CCDC120

gene
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Also known as JM11

Summary

CCDC120 (coiled-coil domain containing 120, HGNC:28910) is a protein-coding gene on chromosome Xp11.23, encoding Coiled-coil domain-containing protein 120 (Q96HB5). Centriolar protein required for centriole subdistal appendage assembly and microtubule anchoring in interphase cells.

This gene encodes a protein that contains a coiled-coil domain. Several alternatively spliced transcript variants encoding multiple isoforms have been found for this gene.

Source: NCBI Gene 90060 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): osteopetrosis (Limited, GenCC)
  • Clinical variants (ClinVar): 145 total — 2 pathogenic
  • MANE Select transcript: NM_001163321

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:28910
Approved symbolCCDC120
Namecoiled-coil domain containing 120
LocationXp11.23
Locus typegene with protein product
StatusApproved
AliasesJM11
Ensembl geneENSG00000147144
Ensembl biotypeprotein_coding
OMIM300947
Entrez90060

Gene structure

Transcript identifiers

Ensembl transcripts: 8 — 6 protein_coding, 2 retained_intron

ENST00000482476, ENST00000496529, ENST00000536628, ENST00000597275, ENST00000603906, ENST00000603986, ENST00000606812, ENST00000620388

RefSeq mRNA: 6 — MANE Select: NM_001163321 NM_001163321, NM_001163322, NM_001163323, NM_001271835, NM_001271836, NM_033626

CCDS: CCDS14316, CCDS55413, CCDS55414

Canonical transcript exons

ENST00000603986 — 11 exons

ExonStartEnd
ENSE000035147334906717649068090
ENSE000036050704905899949059095
ENSE000036155464906854449069854
ENSE000036210044906195949062104
ENSE000036587284906223549062325
ENSE000037146614906437049064664
ENSE000037218474906574749065845
ENSE000037404784906246849062601
ENSE000037476594906545449065628
ENSE000037510644906386149064001
ENSE000037548754906503649065098

Expression profiles

Bgee: expression breadth ubiquitous, 162 present calls, max score 94.61.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 7.2465 / max 67.8850, expressed in 1358 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter IDTPM avgSamples expressed
1963133.2966532
1963123.15571049
1963110.7942532

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
lower esophagus mucosaUBERON:003583494.61gold quality
esophagus mucosaUBERON:000246989.93gold quality
skin of legUBERON:000151189.64gold quality
skin of abdomenUBERON:000141688.62gold quality
olfactory segment of nasal mucosaUBERON:000538685.22gold quality
buccal mucosa cellCL:000233685.07gold quality
zone of skinUBERON:000001484.80gold quality
right hemisphere of cerebellumUBERON:001489084.70gold quality
cerebellar hemisphereUBERON:000224584.41gold quality
cerebellar cortexUBERON:000212984.30gold quality
metanephros cortexUBERON:001053383.64gold quality
minor salivary glandUBERON:000183083.53gold quality
cerebellumUBERON:000203782.67gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099182.52gold quality
adenohypophysisUBERON:000219682.52gold quality
esophagusUBERON:000104382.34gold quality
vaginaUBERON:000099681.86gold quality
cortical plateUBERON:000534381.64gold quality
ectocervixUBERON:001224981.04gold quality
pituitary glandUBERON:000000780.99gold quality
body of pancreasUBERON:000115080.68gold quality
body of stomachUBERON:000116180.61gold quality
mouth mucosaUBERON:000372979.31gold quality
right lobe of thyroid glandUBERON:000111979.01gold quality
mucosa of transverse colonUBERON:000499178.95gold quality
small intestine Peyer’s patchUBERON:000345478.72gold quality
left lobe of thyroid glandUBERON:000112078.62gold quality
saliva-secreting glandUBERON:000104478.31gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047378.09gold quality
left ovaryUBERON:000211978.02gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes3.67

