CCDC89

Summary

CCDC89 (coiled-coil domain containing 89, HGNC:26762) is a protein-coding gene on chromosome 11q14.1, encoding Coiled-coil domain-containing protein 89 (Q8N998).

Predicted to be located in cytoplasm and nucleus.

Source: NCBI Gene 220388 — RefSeq curated summary.

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 55 total
• MANE Select transcript: NM_152723

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:26762
Approved symbol	CCDC89
Name	coiled-coil domain containing 89
Location	11q14.1
Locus type	gene with protein product
Status	Approved
Aliases	FLJ38159
Ensembl gene	ENSG00000179071
Ensembl biotype	protein_coding
Entrez	220388

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000316398

RefSeq mRNA: 1 — MANE Select: NM_152723 NM_152723

CCDS: CCDS8270

Canonical transcript exons

ENST00000316398 — 1 exons

Exon	Start	End
ENSE00001236152	85683848	85686195

Expression profiles

Bgee: expression breadth ubiquitous, 156 present calls, max score 85.92.

FANTOM5 (CAGE): breadth broad, TPM avg 0.4767 / max 69.0160, expressed in 242 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
121687	0.4767	242

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
left testis	UBERON:0004533	85.92	gold quality
right testis	UBERON:0004534	85.04	gold quality
oviduct epithelium	UBERON:0004804	83.46	gold quality
testis	UBERON:0000473	83.17	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	80.96	silver quality
right uterine tube	UBERON:0001302	80.47	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	77.26	silver quality
fallopian tube	UBERON:0003889	73.50	gold quality
bronchial epithelial cell	CL:0002328	73.14	gold quality
calcaneal tendon	UBERON:0003701	72.02	gold quality
bronchus	UBERON:0002185	71.67	gold quality
stromal cell of endometrium	CL:0002255	70.61	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	70.37	gold quality
smooth muscle tissue	UBERON:0001135	68.13	gold quality
body of uterus	UBERON:0009853	65.02	gold quality
mucosa of paranasal sinus	UBERON:0005030	64.82	gold quality
right ovary	UBERON:0002118	63.82	gold quality
left ovary	UBERON:0002119	63.40	gold quality
ovary	UBERON:0000992	63.06	gold quality
left coronary artery	UBERON:0001626	62.46	gold quality
right coronary artery	UBERON:0001625	61.64	gold quality
gall bladder	UBERON:0002110	61.53	gold quality
descending thoracic aorta	UBERON:0002345	61.47	gold quality
coronary artery	UBERON:0001621	61.19	gold quality
left uterine tube	UBERON:0001303	61.01	gold quality
right adrenal gland	UBERON:0001233	60.35	gold quality
tendon	UBERON:0000043	60.02	gold quality
epithelium of nasopharynx	UBERON:0001951	60.01	silver quality
right adrenal gland cortex	UBERON:0035827	58.80	gold quality
cerebellar cortex	UBERON:0002129	58.63	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	5.08

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

93 targeting CCDC89, 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-5011-5P	100.00	83.46	5820
HSA-MIR-3646	100.00	73.56	5283
HSA-MIR-190A-3P	100.00	80.35	5520
HSA-MIR-4682	100.00	68.89	1258
HSA-MIR-4668-3P	100.00	68.74	2635
HSA-MIR-1252-5P	100.00	69.80	2774
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-196A-1-3P	99.99	72.15	2772
HSA-MIR-4803	99.98	71.99	3117
HSA-MIR-32-5P	99.98	75.21	1964
HSA-MIR-92A-3P	99.98	75.21	1960
HSA-MIR-92B-3P	99.98	75.25	1955
HSA-MIR-25-3P	99.98	74.60	1817
HSA-MIR-363-3P	99.98	74.72	1821
HSA-MIR-367-3P	99.98	74.83	1819
HSA-MIR-146A-5P	99.96	68.93	988
HSA-MIR-146B-5P	99.96	69.13	977
HSA-MIR-3658	99.96	73.87	4379
HSA-MIR-1468-3P	99.96	72.74	3797
HSA-MIR-545-3P	99.95	70.74	2783
HSA-MIR-7153-5P	99.94	68.89	1006
HSA-MIR-651-3P	99.94	73.48	5177
HSA-MIR-218-5P	99.93	72.22	2103
HSA-MIR-4760-3P	99.93	70.50	2385
HSA-MIR-338-5P	99.92	72.34	2951
HSA-MIR-5680	99.91	69.83	3421
HSA-MIR-3529-3P	99.90	73.55	3045
HSA-MIR-124-3P	99.89	73.74	3043
HSA-MIR-506-3P	99.89	73.55	3057
HSA-MIR-7162-3P	99.89	68.16	1682

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Ccdc89	ENSMUSG00000044362
rattus_norvegicus	Ccdc89	ENSRNOG00000048071

Protein

Protein identifiers

Coiled-coil domain-containing protein 89 — Q8N998 (reviewed: Q8N998)

Alternative names: Bc8 orange-interacting protein

All UniProt accessions (1): Q8N998

UniProt curated annotations — full annotation on UniProt →

Subunit / interactions. Interacts with HEY1.

