CENPV

Summary

CENPV (centromere protein V, HGNC:29920) is a protein-coding gene on chromosome 17p11.2, encoding Centromere protein V (Q7Z7K6). Required for distribution of pericentromeric heterochromatin in interphase nuclei and for centromere formation and organization, chromosome alignment and cytokinesis.

Predicted to enable carbon-sulfur lyase activity and metal ion binding activity. Involved in several processes, including centromere complex assembly; pericentric heterochromatin formation; and positive regulation of cytokinesis. Acts upstream of or within ameboidal-type cell migration. Located in several cellular components, including midbody; nucleus; and spindle midzone.

Source: NCBI Gene 201161 — RefSeq curated summary.

At a glance

• GWAS associations: 5
• Clinical variants (ClinVar): 46 total — 1 pathogenic
• MANE Select transcript: NM_181716

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:29920
Approved symbol	CENPV
Name	centromere protein V
Location	17p11.2
Locus type	gene with protein product
Status	Approved
Aliases	p30, CENP-V
Ensembl gene	ENSG00000166582
Ensembl biotype	protein_coding
OMIM	608139
Entrez	201161

Gene structure

Transcript identifiers

Ensembl transcripts: 8 — 3 retained_intron, 2 protein_coding, 2 nonsense_mediated_decay, 1 protein_coding_CDS_not_defined

ENST00000299736, ENST00000472570, ENST00000476243, ENST00000482983, ENST00000582062, ENST00000584214, ENST00000631687, ENST00000928025

RefSeq mRNA: 1 — MANE Select: NM_181716 NM_181716

CCDS: CCDS32575

Canonical transcript exons

ENST00000299736 — 5 exons

Exon	Start	End
ENSE00001104396	16353027	16353469
ENSE00003466885	16349931	16350029
ENSE00003553350	16348616	16348685
ENSE00003629710	16342537	16342941
ENSE00003635618	16344597	16344711

Expression profiles

Bgee: expression breadth ubiquitous, 234 present calls, max score 99.32.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 28.6226 / max 646.0348, expressed in 1610 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
164725	27.2547	1606
164723	1.0561	225
164724	0.3118	159

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
ganglionic eminence	UBERON:0004023	99.32	gold quality
embryo	UBERON:0000922	99.31	gold quality
ventricular zone	UBERON:0003053	99.19	gold quality
cortical plate	UBERON:0005343	98.68	gold quality
pancreatic ductal cell	CL:0002079	98.57	gold quality
ileal mucosa	UBERON:0000331	97.61	gold quality
mucosa of transverse colon	UBERON:0004991	96.14	gold quality
cerebellar hemisphere	UBERON:0002245	96.09	gold quality
cerebellar cortex	UBERON:0002129	95.99	gold quality
right hemisphere of cerebellum	UBERON:0014890	95.88	gold quality
jejunal mucosa	UBERON:0000399	95.61	gold quality
right lobe of liver	UBERON:0001114	95.33	gold quality
cerebellum	UBERON:0002037	95.27	gold quality
thymus	UBERON:0002370	94.82	gold quality
prefrontal cortex	UBERON:0000451	94.77	gold quality
duodenum	UBERON:0002114	94.72	gold quality
right frontal lobe	UBERON:0002810	94.56	gold quality
Brodmann (1909) area 9	UBERON:0013540	94.47	gold quality
nucleus accumbens	UBERON:0001882	94.39	gold quality
left testis	UBERON:0004533	94.39	gold quality
rectum	UBERON:0001052	94.37	gold quality
right testis	UBERON:0004534	94.32	gold quality
anterior cingulate cortex	UBERON:0009835	94.21	gold quality
amygdala	UBERON:0001876	93.75	gold quality
hindlimb stylopod muscle	UBERON:0004252	93.75	gold quality
hypothalamus	UBERON:0001898	93.50	gold quality
putamen	UBERON:0001874	93.49	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	93.41	gold quality
caudate nucleus	UBERON:0001873	93.38	gold quality
small intestine Peyer’s patch	UBERON:0003454	93.38	gold quality

Single-cell (SCXA)

Detected in 5 experiment(s), a significant marker in 3.

