CNTLN

Summary

CNTLN (centlein, HGNC:23432) is a protein-coding gene on chromosome 9p22.2, encoding Centlein (Q9NXG0). Required for centrosome cohesion and recruitment of CEP68 to centrosomes.

Enables protein domain specific binding activity; protein kinase binding activity; and protein-macromolecule adaptor activity. Involved in centriole-centriole cohesion and protein localization to organelle. Located in cytosol; microtubule organizing center; and nucleoplasm.

Source: NCBI Gene 54875 — RefSeq curated summary.

At a glance

• GWAS associations: 18
• Clinical variants (ClinVar): 300 total
• MANE Select transcript: NM_017738

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:23432
Approved symbol	CNTLN
Name	centlein
Location	9p22.2
Locus type	gene with protein product
Status	Approved
Aliases	FLJ20276, bA340N12.1, OTTHUMG00000019597
Ensembl gene	ENSG00000044459
Ensembl biotype	protein_coding
OMIM	611870
Entrez	54875

Gene structure

Transcript identifiers

Ensembl transcripts: 5 — 3 protein_coding, 2 protein_coding_CDS_not_defined

ENST00000380641, ENST00000380647, ENST00000461247, ENST00000484374, ENST00000918050

RefSeq mRNA: 5 — MANE Select: NM_017738 NM_001114395, NM_001286984, NM_001286985, NM_001365029, NM_017738

CCDS: CCDS43789, CCDS47953

Canonical transcript exons

ENST00000380647 — 26 exons

Exon	Start	End
ENSE00000927954	17309058	17309252
ENSE00000982165	17330632	17330808
ENSE00000982166	17332605	17332730
ENSE00000982167	17340827	17340948
ENSE00000982180	17484295	17484480
ENSE00000982181	17486989	17487066
ENSE00001089185	17235658	17235792
ENSE00001089186	17226203	17226287
ENSE00001089190	17236409	17236588
ENSE00001089199	17298190	17298352
ENSE00001089201	17457524	17457715
ENSE00001089202	17466706	17466891
ENSE00001089204	17462916	17463013
ENSE00001089206	17465981	17466118
ENSE00001089207	17394534	17395069
ENSE00001089209	17464497	17464623
ENSE00001089211	17415788	17415881
ENSE00001089216	17409293	17409473
ENSE00001132510	17388162	17388253
ENSE00001132517	17366617	17366717
ENSE00001132526	17342325	17342444
ENSE00001426462	17273733	17273866
ENSE00001485715	17135040	17135425
ENSE00001852268	17502551	17503923
ENSE00003573052	17143288	17143376
ENSE00003640081	17415966	17416189

Expression profiles

Bgee: expression breadth ubiquitous, 195 present calls, max score 94.41.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 11.9474 / max 243.7495, expressed in 1590 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
96202	11.2345	1581
96201	0.4795	241
96203	0.2334	53

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
buccal mucosa cell	CL:0002336	94.41	gold quality
calcaneal tendon	UBERON:0003701	93.74	gold quality
ventricular zone	UBERON:0003053	91.26	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	86.83	gold quality
sural nerve	UBERON:0015488	86.53	gold quality
ganglionic eminence	UBERON:0004023	86.02	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	85.74	gold quality
tendon	UBERON:0000043	81.62	gold quality
monocyte	CL:0000576	81.02	gold quality
mononuclear cell	CL:0000842	80.73	gold quality
secondary oocyte	CL:0000655	80.00	silver quality
leukocyte	CL:0000738	79.83	gold quality
right lobe of liver	UBERON:0001114	79.49	gold quality
left ovary	UBERON:0002119	78.25	gold quality
right ovary	UBERON:0002118	78.12	gold quality
adrenal tissue	UBERON:0018303	78.00	gold quality
ovary	UBERON:0000992	77.69	gold quality
colonic epithelium	UBERON:0000397	77.51	gold quality
popliteal artery	UBERON:0002250	77.09	gold quality
tibial artery	UBERON:0007610	77.09	gold quality
body of uterus	UBERON:0009853	76.39	gold quality
stromal cell of endometrium	CL:0002255	76.31	gold quality
tibial nerve	UBERON:0001323	76.06	gold quality
mucosa of stomach	UBERON:0001199	75.90	gold quality
liver	UBERON:0002107	75.81	gold quality
endocervix	UBERON:0000458	75.61	gold quality
aorta	UBERON:0000947	75.52	gold quality
left uterine tube	UBERON:0001303	75.40	gold quality
muscle layer of sigmoid colon	UBERON:0035805	75.19	gold quality
gall bladder	UBERON:0002110	75.16	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	8.32