Subcellular location. Cytoplasm. Nucleus.

Similarity. Belongs to the CCDC89 family.

RefSeq proteins (1): NP_689936* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR043450	CCDC89-like	Family

UniProt features (7 total): chain 1, region of interest 1, coiled-coil region 1, compositionally biased region 1, modified residue 1, helix 1, turn 1

Structure

Experimental structures (PDB)

4 structures.

PDB	Method	Resolution (Å)
8WQB	ELECTRON MICROSCOPY	3.37
8WQA	ELECTRON MICROSCOPY	3.39
8WQH	ELECTRON MICROSCOPY	3.44
8WQD	ELECTRON MICROSCOPY	3.55

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8N998-F1	83.06	0.57

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 (1): 16

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 44 (showing top): FOXO1_01, NIKOLSKY_BREAST_CANCER_11Q12_Q14_AMPLICON, FOXO4_02, DODD_NASOPHARYNGEAL_CARCINOMA_DN, MIR3646, MIR506_3P, MIR124_3P, MIR5680, MIR196A_1_3P, MIR33A_3P, MIR545_3P, CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_2, MIR379_3P_MIR411_3P, MIR636, MIR5590_5P

GO Biological Process (0):

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

GO Cellular Component (2): nucleus (GO:0005634), cytoplasm (GO:0005737)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	1
intracellular membrane-bounded organelle	1
intracellular anatomical structure	1
cellular anatomical structure	1

Protein interactions and networks

STRING

234 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CCDC89	SPACA7	Q96KW9	558
CCDC89	CCDC182	A6NF36	543
CCDC89	KRTAP10-1	P60331	507
CCDC89	FRG2B	Q96QU4	507
CCDC89	HEY1	Q9Y5J3	491
CCDC89	A6NEC3	A6NEC3	477
CCDC89	CFAP276	Q5T5A4	447
CCDC89	KRTAP4-3	Q9BYR4	445
CCDC89	MFSD6L	Q8IWD5	438
CCDC89	TSPY4	P0CV99	436
CCDC89	KIAA1671	Q9BY89	417
CCDC89	XKR3	Q5GH77	410
CCDC89	TSPYL4	Q9UJ04	406
CCDC89	TPD52L3	Q96J77	393
CCDC89	ZNF595	Q8IYB9	376

IntAct

18 interactions, top by confidence:

A	B	Type	Score
CCDC89	LRRC45	psi-mi:“MI:0915”(physical association)	0.670
CCDC89	PIK3R3	psi-mi:“MI:0915”(physical association)	0.560
CCDC89	FAM50B	psi-mi:“MI:0915”(physical association)	0.560
TSFM	CCDC89	psi-mi:“MI:0915”(physical association)	0.560
CCDC89	ZMYM6	psi-mi:“MI:0914”(association)	0.530
CCDC89	H1-5	psi-mi:“MI:0915”(physical association)	0.400
CCDC89	H2BC9	psi-mi:“MI:0915”(physical association)	0.400
CCDC89	PLEKHG3	psi-mi:“MI:0914”(association)	0.350
PIK3R3	CCDC89	psi-mi:“MI:0915”(physical association)	0.000
LRRC45	CCDC89	psi-mi:“MI:0915”(physical association)	0.000
FAM50B	CCDC89	psi-mi:“MI:0915”(physical association)	0.000
TSFM	CCDC89	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (28): KIF20B (Affinity Capture-MS), KIF14 (Affinity Capture-MS), RPS27A (Affinity Capture-MS), CEP44 (Affinity Capture-MS), SPAG5 (Affinity Capture-MS), ZMYM6 (Affinity Capture-MS), KIAA1279 (Affinity Capture-MS), KNSTRN (Affinity Capture-MS), FBXO28 (Affinity Capture-MS), SLMAP (Affinity Capture-MS), FBLN1 (Affinity Capture-MS), CCDC89 (Two-hybrid), CCDC89 (Two-hybrid), CCDC89 (Two-hybrid), CCDC89 (Two-hybrid)

ESM2 similar proteins: A2AIV8, A2AL36, A2AM05, A3KNA5, A6PWD2, B1AJZ9, B2RZ86, B9V5F5, E9Q1U1, O35550, O35551, P0CAP1, P27628, P55937, Q08DR9, Q0IHN7, Q0VF96, Q15276, Q19UN5, Q29RS0, Q4L180, Q5BIX7, Q5R923, Q6AW69, Q6NRC9, Q6P6L0, Q6PHN1, Q6TFL3, Q70FJ1, Q7YS99, Q7Z7A1, Q7Z7B0, Q861Q8, Q86SQ7, Q8BI22, Q8K3K8, Q8K4T4, Q8N998, Q8R5M4, Q95JI9

Diamond homologs: A8WG43, B2RZ86, Q29RS0, Q7ZW57, Q8N998, Q95JI9, Q9DA73

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	54
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

