CCDC86

Summary

CCDC86 (coiled-coil domain containing 86, HGNC:28359) is a protein-coding gene on chromosome 11q12.2, encoding Coiled-coil domain-containing protein 86 (Q9H6F5). Required for proper chromosome segregation during mitosis and error-free mitotic progression. It is a selective cancer dependency (DepMap: 89.5% of cell lines).

Enables RNA binding activity. Located in chromosome; nucleolus; and nucleoplasm.

Source: NCBI Gene 79080 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 73 total
• Cancer dependency (DepMap): dependent in 89.5% of screened cell lines
• MANE Select transcript: NM_024098

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:28359
Approved symbol	CCDC86
Name	coiled-coil domain containing 86
Location	11q12.2
Locus type	gene with protein product
Status	Approved
Aliases	MGC2574, cyclon, Cgr1
Ensembl gene	ENSG00000110104
Ensembl biotype	protein_coding
OMIM	611293
Entrez	79080

Gene structure

Transcript identifiers

Ensembl transcripts: 4 — 2 protein_coding, 1 nonsense_mediated_decay, 1 retained_intron

ENST00000227520, ENST00000535217, ENST00000545580, ENST00000649393

RefSeq mRNA: 1 — MANE Select: NM_024098 NM_024098

CCDS: CCDS7993

Canonical transcript exons

ENST00000227520 — 4 exons

Exon	Start	End
ENSE00000851430	60842113	60842882
ENSE00000851431	60850206	60851081
ENSE00003550038	60849940	60850014
ENSE00003550301	60847924	60848053

Expression profiles

Bgee: expression breadth ubiquitous, 277 present calls, max score 92.25.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 36.2654 / max 326.2249, expressed in 1808 samples.

FANTOM5 promoters (9 alternative TSS)

Promoter ID	TPM avg	Samples expressed
114503	20.8619	1786
114502	10.8812	1751
114501	3.5279	1583
114500	0.4020	242
114508	0.2432	109
114504	0.2109	69
114505	0.0969	33
114507	0.0214	8
114506	0.0200	6

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
left testis	UBERON:0004533	92.25	gold quality
right testis	UBERON:0004534	91.81	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	90.89	gold quality
testis	UBERON:0000473	90.68	gold quality
gastrocnemius	UBERON:0001388	89.62	gold quality
cervix squamous epithelium	UBERON:0006922	88.43	silver quality
muscle of leg	UBERON:0001383	88.31	gold quality
left adrenal gland cortex	UBERON:0035825	88.23	gold quality
left adrenal gland	UBERON:0001234	88.21	gold quality
pancreatic ductal cell	CL:0002079	87.99	gold quality
adrenal cortex	UBERON:0001235	87.74	gold quality
right adrenal gland	UBERON:0001233	87.69	gold quality
right adrenal gland cortex	UBERON:0035827	87.62	gold quality
pituitary gland	UBERON:0000007	87.01	gold quality
adrenal gland	UBERON:0002369	86.98	gold quality
muscle organ	UBERON:0001630	86.22	gold quality
skeletal muscle organ	UBERON:0014892	86.21	gold quality
gluteal muscle	UBERON:0002000	86.16	silver quality
triceps brachii	UBERON:0001509	86.15	gold quality
omental fat pad	UBERON:0010414	86.06	gold quality
peritoneum	UBERON:0002358	86.04	gold quality
adenohypophysis	UBERON:0002196	86.01	gold quality
hindlimb stylopod muscle	UBERON:0004252	85.98	gold quality
sperm	CL:0000019	85.97	silver quality
islet of Langerhans	UBERON:0000006	85.91	gold quality
skin of leg	UBERON:0001511	85.79	gold quality
skin of abdomen	UBERON:0001416	85.46	gold quality
adipose tissue of abdominal region	UBERON:0007808	85.37	gold quality
male germ cell	CL:0000015	85.36	silver quality
gingival epithelium	UBERON:0001949	85.31	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-MTAB-6379	no	144.49
E-ANND-3	no	2.78

