CCNP

Summary

CCNP (cyclin P, HGNC:25805) is a protein-coding gene on chromosome 19q13.2, encoding Cyclin-P (Q9H8S5). Seems to be involved in the regulation of proliferation and migration.

Predicted to enable cyclin-dependent protein serine/threonine kinase regulator activity. Predicted to be involved in G1/S transition of mitotic cell cycle. Located in nucleus.

Source: NCBI Gene 79935 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 58 total
• MANE Select transcript: NM_024877

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:25805
Approved symbol	CCNP
Name	cyclin P
Location	19q13.2
Locus type	gene with protein product
Status	Approved
Aliases	FLJ13265
Ensembl gene	ENSG00000105219
Ensembl biotype	protein_coding
OMIM	620396
Entrez	79935

Gene structure

Transcript identifiers

Ensembl transcripts: 7 — 5 protein_coding, 1 nonsense_mediated_decay, 1 retained_intron

ENST00000221818, ENST00000430325, ENST00000513948, ENST00000593335, ENST00000599263, ENST00000921917, ENST00000921918

RefSeq mRNA: 2 — MANE Select: NM_024877 NM_001411133, NM_024877

CCDS: CCDS12551, CCDS92618

Canonical transcript exons

ENST00000430325 — 5 exons

Exon	Start	End
ENSE00000706480	40224488	40224643
ENSE00001641476	40226375	40226689
ENSE00001644028	40224722	40224811
ENSE00001788472	40223388	40223546
ENSE00002028229	40222208	40223303

Expression profiles

Bgee: expression breadth ubiquitous, 153 present calls, max score 98.38.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.2303 / max 17.6767, expressed in 88 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
180951	0.1830	75
180950	0.0347	8
180949	0.0126	3

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	98.38	gold quality
oocyte	CL:0000023	89.51	gold quality
pancreatic ductal cell	CL:0002079	86.25	silver quality
right hemisphere of cerebellum	UBERON:0014890	85.85	gold quality
cerebellar hemisphere	UBERON:0002245	85.81	gold quality
cerebellar cortex	UBERON:0002129	85.57	gold quality
cerebellum	UBERON:0002037	83.56	gold quality
type B pancreatic cell	CL:0000169	81.34	gold quality
olfactory bulb	UBERON:0002264	81.30	gold quality
secondary oocyte	CL:0000655	81.26	gold quality
metanephros cortex	UBERON:0010533	80.99	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	79.12	gold quality
tibialis anterior	UBERON:0001385	78.75	silver quality
superficial temporal artery	UBERON:0001614	75.18	gold quality
right lobe of liver	UBERON:0001114	74.35	gold quality
orbitofrontal cortex	UBERON:0004167	74.16	gold quality
ileal mucosa	UBERON:0000331	72.68	silver quality
pituitary gland	UBERON:0000007	71.55	gold quality
triceps brachii	UBERON:0001509	71.07	gold quality
right uterine tube	UBERON:0001302	71.03	gold quality
vastus lateralis	UBERON:0001379	71.02	gold quality
biceps brachii	UBERON:0001507	71.02	gold quality
CA1 field of hippocampus	UBERON:0003881	71.02	gold quality
adenohypophysis	UBERON:0002196	70.04	gold quality
metanephros	UBERON:0000081	69.61	gold quality
gluteal muscle	UBERON:0002000	69.59	gold quality
tongue squamous epithelium	UBERON:0006919	69.45	gold quality
upper arm skin	UBERON:0004263	69.40	gold quality
parotid gland	UBERON:0001831	69.08	gold quality
myocardium	UBERON:0002349	67.78	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.27