66 predictions. Top by Δscore:

Variant	Effect	Δscore
11:85685238:T:A	donor_gain	0.5100
11:85685388:G:C	donor_gain	0.5000
11:85685259:G:A	donor_gain	0.4300
11:85685310:T:TA	donor_gain	0.4300
11:85685446:G:C	donor_gain	0.4300
11:85685188:CAA:C	donor_gain	0.4200
11:85685189:AAA:A	donor_gain	0.4200
11:85685783:AC:A	donor_gain	0.4100
11:85685784:CC:C	donor_gain	0.4100
11:85685178:G:GA	donor_gain	0.4000
11:85685282:G:A	donor_gain	0.3800
11:85685403:G:GA	donor_gain	0.3800
11:85685777:GTACT:G	donor_loss	0.3800
11:85685778:TACT:T	donor_loss	0.3800
11:85685779:ACTC:A	donor_loss	0.3800
11:85685780:CTCA:C	donor_loss	0.3800
11:85685781:TCACC:T	donor_loss	0.3800
11:85685782:C:CG	donor_loss	0.3800
11:85685783:A:AG	donor_loss	0.3800
11:85685784:C:T	donor_loss	0.3800
11:85685311:C:CA	donor_gain	0.3700
11:85685613:T:TA	donor_gain	0.3700
11:85685776:TGTAC:T	donor_loss	0.3700
11:85685392:T:C	donor_gain	0.3600
11:85685783:A:AC	donor_gain	0.3400
11:85685784:C:CC	donor_gain	0.3400
11:85685608:T:A	donor_gain	0.3300
11:85685712:T:TG	acceptor_gain	0.3300
11:85685110:AGG:A	donor_gain	0.3200
11:85685176:C:CT	donor_gain	0.3200

AlphaMissense

2483 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
11:85685888:C:A	K81N	0.971
11:85685888:C:G	K81N	0.971
11:85685753:A:C	F126L	0.944
11:85685753:A:T	F126L	0.944
11:85685755:A:G	F126L	0.944
11:85685886:C:G	R82P	0.930
11:85685881:A:G	S84P	0.919
11:85685904:A:G	L76P	0.916
11:85685636:G:C	F165L	0.915
11:85685636:G:T	F165L	0.915
11:85685638:A:G	F165L	0.915
11:85685925:C:G	R69P	0.915
11:85685661:A:G	L157P	0.912
11:85685889:T:G	K81T	0.909
11:85685926:G:T	R69S	0.909
11:85685189:A:C	F314L	0.907
11:85685189:A:T	F314L	0.907
11:85685191:A:G	F314L	0.907
11:85685682:A:G	L150P	0.903
11:85685912:C:A	Q73H	0.903
11:85685912:C:G	Q73H	0.903
11:85685142:A:G	L330P	0.898
11:85685711:C:A	K140N	0.896
11:85685711:C:G	K140N	0.896
11:85685066:G:C	S355R	0.891
11:85685066:G:T	S355R	0.891
11:85685068:T:G	S355R	0.891
11:85685911:A:G	S74P	0.889
11:85685890:T:C	K81E	0.887
11:85685089:A:G	S348P	0.879

dbSNP variants (sampled 300 via entrez): RS1000569497 (11:85683793 C>T), RS1000633341 (11:85687862 G>C,T), RS1001739940 (11:85688147 A>G), RS1001811403 (11:85684931 T>C), RS1001918183 (11:85686960 C>A,G), RS1003710494 (11:85685791 C>A,T), RS1004810252 (11:85687963 C>T), RS1005154413 (11:85688106 G>T), RS1005160255 (11:85688142 T>C), RS1006423980 (11:85686637 C>T), RS1007841658 (11:85684694 A>C), RS1007959259 (11:85685150 G>A,C), RS1008057775 (11:85685889 T>C,G), RS1008465061 (11:85683853 T>A), RS1009285911 (11:85687598 C>T)

Disease associations

OMIM: gene `` | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

2 associations (top):

Study	Trait	p-value
GCST010002_244	Refractive error	2.000000e-53
GCST90000046_5	Age at first sexual intercourse	1.000000e-09

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0009749	age at first sexual intercourse measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

16 total (human), top 16 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Smoke	increases abundance, increases expression	2
aristolochic acid I	increases expression	1
sotorasib	affects cotreatment, increases expression	1
ferrous chloride	decreases expression	1
CGP 52608	affects binding, increases reaction	1
trametinib	affects cotreatment, increases expression	1
NVP-BKM120	increases expression, affects cotreatment	1
Temozolomide	decreases expression	1
Air Pollutants	increases abundance, increases expression	1
Arsenic	affects methylation	1
Benzo(a)pyrene	increases methylation	1
Oxygen	increases expression	1
Rotenone	decreases expression	1
Tobacco Smoke Pollution	decreases expression	1
Aflatoxin B1	decreases expression	1
Okadaic Acid	increases expression	1

Clinical trials (associated diseases)

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