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

33 targeting CCDC86, 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-450A-1-3P	100.00	69.33	1837
HSA-MIR-4531	99.99	69.70	3181
HSA-MIR-4267	99.96	66.53	2368
HSA-MIR-95-5P	99.89	72.17	3973
HSA-MIR-124-3P	99.89	73.74	3043
HSA-MIR-506-3P	99.89	73.55	3057
HSA-MIR-4731-5P	99.89	67.23	2537
HSA-MIR-605-3P	99.88	69.22	1833
HSA-MIR-4779	99.86	66.50	1583
HSA-MIR-4447	99.85	67.81	2900
HSA-MIR-6885-3P	99.75	70.36	3187
HSA-MIR-6715B-5P	99.64	69.63	1420
HSA-MIR-6126	99.62	68.09	996
HSA-MIR-4516	99.61	67.78	3390
HSA-MIR-4472	99.56	66.08	1478
HSA-MIR-4269	99.55	69.89	1373
HSA-MIR-671-5P	99.52	67.11	1277
HSA-MIR-3614-5P	99.30	65.25	837
HSA-MIR-6719-3P	99.29	67.78	1387
HSA-MIR-5703	99.10	67.09	2053
HSA-MIR-4796-3P	99.08	68.38	1681
HSA-MIR-6770-5P	98.97	66.76	1853
HSA-MIR-16-1-3P	98.70	69.23	1538
HSA-MIR-4463	98.56	66.05	1071
HSA-MIR-432-5P	98.00	68.13	989
HSA-MIR-1271-3P	97.56	64.85	865
HSA-MIR-550A-3-5P	97.56	65.35	823
HSA-MIR-550A-5P	97.56	65.35	823
HSA-MIR-505-5P	97.01	65.54	778
HSA-MIR-550B-2-5P	96.56	64.61	646

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 89.5% of screened cell lines.

Literature-anchored findings (GeneRIF, showing 4)

• cyclon gene encodes a phosphorylated nuclear protein consisting of repetitive sequences in the amino-terminus and a coiled-coil domain in the carboxyl-terminus (PMID:17300783)
• Cyclon/CCDC68 levels correlate with the clinical presentation of relapsed schizophrenia (PMID:23439384)
• CCDC86 is a novel Ki-67-interacting protein important for cell division. (PMID:36695333)
• CCDC86 promotes the aggressive behavior of nasopharyngeal carcinoma by positively regulating EGFR and activating the PI3K/Akt signaling. (PMID:38247332)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	ccdc86	ENSDARG00000059908
mus_musculus	Ccdc86	ENSMUSG00000024732
rattus_norvegicus	Ccdc86	ENSRNOG00000020925
drosophila_melanogaster	CG14210	FBGN0031040
caenorhabditis_elegans	Y40B1B.7	WBGENE00012739

Protein

Protein identifiers

Coiled-coil domain-containing protein 86 — Q9H6F5 (reviewed: Q9H6F5)

Alternative names: Cytokine-induced protein with coiled-coil domain

All UniProt accessions (2): Q9H6F5, H0YG79

UniProt curated annotations — full annotation on UniProt →

Function. Required for proper chromosome segregation during mitosis and error-free mitotic progression.

Subunit / interactions. (Microbial infection) Interacts with hepatitis C virus (HCV) protein NS5A.

Subcellular location. Nucleus. Chromosome. Nucleolus.

Post-translational modifications. Citrullinated by PADI4.

Isoforms (2)

UniProt ID	Names	Canonical?
Q9H6F5-1	1	yes
Q9H6F5-2	2

RefSeq proteins (1): NP_077003* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR026570	CCDC86	Family

UniProt features (32 total): modified residue 19, compositionally biased region 6, region of interest 2, chain 1, splice variant 1, coiled-coil region 1, sequence variant 1, mutagenesis site 1

Structure

Experimental structures (PDB)

10 structures.

PDB	Method	Resolution (Å)
8FL3	ELECTRON MICROSCOPY	2.53
8FL2	ELECTRON MICROSCOPY	2.67
8FL4	ELECTRON MICROSCOPY	2.89
8FL0	ELECTRON MICROSCOPY	2.91
8INK	ELECTRON MICROSCOPY	3.2
8IPD	ELECTRON MICROSCOPY	3.2
8IPY	ELECTRON MICROSCOPY	3.2
8IR1	ELECTRON MICROSCOPY	3.3
8IR3	ELECTRON MICROSCOPY	3.5
8IPX	ELECTRON MICROSCOPY	4.3

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9H6F5-F1	62.88	0.16

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 (19): 18, 21, 24, 47, 50, 58, 65, 66, 69, 80, 91, 102, 110, 113, 128, 188, 217, 218, 342

Mutagenesis-validated functional residues (1):

Position	Phenotype
1–63	loss of localization to chromosomes during mitosis.