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

36 targeting CCNP, 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-4534	99.99	66.58	1907
HSA-MIR-4531	99.99	69.70	3181
HSA-MIR-605-3P	99.88	69.22	1833
HSA-MIR-4728-5P	99.85	69.39	4718
HSA-MIR-6785-5P	99.82	68.68	4428
HSA-MIR-149-3P	99.72	68.22	3963
HSA-MIR-6883-5P	99.69	68.05	3785
HSA-MIR-646	99.68	67.84	1645
HSA-MIR-4441	99.49	66.56	3216
HSA-MIR-3915	99.45	68.49	1905
HSA-MIR-3960	99.41	66.11	96
HSA-MIR-584-3P	99.35	67.69	1082
HSA-MIR-532-3P	99.34	65.76	1195
HSA-MIR-422A	99.18	65.83	550
HSA-MIR-6809-5P	99.13	68.45	1223
HSA-MIR-7160-5P	99.11	67.17	2207
HSA-MIR-4478	99.07	65.16	2320
HSA-MIR-4270	99.02	66.26	1987
HSA-MIR-6754-5P	98.60	65.54	1627
HSA-MIR-4463	98.56	66.05	1071
HSA-MIR-378A-3P	98.43	66.10	548
HSA-MIR-378B	98.43	65.36	573
HSA-MIR-378C	98.43	66.10	548
HSA-MIR-378D	98.43	66.10	548
HSA-MIR-378E	98.43	65.99	551
HSA-MIR-378F	98.43	65.66	554
HSA-MIR-378H	98.43	66.16	545
HSA-MIR-378I	98.43	66.10	548
HSA-MIR-758-3P	98.42	68.60	1122
HSA-MIR-8072	98.27	66.24	83

Literature-anchored findings (GeneRIF, showing 3)

• Study reports that CNTD2 is upregulated in human lung cancer tissues and correlates with worse prognosis. CNTD2 is found to be an oncogenic driver in lung cancer cell lines and mouse xenograft models. (PMID:28860486)
• CNTD2 is significantly upregulated in Colorectal cancer (CRC) tissue compared to the adjacent normal one. CNTD2 overexpression in CRC cell lines increases their proliferation capacity and migration, as well as spheroid formation capacity and anchorage-independent growth. (PMID:30087414)
• Atypical cyclin P regulates cancer cell stemness through activation of the WNT pathway. (PMID:34604945)

Cross-species orthologs

9 orthologs

Organism	Symbol	Gene ID
danio_rerio	ccnp	ENSDARG00000055250
drosophila_melanogaster	CycB	FBGN0000405
drosophila_melanogaster	CycD	FBGN0010315
drosophila_melanogaster	CycE	FBGN0010382
caenorhabditis_elegans		WBGENE00000865
caenorhabditis_elegans		WBGENE00000866
caenorhabditis_elegans	cyb-2.2	WBGENE00000867
caenorhabditis_elegans		WBGENE00000870
caenorhabditis_elegans	cye-1	WBGENE00000871

Paralogs (18): CCNE1 (ENSG00000105173), CCNJ (ENSG00000107443), CCND1 (ENSG00000110092), CCND3 (ENSG00000112576), CCNG1 (ENSG00000113328), CCNI (ENSG00000118816), CCND2 (ENSG00000118971), CCNA1 (ENSG00000133101), CCNB1 (ENSG00000134057), CCNJL (ENSG00000135083), CCNG2 (ENSG00000138764), CCNA2 (ENSG00000145386), CCNB3 (ENSG00000147082), CCNO (ENSG00000152669), CCNB2 (ENSG00000157456), CCNF (ENSG00000162063), CCNE2 (ENSG00000175305), CCNI2 (ENSG00000205089)

Protein

Protein identifiers

Cyclin-P — Q9H8S5 (reviewed: Q9H8S5)

Alternative names: Cyclin N-terminal domain-containing protein 2

All UniProt accessions (3): Q9H8S5, D6RCS3, M0QZM5

UniProt curated annotations — full annotation on UniProt →

Function. Seems to be involved in the regulation of proliferation and migration.

Subcellular location. Nucleus.

Tissue specificity. Expression is induced in lung and colon cancer cells.

Miscellaneous. May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay.

Isoforms (2)

UniProt ID	Names	Canonical?
Q9H8S5-1	1	yes
Q9H8S5-2	2

RefSeq proteins (2): NP_001398062, NP_079153* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR006671	Cyclin_N	Domain
IPR013763	Cyclin-like_dom	Domain
IPR036915	Cyclin-like_sf	Homologous_superfamily
IPR039361	Cyclin	Family

Pfam: PF00134

UniProt features (7 total): splice variant 3, region of interest 2, chain 1, domain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9H8S5-F1	70.87	0.38

