MIR-4283100.0066.422097
HSA-MIR-8485100.0077.574731
HSA-MIR-3646100.0073.565283
HSA-MIR-3120-5P100.0065.56965
HSA-MIR-5193100.0067.261744
HSA-MIR-118499.9968.191458
HSA-MIR-450099.9972.722367
HSA-MIR-548N99.9871.944170
HSA-MIR-433-3P99.9869.371203
HSA-MIR-569699.9872.364487
HSA-MIR-4715-3P99.9866.03670
HSA-MIR-50799.9770.111915
HSA-MIR-3065-5P99.9771.563281
HSA-MIR-365899.9673.874379
HSA-MIR-551B-5P99.9671.283493
HSA-MIR-55799.9670.011640
HSA-MIR-493-5P99.9672.472382
HSA-MIR-570-3P99.9672.414910
HSA-LET-7D-5P99.9671.761632
HSA-MIR-445899.9671.641650
HSA-MIR-548AB99.9571.313488
HSA-MIR-55999.9572.283609
HSA-MIR-548A-5P99.9471.273482
HSA-MIR-548AD-5P99.9471.233502
HSA-MIR-548AE-5P99.9471.233502
HSA-MIR-548AK99.9471.243488
HSA-MIR-548AM-5P99.9471.243488
HSA-MIR-548AP-5P99.9471.143489

Literature-anchored findings (GeneRIF, showing 2)

  • A common variant in CCDC93 protects against myocardial infarction and cardiovascular mortality by regulating endosomal trafficking of low-density lipoprotein receptor. (PMID:31630160)
  • Genetic variation in CCDC93 is associated with elevated central systolic blood pressure, impaired arterial relaxation, and mitochondrial dysfunction. (PMID:39250516)

Cross-species orthologs

7 orthologs

OrganismSymbolGene ID
danio_rerioccdc93ENSDARG00000040678
mus_musculusCcdc93ENSMUSG00000026339
rattus_norvegicusCcdc93ENSRNOG00000002514
drosophila_melanogasterfidipidineFBGN0025519
caenorhabditis_elegansWBGENE00007846
caenorhabditis_elegansWBGENE00007847
caenorhabditis_elegansWBGENE00015815

Protein

Protein identifiers

Coiled-coil domain-containing protein 93Q567U6 (reviewed: Q567U6)

All UniProt accessions (3): Q567U6, F8W9X7, H7C050

UniProt curated annotations — full annotation on UniProt →

Function. Component of the commander complex that is essential for endosomal recycling of transmembrane cargos; the commander complex is composed of composed of the CCC subcomplex and the retriever subcomplex. Component of the CCC complex, which is involved in the regulation of endosomal recycling of surface proteins, including integrins, signaling receptor and channels. The CCC complex associates with SNX17, retriever and WASH complexes to prevent lysosomal degradation and promote cell surface recycling of numerous cargos such as integrins ITGA5:ITGB1. Involved in copper-dependent ATP7A trafficking between the trans-Golgi network and vesicles in the cell periphery; the function is proposed to depend on its association within the CCC complex and cooperation with the WASH complex on early endosomes and is dependent on its interaction with WASHC2C. (Microbial infection) The CCC complex, in collaboration with the heterotrimeric retriever complex, mediates the exit of human papillomavirus to the cell surface.

Subunit / interactions. Component of the commander complex consisting of the CCC subcomplex and the retriever subcomplex. Component of the CCC (COMMD/CCDC22/CCDC93) subcomplex consisting of COMMD1, COMMD2, COMMD3, COMMD4, COMMD5, COMMD6, COMMD7, COMMD8, COMMD9, COMMD10, CCDC22 and CCDC93. Forms a coiled-coil heterodimer with CCDC22; this heterodimer interacts with the guanine nucleotide exchange factor DENND10; the interaction is direct. Interacts with WASHC1. Interacts directly with WASHC2C. Interacts with SNX17 and SNX31.

Subcellular location. Early endosome.

Similarity. Belongs to the CCDC93 family.

RefSeq proteins (1): NP_061917* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR019159CCDC93_CCDomain
IPR039116CCDC93Family
IPR048747CCDC93_NDomain

Pfam: PF09762, PF21673

UniProt features (36 total): helix 11, region of interest 5, sequence variant 5, modified residue 3, strand 3, mutagenesis site 2, sequence conflict 2, compositionally biased region 2, chain 1, turn 1, coiled-coil region 1

Structure

Experimental structures (PDB)

4 structures.