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 186 (showing top): GSE45365_NK_CELL_VS_CD11B_DC_DN, ELVIDGE_HYPOXIA_DN, HORIUCHI_WTAP_TARGETS_DN, ZHAN_MULTIPLE_MYELOMA_MF_UP, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_UP, BROWNE_HCMV_INFECTION_12HR_UP, GTGCCTT_MIR506, GOBP_ORGANELLE_FISSION, GOBP_MITOTIC_NUCLEAR_DIVISION, GOBP_MITOTIC_CELL_CYCLE, SCHLOSSER_MYC_TARGETS_AND_SERUM_RESPONSE_UP, SANSOM_APC_TARGETS_UP, WANG_TARGETS_OF_MLL_CBP_FUSION_DN, TIEN_INTESTINE_PROBIOTICS_24HR_UP, IVANOVA_HEMATOPOIESIS_EARLY_PROGENITOR

GO Biological Process (2): chromosome segregation (GO:0007059), mitotic nuclear division (GO:0140014)

GO Molecular Function (2): RNA binding (GO:0003723), protein binding (GO:0005515)

GO Cellular Component (4): nucleus (GO:0005634), nucleoplasm (GO:0005654), chromosome (GO:0005694), nucleolus (GO:0005730)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
nuclear lumen	2
intracellular membraneless organelle	2
cell cycle process	1
mitotic cell cycle	1
nuclear division	1
mitotic cell cycle process	1
nucleic acid binding	1
binding	1
intracellular membrane-bounded organelle	1
cellular anatomical structure	1

Protein interactions and networks

STRING

1030 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CCDC86	IL3	P08700	545
CCDC86	ETFA	P13804	471
CCDC86	UFSP2	Q9NUQ7	467
CCDC86	TM2D1	Q9BX74	458
CCDC86	NUP210	Q8TEM1	437
CCDC86	MS4A10	Q96PG2	432
CCDC86	PTGES2	Q9H7Z7	412
CCDC86	CFAP184	Q2M329	408
CCDC86	APTX	Q7Z2E3	397
CCDC86	SPMIP4	Q8N865	394
CCDC86	CDK2AP2	O75956	385
CCDC86	TMEM217	Q8N7C4	385
CCDC86	TMEM217B	A0A494BZU4	383
CCDC86	APOF	Q13790	383
CCDC86	CCDC116	Q8IYX3	377

IntAct

133 interactions, top by confidence:

A	B	Type	Score
LARP7	CCNT1	psi-mi:“MI:0914”(association)	0.850
H2AX	PPM1G	psi-mi:“MI:0914”(association)	0.730
H2AC4	PPM1G	psi-mi:“MI:0914”(association)	0.670
rep	MPHOSPH10	psi-mi:“MI:0914”(association)	0.660
NSA2	TYW5	psi-mi:“MI:0914”(association)	0.530
ZCRB1	DKC1	psi-mi:“MI:0914”(association)	0.530
N	RBM47	psi-mi:“MI:0914”(association)	0.530
H2BC26	PPM1G	psi-mi:“MI:0914”(association)	0.530
H2AC20	PPM1G	psi-mi:“MI:0914”(association)	0.530
PRR11	NVL	psi-mi:“MI:0914”(association)	0.530
ABT1	ZNF316	psi-mi:“MI:0914”(association)	0.530
DAXX	TNRC18	psi-mi:“MI:0914”(association)	0.530
	CCDC86	psi-mi:“MI:0915”(physical association)	0.510
CCDC86		psi-mi:“MI:0915”(physical association)	0.510
ORF20	CCDC86	psi-mi:“MI:0915”(physical association)	0.400
MRTO4	CCDC86	psi-mi:“MI:0915”(physical association)	0.400
CCDC102B	CCDC86	psi-mi:“MI:0915”(physical association)	0.400
Rpl35	RPS6	psi-mi:“MI:0914”(association)	0.350
Srp72		psi-mi:“MI:0914”(association)	0.350
Gspt1	MRPL27	psi-mi:“MI:0914”(association)	0.350
HNRNPU		psi-mi:“MI:0914”(association)	0.350
NLRP3	PHRF1	psi-mi:“MI:0914”(association)	0.350
NPM1	RPSA	psi-mi:“MI:0914”(association)	0.350
FOXQ1	ARHGAP10	psi-mi:“MI:0914”(association)	0.350
KSR1	FBLL1	psi-mi:“MI:0914”(association)	0.350