Experiment	Marker?	Max mean expression
E-MTAB-8271	yes	305.96
E-HCAD-5	yes	21.11
E-MTAB-6108	no	466.88
E-MTAB-9388	no	9.39
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

22 targeting CENPV, 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-4425	100.00	67.59	1049
HSA-MIR-22-3P	99.93	68.13	917
HSA-MIR-6721-5P	99.93	68.92	2981
HSA-MIR-8063	99.91	69.76	3146
HSA-MIR-377-3P	99.37	70.18	1905
HSA-MIR-7702	99.06	65.95	698
HSA-MIR-6770-5P	98.97	66.76	1853
HSA-MIR-2467-3P	98.65	67.18	1969
HSA-MIR-3187-5P	98.36	65.74	1776
HSA-MIR-6882-3P	98.23	67.01	1119
HSA-MIR-4691-3P	98.11	66.83	1204
HSA-MIR-1285-3P	97.72	67.02	1932
HSA-MIR-5189-5P	97.72	66.96	1814
HSA-MIR-3127-5P	97.52	65.24	786
HSA-MIR-558	97.50	67.16	977
HSA-MIR-612	97.26	65.95	1597
HSA-MIR-509-3-5P	97.21	67.74	1517
HSA-MIR-509-5P	97.21	67.90	1512
HSA-MIR-6860	97.21	66.31	1656
HSA-MIR-4418	97.04	67.16	1372
HSA-MIR-874-5P	96.93	63.92	1014
HSA-MIR-4259	95.68	65.25	582

Literature-anchored findings (GeneRIF, showing 1)

• Results suggest that CENP-V (nuclear protein p30) is required for centromere organization, chromosome alignment and cytokinesis in human cells (PMID:18772885)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	cenpv	ENSDARG00000092285
mus_musculus	Cenpv	ENSMUSG00000018509
rattus_norvegicus	Cenpv	ENSRNOG00000003086
caenorhabditis_elegans		WBGENE00017771

Paralogs (3): CENPVL1 (ENSG00000223591), CENPVL3 (ENSG00000224109), CENPVL2 (ENSG00000283093)

Protein

Protein identifiers

Centromere protein V — Q7Z7K6 (reviewed: Q7Z7K6)

Alternative names: Nuclear protein p30, Proline-rich protein 6

All UniProt accessions (3): A0A0M3HER2, Q7Z7K6, K7ERN6

UniProt curated annotations — full annotation on UniProt →

Function. Required for distribution of pericentromeric heterochromatin in interphase nuclei and for centromere formation and organization, chromosome alignment and cytokinesis.

Subcellular location. Chromosome. Centromere. Kinetochore. Nucleus. Cytoplasm. Cytoskeleton. Spindle.

Cofactor. Binds 2 Zn(2+) ions per subunit.

Similarity. Belongs to the Gfa family.

Isoforms (3)

UniProt ID	Names	Canonical?
Q7Z7K6-1	1	yes
Q7Z7K6-2	2
Q7Z7K6-3	3

RefSeq proteins (1): NP_859067* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR006913	CENP-V/GFA	Domain
IPR011057	Mss4-like_sf	Homologous_superfamily
IPR052355	CENP-V-like	Family

Pfam: PF04828

UniProt features (25 total): binding site 7, modified residue 7, mutagenesis site 3, compositionally biased region 3, splice variant 2, chain 1, domain 1, region of interest 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q7Z7K6-F1	80.30	0.58

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Ligand- & substrate-binding residues (7): 177; 216; 219; 152; 154; 172; 174

Post-translational modifications (7): 18, 21, 43, 98, 101, 103, 257

Mutagenesis-validated functional residues (3):

Position	Phenotype
172	abolishes chromatin hypercondensation phenotype induced by overexpression of wild-type protein; when associated with a-1
174	abolishes chromatin hypercondensation phenotype induced by overexpression of wild-type protein.
177	abolishes chromatin hypercondensation phenotype induced by overexpression of wild-type protein; when associated with a-1

