CCDC69

Summary

CCDC69 (coiled-coil domain containing 69, HGNC:24487) is a protein-coding gene on chromosome 5q33.1, encoding Coiled-coil domain-containing protein 69 (A6NI79). May act as a scaffold to regulate the recruitment and assembly of spindle midzone components.

Predicted to enable microtubule binding activity. Involved in spindle midzone assembly. Located in spindle midzone.

Source: NCBI Gene 26112 — RefSeq curated summary.

At a glance

• GWAS associations: 13
• Clinical variants (ClinVar): 62 total
• MANE Select transcript: NM_015621

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:24487
Approved symbol	CCDC69
Name	coiled-coil domain containing 69
Location	5q33.1
Locus type	gene with protein product
Status	Approved
Aliases	FLJ13705, DKFZP434C171
Ensembl gene	ENSG00000198624
Ensembl biotype	protein_coding
OMIM	619288
Entrez	26112

Gene structure

Transcript identifiers

Ensembl transcripts: 13 — 6 protein_coding, 3 protein_coding_CDS_not_defined, 2 nonsense_mediated_decay, 2 retained_intron

ENST00000355417, ENST00000518189, ENST00000519448, ENST00000519740, ENST00000521308, ENST00000522179, ENST00000522964, ENST00000524344, ENST00000900832, ENST00000900833, ENST00000900834, ENST00000900835, ENST00000964027

RefSeq mRNA: 1 — MANE Select: NM_015621 NM_015621

CCDS: CCDS4312

Canonical transcript exons

ENST00000355417 — 9 exons

Exon	Start	End
ENSE00002094133	151223923	151224092
ENSE00003506688	151198997	151199084
ENSE00003527379	151181052	151183614
ENSE00003560893	151186023	151186124
ENSE00003632058	151184344	151184441
ENSE00003639490	151201582	151201688
ENSE00003642702	151187386	151187459
ENSE00003647090	151205400	151205475
ENSE00003668013	151185422	151185541

Expression profiles

Bgee: expression breadth ubiquitous, 271 present calls, max score 98.37.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 22.2135 / max 423.9356, expressed in 1341 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
64352	21.6812	1322
64353	0.5324	272

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
mucosa of stomach	UBERON:0001199	98.37	gold quality
lower esophagus muscularis layer	UBERON:0035833	98.34	gold quality
lower esophagus	UBERON:0013473	98.31	gold quality
muscle layer of sigmoid colon	UBERON:0035805	97.68	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	97.57	gold quality
left adrenal gland cortex	UBERON:0035825	97.31	gold quality
adrenal cortex	UBERON:0001235	97.27	gold quality
left adrenal gland	UBERON:0001234	97.17	gold quality
right adrenal gland cortex	UBERON:0035827	97.12	gold quality
right adrenal gland	UBERON:0001233	97.02	gold quality
adrenal gland	UBERON:0002369	97.00	gold quality
monocyte	CL:0000576	96.76	gold quality
leukocyte	CL:0000738	96.76	gold quality
right atrium auricular region	UBERON:0006631	96.75	gold quality
mononuclear cell	CL:0000842	96.71	gold quality
granulocyte	CL:0000094	96.68	gold quality
apex of heart	UBERON:0002098	96.64	gold quality
hindlimb stylopod muscle	UBERON:0004252	96.52	gold quality
cardiac atrium	UBERON:0002081	96.37	gold quality
gastrocnemius	UBERON:0001388	96.34	gold quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	96.29	gold quality
muscle of leg	UBERON:0001383	96.01	gold quality
heart left ventricle	UBERON:0002084	95.96	gold quality
cardiac ventricle	UBERON:0002082	95.90	gold quality
blood	UBERON:0000178	95.86	gold quality
adipose tissue	UBERON:0001013	95.86	gold quality
vastus lateralis	UBERON:0001379	95.84	gold quality
biceps brachii	UBERON:0001507	95.78	gold quality
adrenal tissue	UBERON:0018303	95.59	gold quality
muscle organ	UBERON:0001630	95.54	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 2.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	15.34
E-CURD-88	yes	4.29

