CEP44

Summary

CEP44 (centrosomal protein 44, HGNC:29356) is a protein-coding gene on chromosome 4q34.1, encoding Centrosomal protein of 44 kDa (Q9C0F1). Centriole-enriched microtubule-binding protein involved in centriole biogenesis.

Enables microtubule binding activity. Involved in centriole replication and centriole-centriole cohesion. Located in cytosol and microtubule cytoskeleton.

Source: NCBI Gene 80817 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 54 total — 1 pathogenic
• MANE Select transcript: NM_001040157

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:29356
Approved symbol	CEP44
Name	centrosomal protein 44
Location	4q34.1
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000164118
Ensembl biotype	protein_coding
OMIM	620217
Entrez	80817

Gene structure

Transcript identifiers

Ensembl transcripts: 20 — 18 protein_coding, 1 nonsense_mediated_decay, 1 retained_intron

ENST00000296519, ENST00000396791, ENST00000426172, ENST00000457424, ENST00000503053, ENST00000503780, ENST00000505124, ENST00000508483, ENST00000514712, ENST00000515299, ENST00000853407, ENST00000853408, ENST00000853409, ENST00000927478, ENST00000927479, ENST00000927480, ENST00000927481, ENST00000927482, ENST00000927483, ENST00000961153

RefSeq mRNA: 2 — MANE Select: NM_001040157 NM_001040157, NM_001145314

CCDS: CCDS34106, CCDS47163

Canonical transcript exons

ENST00000503780 — 12 exons

Exon	Start	End
ENSE00001081599	174304247	174304369
ENSE00001081601	174316530	174316567
ENSE00001081602	174302039	174302186
ENSE00001081603	174316166	174316290
ENSE00001081605	174308689	174308859
ENSE00001081609	174303703	174303849
ENSE00001547096	174297966	174298062
ENSE00001557683	174299072	174299210
ENSE00002019729	174283911	174283943
ENSE00002058980	174317335	174320328
ENSE00003649126	174309850	174310056
ENSE00003665645	174310783	174310858

Expression profiles

Bgee: expression breadth ubiquitous, 248 present calls, max score 90.47.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 13.5818 / max 497.8515, expressed in 1742 samples.

FANTOM5 promoters (10 alternative TSS)

Promoter ID	TPM avg	Samples expressed
50657	6.2694	1603
50655	3.1007	1136
50658	1.6984	802
50650	0.6600	333
50651	0.5998	120
50653	0.5488	285
50654	0.4230	207
50659	0.1200	39
50656	0.1047	27
50652	0.0572	15

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
bronchial epithelial cell	CL:0002328	90.47	gold quality
calcaneal tendon	UBERON:0003701	90.39	gold quality
bronchus	UBERON:0002185	89.52	gold quality
secondary oocyte	CL:0000655	87.71	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	87.47	gold quality
ventricular zone	UBERON:0003053	87.01	gold quality
ileal mucosa	UBERON:0000331	86.97	gold quality
upper leg skin	UBERON:0004262	86.74	gold quality
oocyte	CL:0000023	86.43	gold quality
endometrium	UBERON:0001295	85.97	gold quality
epithelium of nasopharynx	UBERON:0001951	85.91	gold quality
mucosa of paranasal sinus	UBERON:0005030	85.77	gold quality
adrenal tissue	UBERON:0018303	85.62	gold quality
skin of hip	UBERON:0001554	85.60	gold quality
upper arm skin	UBERON:0004263	85.46	gold quality
jejunal mucosa	UBERON:0000399	85.20	gold quality
tendon	UBERON:0000043	84.98	gold quality
tibia	UBERON:0000979	84.80	gold quality
muscle layer of sigmoid colon	UBERON:0035805	84.60	gold quality
left ovary	UBERON:0002119	84.49	gold quality
seminal vesicle	UBERON:0000998	84.44	gold quality
stromal cell of endometrium	CL:0002255	84.32	gold quality
right ovary	UBERON:0002118	84.17	gold quality
bone marrow cell	CL:0002092	84.12	gold quality
rectum	UBERON:0001052	83.94	gold quality
ovary	UBERON:0000992	83.73	gold quality
smooth muscle tissue	UBERON:0001135	83.63	gold quality
body of pancreas	UBERON:0001150	83.63	gold quality
corpus callosum	UBERON:0002336	83.62	gold quality
uterus	UBERON:0000995	83.60	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	4.92
E-GEOD-75140	no	176.36

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 2)

• Cep44 functions in centrosome cohesion by stabilizing rootletin. (PMID:31974111)
• CEP44 was identified as a luminal centriolar protein that binds to A-MTs and the inner centriole protein POC1B. (PMID:32060285)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	cep44	ENSDARG00000053106
mus_musculus	Cep44	ENSMUSG00000038215
rattus_norvegicus	Cep44	ENSRNOG00000010566