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 222 (showing top): GOBP_MEIOTIC_CHROMOSOME_SEGREGATION, GOBP_CHROMOSOME_ORGANIZATION, GOBP_CHROMOSOME_LOCALIZATION, ACEVEDO_NORMAL_TISSUE_ADJACENT_TO_LIVER_TUMOR_DN, GOCC_MICROTUBULE_ORGANIZING_CENTER, GOBP_AMEBOIDAL_TYPE_CELL_MIGRATION, WEI_MYCN_TARGETS_WITH_E_BOX, MARTINEZ_RB1_TARGETS_UP, GOBP_NEGATIVE_REGULATION_OF_GENE_EXPRESSION_EPIGENETIC, GOBP_ORGANELLE_FISSION, GOBP_CYTOKINESIS, GOBP_POSITIVE_REGULATION_OF_CELL_DIVISION, GOBP_REGULATION_OF_CELL_CYCLE, GOBP_POSITIVE_REGULATION_OF_CELL_CYCLE_PROCESS, GOBP_REGULATION_OF_CYTOKINESIS

GO Biological Process (6): ameboidal-type cell migration (GO:0001667), pericentric heterochromatin formation (GO:0031508), positive regulation of cytokinesis (GO:0032467), regulation of chromosome organization (GO:0033044), cell division (GO:0051301), obsolete centromere complex assembly (GO:0034508)

GO Molecular Function (3): carbon-sulfur lyase activity (GO:0016846), metal ion binding (GO:0046872), protein binding (GO:0005515)

GO Cellular Component (13): kinetochore (GO:0000776), nucleus (GO:0005634), nucleoplasm (GO:0005654), cytosol (GO:0005829), microtubule cytoskeleton (GO:0015630), midbody (GO:0030496), nuclear membrane (GO:0031965), spindle midzone (GO:0051233), chromosome, centromeric region (GO:0000775), chromosome (GO:0005694), cytoplasm (GO:0005737), spindle (GO:0005819), cytoskeleton (GO:0005856)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	5
intracellular membraneless organelle	4
cell migration	1
constitutive heterochromatin formation	1
cytokinesis	1
regulation of cytokinesis	1
positive regulation of cell division	1
positive regulation of cell cycle process	1
regulation of organelle organization	1
chromosome organization	1
cellular process	1
lyase activity	1
cation binding	1
binding	1
condensed chromosome, centromeric region	1
supramolecular complex	1
intracellular membrane-bounded organelle	1
nuclear lumen	1
cytoplasm	1
cytoskeleton	1
nucleus	1
nuclear envelope	1
organelle membrane	1
spindle	1
chromosomal region	1
intracellular anatomical structure	1
microtubule cytoskeleton	1

Protein interactions and networks

STRING

756 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CENPV	SPI1	P17947	880
CENPV	CEBPE	Q15744	785
CENPV	HBZ	P02008	720
CENPV	EMB	Q6PCB8	670
CENPV	CD99	P14209	654
CENPV	POLDIP3	Q9BY77	614
CENPV	PSME3	P61289	596
CENPV	CEBPA	P49715	576
CENPV	RPL18A	Q02543	552
CENPV	WDR5	P61964	542
CENPV	CDK2	P24941	511
CENPV	ATM	Q13315	511
CENPV	GSDMD	P57764	507
CENPV	CDKN2A	P42771	502
CENPV	CREBBP	Q92793	481

IntAct

149 interactions, top by confidence:

A	B	Type	Score
STK3	RASSF2	psi-mi:“MI:0914”(association)	0.950
SOD1	CCS	psi-mi:“MI:0914”(association)	0.830
EZH2	EPOP	psi-mi:“MI:0914”(association)	0.730
CHCHD10	CLPX	psi-mi:“MI:0914”(association)	0.640
SNCA	CENPV	psi-mi:“MI:0915”(physical association)	0.610
NPM1	MPHOSPH10	psi-mi:“MI:0914”(association)	0.610
DMWD	CENPV	psi-mi:“MI:0915”(physical association)	0.560
	CENPV	psi-mi:“MI:0915”(physical association)	0.560
CENPV		psi-mi:“MI:0915”(physical association)	0.560
HLA-A	CENPV	psi-mi:“MI:0915”(physical association)	0.560
LSAMP	CENPV	psi-mi:“MI:0915”(physical association)	0.560
PPIB	CENPV	psi-mi:“MI:0915”(physical association)	0.560
CENPV	PRPH	psi-mi:“MI:0915”(physical association)	0.560
YWHAG	CENPV	psi-mi:“MI:0915”(physical association)	0.560
DNALI1	CENPV	psi-mi:“MI:0915”(physical association)	0.560
BAG6	CENPV	psi-mi:“MI:0915”(physical association)	0.560
KLF11	CENPV	psi-mi:“MI:0915”(physical association)	0.560
SETDB1	CENPV	psi-mi:“MI:0915”(physical association)	0.560
KAT5	CENPV	psi-mi:“MI:0915”(physical association)	0.560
CENPV	ATXN10	psi-mi:“MI:0915”(physical association)	0.560
CENPV	HTRA2	psi-mi:“MI:0915”(physical association)	0.560
LMO3	CENPV	psi-mi:“MI:0915”(physical association)	0.560
CENPV	JPH3	psi-mi:“MI:0915”(physical association)	0.560
CENPV	SPRED1	psi-mi:“MI:0915”(physical association)	0.560
HTT	CENPV	psi-mi:“MI:0915”(physical association)	0.560

BioGRID (164): CENPV (Affinity Capture-MS), CENPV (Affinity Capture-MS), CENPV (Affinity Capture-MS), CENPV (Affinity Capture-MS), CENPV (Proximity Label-MS), CENPV (Affinity Capture-MS), CENPV (Affinity Capture-MS), CENPV (Affinity Capture-MS), CENPV (Affinity Capture-MS), CENPV (Affinity Capture-MS), CENPV (Affinity Capture-MS), CENPV (Affinity Capture-MS), CENPV (Affinity Capture-MS), CENPV (Affinity Capture-MS), CENPV (Affinity Capture-MS)

ESM2 similar proteins: A4Q9F3, A8IHN8, D3YYI7, M0R7T9, O09112, O60347, O88751, P51509, Q09YL6, Q0IHH1, Q13202, Q13505, Q14190, Q147X3, Q17QD9, Q3TZ87, Q3UPL5, Q3V1H9, Q5TGI4, Q5VUJ9, Q5VV17, Q5XI57, Q61079, Q6A039, Q6PDS0, Q6ZVT0, Q7Z7K6, Q80UW0, Q86YJ5, Q8C4U2, Q8CES0, Q8N554, Q8N8J7, Q8TC41, Q8TDR2, Q8WWW0, Q96AQ8, Q96ET8, Q96KN8, Q96MM7

Diamond homologs: A0A0U1RR11, A0A0U1RRI6, E1VBT6, P0DPI3, Q7Z7K6, Q9CXS4

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 118 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.

GO biological processes:

GO term	Partners	Fold	FDR
rRNA processing	8	10.8×	9e-04
positive regulation of apoptotic process	10	5.4×	6e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	1
Likely pathogenic	0
Uncertain significance	38
Likely benign	1
Benign	1

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
815908	GRCh37/hg19 17p12-11.2(chr17:15632431-18726389)x1	Pathogenic

SpliceAI

998 predictions. Top by Δscore:

Variant	Effect	Δscore
17:16342939:TTC:T	acceptor_gain	1.0000
17:16342941:CCT:C	acceptor_loss	1.0000
17:16342942:C:CC	acceptor_gain	1.0000
17:16342943:T:C	acceptor_loss	1.0000
17:16342952:G:C	acceptor_gain	1.0000
17:16344591:ACTC:A	donor_loss	1.0000
17:16344592:CTC:C	donor_loss	1.0000
17:16344593:T:TC	donor_loss	1.0000
17:16344594:CAC:C	donor_loss	1.0000
17:16344595:A:AC	donor_gain	1.0000
17:16344596:C:CC	donor_gain	1.0000
17:16344708:CTCC:C	acceptor_gain	1.0000
17:16344710:CC:C	acceptor_gain	1.0000
17:16344711:CC:C	acceptor_gain	1.0000
17:16344712:C:CA	acceptor_loss	1.0000
17:16344713:T:A	acceptor_loss	1.0000
17:16344716:G:GC	acceptor_gain	1.0000
17:16348686:C:CC	acceptor_gain	1.0000
17:16349929:A:AC	donor_gain	1.0000
17:16349930:C:CC	donor_gain	1.0000
17:16350027:TCA:T	acceptor_gain	1.0000
17:16350028:CA:C	acceptor_gain	1.0000
17:16350028:CAC:C	acceptor_gain	1.0000
17:16350030:C:CC	acceptor_gain	1.0000
17:16353025:A:AC	donor_gain	1.0000
17:16353026:C:CC	donor_gain	1.0000
17:16342937:AATTC:A	acceptor_gain	0.9900
17:16342938:ATTC:A	acceptor_gain	0.9900
17:16342940:TC:T	acceptor_gain	0.9900
17:16342941:CC:C	acceptor_gain	0.9900

AlphaMissense

1753 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000119487 (17:16351874 G>A), RS1000255906 (17:16351627 A>G), RS1000340783 (17:16343552 G>A), RS1000341057 (17:16345396 C>G), RS1000371755 (17:16343325 T>C), RS1000446701 (17:16353226 G>C), RS1000581703 (17:16352965 G>A,T), RS1000814611 (17:16346427 A>G), RS1000880122 (17:16345208 G>A), RS1001099986 (17:16354932 A>T), RS1001625816 (17:16348560 C>T), RS1001678433 (17:16351511 TC>T), RS1001724331 (17:16342678 G>C), RS1002140741 (17:16352674 T>G), RS1002321292 (17:16346066 T>C,G)

Disease associations

OMIM: gene MIM:608139 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

5 associations (top):

Study	Trait	p-value
GCST001664_12	Amyotrophic lateral sclerosis	3.000000e-07
GCST002509_4	Amyotrophic lateral sclerosis	3.000000e-07
GCST007001_11	Cerebrospinal AB1-42 levels in normal cognition	6.000000e-07
GCST007324_144	Adventurousness	2.000000e-09
GCST007325_158	General risk tolerance (MTAG)	1.000000e-11

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0004670	beta-amyloid 1-42 measurement
EFO:0008579	risk-taking behaviour

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	decreases expression, affects expression, increases methylation, affects cotreatment	10
trichostatin A	affects cotreatment, decreases expression	3
Benzo(a)pyrene	decreases expression, increases methylation	3
bisphenol A	decreases methylation, decreases expression	2
sodium arsenite	decreases expression, increases abundance	2
entinostat	decreases expression, affects cotreatment	2
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	increases expression, decreases expression, affects cotreatment	2
Acetaminophen	decreases expression	2
Cyclosporine	decreases expression, increases expression	2
alpha-pinene	affects cotreatment, increases oxidation, increases abundance	1
cobaltous chloride	decreases expression	1
coumarin	increases phosphorylation	1
methacrylaldehyde	affects cotreatment, increases oxidation, increases abundance	1
K 7174	decreases expression	1
2-amino-14,16-dimethyloctadecan-3-ol	decreases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
LDN 193189	affects cotreatment, increases expression	1
Acrolein	affects cotreatment, increases oxidation, increases abundance	1
Air Pollutants	increases oxidation, affects cotreatment, increases abundance	1
Arsenic	increases abundance, decreases expression	1
Benztropine	increases expression	1
Caffeine	decreases phosphorylation	1
Carbamazepine	affects expression	1
Cisplatin	decreases expression	1
Clozapine	increases expression	1
Dichlorodiphenyl Dichloroethylene	increases expression	1
Demecolcine	decreases expression	1
Diethylhexyl Phthalate	decreases expression, increases expression	1
Doxorubicin	decreases expression	1
Estradiol	affects cotreatment, decreases expression	1

Clinical trials (associated diseases)

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