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

79 targeting CCDC69, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-6748-5P	100.00	65.81	1057
HSA-MIR-1184	99.99	68.19	1458
HSA-MIR-4531	99.99	69.70	3181
HSA-MIR-150-5P	99.99	66.69	1976
HSA-MIR-3667-3P	99.99	67.17	1636
HSA-MIR-4267	99.96	66.53	2368
HSA-MIR-6778-3P	99.96	67.29	2693
HSA-MIR-185-3P	99.95	67.01	1743
HSA-MIR-627-3P	99.90	71.42	3316
HSA-MIR-95-5P	99.89	72.17	3973
HSA-MIR-4731-5P	99.89	67.23	2537
HSA-MIR-6783-3P	99.89	67.92	2059
HSA-MIR-1343-3P	99.89	66.78	1815
HSA-MIR-4728-5P	99.85	69.39	4718
HSA-MIR-3663-3P	99.84	70.39	798
HSA-MIR-6785-5P	99.82	68.68	4428
HSA-MIR-4420	99.82	70.08	1624
HSA-MIR-181B-2-3P	99.81	70.06	1646
HSA-MIR-181B-3P	99.81	70.06	1646
HSA-MIR-149-3P	99.72	68.22	3963
HSA-MIR-1200	99.71	70.42	1838
HSA-MIR-6883-5P	99.69	68.05	3785
HSA-MIR-7154-5P	99.69	70.52	1900
HSA-MIR-4502	99.65	66.99	1021
HSA-MIR-1251-3P	99.64	67.21	1408
HSA-MIR-9851-3P	99.63	69.68	1110
HSA-MIR-4516	99.61	67.78	3390
HSA-MIR-7106-5P	99.53	67.47	3574
HSA-MIR-136-5P	99.50	67.26	1153
HSA-MIR-4441	99.49	66.56	3216

Literature-anchored findings (GeneRIF, showing 3)

• Results indicate that CCDC69 acts as a scaffold to regulate the recruitment of midzone components and the assembly of central spindles. (PMID:20962590)
• CCDC69 could play an important role in regulating chemoresistance in ovarian cancer through activation of p14ARF/MDM2/p53 signaling pathway (PMID:30651135)
• Study on CCDC69 interfering with the prognosis of patients with breast cancer through PPAR signal pathway. (PMID:33634680)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio		ENSDARG00000111091
mus_musculus	Ccdc69	ENSMUSG00000049588
rattus_norvegicus	Ccdc69	ENSRNOG00000021370

Paralogs (2): MTUS1 (ENSG00000129422), MTUS2 (ENSG00000132938)

Protein

Protein identifiers

Coiled-coil domain-containing protein 69 — A6NI79 (reviewed: A6NI79)

All UniProt accessions (3): A6NI79, H0YB32, H0YBY5

UniProt curated annotations — full annotation on UniProt →

Function. May act as a scaffold to regulate the recruitment and assembly of spindle midzone components. Required for the localization of AURKB and PLK1 to the spindle midzone.

Subcellular location. Cytoplasm. Cytoskeleton. Spindle. Midbody.

Tissue specificity. Highly expressed in duodenum, esophagus, pancreas, prostate, salivary gland, thymus and urinary bladder.

Similarity. Belongs to the CCDC69 family.

RefSeq proteins (1): NP_056436* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR051293	MTUS1/CCDC69	Family

UniProt features (10 total): compositionally biased region 2, modified residue 2, initiator methionine 1, chain 1, region of interest 1, coiled-coil region 1, lipid moiety-binding region 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-A6NI79-F1	85.55	0.70

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): 154, 241, 2

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 136 (showing top): RNGTGGGC_UNKNOWN, TGACCTY_ERR1_Q2, BLALOCK_ALZHEIMERS_DISEASE_UP, MARTIN_VIRAL_GPCR_SIGNALING_UP, GOBP_ORGANELLE_ASSEMBLY, SCHLOSSER_SERUM_RESPONSE_DN, BERTUCCI_MEDULLARY_VS_DUCTAL_BREAST_CANCER_UP, FLECHNER_BIOPSY_KIDNEY_TRANSPLANT_REJECTED_VS_OK_DN, GOBP_SPINDLE_ASSEMBLY, HAN_SATB1_TARGETS_DN, GOCC_SPINDLE, WANG_HCP_PROSTATE_CANCER, GOCC_SPINDLE_MIDZONE, GOCC_MIDBODY, GOBP_CELL_CYCLE_PROCESS

GO Biological Process (1): spindle midzone assembly (GO:0051255)

GO Molecular Function (1): microtubule binding (GO:0008017)

GO Cellular Component (6): nucleus (GO:0005634), midbody (GO:0030496), spindle midzone (GO:0051233), cytoplasm (GO:0005737), spindle (GO:0005819), cytoskeleton (GO:0005856)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	3
intracellular membraneless organelle	2
microtubule-based process	1
cell cycle process	1
cellular component assembly	1
spindle assembly	1
tubulin binding	1
intracellular membrane-bounded organelle	1
spindle	1
intracellular anatomical structure	1
microtubule cytoskeleton	1

Protein interactions and networks

STRING

528 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CCDC69	ARMCX2	Q7L311	491
CCDC69	LRRC17	Q8N6Y2	455
CCDC69	FAM219B	Q5XKK7	428
CCDC69	PAIP2	Q9BPZ3	403
CCDC69	SRD5A3	Q9H8P0	398
CCDC69	CCDC192	P0DO97	394
CCDC69	CCDC167	Q9P0B6	394
CCDC69	YJU2	Q9BW85	386
CCDC69	TP53I13	Q8NBR0	377
CCDC69	ELMOD3	Q96FG2	374
CCDC69	TSGA10IP	Q3SY00	370
CCDC69	CCDC178	Q5BJE1	369
CCDC69	ZNF623	O75123	358
CCDC69	TBCK	Q8TEA7	334
CCDC69	PERP	Q96FX8	333

