SPICE1

Summary

SPICE1 (spindle and centriole associated protein 1, HGNC:25083) is a protein-coding gene on chromosome 3q13.2, encoding Spindle and centriole-associated protein 1 (Q8N0Z3). Regulator required for centriole duplication, for proper bipolar spindle formation and chromosome congression in mitosis. It is a selective cancer dependency (DepMap: 13.7% of cell lines).

Involved in metaphase chromosome alignment; mitotic spindle assembly; and regulation of centriole replication. Located in intracellular membrane-bounded organelle; microtubule cytoskeleton; and plasma membrane.

Source: NCBI Gene 152185 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 144 total — 1 pathogenic
• Cancer dependency (DepMap): dependent in 13.7% of screened cell lines
• MANE Select transcript: NM_144718

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:25083
Approved symbol	SPICE1
Name	spindle and centriole associated protein 1
Location	3q13.2
Locus type	gene with protein product
Status	Approved
Aliases	SPICE
Ensembl gene	ENSG00000163611
Ensembl biotype	protein_coding
OMIM	613447
Entrez	152185

Gene structure

Transcript identifiers

Ensembl transcripts: 22 — 20 protein_coding, 2 retained_intron

ENST00000295872, ENST00000460832, ENST00000467618, ENST00000480527, ENST00000495812, ENST00000496105, ENST00000496859, ENST00000854918, ENST00000854919, ENST00000854920, ENST00000854921, ENST00000854922, ENST00000854923, ENST00000854924, ENST00000854925, ENST00000854926, ENST00000854927, ENST00000930826, ENST00000930827, ENST00000930828, ENST00000930829, ENST00000968436

RefSeq mRNA: 4 — MANE Select: NM_144718 NM_001331078, NM_001331079, NM_001387939, NM_144718

CCDS: CCDS2973

Canonical transcript exons

ENST00000295872 — 18 exons

Exon	Start	End
ENSE00001156013	113446589	113446676
ENSE00001156020	113448038	113448140
ENSE00001175104	113450336	113450516
ENSE00001199378	113494049	113494142
ENSE00001199381	113499439	113499582
ENSE00001277405	113514897	113515156
ENSE00001277415	113442718	113445360
ENSE00003489197	113469099	113469238
ENSE00003511105	113488945	113489063
ENSE00003514332	113468762	113468899
ENSE00003515593	113457136	113457357
ENSE00003591537	113503180	113503227
ENSE00003623440	113506507	113506605
ENSE00003627107	113453466	113453950
ENSE00003628863	113460617	113460764
ENSE00003640608	113465653	113465784
ENSE00003647241	113493206	113493312
ENSE00003690638	113468139	113468404

Expression profiles

Bgee: expression breadth ubiquitous, 230 present calls, max score 90.44.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 11.4811 / max 266.7659, expressed in 1704 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
43846	7.8939	1636
43845	3.5872	1155

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
oocyte	CL:0000023	90.44	gold quality
secondary oocyte	CL:0000655	90.29	gold quality
calcaneal tendon	UBERON:0003701	87.84	gold quality
ventricular zone	UBERON:0003053	87.04	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	86.88	gold quality
sural nerve	UBERON:0015488	83.97	gold quality
colonic epithelium	UBERON:0000397	83.65	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	82.54	gold quality
ganglionic eminence	UBERON:0004023	81.99	gold quality
islet of Langerhans	UBERON:0000006	80.09	gold quality
gall bladder	UBERON:0002110	80.04	gold quality
stromal cell of endometrium	CL:0002255	79.13	gold quality
tendon	UBERON:0000043	78.94	gold quality
rectum	UBERON:0001052	78.76	gold quality
right uterine tube	UBERON:0001302	77.97	gold quality
bronchial epithelial cell	CL:0002328	77.87	gold quality
vagina	UBERON:0000996	77.36	gold quality
ovary	UBERON:0000992	76.60	gold quality
endometrium	UBERON:0001295	76.49	gold quality
tonsil	UBERON:0002372	76.40	gold quality
minor salivary gland	UBERON:0001830	76.23	gold quality
pancreas	UBERON:0001264	76.22	gold quality
left ovary	UBERON:0002119	76.02	gold quality
ectocervix	UBERON:0012249	75.92	gold quality
endocervix	UBERON:0000458	75.59	gold quality
body of uterus	UBERON:0009853	75.41	gold quality
body of pancreas	UBERON:0001150	75.27	gold quality
mucosa of paranasal sinus	UBERON:0005030	75.15	gold quality
bone marrow cell	CL:0002092	75.11	gold quality
pituitary gland	UBERON:0000007	75.00	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	4.67
E-MTAB-7249	no	204.07