BioGRID (189): CCDC86 (Affinity Capture-MS), CCDC86 (Affinity Capture-MS), CCDC86 (Affinity Capture-MS), CCDC86 (Affinity Capture-MS), CCDC86 (Affinity Capture-MS), CCDC86 (Co-fractionation), CCDC86 (Affinity Capture-MS), CCDC86 (Proximity Label-MS), CCDC86 (Biochemical Activity), CCDC86 (Affinity Capture-MS), CCDC86 (Affinity Capture-MS), CCDC86 (Affinity Capture-MS), CCDC86 (Affinity Capture-MS), CCDC86 (Affinity Capture-MS), CCDC86 (Affinity Capture-MS)

ESM2 similar proteins: A2TJV2, A5D7J3, A5D7L8, A6NDB9, A6QPT6, A7E321, B1ASB6, F1MGG3, O08784, O15446, P0C671, P48382, P48681, Q14676, Q14684, Q149B8, Q1ED39, Q3UY34, Q4R729, Q5I034, Q5SV97, Q5TM66, Q5TM68, Q5U2M8, Q5XFX8, Q5XIB5, Q68A65, Q68FX5, Q6NYC8, Q767L8, Q767M0, Q76KJ5, Q7YR40, Q7Z6P3, Q80VR2, Q86VY4, Q86Y26, Q8BQ30, Q8CB87, Q8IY92

Diamond homologs: Q2TBX7, Q5RB69, Q5XIB5, Q9H6F5, Q9JJ89

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 142 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:

Pathway	Partners	Fold	FDR
Eukaryotic Translation Initiation	6	21.5×	5e-06
Cap-dependent Translation Initiation	6	21.5×	5e-06
SARS-CoV-1 modulates host translation machinery	6	21.5×	5e-06
Eukaryotic Translation Elongation	6	19.4×	8e-06
Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S	6	19.0×	9e-06
Peptide chain elongation	12	17.7×	2e-10
Viral mRNA Translation	12	17.7×	2e-10
Formation of the ternary complex, and subsequently, the 43S complex	7	17.5×	3e-06

GO biological processes:

GO term	Partners	Fold	FDR
ribosomal large subunit biogenesis	6	21.1×	5e-05
cytoplasmic translation	13	19.1×	1e-10
ribosomal small subunit biogenesis	10	18.1×	3e-08
rRNA processing	13	14.6×	2e-09
regulation of alternative mRNA splicing, via spliceosome	7	13.6×	8e-05
RNA processing	7	12.2×	1e-04
translation	14	11.4×	5e-09
RNA splicing	8	5.6×	6e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	64
Likely benign	3
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

300 predictions. Top by Δscore:

Variant	Effect	Δscore
11:60847922:A:AG	acceptor_gain	1.0000
11:60847923:G:GC	acceptor_gain	1.0000
11:60847923:GATTC:G	acceptor_gain	1.0000
11:60848051:CAGG:C	donor_loss	1.0000
11:60848052:AGGTG:A	donor_loss	1.0000
11:60848054:G:A	donor_loss	1.0000
11:60848054:G:GG	donor_gain	1.0000
11:60848055:T:A	donor_loss	1.0000
11:60849929:A:AG	acceptor_gain	1.0000
11:60849929:ACAT:A	acceptor_gain	1.0000
11:60849930:C:G	acceptor_gain	1.0000
11:60849931:A:AG	acceptor_gain	1.0000
11:60849931:AT:A	acceptor_gain	1.0000
11:60849932:T:G	acceptor_gain	1.0000
11:60849932:T:TA	acceptor_gain	1.0000
11:60849938:A:AG	acceptor_gain	1.0000
11:60849938:A:G	acceptor_loss	1.0000
11:60849938:AG:A	acceptor_gain	1.0000
11:60849939:G:GA	acceptor_gain	1.0000
11:60849939:GG:G	acceptor_gain	1.0000
11:60849939:GGA:G	acceptor_gain	1.0000
11:60849939:GGAGA:G	acceptor_gain	1.0000
11:60850010:AAGTG:A	donor_gain	1.0000
11:60850012:GTG:G	donor_gain	1.0000
11:60850013:TG:T	donor_gain	1.0000
11:60850014:GG:G	donor_gain	1.0000
11:60850015:G:GG	donor_gain	1.0000
11:60850016:T:A	donor_loss	1.0000
11:60850195:A:AG	acceptor_gain	1.0000
11:60850196:C:G	acceptor_gain	1.0000