Protein

Protein identifiers

Centrosomal protein of 44 kDa — Q9C0F1 (reviewed: Q9C0F1)

Alternative names: HBV PreS1-transactivated protein 3

All UniProt accessions (4): Q9C0F1, D6RBX1, D6RC25, D6RGX6

UniProt curated annotations — full annotation on UniProt →

Function. Centriole-enriched microtubule-binding protein involved in centriole biogenesis. In collaboration with CEP295 and POC1B, is required for the centriole-to-centrosome conversion by ensuring the formation of bona fide centriole wall. Functions as a linker component that maintains centrosome cohesion. Associates with CROCC and regulates its stability and localization to the centrosome.

Subunit / interactions. Interacts with CROCC. Interacts with POC1B; the interaction is direct and recruits POC1B to centriolar microtubules. Binds to centriolar microtubules.

Subcellular location. Cytoplasm. Cytoskeleton. Microtubule organizing center. Centrosome. Centriole. Spindle pole. Midbody.

Isoforms (2)

UniProt ID	Names	Canonical?
Q9C0F1-1	1	yes
Q9C0F1-2	2

RefSeq proteins (2): NP_001035247, NP_001138786 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR029157	CEP44_CC	Domain
IPR033603	CEP44	Family

Pfam: PF15007

UniProt features (19 total): helix 7, modified residue 3, region of interest 2, coiled-coil region 2, chain 1, sequence variant 1, mutagenesis site 1, compositionally biased region 1, splice variant 1

Structure

Experimental structures (PDB)

1 structures.

PDB	Method	Resolution (Å)
7PT5	X-RAY DIFFRACTION	2.3

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9C0F1-F1	68.41	0.31

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): 331, 345, 346

Mutagenesis-validated functional residues (1):

Position	Phenotype
68–88	loss of binding to microtubules and location to centrioles.

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 151 (showing top): chr4q34, GOCC_MICROTUBULE_ORGANIZING_CENTER, GOBP_CENTRIOLE_ASSEMBLY, WCTCNATGGY_UNKNOWN, GTGTTGA_MIR505, GOCC_CENTROSOME, GOBP_ORGANELLE_ASSEMBLY, PYEON_CANCER_HEAD_AND_NECK_VS_CERVICAL_UP, ZHOU_INFLAMMATORY_RESPONSE_LIVE_DN, HAND1E47_01, GOBP_CENTROSOME_DUPLICATION, GOCC_SPINDLE, GOCC_CENTRIOLE, NUYTTEN_EZH2_TARGETS_DN, GOCC_MIDBODY

GO Biological Process (3): centrosome cycle (GO:0007098), centriole replication (GO:0007099), centriole-centriole cohesion (GO:0010457)

GO Molecular Function (2): microtubule binding (GO:0008017), protein binding (GO:0005515)

GO Cellular Component (8): spindle pole (GO:0000922), centrosome (GO:0005813), centriole (GO:0005814), cytosol (GO:0005829), midbody (GO:0030496), ciliary basal body (GO:0036064), cytoplasm (GO:0005737), cytoskeleton (GO:0005856)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	4
cell cycle process	3
microtubule organizing center	3
intracellular membraneless organelle	2
microtubule organizing center organization	1
centrosome duplication	1
centriole assembly	1
centrosome cycle	1
tubulin binding	1
binding	1
spindle	1
centriole	1
cytoplasm	1
cilium	1
intracellular anatomical structure	1

Protein interactions and networks

STRING

1088 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CEP44	FBXO8	Q9NRD0	593
CEP44	CEP295	Q9C0D2	528
CEP44	TEDC1	Q86SX3	511
CEP44	CCDC102B	Q68D86	500
CEP44	CNTLN	Q9NXG0	492
CEP44	SKIDA1	Q1XH10	483
CEP44	CEP120	Q8N960	479
CEP44	CEP164	Q9UPV0	478
CEP44	TUBD1	Q9UJT1	475
CEP44	SPICE1	Q8N0Z3	461
CEP44	TEDC2	Q7L2K0	453
CEP44	ELMOD2	Q8IZ81	450
CEP44	CEP97	Q8IW35	446
CEP44	PCNX4	Q63HM2	445
CEP44	RTTN	Q86VV8	440
CEP44	HYLS1	Q96M11	440

IntAct

300 interactions, top by confidence:

A	B	Type	Score
MAPK9	CEP44	psi-mi:“MI:0915”(physical association)	0.780
CEP44	ABI3	psi-mi:“MI:0915”(physical association)	0.780
CEP44	MAPK9	psi-mi:“MI:0915”(physical association)	0.780
CEP44	H2AP	psi-mi:“MI:0915”(physical association)	0.720
TXLNA	CEP44	psi-mi:“MI:0915”(physical association)	0.720
POP5	CEP44	psi-mi:“MI:0915”(physical association)	0.720
CEP44	ZFYVE26	psi-mi:“MI:0915”(physical association)	0.720
CEP44	ZNF587	psi-mi:“MI:0915”(physical association)	0.720
TSGA10	CEP44	psi-mi:“MI:0915”(physical association)	0.720
CEP44	TXLNA	psi-mi:“MI:0915”(physical association)	0.720
ZFYVE26	CEP44	psi-mi:“MI:0915”(physical association)	0.720
ZNF587	CEP44	psi-mi:“MI:0915”(physical association)	0.720
H2AP	CEP44	psi-mi:“MI:0915”(physical association)	0.720
CEP44	CBY2	psi-mi:“MI:0915”(physical association)	0.670
ZNF417	CEP44	psi-mi:“MI:0915”(physical association)	0.670
CBY2	CEP44	psi-mi:“MI:0915”(physical association)	0.670
CEP44	ZNF417	psi-mi:“MI:0915”(physical association)	0.670

BioGRID (254): CEP44 (Two-hybrid), CEP44 (Two-hybrid), CEP44 (Two-hybrid), CEP44 (Two-hybrid), CEP44 (Two-hybrid), CEP44 (Two-hybrid), CEP44 (Two-hybrid), CEP44 (Two-hybrid), CEP44 (Two-hybrid), CEP44 (Two-hybrid), CEP44 (Two-hybrid), CEP44 (Two-hybrid), CEP44 (Two-hybrid), CEP44 (Two-hybrid), CEP44 (Two-hybrid)

ESM2 similar proteins: A0A1B0GW35, A6QNM3, B0R034, B1ANS9, B9EK06, D2KC46, D3ZY60, F1MS15, F1P065, F1REV3, O00522, O15091, O75747, P10911, P58069, Q008S8, Q14449, Q14D04, Q15283, Q32NR9, Q45GW3, Q4R366, Q4R6T7, Q5H9U9, Q5K651, Q5PQS3, Q5XGX5, Q5XIZ9, Q5ZLD2, Q60862, Q63713, Q69Z37, Q6DCF6, Q6S5J6, Q6TNJ1, Q75PQ8, Q80W71, Q86VD1, Q86YR7, Q8C5W4

Diamond homologs: A2RVA7, Q08DB0, Q0P4I1, Q3B7T8, Q4R7I0, Q5HZK1, Q9C0F1

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 91 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
Loss of Nlp from mitotic centrosomes	7	25.8×	9e-07
Loss of proteins required for interphase microtubule organization from the centrosome	7	25.8×	9e-07
AURKA Activation by TPX2	7	24.8×	9e-07
Recruitment of mitotic centrosome proteins and complexes	7	22.1×	2e-06
Anchoring of the basal body to the plasma membrane	8	21.0×	9e-07
Regulation of PLK1 Activity at G2/M Transition	7	20.7×	2e-06
Recruitment of NuMA to mitotic centrosomes	7	19.0×	3e-06

GO biological processes:

GO term	Partners	Fold	FDR
cilium assembly	8	8.1×	2e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	1
Likely pathogenic	0
Uncertain significance	41
Likely benign	6
Benign	0

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
2423427	NC_000004.11:g.(?174448428)(175443602_?)del	Pathogenic

SpliceAI

2188 predictions. Top by Δscore:

Variant	Effect	Δscore
4:174299066:TTTCA:T	acceptor_loss	1.0000
4:174299067:TTCA:T	acceptor_loss	1.0000
4:174299068:TCA:T	acceptor_loss	1.0000
4:174299069:CAGGT:C	acceptor_loss	1.0000
4:174299070:A:AT	acceptor_loss	1.0000
4:174299071:G:GC	acceptor_loss	1.0000
4:174299206:GTAGG:G	donor_gain	1.0000
4:174299209:GG:G	donor_gain	1.0000
4:174299210:GG:G	donor_gain	1.0000
4:174299211:G:GC	donor_loss	1.0000
4:174299211:G:GG	donor_gain	1.0000
4:174302037:A:AG	acceptor_gain	1.0000
4:174302037:AGTTT:A	acceptor_gain	1.0000
4:174302038:G:GG	acceptor_gain	1.0000
4:174302038:GT:G	acceptor_gain	1.0000
4:174302038:GTT:G	acceptor_gain	1.0000
4:174302038:GTTT:G	acceptor_gain	1.0000
4:174302038:GTTTG:G	acceptor_gain	1.0000
4:174302182:ATAAG:A	donor_loss	1.0000
4:174302183:TAAG:T	donor_loss	1.0000
4:174302184:AAGG:A	donor_loss	1.0000
4:174302185:AGG:A	donor_loss	1.0000
4:174302186:GGT:G	donor_loss	1.0000
4:174302187:G:C	donor_loss	1.0000
4:174302188:T:A	donor_loss	1.0000
4:174305599:A:AG	donor_gain	1.0000
4:174308684:T:G	acceptor_gain	1.0000
4:174308684:TGCA:T	acceptor_loss	1.0000
4:174308685:GCA:G	acceptor_loss	1.0000
4:174308686:CA:C	acceptor_loss	1.0000