IntAct

6 interactions, top by confidence:

A	B	Type	Score
MAP3K20	CCDC69	psi-mi:“MI:0915”(physical association)	0.370
CCDC69	PMPCB	psi-mi:“MI:0914”(association)	0.350
CCDC69	MYL1	psi-mi:“MI:0914”(association)	0.350
ACO1	CCDC69	psi-mi:“MI:0915”(physical association)	0.000
CCDC69	UBA1	psi-mi:“MI:0220”(ubiquitination reaction)	0.000

BioGRID (46): CCDC69 (Two-hybrid), CCDC69 (Biochemical Activity), CCDC69 (Biochemical Activity), RMI1 (Affinity Capture-MS), TOP3A (Affinity Capture-MS), MMADHC (Affinity Capture-MS), PSMG4 (Affinity Capture-MS), NUDT8 (Affinity Capture-MS), PSMG3 (Affinity Capture-MS), FAM192A (Affinity Capture-MS), CLTCL1 (Affinity Capture-MS), GGPS1 (Affinity Capture-MS), RMI2 (Affinity Capture-MS), PSME3 (Affinity Capture-MS), ASH2L (Affinity Capture-MS)

ESM2 similar proteins: A0JMK8, A0JNT9, A2AIV8, A6NI79, A9QT41, B2RZ86, B3DLE8, B8JK76, B9V5F5, F1R4Y7, O35550, O35551, O88522, P0CF95, Q08DR9, Q0IHN7, Q0V9T6, Q15276, Q29RS0, Q2MJU7, Q3KR99, Q3SWS9, Q502I3, Q5BIX7, Q5HZK9, Q5U4E6, Q60952, Q6DCD4, Q6DIX6, Q6GLX3, Q6NRW2, Q6P402, Q6PGZ0, Q6TMG5, Q6ZP65, Q6ZU80, Q86SQ7, Q8BI22, Q8BVL9, Q8CHW5

Diamond homologs: A0JMQ7, A6NI79, A6QNP9, A7MC22, Q08AV7, Q0IHN7, Q17QT2, Q3TCJ8, Q3UHD3, Q5HZI1, Q5JR59, Q5R9I1, Q6DCD4, Q6IMY1, Q7SZL5, Q9ULD2

SIGNOR signaling

1 interactions.

A	Effect	B	Mechanism
SMURF1	unknown	CCDC69	ubiquitination

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	47
Likely benign	7
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1718 predictions. Top by Δscore:

Variant	Effect	Δscore
5:151183615:C:CC	acceptor_gain	1.0000
5:151184438:CTTT:C	acceptor_gain	1.0000
5:151184442:C:CC	acceptor_gain	1.0000
5:151185409:C:CA	donor_gain	1.0000
5:151185410:C:A	donor_gain	1.0000
5:151185421:CCA:C	donor_gain	1.0000
5:151185429:T:TA	donor_gain	1.0000
5:151187460:C:CC	acceptor_gain	1.0000
5:151201578:TTA:T	donor_loss	1.0000
5:151201580:A:AC	donor_gain	1.0000
5:151201580:AC:A	donor_gain	1.0000
5:151201581:C:CA	donor_gain	1.0000
5:151201581:CC:C	donor_gain	1.0000
5:151201581:CCT:C	donor_gain	1.0000
5:151201581:CCTG:C	donor_gain	1.0000
5:151201581:CCTGT:C	donor_gain	1.0000
5:151201684:TATAG:T	acceptor_gain	1.0000
5:151201685:ATAG:A	acceptor_gain	1.0000
5:151201686:TAG:T	acceptor_gain	1.0000
5:151201687:AG:A	acceptor_gain	1.0000
5:151201689:C:CC	acceptor_gain	1.0000
5:151201689:CTAGA:C	acceptor_loss	1.0000
5:151201690:T:C	acceptor_loss	1.0000
5:151201695:A:C	acceptor_gain	1.0000
5:151205049:T:A	donor_gain	1.0000
5:151183531:T:TA	donor_gain	0.9900
5:151183611:CTGC:C	acceptor_gain	0.9900
5:151183612:TGC:T	acceptor_gain	0.9900
5:151183612:TGCC:T	acceptor_loss	0.9900
5:151183613:GCC:G	acceptor_loss	0.9900