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

46 targeting CCDC120, 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-30A-5P100.0076.313233
HSA-MIR-30B-5P100.0076.293248
HSA-MIR-30C-5P100.0076.293248
HSA-MIR-30D-5P100.0076.323233
HSA-MIR-30E-5P100.0076.323242
HSA-MIR-10401-5P99.9965.79948
HSA-MIR-453199.9969.703181
HSA-MIR-318599.9968.121959
HSA-MIR-6759-5P99.9966.54785
HSA-MIR-1213699.9872.815713
HSA-MIR-6793-5P99.9765.95758
HSA-MIR-430299.8967.941187
HSA-MIR-383-3P99.8565.841359
HSA-MIR-204-5P99.7971.622439
HSA-MIR-211-5P99.7971.652440
HSA-MIR-3934-3P99.7665.511351
HSA-MIR-4755-5P99.7170.342716
HSA-MIR-5006-3P99.7170.262728
HSA-MIR-46699.6770.852863
HSA-MIR-7-5P99.6770.531809
HSA-MIR-6887-3P99.6667.831778
HSA-MIR-182799.6368.573265
HSA-MIR-451699.6167.783390
HSA-MIR-6832-3P99.5270.441726
HSA-MIR-199A-5P99.5169.711107
HSA-MIR-199B-5P99.5169.741098
HSA-MIR-766-5P99.4767.912225
HSA-MIR-570399.1067.092053
HSA-MIR-143-5P98.9868.87946
HSA-MIR-3127-3P98.9467.341055

Literature-anchored findings (GeneRIF, showing 2)

  • Arf6 guanine nucleotide exchange factor cytohesin-2 binds to CCDC120 and is transported along neurites to mediate neurite growth. (PMID:25326380)
  • centrosome-binding proteins, coiled-coil domain containing (CCDC) 120 and CCDC68 are two novel subdistal appendages (SDA) components required for hierarchical SDA assembly in human cells. (PMID:28422092)

Cross-species orthologs

4 orthologs

OrganismSymbolGene ID
danio_rerioccdc120aENSDARG00000012449
danio_rerioccdc120bENSDARG00000032856
mus_musculusCcdc120ENSMUSG00000031150
rattus_norvegicusCcdc120ENSRNOG00000009687

Paralogs (1): INAVA (ENSG00000163362)

Protein

Protein identifiers

Coiled-coil domain-containing protein 120Q96HB5 (reviewed: Q96HB5)

All UniProt accessions (2): Q96HB5, S4R3T7

UniProt curated annotations — full annotation on UniProt →

Function. Centriolar protein required for centriole subdistal appendage assembly and microtubule anchoring in interphase cells. Together with CCDC68, cooperate with subdistal appendage components ODF2, NIN and CEP170 for hierarchical subdistal appendage assembly. Recruits NIN and CEP170 to centrosomes. Also required for neurite growth. Localizes CYTH2 to vesicles to allow its transport along neurites, and subsequent ARF6 activation and neurite growth.

Subunit / interactions. Interacts with NIN and CEP170; leading to recruit them to centrosomes. Directly interacts with CYTH2; this interaction stabilizes CCDC120, possibly by preventing ubiquitination.

Subcellular location. Cytoplasm. Cytoskeleton. Microtubule organizing center. Centrosome. Centriole. Cell projection. Neuron projection. Growth cone. Endosome.

Post-translational modifications. Ubiquitinated; interaction with CYTH2 may prevent ubiquitination.

Isoforms (5)

UniProt IDNamesCanonical?
Q96HB5-11yes
Q96HB5-22
Q96HB5-33
Q96HB5-44
Q96HB5-55

RefSeq proteins (6): NP_001156793, NP_001156794, NP_001156795, NP_001258764, NP_001258765, NP_296375 (=MANE)

Domains & families (InterPro)

IDNameType
IPR021774CUPIDDomain
IPR043447CCDC120/INAVAFamily

Pfam: PF11819

UniProt features (15 total): compositionally biased region 4, region of interest 3, modified residue 3, splice variant 3, chain 1, coiled-coil region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q96HB5-F156.340.15

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): 360, 435, 358

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 107 (showing top): RNGTGGGC_UNKNOWN, GOBP_MICROTUBULE_ANCHORING, AREB6_01, GOCC_MICROTUBULE_ORGANIZING_CENTER, AP1_Q4_01, SHETH_LIVER_CANCER_VS_TXNIP_LOSS_PAM3, BACH2_01, AAAGGGA_MIR204_MIR211, ARGGGTTAA_UNKNOWN, TGANTCA_AP1_C, TGTTTAC_MIR30A5P_MIR30C_MIR30D_MIR30B_MIR30E5P, GOCC_NEURON_PROJECTION, GOCC_CENTRIOLE, GOCC_CILIUM, GOCC_AXON

GO Biological Process (2): intracellular protein localization (GO:0008104), microtubule anchoring at centrosome (GO:0034454)