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

64 targeting CNTLN, 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-3185	99.99	68.12	1959
HSA-MIR-12136	99.98	72.81	5713
HSA-MIR-570-3P	99.96	72.41	4910
HSA-MIR-1250-3P	99.96	70.04	4038
HSA-MIR-548AA	99.96	70.64	3753
HSA-MIR-548AP-3P	99.96	70.64	3753
HSA-MIR-548T-3P	99.96	70.64	3753
HSA-MIR-590-3P	99.96	74.34	6478
HSA-MIR-23A-3P	99.95	74.24	3163
HSA-MIR-23B-3P	99.95	74.24	3163
HSA-MIR-23C	99.95	73.92	3192
HSA-MIR-6508-5P	99.92	70.67	2465
HSA-MIR-7-1-3P	99.91	71.53	4384
HSA-MIR-7-2-3P	99.91	71.40	4394
HSA-MIR-153-5P	99.89	73.86	6317
HSA-MIR-95-5P	99.89	72.17	3973
HSA-MIR-548D-3P	99.87	70.67	4362
HSA-MIR-548BB-3P	99.86	70.58	4354
HSA-MIR-5582-3P	99.86	72.48	4221
HSA-MIR-548AC	99.84	70.77	4351
HSA-MIR-548H-3P	99.84	70.80	4349
HSA-MIR-548Z	99.84	70.80	4349
HSA-MIR-944	99.82	70.85	3042
HSA-MIR-4495	99.82	72.08	3080
HSA-MIR-4799-5P	99.82	70.60	2663
HSA-MIR-489-3P	99.80	66.46	839
HSA-MIR-4659A-3P	99.80	72.62	4248
HSA-MIR-4659B-3P	99.80	72.62	4248
HSA-MIR-187-5P	99.74	70.26	1404
HSA-MIR-12129	99.72	67.45	1311

Literature-anchored findings (GeneRIF, showing 3)

• identified a SNP (rs894379) in the intronic region of the centlein, centrosomal protein (CNTLN) gene on chromosome 9p22, whose minor allele G is associated with an increased left ventricular mass (PMID:22940680)
• Centlein complexes with C-Nap1 and Cep68 at the proximal ends of centrioles during interphase. (PMID:24554434)
• Taken together, we propose that centlein is involved in MT stability and neuritogenesis in vivo. (PMID:26915804)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	cntln	ENSDARG00000033345
mus_musculus	Cntln	ENSMUSG00000038070
rattus_norvegicus	Cntln	ENSRNOG00000043151

Protein

Protein identifiers

Centlein — Q9NXG0 (reviewed: Q9NXG0)

Alternative names: Centrosomal protein

All UniProt accessions (1): Q9NXG0

UniProt curated annotations — full annotation on UniProt →

Function. Required for centrosome cohesion and recruitment of CEP68 to centrosomes.

Subunit / interactions. Interacts with CEP250 and CEP68. Interacts with NEK2; the interaction leads to phosphorylation of CNTLN.

Subcellular location. Cytoplasm. Cytoskeleton. Microtubule organizing center. Centrosome. Centriole.

Post-translational modifications. Phosphorylated directly or indirectly by NEK2.