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

129 targeting SPICE1, 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-3613-3P	100.00	76.36	7965
HSA-MIR-513A-5P	100.00	69.77	2465
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-126-5P	100.00	72.71	3180
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-34A-5P	99.99	71.21	1784
HSA-MIR-449A	99.99	71.05	1776
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-4531	99.99	69.70	3181
HSA-MIR-3692-3P	99.98	70.27	2139
HSA-MIR-373-5P	99.98	75.36	4753
HSA-MIR-616-5P	99.98	75.58	4775
HSA-MIR-4482-3P	99.98	72.50	3147
HSA-MIR-27A-3P	99.98	72.13	2955
HSA-MIR-27B-3P	99.98	72.13	2955
HSA-MIR-9985	99.98	72.11	2939
HSA-MIR-34C-5P	99.97	70.45	1577
HSA-MIR-449B-5P	99.97	70.26	1580
HSA-MIR-3148	99.97	75.06	6478
HSA-MIR-607	99.97	73.62	5593
HSA-MIR-548AJ-3P	99.96	73.38	5345
HSA-MIR-548X-3P	99.96	73.38	5345
HSA-MIR-4666A-3P	99.96	71.71	3434
HSA-MIR-1250-3P	99.96	70.04	4038
HSA-MIR-570-3P	99.96	72.41	4910
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-548J-3P	99.94	72.61	4881
HSA-MIR-4525	99.94	64.38	675

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 13.7% of screened cell lines.

Literature-anchored findings (GeneRIF, showing 3)

• SPICE is required for centriole duplication and mitotic chromosome congression. (PMID:20736305)
• CEP120 associates with SPICE1 and CPAP, and depletion of any of these proteins results in short procentrioles. Furthermore, CEP120 or CPAP overexpression results in excessive centriole elongation, a process dependent on CEP120, SPICE1, and CPAP. (PMID:23810536)
• temporal and spatial Aurora kinase-mediated regulation of SPICE1 is important for correct chromosome segregation. (PMID:30485161)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	spice1	ENSDARG00000004647
mus_musculus	Spice1	ENSMUSG00000043065
rattus_norvegicus	Spice1	ENSRNOG00000039024

Protein

Protein identifiers

Spindle and centriole-associated protein 1 — Q8N0Z3 (reviewed: Q8N0Z3)

Alternative names: Coiled-coil domain-containing protein 52, Spindle and centriole-associated protein

All UniProt accessions (5): Q8N0Z3, C9IZF0, C9J4W3, C9J5T2, H7C5N4

UniProt curated annotations — full annotation on UniProt →

Function. Regulator required for centriole duplication, for proper bipolar spindle formation and chromosome congression in mitosis.

Subunit / interactions. Interacts with CEP120.

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

RefSeq proteins (4): NP_001318007, NP_001318008, NP_001374868, NP_653319* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR031387	SPICE1	Family

Pfam: PF15678

UniProt features (18 total): modified residue 6, region of interest 3, compositionally biased region 3, sequence variant 2, coiled-coil region 2, chain 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8N0Z3-F1	57.38	0.13

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 (6): 640, 644, 760, 764, 819, 235