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

GO Cellular Component (8): endosome (GO:0005768), centriole (GO:0005814), growth cone (GO:0030426), centriolar subdistal appendage (GO:0120103), cytoplasm (GO:0005737), cytoskeleton (GO:0005856), cell projection (GO:0042995), neuron projection (GO:0043005)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
intracellular membraneless organelle2
cellular anatomical structure2
macromolecule localization1
microtubule anchoring at microtubule organizing center1
binding1
endomembrane system1
cytoplasmic vesicle1
microtubule organizing center1
site of polarized growth1
distal axon1
cilium1
intracellular protein-containing complex1
intracellular anatomical structure1
plasma membrane bounded cell projection1

Protein interactions and networks

STRING

574 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
CCDC120CCDC68Q9H2F9919
CCDC120CEP128Q6ZU80898
CCDC120CEP170Q5SW79806
CCDC120NINQ8N4C6785
CCDC120CNTRLQ7Z7A1739
CCDC120CYTH2Q99418643
CCDC120SCLT1Q96NL6636
CCDC120CEP89Q96ST8634
CCDC120CEP83Q9Y592615
CCDC120FBF1Q8TES7583
CCDC120CEP164Q9UPV0562
CCDC120CYTH4Q9UIA0556
CCDC120CMTM5Q96DZ9555
CCDC120C2CD3Q4AC94547
CCDC120CC2D2AQ9P2K1536

IntAct

401 interactions, top by confidence:

ABTypeScore
CCDC120CEP170psi-mi:“MI:0403”(colocalization)0.820
CCDC120CEP170psi-mi:“MI:0914”(association)0.820
CEP170CCDC120psi-mi:“MI:0915”(physical association)0.820
CCDC120CEP170psi-mi:“MI:0915”(physical association)0.820
CCDC120CEP170psi-mi:“MI:0407”(direct interaction)0.820
CEP170CCDC120psi-mi:“MI:0914”(association)0.820
CEP170CCDC120psi-mi:“MI:0403”(colocalization)0.820
CCDC120NINpsi-mi:“MI:0403”(colocalization)0.680
NINCCDC120psi-mi:“MI:0915”(physical association)0.680
NINCCDC120psi-mi:“MI:0407”(direct interaction)0.680
CCDC120NINpsi-mi:“MI:0915”(physical association)0.680
NINCCDC120psi-mi:“MI:0403”(colocalization)0.680
CCDC120AIPpsi-mi:“MI:0914”(association)0.640
CCDC120ODF2psi-mi:“MI:0403”(colocalization)0.600
CCDC120ODF2psi-mi:“MI:0915”(physical association)0.600
CCDC120PAC1psi-mi:“MI:0915”(physical association)0.560
PAC1CCDC120psi-mi:“MI:0915”(physical association)0.560
ZNF417CCDC120psi-mi:“MI:0915”(physical association)0.560
GAS2L2CCDC120psi-mi:“MI:0915”(physical association)0.560

BioGRID (243): CCDC120 (Two-hybrid), CCDC120 (Two-hybrid), CCDC120 (Two-hybrid), CCDC120 (Two-hybrid), CCDC120 (Two-hybrid), CCDC120 (Two-hybrid), CCDC120 (Two-hybrid), CCDC120 (Two-hybrid), CCDC120 (Two-hybrid), KRT40 (Two-hybrid), CCDC57 (Two-hybrid), CEP170P1 (Two-hybrid), BRCA1 (Two-hybrid), CCDC120 (Two-hybrid), CCDC120 (Two-hybrid)

ESM2 similar proteins: A0A0U1RQ45, A0A0U1RQS6, A0A2R8YCJ5, A2A699, A2AEV7, A6NGB7, A6NJG2, A6NKF7, A6NKL6, A6NL88, A8MVW0, A9JSM3, B2RU40, B8ZZ34, C9JH25, D4A9R4, J3QNX5, P0CG09, P98077, Q0VD38, Q14761, Q17QH7, Q29RK8, Q2KJ18, Q2M3V2, Q3SX20, Q5BJT1, Q5HZJ5, Q5RKR3, Q5T442, Q64697, Q69YZ2, Q6PB97, Q6PCT2, Q6UXK2, Q6ZMQ8, Q6ZVH7, Q6ZW31, Q80XF7, Q8BLS7

Diamond homologs: A2AEV7, Q3KP66, Q7TN12, Q920B0, Q96HB5, Q9Y2L6, Q8BIE6, Q9P2Q2, P26038, P26042, Q2HJ49, P26040, P31977, Q8HZQ5