Isoforms (3)

UniProt ID	Names	Canonical?
Q9NXG0-1	1	yes
Q9NXG0-2	2
Q9NXG0-3	3

RefSeq proteins (3): NP_001107867, NP_001351958, NP_060208* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR038810	CNTLN	Family

UniProt features (32 total): compositionally biased region 5, sequence variant 5, sequence conflict 5, modified residue 4, region of interest 4, coiled-coil region 4, splice variant 3, initiator methionine 1, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9NXG0-F1	71.14	0.23

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 (4): 2, 5, 22, 1343

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 213 (showing top): GSE45365_HEALTHY_VS_MCMV_INFECTION_CD8_TCELL_IFNAR_KO_DN, GSE45365_CTRL_VS_MCMV_INFECTION_NK_CELL_UP, GOBP_SINGLE_FERTILIZATION, RORA1_01, TTTGTAG_MIR520D, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, TGACCTY_ERR1_Q2, HNF1_Q6, GOBP_MALE_GAMETE_GENERATION, AAAYRNCTG_UNKNOWN, GOCC_MICROTUBULE_ORGANIZING_CENTER, NKX61_01, EVI1_05, TCF4_Q5, CDP_01

GO Biological Process (7): spermatogenesis (GO:0007283), single fertilization (GO:0007338), intracellular protein localization (GO:0008104), centriole-centriole cohesion (GO:0010457), regulation of protein localization (GO:0032880), protein-containing complex assembly (GO:0065003), protein localization to organelle (GO:0033365)

GO Molecular Function (4): protein kinase binding (GO:0019901), protein domain specific binding (GO:0019904), protein-macromolecule adaptor activity (GO:0030674), protein binding (GO:0005515)

GO Cellular Component (8): nucleoplasm (GO:0005654), cytoplasm (GO:0005737), centrosome (GO:0005813), centriole (GO:0005814), cytosol (GO:0005829), extracellular exosome (GO:0070062), sperm head-tail coupling apparatus (GO:0120212), cytoskeleton (GO:0005856)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	4
intracellular protein localization	2
protein binding	2
microtubule organizing center	2
intracellular membraneless organelle	2
developmental process involved in reproduction	1
male gamete generation	1
fertilization	1
macromolecule localization	1
centrosome cycle	1
cell cycle process	1
regulation of localization	1
cellular component assembly	1
protein-containing complex organization	1
kinase binding	1
molecular adaptor activity	1
binding	1
nuclear lumen	1
intracellular anatomical structure	1
centriole	1
cytoplasm	1
extracellular vesicle	1

Protein interactions and networks

STRING

1090 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CNTLN	PCNT	O95613	969
CNTLN	LRRC45	Q96CN5	924
CNTLN	CROCC	Q5TZA2	922
CNTLN	NIN	Q8N4C6	898
CNTLN	CEP250	Q9BV73	882
CNTLN	CEP170	Q5SW79	878
CNTLN	CCP110	O43303	878
CNTLN	CPAP	Q9HC77	874
CNTLN	CEP135	Q66GS9	870
CNTLN	PLK4	O00444	849
CNTLN	CNTROB	Q8N137	845
CNTLN	SASS6	Q6UVJ0	821
CNTLN	CEP290	O15078	816
CNTLN	CEP152	O94986	815
CNTLN	CEP120	Q8N960	802

IntAct

10 interactions, top by confidence:

A	B	Type	Score
ATG101	ATG13	psi-mi:“MI:0914”(association)	0.950
PPP5C	IRS4	psi-mi:“MI:0914”(association)	0.570
LAS2	CNTLN	psi-mi:“MI:0915”(physical association)	0.400
YWHAB	BRAF	psi-mi:“MI:0914”(association)	0.350
YWHAE	DEPDC5	psi-mi:“MI:0914”(association)	0.350
YWHAG	BRAF	psi-mi:“MI:0914”(association)	0.350
CARNMT1	LENG9	psi-mi:“MI:0914”(association)	0.350
GOPC	ZBTB5	psi-mi:“MI:0914”(association)	0.350
TPM1	SPAG9	psi-mi:“MI:0914”(association)	0.350

BioGRID (35): CNTLN (Affinity Capture-MS), CNTLN (Affinity Capture-MS), CNTLN (Affinity Capture-MS), CNTLN (Affinity Capture-MS), CNTLN (Affinity Capture-MS), CNTLN (Affinity Capture-MS), CNTLN (Affinity Capture-MS), CNTLN (Affinity Capture-MS), CNTLN (Affinity Capture-MS), CNTLN (Affinity Capture-MS), CNTLN (Proximity Label-MS), RFK (Two-hybrid), C18orf54 (Two-hybrid), CNTLN (Proximity Label-MS), CNTLN (Proximity Label-MS)