AlphaMissense

1930 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
5:151185497:G:C	S180R	0.989
5:151185497:G:T	S180R	0.989
5:151185499:T:G	S180R	0.989
5:151185518:G:C	F173L	0.981
5:151185518:G:T	F173L	0.981
5:151185520:A:G	F173L	0.981
5:151185515:C:A	W174C	0.968
5:151185515:C:G	W174C	0.968
5:151185504:A:G	L178P	0.965
5:151183525:A:G	L268P	0.955
5:151185517:A:G	W174R	0.955
5:151185517:A:T	W174R	0.955
5:151185486:A:T	V184D	0.953
5:151184380:A:G	L226P	0.952
5:151185441:A:G	L199P	0.950
5:151185477:A:G	M187T	0.950
5:151185488:A:C	F183L	0.949
5:151185488:A:T	F183L	0.949
5:151185490:A:G	F183L	0.949
5:151185507:T:A	E177V	0.944
5:151186058:A:G	S154P	0.941
5:151186086:G:C	F144L	0.940
5:151186086:G:T	F144L	0.940
5:151186088:A:G	F144L	0.940
5:151185495:A:G	L181S	0.937
5:151186108:A:G	L137P	0.935
5:151185473:C:A	K188N	0.934
5:151185473:C:G	K188N	0.934
5:151185453:A:G	L195P	0.933
5:151184395:T:G	Q221P	0.932

dbSNP variants (sampled 300 via entrez): RS1000017543 (5:151219326 C>A), RS1000051295 (5:151200062 G>A), RS1000083459 (5:151199859 T>C), RS1000171992 (5:151212645 G>A), RS1000198793 (5:151193733 A>G), RS1000204513 (5:151212377 G>T), RS1000246853 (5:151181531 T>C), RS1000280557 (5:151206345 C>T), RS1000340056 (5:151193832 T>C), RS1000400351 (5:151206620 G>A), RS1000405344 (5:151218508 G>A,C), RS1000487223 (5:151223684 A>G,T), RS1000618129 (5:151193410 G>A), RS1000624078 (5:151185643 C>A,T), RS1000657056 (5:151185256 C>CCG)

Disease associations

OMIM: gene MIM:619288 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

13 associations (top):

Study	Trait	p-value
GCST001762_742	Obesity-related traits	9.000000e-06
GCST001958_11	Bulimia nervosa	7.000000e-06
GCST003772_8	Loneliness (linear analysis)	3.000000e-06
GCST004131_47	Inflammatory bowel disease	3.000000e-15
GCST004132_24	Crohn’s disease	2.000000e-19
GCST004610_4	White blood cell count	1.000000e-10
GCST004625_18	Monocyte count	3.000000e-12
GCST007692_117	Chronic obstructive pulmonary disease	1.000000e-08
GCST90002388_329	Lymphocyte count	1.000000e-14
GCST90002393_108	Monocyte count	1.000000e-15
GCST90002398_6	Neutrophil count	4.000000e-09
GCST90002404_217	Red cell distribution width	1.000000e-30
GCST90002407_472	White blood cell count	1.000000e-17

EFO canonical traits (6, from GWAS)

EFO ID	Trait name
EFO:0003939	energy intake
EFO:0007865	loneliness measurement
EFO:0005091	monocyte count
EFO:0004587	lymphocyte count
EFO:0004833	neutrophil count
EFO:0009188	Red cell distribution width

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, increases expression, affects expression	6
bisphenol A	affects expression, affects cotreatment, increases expression	2
sodium arsenite	affects expression, decreases expression	2
entinostat	increases expression, affects cotreatment	2
belinostat	increases expression, affects cotreatment	2
Panobinostat	affects cotreatment, increases expression	2
Air Pollutants	decreases expression, increases abundance, increases expression	2
Cisplatin	affects cotreatment, increases expression	2
Dexamethasone	increases expression, affects cotreatment	2
Phenylmercuric Acetate	affects cotreatment, increases expression	2
Cyclosporine	decreases expression	2
Particulate Matter	increases expression, decreases expression, increases abundance	2
triphenyl phosphate	affects expression	1
lead acetate	decreases expression	1
trichostatin A	increases expression	1
beta-lapachone	increases expression	1
arsenite	affects binding, decreases reaction	1
mono-(2-ethylhexyl)phthalate	increases expression	1
tris(1,3-dichloro-2-propyl)phosphate	decreases expression	1
perfluorooctanoic acid	decreases expression	1
cupric chloride	decreases expression	1
di-n-butylphosphoric acid	affects expression	1
perfluorooctane sulfonic acid	decreases expression	1
perfluoro-n-nonanoic acid	decreases expression	1
K 7174	decreases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	increases expression, affects cotreatment	1
perfluorohexanesulfonic acid	decreases expression	1
nutlin 3	affects cotreatment, increases expression	1
abrine	decreases expression	1
dorsomorphin	affects cotreatment, increases expression	1

Clinical trials (associated diseases)

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