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 106 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
Intra-Golgi traffic523.2×2e-04
Keratinization109.9×8e-06

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic2
Likely pathogenic0
Uncertain significance100
Likely benign6
Benign0

Top pathogenic / likely-pathogenic (2)

Variant IDHGVSClassification
1341233GRCh37/hg19 Xp22.33-q28(chrX:168546-155233731)x1Pathogenic
190973hg18chrX:g.(48,802,381_48,809,279)_(48,829,265_48,854,335)delPathogenic

SpliceAI

1545 predictions. Top by Δscore:

VariantEffectΔscore
X:49062232:CA:Cacceptor_loss1.0000
X:49062233:A:AGacceptor_gain1.0000
X:49062234:G:Cacceptor_loss1.0000
X:49062234:G:GGacceptor_gain1.0000
X:49062234:GA:Gacceptor_gain1.0000
X:49062234:GACT:Gacceptor_gain1.0000
X:49062234:GACTT:Gacceptor_gain1.0000
X:49062464:CCAGC:Cacceptor_loss1.0000
X:49062465:CAGCT:Cacceptor_loss1.0000
X:49062466:A:AGacceptor_gain1.0000
X:49062466:AGCT:Aacceptor_gain1.0000
X:49062467:G:GGacceptor_gain1.0000
X:49062467:G:GTacceptor_loss1.0000
X:49062467:GCT:Gacceptor_gain1.0000
X:49062467:GCTG:Gacceptor_gain1.0000
X:49062548:G:GTdonor_gain1.0000
X:49062584:G:GGdonor_gain1.0000
X:49062596:G:GTdonor_gain1.0000
X:49062598:GGCG:Gdonor_gain1.0000
X:49062599:GCGG:Gdonor_gain1.0000
X:49065448:A:AGacceptor_gain1.0000
X:49065449:C:Gacceptor_gain1.0000
X:49065451:CA:Cacceptor_loss1.0000
X:49065452:A:AGacceptor_gain1.0000
X:49065452:A:Tacceptor_loss1.0000
X:49065452:AGAG:Aacceptor_gain1.0000
X:49065453:G:GGacceptor_gain1.0000
X:49065453:GA:Gacceptor_gain1.0000
X:49065453:GAGG:Gacceptor_gain1.0000
X:49065453:GAGGA:Gacceptor_gain1.0000

AlphaMissense

4388 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
X:49062576:T:CL53P0.999
X:49067903:T:AW562R0.998
X:49067903:T:CW562R0.998
X:49067905:G:CW562C0.998
X:49067905:G:TW562C0.998
X:49062599:G:CA61P0.997
X:49065793:A:CS302R0.997
X:49065795:T:AS302R0.997
X:49065795:T:GS302R0.997
X:49067297:A:CS360R0.997
X:49067299:T:AS360R0.997
X:49067299:T:GS360R0.997
X:49067906:T:GY563D0.997
X:49062555:T:CL46P0.996
X:49064502:G:CA153P0.996
X:49067291:A:CS358R0.996
X:49067293:C:AS358R0.996
X:49067293:C:GS358R0.996
X:49067895:T:CL559P0.996
X:49067898:G:CR560P0.996
X:49064431:C:AA129D0.995
X:49062567:T:CL50P0.994
X:49062576:T:AL53H0.994
X:49062587:T:CC57R0.994
X:49064419:T:GI125S0.994
X:49064430:G:CA129P0.994
X:49065627:A:CS286R0.994
X:49065747:C:AS286R0.994
X:49065747:C:GS286R0.994
X:49065787:G:AG300R0.994

dbSNP variants (sampled 300 via entrez): RS1000263512 (X:49052602 C>T), RS1000692841 (X:49069813 C>A), RS1001182264 (X:49063730 G>A), RS1001269192 (X:49054347 C>T), RS1001342996 (X:49054898 C>T), RS1002350111 (X:49057393 C>G), RS1003281689 (X:49059014 C>T), RS1003851663 (X:49052379 G>A), RS1004363207 (X:49061173 C>T), RS1004591159 (X:49068918 C>G,T), RS1004804471 (X:49068506 C>G,T), RS1004811815 (X:49054270 C>G,T), RS1005362030 (X:49063034 A>G), RS1005405982 (X:49053869 G>A,T), RS1005816436 (X:49056819 G>A)

Disease associations

OMIM: gene MIM:300947 | disease phenotypes: MIM:300896

GenCC curated gene-disease

DiseaseClassificationInheritance
osteopetrosisLimitedX-linked

Mondo (2): SLC35A2-congenital disorder of glycosylation (MONDO:0010478), osteopetrosis (MONDO:0017198)

Orphanet (1): SLC35A2-CDG (Orphanet:356961)

HPO phenotypes

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

GWAS associations

0 associations (top):

MeSH disease descriptors (1)

DescriptorNameTree numbers
D010022OsteopetrosisC05.116.099.708.702.678

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

23 total (human), top 23 by PubMed support.