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 200 (showing top): GSE45365_CTRL_VS_MCMV_INFECTION_NK_CELL_UP, GOBP_CHROMOSOME_ORGANIZATION, GOBP_REGULATION_OF_MICROTUBULE_BASED_PROCESS, GOBP_CHROMOSOME_LOCALIZATION, GOBP_REGULATION_OF_CELLULAR_COMPONENT_BIOGENESIS, GOCC_MICROTUBULE_ORGANIZING_CENTER, GOBP_REGULATION_OF_CENTRIOLE_REPLICATION, GOBP_CENTRIOLE_ASSEMBLY, GOBP_MITOTIC_SPINDLE_ASSEMBLY, GOBP_ORGANELLE_FISSION, GOBP_REGULATION_OF_CELL_CYCLE, GOCC_CENTROSOME, GOBP_MITOTIC_NUCLEAR_DIVISION, GOBP_REGULATION_OF_CENTROSOME_CYCLE, GOBP_ORGANELLE_ASSEMBLY

GO Biological Process (4): regulation of centriole replication (GO:0046599), cell division (GO:0051301), metaphase chromosome alignment (GO:0051310), mitotic spindle assembly (GO:0090307)

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

GO Cellular Component (7): centrosome (GO:0005813), centriole (GO:0005814), spindle (GO:0005819), plasma membrane (GO:0005886), ciliary basal body (GO:0036064), cytoplasm (GO:0005737), cytoskeleton (GO:0005856)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
microtubule organizing center	3
intracellular membraneless organelle	3
centriole replication	1
regulation of centrosome duplication	1
regulation of organelle assembly	1
cellular process	1
chromosome localization	1
nuclear chromosome segregation	1
mitotic sister chromatid segregation	1
mitotic spindle organization	1
spindle assembly	1
mitotic nuclear division	1
binding	1
centriole	1
microtubule cytoskeleton	1
membrane	1
cell periphery	1
cilium	1
intracellular anatomical structure	1
cellular anatomical structure	1

Protein interactions and networks

STRING

992 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SPICE1	CEP120	Q8N960	992
SPICE1	TACC1	O75410	786
SPICE1	TACC3	Q9Y6A5	746
SPICE1	CPAP	Q9HC77	738
SPICE1	POC5	Q8NA72	705
SPICE1	PCNT	O95613	661
SPICE1	CNTLN	Q9NXG0	608
SPICE1	CEP135	Q66GS9	603
SPICE1	CEP295	Q9C0D2	579
SPICE1	CEP192	Q8TEP8	578
SPICE1	CEP152	O94986	574
SPICE1	POC1B	Q8TC44	571
SPICE1	CCP110	O43303	570
SPICE1	CEP63	Q96MT8	563
SPICE1	NIN	Q8N4C6	561

IntAct

80 interactions, top by confidence:

A	B	Type	Score
MED4	MED19	psi-mi:“MI:2364”(proximity)	0.900
WRAP73	CEP135	psi-mi:“MI:0914”(association)	0.890
CSNK1E	PER1	psi-mi:“MI:0914”(association)	0.840
KDM1A	SPICE1	psi-mi:“MI:0915”(physical association)	0.670
SPICE1	KDM1A	psi-mi:“MI:0915”(physical association)	0.670
STXBP1	SPICE1	psi-mi:“MI:0915”(physical association)	0.560
Cep120	SPICE1	psi-mi:“MI:0915”(physical association)	0.560
CEP135	SPICE1	psi-mi:“MI:0914”(association)	0.540
CEP135	SPICE1	psi-mi:“MI:0915”(physical association)	0.540
KXD1	HIP1	psi-mi:“MI:0914”(association)	0.530
SPICE1	SERPINB2	psi-mi:“MI:0914”(association)	0.530
TGM5	UBB	psi-mi:“MI:0914”(association)	0.530
KXD1	TRAK2	psi-mi:“MI:0914”(association)	0.530
CEP162	OFD1	psi-mi:“MI:0914”(association)	0.420
SSX2IP	SPICE1	psi-mi:“MI:0914”(association)	0.420
SPICE1	IPO5	psi-mi:“MI:0914”(association)	0.420
SPICE1	Them6	psi-mi:“MI:0915”(physical association)	0.400
SPICE1	GSK3A	psi-mi:“MI:0915”(physical association)	0.400
GSK3B	SPICE1	psi-mi:“MI:0915”(physical association)	0.400
SPICE1	STAT2	psi-mi:“MI:0915”(physical association)	0.400
SPICE1	USP20	psi-mi:“MI:0915”(physical association)	0.400
	SPICE1	psi-mi:“MI:0915”(physical association)	0.370
Cep120	TBC1D31	psi-mi:“MI:0914”(association)	0.350
CEP43	CCHCR1	psi-mi:“MI:0914”(association)	0.350
MYH6	ELOC	psi-mi:“MI:0914”(association)	0.350
STAT5A	R3HDM2	psi-mi:“MI:0914”(association)	0.350
OFD1	CCDC14	psi-mi:“MI:0914”(association)	0.350
RGMA	BDP1	psi-mi:“MI:0914”(association)	0.350
Ccn1	SRGAP3	psi-mi:“MI:0914”(association)	0.350