PDBMethodResolution (Å)
8P0WELECTRON MICROSCOPY2.9
8F2UELECTRON MICROSCOPY3.53
8P0VELECTRON MICROSCOPY6.5
8P0XELECTRON MICROSCOPY7.5

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q567U6-F178.490.32

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (3): 301, 305, 298

Mutagenesis-validated functional residues (2):

PositionPhenotype
406impairs interaction with dennd10.
410impairs interaction with dennd10.

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 154 (showing top): GOBP_RESPONSE_TO_NITROGEN_COMPOUND, GOBP_EMBRYO_DEVELOPMENT_ENDING_IN_BIRTH_OR_EGG_HATCHING, ACTACCT_MIR196A_MIR196B, GOBP_REGULATION_OF_BLOOD_PRESSURE, GOBP_CIRCULATORY_SYSTEM_PROCESS, GOBP_ARTERY_DEVELOPMENT, GOBP_VESICLE_MEDIATED_TRANSPORT, GOBP_MONOCARBOXYLIC_ACID_METABOLIC_PROCESS, GGGTGGRR_PAX4_03, MONNIER_POSTRADIATION_TUMOR_ESCAPE_UP, PATIL_LIVER_CANCER, GOBP_AORTA_DEVELOPMENT, GOBP_GOLGI_TO_PLASMA_MEMBRANE_TRANSPORT, ONKEN_UVEAL_MELANOMA_UP, GOBP_IN_UTERO_EMBRYONIC_DEVELOPMENT

GO Biological Process (3): Golgi to plasma membrane transport (GO:0006893), protein transport (GO:0015031), endocytic recycling (GO:0032456)

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (2): early endosome (GO:0005769), endosome (GO:0005768)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
vesicle-mediated transport to the plasma membrane2
post-Golgi vesicle-mediated transport1
transport1
intracellular protein localization1
establishment of protein localization1
endosomal transport1
binding1
endosome1
endomembrane system1
cytoplasmic vesicle1

Protein interactions and networks

STRING

734 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
CCDC93CCDC22O60826998
CCDC93VPS35LQ7Z3J2981
CCDC93COMMD1Q8N668918
CCDC93VPS26CO14972913
CCDC93COMMD9Q9P000834
CCDC93SNX17Q15036757
CCDC93WASHC2AQ641Q2752
CCDC93WASHC2CQ9Y4E1723
CCDC93COMMD6Q7Z4G1708
CCDC93COMMD10Q9Y6G5668
CCDC93WASHC1A8K0Z3658
CCDC93VPS29Q9UBQ0636
CCDC93WASHC3Q9Y3C0621
CCDC93WASHC5Q12768611
CCDC93COMMD5Q9GZQ3566

IntAct

177 interactions, top by confidence:

ABTypeScore
COMMD1CCDC22psi-mi:“MI:0914”(association)0.970
CCDC22CCDC93psi-mi:“MI:0914”(association)0.960
CCDC93CCDC22psi-mi:“MI:0914”(association)0.960
CCDC93CCDC22psi-mi:“MI:0915”(physical association)0.960
CCDC93CCDC22psi-mi:“MI:0407”(direct interaction)0.960
CCDC22CCDC93psi-mi:“MI:0403”(colocalization)0.960
CCDC22CCDC93psi-mi:“MI:0915”(physical association)0.960
COMMD2CCDC22psi-mi:“MI:0914”(association)0.930
COMMD5CCDC22psi-mi:“MI:0914”(association)0.930
VPS35LCCDC22psi-mi:“MI:0914”(association)0.900
COMMD1CCDC93psi-mi:“MI:0403”(colocalization)0.900
COMMD1CCDC93psi-mi:“MI:0915”(physical association)0.900

BioGRID (179): CCDC93 (Two-hybrid), KRT40 (Two-hybrid), NOTCH2NL (Two-hybrid), CCDC93 (Affinity Capture-Western), CCDC22 (Affinity Capture-Western), C16orf62 (Affinity Capture-Western), CCDC93 (Affinity Capture-Western), COMMD1 (Affinity Capture-Western), COMMD6 (Affinity Capture-Western), CCDC93 (Affinity Capture-Western), CCDC93 (Affinity Capture-MS), CCDC93 (Affinity Capture-MS), CCDC93 (Affinity Capture-MS), CCDC93 (Affinity Capture-MS), CCDC22 (Co-fractionation)