ESM2 similar proteins: A0A1L8GUX5, A0A1L8GXY6, A0A1W2P884, A2AIW0, A2AM05, A2CE83, A6PWD2, E7F5E1, O60296, P27628, P28290, P60853, Q0VF96, Q28GJ0, Q2KJD6, Q2M243, Q2MJV9, Q3V036, Q4KLH6, Q5R9L2, Q5RHB5, Q5SZL2, Q5U2Y9, Q5U3Z6, Q5U4W1, Q6AW69, Q6DIS8, Q6NRK1, Q6NRX3, Q6P2H3, Q6PCQ0, Q6ZQ06, Q70YC5, Q804T6, Q80ST9, Q86VQ0, Q8BMK0, Q8C115, Q8CFC9, Q8CGZ2

Diamond homologs: A0A096LPI5, A6NIU2, A6NJG6, F2Z398, P0DTE4, P51957, Q09FC8, Q5H9K5, Q5T7P6, Q68CZ1, Q6B4Z3, Q6UX73, Q86U02, Q8IV13, Q8N7M2, Q8N9N2, Q8NDZ0, Q8NEM8, Q8TDM0, Q92918, Q96J02, Q96MD7, Q9BUA6, Q9NXG0, A2AM05, A9ZSY0

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	239
Likely benign	16
Benign	8

Top pathogenic / likely-pathogenic (0)

SpliceAI

7105 predictions. Top by Δscore:

Variant	Effect	Δscore
9:17135220:A:T	donor_gain	1.0000
9:17143286:A:G	acceptor_gain	1.0000
9:17166963:AGC:A	donor_gain	1.0000
9:17167009:G:GT	donor_gain	1.0000
9:17226195:A:AG	acceptor_gain	1.0000
9:17226196:T:G	acceptor_gain	1.0000
9:17226197:A:AG	acceptor_gain	1.0000
9:17226198:T:G	acceptor_gain	1.0000
9:17226201:A:AG	acceptor_gain	1.0000
9:17226202:G:GA	acceptor_gain	1.0000
9:17226202:GA:G	acceptor_gain	1.0000
9:17226202:GAGA:G	acceptor_gain	1.0000
9:17226202:GAGAA:G	acceptor_gain	1.0000
9:17226283:AACAG:A	donor_loss	1.0000
9:17226284:ACAGG:A	donor_loss	1.0000
9:17226285:CAGGT:C	donor_loss	1.0000
9:17226287:GG:G	donor_loss	1.0000
9:17226288:G:GA	donor_loss	1.0000
9:17226289:T:A	donor_loss	1.0000
9:17235654:ACAG:A	acceptor_loss	1.0000
9:17235656:A:AG	acceptor_gain	1.0000
9:17235656:AG:A	acceptor_loss	1.0000
9:17235657:G:A	acceptor_loss	1.0000
9:17235657:G:GG	acceptor_gain	1.0000
9:17235657:GA:G	acceptor_gain	1.0000
9:17235657:GAGA:G	acceptor_gain	1.0000
9:17235739:A:T	donor_gain	1.0000
9:17235788:TTAAG:T	donor_loss	1.0000
9:17235790:AAG:A	donor_loss	1.0000
9:17235791:AGG:A	donor_loss	1.0000

AlphaMissense

9334 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000006664 (9:17175781 T>G), RS1000010459 (9:17388436 G>A), RS1000011270 (9:17252623 T>C), RS1000023909 (9:17181887 C>T), RS1000031175 (9:17213579 G>T), RS1000032596 (9:17448312 G>A), RS1000039389 (9:17245954 T>G), RS1000043321 (9:17144699 G>A), RS1000049342 (9:17522338 G>A), RS1000057464 (9:17252821 T>A), RS1000057877 (9:17351779 T>C), RS1000061937 (9:17296339 A>C,G), RS1000062672 (9:17443520 T>C), RS1000073838 (9:17408178 A>G), RS1000074494 (9:17337561 A>G)