BioGRID (248): SPICE1 (Proximity Label-MS), SPICE1 (Proximity Label-MS), SPICE1 (Proximity Label-MS), SPICE1 (Affinity Capture-Western), SPICE1 (Affinity Capture-MS), PCM1 (Affinity Capture-MS), IPO5 (Affinity Capture-MS), PTCD3 (Affinity Capture-MS), PA2G4 (Affinity Capture-MS), SPICE1 (Affinity Capture-Western), SPICE1 (Proximity Label-MS), SPICE1 (Proximity Label-MS), SPICE1 (Proximity Label-MS), ARHGAP21 (Proximity Label-MS), ARID1B (Proximity Label-MS)

ESM2 similar proteins: A1YF19, A2T767, B0K035, F1RCE7, F7BHS0, O95997, P0DPK0, P23999, P97613, Q08B36, Q08BD8, Q09HN1, Q0VA20, Q14140, Q2KHM9, Q2QD14, Q2QD15, Q2T9X8, Q2WG80, Q3SZY3, Q3UHI0, Q3V1H1, Q5R7F8, Q5RBY6, Q5RKG1, Q5XG16, Q5ZJU5, Q6A000, Q6AYH4, Q6DF94, Q7SXC6, Q8BHE0, Q8BHZ5, Q8C804, Q8N0Z3, Q8QGU6, Q8R080, Q8WWK9, Q96C57, Q96FF9

Diamond homologs: Q2T9X8, Q5RBY6, Q5RKG1, Q6DF94, Q8C804, Q8N0Z3

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 101 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	8	20.8×	5e-07
Loss of proteins required for interphase microtubule organization from the centrosome	8	20.8×	5e-07
Centrosome maturation	5	20.8×	2e-04
AURKA Activation by TPX2	8	20.0×	5e-07
Regulation of PLK1 Activity at G2/M Transition	9	18.7×	5e-07
Recruitment of mitotic centrosome proteins and complexes	8	17.8×	1e-06
Anchoring of the basal body to the plasma membrane	9	16.7×	5e-07
Recruitment of NuMA to mitotic centrosomes	8	15.3×	3e-06

GO biological processes:

GO term	Partners	Fold	FDR
positive regulation of autophagy	7	17.3×	7e-05
cilium assembly	10	8.8×	7e-05

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	1
Likely pathogenic	0
Uncertain significance	116
Likely benign	13
Benign	0

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
1527035	GRCh37/hg19 3q13.2-13.31(chr3:112144081-115514432)	Pathogenic

SpliceAI

3440 predictions. Top by Δscore:

Variant	Effect	Δscore
3:113444837:C:CT	acceptor_gain	1.0000
3:113444837:C:T	acceptor_gain	1.0000
3:113444838:A:T	acceptor_gain	1.0000
3:113448033:CTTA:C	donor_loss	1.0000
3:113448036:A:AC	donor_gain	1.0000
3:113448037:C:CC	donor_gain	1.0000
3:113448037:CCTT:C	donor_gain	1.0000
3:113448136:TCCTT:T	acceptor_gain	1.0000
3:113448137:CCTTC:C	acceptor_gain	1.0000
3:113448138:CTT:C	acceptor_gain	1.0000
3:113448141:C:CC	acceptor_gain	1.0000
3:113450357:A:C	donor_gain	1.0000
3:113453457:GGTAC:G	donor_loss	1.0000
3:113453458:GTACT:G	donor_loss	1.0000
3:113453459:TAC:T	donor_loss	1.0000
3:113453460:AC:A	donor_loss	1.0000
3:113453461:CTC:C	donor_loss	1.0000
3:113453462:TCAC:T	donor_loss	1.0000
3:113453463:CACAG:C	donor_loss	1.0000
3:113453464:A:AC	donor_gain	1.0000
3:113453464:AC:A	donor_loss	1.0000
3:113453465:C:CC	donor_gain	1.0000
3:113453465:C:CT	donor_loss	1.0000
3:113453465:CAGA:C	donor_gain	1.0000
3:113453465:CAGAA:C	donor_gain	1.0000
3:113453488:T:A	donor_gain	1.0000
3:113457129:GACTT:G	donor_loss	1.0000
3:113457130:ACTTA:A	donor_loss	1.0000
3:113457133:TA:T	donor_loss	1.0000
3:113457134:A:AC	donor_gain	1.0000