ESM2 similar proteins: A7RNG8, B0WTU5, F1RKB1, O14777, O35594, O60826, P58501, P83829, P86182, Q16VW9, Q17QH9, Q28G12, Q3T0L1, Q3TDD9, Q4QQS3, Q4R630, Q4R6I5, Q4R8Y5, Q4V909, Q502W7, Q567U6, Q5BJT7, Q5XIR8, Q5ZKI4, Q640U7, Q68CZ6, Q6DCY9, Q6GQI5, Q6IR70, Q6PA15, Q6ZMI0, Q753N1, Q76I89, Q7PZ96, Q7TQK5, Q8CDN8, Q8I145, Q8I1C8, Q8I1H7, Q8LDS5

Diamond homologs: Q54CV3, Q567U6, Q5BJT7, Q5ZKI4, Q640U7, Q6GQI5, Q7TQK5

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 97 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

PathwayPartnersFoldFDR
Regulation of PTEN gene transcription513.7×5e-03
Neddylation118.0×3e-05

GO biological processes:

GO termPartnersFoldFDR
Golgi to plasma membrane transport533.0×8e-05
endocytic recycling1031.5×3e-10
retrograde transport, endosome to Golgi614.5×4e-04
protein transport126.2×8e-05

Disease & clinical

Clinical variants and AI predictions

ClinVar

114 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance90
Likely benign1
Benign1

Top pathogenic / likely-pathogenic (0)

SpliceAI

4340 predictions. Top by Δscore:

VariantEffectΔscore
2:117935513:AATT:Adonor_gain1.0000
2:117936700:A:ACdonor_gain1.0000
2:117936701:C:CCdonor_gain1.0000
2:117936735:CTAAT:Cacceptor_gain1.0000
2:117939112:C:CCacceptor_gain1.0000
2:117941187:A:ACdonor_gain1.0000
2:117941188:C:CCdonor_gain1.0000
2:117941188:CT:Cdonor_gain1.0000
2:117944085:TCCTA:Tacceptor_loss1.0000
2:117944087:C:CAacceptor_loss1.0000
2:117944087:C:CCacceptor_gain1.0000
2:117944088:T:Aacceptor_loss1.0000
2:117945527:A:ACdonor_gain1.0000
2:117945528:C:CCdonor_gain1.0000
2:117945528:CGT:Cdonor_gain1.0000
2:117946902:T:Cacceptor_gain1.0000
2:117946904:T:Cacceptor_gain1.0000
2:117946904:T:TCacceptor_gain1.0000
2:117948098:CACT:Cdonor_loss1.0000
2:117948099:ACTT:Adonor_loss1.0000
2:117948100:CT:Cdonor_loss1.0000
2:117948101:TT:Tdonor_loss1.0000
2:117948102:T:TGdonor_loss1.0000
2:117948103:A:ACdonor_gain1.0000
2:117948103:AC:Adonor_loss1.0000
2:117948104:C:CTdonor_gain1.0000
2:117948104:CT:Cdonor_gain1.0000
2:117948104:CTCGA:Cdonor_gain1.0000
2:117948182:GGATA:Gacceptor_gain1.0000
2:117948183:GATA:Gacceptor_gain1.0000

AlphaMissense

4162 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
2:117996358:A:GL123P1.000
2:117996362:A:GW122R1.000
2:117996362:A:TW122R1.000
2:118006798:A:GW59R1.000
2:118006798:A:TW59R1.000
2:118006806:C:TG56E1.000
2:118006807:C:GG56R1.000
2:118006807:C:TG56R1.000
2:118006809:C:TG55E1.000
2:118008588:C:TG38E1.000
2:118008589:C:AG38W1.000
2:117941230:A:GL494P0.999
2:117996347:C:GA127P0.999
2:117996360:C:AW122C0.999
2:117996360:C:GW122C0.999
2:118000828:A:TV119D0.999
2:118000837:A:TI116K0.999
2:118000855:C:TG110E0.999
2:118000856:C:AG110W0.999
2:118000856:C:GG110R0.999
2:118000856:C:TG110R0.999
2:118000861:A:CI108S0.999
2:118000861:A:TI108N0.999
2:118000864:T:GQ107P0.999
2:118000868:G:CH106D0.999
2:118000889:A:GC99R0.999
2:118000927:A:GL86P0.999
2:118006722:A:TI84K0.999
2:118006731:C:TG81D0.999
2:118006751:A:CF74L0.999