AlphaMissense

2272 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
11:60842862:G:C	W246C	0.994
11:60842862:G:T	W246C	0.994
11:60842865:G:C	K247N	0.994
11:60842865:G:T	K247N	0.994
11:60842860:T:A	W246R	0.993
11:60842860:T:C	W246R	0.993
11:60847925:T:C	F254L	0.993
11:60847927:C:A	F254L	0.993
11:60847927:C:G	F254L	0.993
11:60849974:G:C	R308P	0.992
11:60849992:G:C	R314P	0.991
11:60850229:G:C	K329N	0.991
11:60850229:G:T	K329N	0.991
11:60849953:G:C	R301P	0.990
11:60847966:G:C	W267C	0.989
11:60847966:G:T	W267C	0.989
11:60850007:T:A	V319D	0.988
11:60847964:T:A	W267R	0.986
11:60847964:T:C	W267R	0.986
11:60850207:T:C	I322T	0.986
11:60849977:G:C	R309P	0.985
11:60849997:G:C	A316P	0.985
11:60849956:G:C	R302P	0.984
11:60850207:T:A	I322N	0.984
11:60842847:A:C	K241N	0.983
11:60842847:A:T	K241N	0.983
11:60842855:G:C	R244P	0.983
11:60842852:G:A	G243E	0.981
11:60850207:T:G	I322S	0.980
11:60847975:G:C	K270N	0.979

dbSNP variants (sampled 300 via entrez): RS1000406199 (11:60851281 T>C), RS1000583688 (11:60845786 C>A,G), RS1001491769 (11:60847788 C>T), RS1001640324 (11:60841970 C>G,T), RS1001745720 (11:60850388 C>G,T), RS1001978781 (11:60843115 C>T), RS1002406908 (11:60845529 C>G,T), RS1002467307 (11:60849730 A>C,G), RS1002511117 (11:60846750 T>A), RS1002654369 (11:60840580 G>A,C), RS1002750228 (11:60849318 G>A,T), RS1003473633 (11:60848134 C>G), RS1003999984 (11:60849394 A>G), RS1004360604 (11:60849269 A>G), RS1004377097 (11:60848873 T>G)

Disease associations

OMIM: gene MIM:611293 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

1 associations (top):

Study	Trait	p-value
GCST002160_3	Wegener’s granulomatosis	2.000000e-07

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	affects expression, decreases expression, affects cotreatment, increases abundance, increases expression	3
(+)-JQ1 compound	decreases expression	3
Benzo(a)pyrene	affects methylation, increases expression	3
Estradiol	increases expression	2
Valproic Acid	increases expression, affects expression	2
Aflatoxin B1	increases expression	2
aristolochic acid I	increases expression	1
GSK-J4	decreases expression	1
FR900359	affects phosphorylation	1
beauvericin	decreases expression	1
alpha-pinene	affects cotreatment, increases oxidation, increases abundance	1
deoxynivalenol	increases expression	1
2-bromopalmitate	decreases reaction, increases abundance, increases palmitoylation	1
manganese chloride	affects cotreatment, increases abundance, increases expression	1
potassium chromate(VI)	affects cotreatment, increases expression	1
coumarin	increases phosphorylation	1
methacrylaldehyde	affects cotreatment, increases oxidation, increases abundance	1
epigallocatechin gallate	affects cotreatment, increases expression	1
di-n-butylphosphoric acid	affects expression	1
cylindrospermopsin	increases expression	1
chloropicrin	decreases expression	1
AM 251	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	affects cotreatment, decreases expression	1
ICG 001	decreases expression	1
abrine	increases expression	1
2-(1H-indazol-4-yl)-6-(4-methanesulfonylpiperazin-1-ylmethyl)-4-morpholin-4-ylthieno(3,2-d)pyrimidine	decreases expression, increases response to substance	1
LDN 193189	affects cotreatment, decreases expression	1
4-(4-((5-(4,5-dimethyl-2-nitrophenyl)-2-furanyl)methylene)-4,5-dihydro-3-methyl-5-oxo-1H-pyrazol-1-yl)benzoic acid	decreases expression	1
Sunitinib	increases expression	1

Cellosaurus cell lines

2 cell lines: 2 cancer cell line

First 10 cell lines (id-ordered, not curated):

Cellosaurus	Name	Category	Sex
CVCL_D7LV	Ubigene A-549 CCDC86 KO	Cancer cell line	Male
CVCL_E0ZI	Ubigene NCI-H1299 CCDC86 KO	Cancer cell line	Male

Clinical trials (associated diseases)

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