AlphaMissense

5592 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
3:113506512:A:G	W32R	0.994
3:113506512:A:T	W32R	0.994
3:113468146:A:G	L383P	0.993
3:113506510:C:A	W32C	0.993
3:113506510:C:G	W32C	0.993
3:113468179:A:G	L372P	0.992
3:113465699:A:G	L414P	0.989
3:113445331:A:C	F848L	0.988
3:113445331:A:T	F848L	0.988
3:113445333:A:G	F848L	0.988
3:113499576:G:T	R52S	0.988
3:113445336:A:G	W847R	0.986
3:113445336:A:T	W847R	0.986
3:113450438:C:G	A741P	0.986
3:113468190:G:C	F368L	0.986
3:113468190:G:T	F368L	0.986
3:113468192:A:G	F368L	0.986
3:113450452:C:G	R736P	0.985
3:113450458:A:G	L734S	0.985
3:113450425:A:G	L745P	0.984
3:113465711:A:G	L410P	0.984
3:113499575:C:G	R52P	0.984
3:113503211:A:G	L39P	0.984
3:113468158:A:G	L379P	0.983
3:113465717:C:G	R408P	0.981
3:113468167:A:G	L376P	0.979
3:113503181:A:G	L49P	0.979
3:113445332:A:G	F848S	0.978
3:113465703:C:G	A413P	0.978
3:113450445:A:C	S738R	0.977

dbSNP variants (sampled 300 via entrez): RS1000041775 (3:113454993 G>C), RS1000064088 (3:113495050 T>C), RS1000067093 (3:113445183 T>C), RS1000074581 (3:113454765 T>G), RS1000081788 (3:113487379 G>A), RS1000134076 (3:113458223 C>T), RS1000161594 (3:113507038 C>A), RS1000179278 (3:113482421 T>C), RS1000322135 (3:113461005 C>T), RS1000422897 (3:113481981 A>G), RS1000480566 (3:113513861 A>C,G), RS1000497575 (3:113444977 T>C), RS1000513111 (3:113462809 G>A,C), RS1000518373 (3:113494705 CAAAAT>C), RS1000579426 (3:113468894 G>C)

Disease associations

OMIM: gene MIM:613447 | 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
GCST001942_7	Prostate cancer	4.000000e-13

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

22 total (human), top 22 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects expression, decreases expression, increases methylation	3
Arsenic Trioxide	decreases expression, increases expression	2
Tretinoin	decreases expression	2
aristolochic acid I	decreases expression	1
FR900359	affects phosphorylation	1
bisphenol F	decreases methylation	1
dicrotophos	decreases expression	1
zinc chloride	decreases expression	1
butyraldehyde	decreases expression	1
di-n-butylphosphoric acid	affects expression	1
CGP 52608	affects binding, increases reaction	1
Acetaminophen	increases expression	1
Arsenic	affects methylation	1
Caffeine	decreases phosphorylation	1
Cisplatin	increases expression	1
Doxorubicin	decreases expression	1
Ethyl Methanesulfonate	increases expression	1
Methyl Methanesulfonate	increases expression	1
Urethane	decreases expression	1
Zinc	decreases expression	1
Aflatoxin B1	decreases methylation	1
Acrylamide	decreases expression	1

Clinical trials (associated diseases)

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