dbSNP variants (sampled 300 via entrez): RS1000022072 (2:118012946 T>A), RS1000031782 (2:117978321 T>C), RS1000042314 (2:117992155 C>T), RS1000072122 (2:117927642 T>A,C), RS1000101817 (2:117970579 G>A), RS1000118731 (2:118013090 A>G), RS1000199773 (2:117995732 G>A), RS1000214571 (2:117920921 T>C), RS1000220382 (2:117959527 A>G), RS1000245487 (2:117945687 C>T), RS1000257723 (2:117988903 G>C), RS1000275221 (2:117952536 A>G), RS1000297596 (2:117976123 A>G), RS1000319968 (2:117915352 C>T), RS1000342311 (2:117965539 T>G)

Disease associations

OMIM: gene MIM:620553 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

12 associations (top):

StudyTraitp-value
GCST001168_2Recombination measurement3.000000e-08
GCST006613_17Triglycerides1.000000e-08
GCST008077_17LDL cholesterol levels1.000000e-09
GCST008077_66LDL cholesterol levels2.000000e-09
GCST008078_113LDL cholesterol levels x alcohol consumption (regular vs non-regular drinkers) interaction (2df)2.000000e-12
GCST008078_20LDL cholesterol levels x alcohol consumption (regular vs non-regular drinkers) interaction (2df)4.000000e-12
GCST008079_149LDL cholesterol levels x alcohol consumption (drinkers vs non-drinkers) interaction (2df)5.000000e-16
GCST008079_16LDL cholesterol levels x alcohol consumption (drinkers vs non-drinkers) interaction (2df)6.000000e-15
GCST008086_43LDL cholesterol levels in current drinkers1.000000e-09
GCST008086_62LDL cholesterol levels in current drinkers5.000000e-10
GCST009936_22Venous thromboembolism4.000000e-06
GCST011347_17Low density lipoprotein cholesterol levels1.000000e-09

EFO canonical traits (4, from GWAS)

EFO IDTrait name
EFO:0005919recombination measurement
EFO:0004530triglyceride measurement
EFO:0004611low density lipoprotein cholesterol measurement
EFO:0004329alcohol drinking

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

39 total (human), top 30 by PubMed support.

ChemicalActions (top 5)PubMed papers
bisphenol Adecreases expression2
sodium arsenitedecreases expression, increases expression2
Particulate Matterdecreases expression, increases abundance, increases expression, affects cotreatment2
FR900359decreases phosphorylation1
2,4,6-tribromophenolincreases expression1
methylmercuric chlorideincreases expression1
triphenyl phosphateaffects expression1
arsenitedecreases reaction, affects binding1
isobutyl alcoholdecreases expression, increases abundance, affects cotreatment1
tamibarotenedecreases expression1
di-n-butylphosphoric acidaffects expression1
perfluorooctane sulfonic acidincreases expression1
CGP 52608affects binding, increases reaction1
pentabrominated diphenyl ether 100decreases expression1
PCI 5002affects cotreatment, increases expression1
Resveratrolaffects cotreatment, increases expression1
Sunitinibincreases expression1
Acetaminophenincreases expression1
Air Pollutantsincreases abundance, increases expression1
Calcitriolincreases expression1
Doxorubicindecreases expression1
Ethyl Methanesulfonateincreases expression1
Gasolineaffects cotreatment, decreases expression, increases abundance1
Hydrogen Peroxideaffects cotreatment, decreases expression1
Methyl Methanesulfonateincreases expression1
Plant Extractsaffects cotreatment, increases expression1
Polycyclic Aromatic Hydrocarbonsaffects cotreatment, decreases expression, increases abundance1
Rotenonedecreases expression1
Silicon Dioxideincreases expression1
Theophyllineaffects cotreatment, decreases expression1

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.

No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.