AlphaMissense

2602 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
4:174303766:T:C	F101L	0.998
4:174303768:T:A	F101L	0.998
4:174303768:T:G	F101L	0.998
4:174302049:G:A	G34R	0.997
4:174302049:G:C	G34R	0.997
4:174303707:T:C	L81P	0.997
4:174303710:G:C	R82P	0.997
4:174303737:T:C	L91S	0.997
4:174303752:T:C	F96S	0.997
4:174299159:T:C	L13P	0.996
4:174302050:G:A	G34E	0.996
4:174303731:C:G	P89R	0.996
4:174310016:G:C	R282P	0.996
4:174302050:G:T	G34V	0.995
4:174302166:T:C	F73L	0.995
4:174302167:T:C	F73S	0.995
4:174302168:T:A	F73L	0.995
4:174302168:T:G	F73L	0.995
4:174303709:C:A	R82S	0.995
4:174303731:C:A	P89Q	0.995
4:174303737:T:G	L91W	0.994
4:174310007:T:C	L279P	0.994
4:174299132:G:A	G4D	0.993
4:174303767:T:C	F101S	0.993
4:174299153:G:C	R11P	0.992
4:174299171:T:C	L17P	0.992
4:174303704:T:C	L80P	0.992
4:174303707:T:G	L81R	0.992
4:174303779:A:T	K105I	0.992
4:174309997:T:A	W276R	0.992

dbSNP variants (sampled 300 via entrez): RS1000037425 (4:174329349 C>A,T), RS1000226578 (4:174305609 G>A), RS1000243438 (4:174303674 AT>A), RS1000336997 (4:174312078 C>T), RS1000403101 (4:174311277 A>G), RS1000519862 (4:174289966 G>T), RS1000608535 (4:174329430 A>G), RS1000654013 (4:174317603 G>A,C,T), RS1000668254 (4:174310426 C>G,T), RS1000716933 (4:174323307 C>A,T), RS1000849380 (4:174305322 C>G,T), RS1000910728 (4:174298328 A>C,G), RS1000963962 (4:174298504 G>C), RS1000964492 (4:174303913 G>A), RS1001032605 (4:174322132 A>G)

Disease associations

OMIM: gene MIM:620217 | 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
GCST000924_1	Response to acetaminophen (hepatotoxicity)	6.000000e-06

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	decreases methylation, affects cotreatment, increases expression, decreases expression	4
bisphenol A	increases expression, decreases expression	2
sodium arsenite	decreases expression, affects cotreatment, increases abundance	2
Benzo(a)pyrene	decreases expression	2
Tretinoin	decreases expression	2
aristolochic acid I	decreases expression	1
triphenyl phosphate	affects expression	1
arsenite	affects binding, decreases reaction	1
tris(1,3-dichloro-2-propyl)phosphate	decreases expression	1
butyraldehyde	decreases expression	1
manganese chloride	affects cotreatment, decreases expression, increases abundance	1
potassium chromate(VI)	decreases expression	1
N-acetyl-4-benzoquinoneimine	affects response to substance	1
pentanal	decreases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, increases expression	1
dorsomorphin	affects cotreatment, increases expression	1
Temozolomide	decreases expression	1
Sunitinib	increases expression	1
Vorinostat	increases expression	1
Air Pollutants	decreases expression	1
Arsenic	decreases expression, increases abundance, affects cotreatment	1
Atrazine	decreases expression	1
Enzyme Inhibitors	decreases activity, increases O-linked glycosylation	1
Folic Acid	decreases expression	1
Manganese	decreases expression, increases abundance, affects cotreatment	1
Silicon Dioxide	decreases expression	1
Testosterone	decreases expression	1
Tobacco Smoke Pollution	decreases expression	1
Tunicamycin	decreases expression	1
Urethane	increases expression	1

Clinical trials (associated diseases)

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