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 43 (showing top): GSE45365_CD8A_DC_VS_CD11B_DC_IFNAR_KO_MCMV_INFECTION_DN, GOBP_CELL_CYCLE_PHASE_TRANSITION, GOBP_CELL_CYCLE_G1_S_PHASE_TRANSITION, GOBP_MITOTIC_CELL_CYCLE, KUUSELO_PANCREATIC_CANCER_19Q13_AMPLIFICATION, GOCC_TRANSFERASE_COMPLEX_TRANSFERRING_PHOSPHORUS_CONTAINING_GROUPS, GOCC_TRANSFERASE_COMPLEX, GOCC_PROTEIN_KINASE_COMPLEX, GOBP_CELL_CYCLE_PROCESS, GOCC_CYCLIN_DEPENDENT_PROTEIN_KINASE_HOLOENZYME_COMPLEX, GOMF_ENZYME_REGULATOR_ACTIVITY, MOREAUX_MULTIPLE_MYELOMA_BY_TACI_UP, BHAT_ESR1_TARGETS_VIA_AKT1_UP, ZWANG_TRANSIENTLY_UP_BY_2ND_EGF_PULSE_ONLY, PTEN_DN.V1_UP

GO Biological Process (1): G1/S transition of mitotic cell cycle (GO:0000082)

GO Molecular Function (1): cyclin-dependent protein serine/threonine kinase regulator activity (GO:0016538)

GO Cellular Component (3): cyclin-dependent protein kinase holoenzyme complex (GO:0000307), nucleus (GO:0005634), cytoplasm (GO:0005737)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
mitotic cell cycle	1
mitotic cell cycle phase transition	1
cell cycle G1/S phase transition	1
cyclin-dependent protein serine/threonine kinase activity	1
cyclin-dependent protein kinase regulator activity	1
serine/threonine protein kinase complex	1
intracellular membrane-bounded organelle	1
intracellular anatomical structure	1
cellular anatomical structure	1

Protein interactions and networks

STRING

1921 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CCNP	SVOP	Q8N4V2	478
CCNP	NAT9	Q9BTE0	457
CCNP	ZNF205	O95201	439
CCNP	STRADA	Q7RTN6	409
CCNP	RAD51AP1	Q96B01	391
CCNP	ZFYVE9	O95405	377
CCNP	TMEM220	Q6QAJ8	377
CCNP	C1orf115	Q9H7X2	369
CCNP	SVOPL	Q8N434	358
CCNP	COQ9	O75208	349
CCNP	NEU2	Q9Y3R4	323
CCNP	SEC61G	P38384	323
CCNP	CDK1	P06493	320
CCNP	PYCR1	P32322	300
CCNP	PLA2G1B	P04054	289
CCNP	STK17A	Q9UEE5	289

IntAct

0 interactions, top by confidence:

ESM2 similar proteins: A6QP75, E1BDF2, E2RD63, P0C242, P22674, P29590, P30282, P41155, P48961, P49593, Q13505, Q14094, Q1LZ97, Q32NJ2, Q32NM1, Q3MHH5, Q3TAA7, Q4FZD7, Q52WX2, Q5F2F2, Q5SRT8, Q60I26, Q60I27, Q69Z89, Q6IN84, Q6UXT9, Q70EL4, Q86UR1, Q8BQX5, Q8BTM9, Q8BUM9, Q8N1F8, Q8N2A8, Q8N9H8, Q8TCX5, Q8TDF6, Q8WXI3, Q91ZT7, Q969S2, Q96DC7

Diamond homologs: A0MEB5, A5PK16, O48790, P18606, P20248, P25010, P25011, P30274, P34638, P34800, P34801, P37881, P39963, P41002, P43062, P47827, P51943, P51944, P51986, P78396, Q01J96, Q0DJR9, Q0INT0, Q0JPA4, Q38819, Q39069, Q39071, Q3ECW2, Q5A1N6, Q5XGG5, Q61456, Q6AY13, Q6NYX6, Q7F830, Q7T0L6, Q7TMA5, Q7XSJ6, Q8K4F8, Q92161, Q9C6A9

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	48
Likely benign	6
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1256 predictions. Top by Δscore:

Variant	Effect	Δscore
19:40223382:GCTCA:G	donor_loss	1.0000
19:40223383:CTCA:C	donor_loss	1.0000
19:40223384:TCA:T	donor_loss	1.0000
19:40223385:CA:C	donor_loss	1.0000
19:40223386:A:AT	donor_loss	1.0000
19:40223506:C:CT	acceptor_gain	1.0000
19:40223506:C:T	acceptor_gain	1.0000
19:40223543:CGGG:C	acceptor_gain	1.0000
19:40223547:C:CC	acceptor_gain	1.0000
19:40224502:A:AC	donor_gain	1.0000
19:40224503:C:CC	donor_gain	1.0000
19:40224503:CT:C	donor_gain	1.0000
19:40224507:T:TA	donor_gain	1.0000
19:40224641:CTC:C	acceptor_gain	1.0000
19:40223133:T:TA	donor_gain	0.9900
19:40223300:TCAC:T	acceptor_gain	0.9900
19:40223300:TCACC:T	acceptor_loss	0.9900
19:40223301:CACC:C	acceptor_gain	0.9900
19:40223301:CACCT:C	acceptor_loss	0.9900
19:40223302:ACCTG:A	acceptor_loss	0.9900
19:40223303:CCTG:C	acceptor_loss	0.9900
19:40223304:C:CC	acceptor_gain	0.9900
19:40223305:T:A	acceptor_loss	0.9900
19:40223386:A:AC	donor_gain	0.9900
19:40223387:C:CC	donor_gain	0.9900
19:40223400:C:CA	donor_gain	0.9900
19:40223542:GCGGG:G	acceptor_gain	0.9900
19:40223543:CGGGC:C	acceptor_gain	0.9900
19:40223544:GGG:G	acceptor_gain	0.9900
19:40223545:GG:G	acceptor_gain	0.9900

AlphaMissense

1926 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:40224512:T:A	K163N	0.995
19:40224512:T:G	K163N	0.995
19:40224513:T:A	K163I	0.994
19:40223457:G:C	F201L	0.987
19:40223457:G:T	F201L	0.987
19:40223459:A:G	F201L	0.987
19:40224530:G:C	C157W	0.987
19:40224531:C:T	C157Y	0.983
19:40224532:A:G	C157R	0.982
19:40223484:C:A	E192D	0.980
19:40223484:C:G	E192D	0.980
19:40224519:G:T	A161E	0.978
19:40224597:A:G	L135P	0.978
19:40224757:G:T	R108S	0.976
19:40223485:T:A	E192V	0.975
19:40223459:A:T	F201I	0.963
19:40223489:C:G	A191P	0.963
19:40223511:G:C	F183L	0.963
19:40223511:G:T	F183L	0.963
19:40223513:A:G	F183L	0.963
19:40224618:G:T	T128K	0.963
19:40226391:A:G	I84T	0.961
19:40224514:T:C	K163E	0.955
19:40223458:A:G	F201S	0.953
19:40224540:C:T	G154D	0.953
19:40223476:A:G	I195T	0.952
19:40224603:A:T	V133D	0.952
19:40226404:A:G	Y80H	0.951
19:40224541:C:G	G154R	0.950
19:40223215:G:T	A254D	0.948

dbSNP variants (sampled 300 via entrez): RS1000264091 (19:40223256 G>A,C), RS1000668647 (19:40224901 G>A), RS1001276678 (19:40224710 C>T), RS1002570477 (19:40227209 C>T), RS1003317256 (19:40227112 G>A), RS1003357973 (19:40222303 G>A,C), RS1003631564 (19:40227326 G>A,T), RS1004492683 (19:40222520 T>A,C), RS1004629956 (19:40222335 A>G), RS1004730129 (19:40227150 G>A), RS1004795959 (19:40225595 T>C), RS1004976916 (19:40225009 A>C), RS1005207339 (19:40227336 G>A,C,T), RS1005482488 (19:40227769 T>C), RS1005495679 (19:40223621 C>T)

Disease associations

OMIM: gene MIM:620396 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

14 total (human), top 14 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
aristolochic acid I	increases expression	1
sodium arsenite	decreases expression	1
CGP 52608	affects binding, increases reaction	1
licochalcone B	increases expression	1
jinfukang	decreases expression	1
Resveratrol	affects cotreatment, decreases expression	1
Benzo(a)pyrene	affects methylation, decreases methylation	1
Plant Extracts	affects cotreatment, decreases expression	1
Potassium Chloride	decreases response to substance, increases expression	1
Smoke	decreases expression	1
Dronabinol	decreases response to substance, increases expression	1
Tobacco Smoke Pollution	decreases expression	1
Okadaic Acid	increases expression	1
Acrylamide	increases expression	1

Clinical trials (associated diseases)

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