Disease associations

OMIM: gene MIM:611870 | disease phenotypes:

GenCC curated gene-disease

Mondo (1): primary amenorrhea (MONDO:1060208)

Orphanet (0):

HPO phenotypes

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

GWAS associations

18 associations (top):

Study	Trait	p-value
GCST000455_1	Ovarian cancer	5.000000e-19
GCST001651_23	Response to amphetamines	6.000000e-06
GCST002337_85	Amyotrophic lateral sclerosis (sporadic)	8.000000e-06
GCST003327_10	Squamous cell carcinoma	8.000000e-09
GCST003485_2	Response to fenofibrate (HDL cholesterol levels)	9.000000e-06
GCST003655_8	Cutaneous squamous cell carcinoma	1.000000e-08
GCST003989_26	Chin dimples	2.000000e-13
GCST004033_10	QRS interval (sulfonylurea treatment interaction)	2.000000e-07
GCST004033_16	QRS interval (sulfonylurea treatment interaction)	6.000000e-08
GCST004744_66	Lung adenocarcinoma	3.000000e-06
GCST005175_17	Coronary artery calcified atherosclerotic plaque (90 or 130 HU threshold) in type 2 diabetes	5.000000e-06
GCST006611_102	HDL cholesterol	3.000000e-08
GCST006979_158	Heel bone mineral density	6.000000e-11
GCST010148_14	Cutaneous squamous cell carcinoma	1.000000e-17
GCST90020025_1127	Waist-to-hip ratio adjusted for BMI	3.000000e-09
GCST90020027_985	Waist-hip index	5.000000e-09
GCST90020029_61	Waist circumference adjusted for body mass index	2.000000e-08
GCST90020029_62	Waist circumference adjusted for body mass index	4.000000e-10

EFO canonical traits (8, from GWAS)

EFO ID	Trait name
EFO:0007805	HDL cholesterol change measurement
EFO:1001927	cutaneous squamous cell carcinoma
EFO:0007922	response to sulfonylurea
EFO:0004723	coronary artery calcification
EFO:0004612	high density lipoprotein cholesterol measurement
EFO:0009270	heel bone mineral density
EFO:0007788	BMI-adjusted waist-hip ratio
EFO:0007789	BMI-adjusted waist circumference

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, increases expression, affects expression, decreases expression	4
trichostatin A	affects cotreatment, increases expression	3
sodium arsenite	decreases expression, affects cotreatment, increases abundance	2
Benzo(a)pyrene	increases expression, increases methylation	2
Phenylmercuric Acetate	affects cotreatment, decreases expression	2
aristolochic acid I	decreases expression	1
methylmercuric chloride	decreases expression	1
bisphenol A	affects expression	1
titanium dioxide	increases methylation	1
butyraldehyde	decreases expression	1
perfluorooctanoic acid	increases expression	1
manganese chloride	affects cotreatment, decreases expression, increases abundance	1
benzo(e)pyrene	decreases methylation	1
potassium chromate(VI)	affects cotreatment, decreases expression	1
epigallocatechin gallate	affects cotreatment, decreases expression	1
pentanal	decreases expression	1
di-n-butylphosphoric acid	affects expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression, increases expression	1
dorsomorphin	decreases expression, increases expression, affects cotreatment	1
bisphenol S	increases methylation	1
jinfukang	affects cotreatment, decreases expression	1
Resveratrol	affects cotreatment, increases expression	1
Sunitinib	increases expression	1
Leflunomide	increases expression	1
Acetaminophen	decreases expression	1
Arsenic	affects cotreatment, decreases expression, increases abundance	1
Cisplatin	affects cotreatment, decreases expression	1
Dichlorodiphenyl Dichloroethylene	increases expression	1
Demecolcine	decreases expression	1
Dimethyl Sulfoxide	increases expression	1

Clinical trials (associated diseases)

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

Trial	Phase	Status	Title
NCT07164248	Not specified	COMPLETED	Evaluation of Bone Mineral Density Indications and Outcomes in Female Adolescents: Implications for Early Detection of Osteopenia/Osteoporosis and Gynecologic Practice