ChemicalActions (top 5)PubMed papers
sodium arseniteaffects cotreatment, decreases expression, increases abundance, increases expression2
GSK-J4decreases expression1
FR900359affects phosphorylation1
bisphenol Faffects cotreatment, increases expression1
dicrotophosincreases expression1
ethyl-p-hydroxybenzoateincreases expression1
butyraldehydedecreases expression1
potassium nitratedecreases expression1
coumarinincreases phosphorylation1
CGP 52608affects binding, increases reaction1
Resveratrolaffects cotreatment, decreases expression1
Leflunomidedecreases expression1
Acetaminophendecreases expression1
Arsenicaffects cotreatment, decreases expression, increases abundance, increases expression1
Benzo(a)pyrenedecreases methylation1
Caffeineincreases phosphorylation1
Dexamethasoneaffects cotreatment, increases expression1
Indomethacinaffects cotreatment, increases expression1
Plant Extractsaffects cotreatment, decreases expression1
Thiramdecreases expression1
Urethaneincreases expression1
1-Methyl-3-isobutylxanthineaffects cotreatment, increases expression1
2,4-Dichlorophenoxyacetic Aciddecreases expression1

Clinical trials (associated diseases)

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

TrialPhaseStatusTitle
NCT00004402PHASE3COMPLETEDPhase III Randomized Study of Interferon Gamma in Children With Severe, Congenital Osteopetrosis
NCT00638820PHASE2TERMINATEDReduced Intensity AlloTransplant For Osteopetrosis
NCT00968864PHASE2TERMINATEDT-cell Depleted Alternative Donor Transplantation
NCT02171104PHASE2ACTIVE_NOT_RECRUITINGMT2013-31: Allo HCT for Metabolic Disorders and Severe Osteopetrosis
NCT02666768PHASE2COMPLETEDACTIMMUNE in Intermediate Osteopetrosis
NCT00145886PHASE1TERMINATEDrhPTH Therapy for Low Turnover Bone Fragility
NCT00775931PHASE2/PHASE3COMPLETEDAllogeneic Transplantation For Severe Osteopetrosis
NCT01019876PHASE2/PHASE3COMPLETEDRisk-Adapted Allogeneic Stem Cell Transplantation For Mixed Donor Chimerism In Patients With Non-Malignant Diseases
NCT01087398PHASE2/PHASE3UNKNOWNHematopoietic Stem Cell Transplantation for Malignant Infantile Osteopetrosis
NCT00730314PHASE1/PHASE2COMPLETEDUnrelated Hematopoietic Stem Cell Transplantation(HSCT) for Genetic Diseases of Blood Cells
NCT02065869PHASE1/PHASE2TERMINATEDSafety Study of Gene Modified Donor T-cells Following TCRαβ+ Depleted Stem Cell Transplant
NCT03301168PHASE1/PHASE2ACTIVE_NOT_RECRUITINGStudy of Gene Modified Donor T-cells Following TCR Alpha Beta Positive Depleted Stem Cell Transplant
NCT00043329Not specifiedCOMPLETEDPost Marketing Surveillance Study of Actimmune in Patients With Severe, Malignant Osteopetrosis
NCT00145587Not specifiedTERMINATEDStem Cell Transplantation for Children Affected With Osteopetrosis
NCT01199094Not specifiedCOMPLETEDClinical Assessment of Patients With High Bone Mass Due to Mutation in Lrp5
NCT01200017Not specifiedNO_LONGER_AVAILABLEExpanded Access Protocol (EAP) Using the CliniMACS® Device for Pediatric Haplocompatible Donor Stem Cell Transplant
NCT03333200Not specifiedRECRUITINGLongitudinal Study of Neurodegenerative Disorders
NCT06521580Not specifiedCOMPLETEDOutcomes of Patients With Osteopetrosis Weight-bearing Bone Fractures