CDK2AP2

Summary

CDK2AP2 (cyclin dependent kinase 2 associated protein 2, HGNC:30833) is a protein-coding gene on chromosome 11q13.2, encoding Cyclin-dependent kinase 2-associated protein 2 (O75956). Acts as a component of the histone deacetylase NuRD complex which participates in the remodeling of chromatin.

This gene encodes a protein that interacts with cyclin-dependent kinase 2 associated protein 1. Pseudogenes associated with this gene are located on chromosomes 7 and 9. Alternatively spliced transcript variants have been observed for this gene.

Source: NCBI Gene 10263 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 19 total
• GTEx eGene: eQTL in 12 tissues, sQTL in 1 (q < 0.05)
• Constraint (gnomAD): pLI 0.98 (loss-of-function intolerant), LOEUF 0.41 (moderately constrained)
• MANE Select transcript: NM_005851

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:30833
Approved symbol	CDK2AP2
Name	cyclin dependent kinase 2 associated protein 2
Location	11q13.2
Locus type	gene with protein product
Status	Approved
Aliases	DOC-1R, p14
Ensembl gene	ENSG00000167797
Ensembl biotype	protein_coding
OMIM	620061
Entrez	10263

Gene structure

Transcript identifiers

Ensembl transcripts: 15 — 8 protein_coding, 5 nonsense_mediated_decay, 2 retained_intron

MANE Select: ENST00000301488

Transcript support level (Ensembl TSL; 1 = fully mRNA-supported): TSL 1: 2, TSL 2: 3

ENST00000301488, ENST00000525402, ENST00000526447, ENST00000531178, ENST00000531506, ENST00000890089, ENST00000935009, ENST00000935010, ENST00000991162, ENST00001027021, ENST00001092095, ENST00001092096, ENST00001092097, ENST00001092098, ENST00001142485

RefSeq mRNA: 2 — MANE Select: NM_005851 NM_001271849, NM_005851

CCDS: CCDS8169

Canonical transcript exons

ENST00000301488 — 4 exons

Exon	Start	End
ENSE00001167405	67506497	67507012
ENSE00001167412	67508001	67508162
ENSE00003556699	67507365	67507497
ENSE00003605861	67507592	67507689

Expression profiles

Bgee: expression breadth ubiquitous, 276 present calls, max score 98.54.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 55.1117 / max 394.6260, expressed in 1816 samples.

Highest expression (Bgee): mucosa of transverse colon, apex of heart, lobe of thyroid gland, lobe of liver, coronary artery.

Genetic regulation across tissues (GTEx eQTL / sQTL)

CDK2AP2 is an eGene in GTEx v10 — its expression is genetically regulated (eQTL) in 12 tissues and its splicing (sQTL) in 1 (q < 0.05). Strongest associations first; slope = normalized effect of the lead variant’s alternative allele.

13 significant tissue × QTL associations:

Tissue	QTL	q-value	Slope	Lead variant
Skin Sun Exposed Lower leg	eqtl	5.9e-15	-0.54	11:67508194:A:C
Liver	eqtl	1.2e-11	-0.29	11:67580441:TGAGGCA:T
Esophagus Mucosa	eqtl	8.3e-10	-0.66	11:67508194:A:C
Skin Not Sun Exposed Suprapubic	eqtl	1.7e-06	-0.49	11:67508194:A:C
Colon Transverse	eqtl	4.4e-04	+0.12	11:67525763:G:A
Heart Atrial Appendage	sqtl	5.3e-03	+2.11	11:67748867:G:A
Brain Caudate basal ganglia	eqtl	6.4e-03	+0.79	11:68443784:G:A
Spleen	eqtl	1.2e-02	-0.46	11:68322940:C:T
Vagina	eqtl	2.3e-02	+0.96	11:67950759:A:G
Brain Cortex	eqtl	2.6e-02	+0.80	11:67713320:C:T
Pituitary	eqtl	2.6e-02	-0.78	11:68143209:C:T
Artery Tibial	eqtl	3.0e-02	+0.07	11:67949932:G:A
Minor Salivary Gland	eqtl	4.1e-02	-0.68	11:67629120:C:CG

FANTOM5 promoters

9 alternative TSS:

Promoter ID	TPM avg	Samples expressed
120947	25.4096	1803
120950	10.3253	1791
120946	5.9386	1676
120944	5.2430	1666
120945	3.6403	1527
120948	2.2660	1336
120942	1.1723	657
120949	0.7017	431
120943	0.4149	211

Top tissues by expression

showing 100 of 293 tissues by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
mucosa of transverse colon	UBERON:0004991	98.54	gold quality
apex of heart	UBERON:0002098	98.02	gold quality
right lobe of thyroid gland	UBERON:0001119	97.90	gold quality
right lobe of liver	UBERON:0001114	97.68	gold quality
right coronary artery	UBERON:0001625	97.63	gold quality
granulocyte	CL:0000094	97.60	gold quality
thoracic aorta	UBERON:0001515	97.54	gold quality
ascending aorta	UBERON:0001496	97.53	gold quality
left coronary artery	UBERON:0001626	97.44	gold quality
left lobe of thyroid gland	UBERON:0001120	97.34	gold quality
aorta	UBERON:0000947	97.29	gold quality
popliteal artery	UBERON:0002250	97.20	gold quality
descending thoracic aorta	UBERON:0002345	97.20	gold quality
endometrium epithelium	UBERON:0004811	97.19	gold quality
tibial artery	UBERON:0007610	97.18	gold quality
oocyte	CL:0000023	97.13	gold quality
coronary artery	UBERON:0001621	97.09	gold quality
body of pancreas	UBERON:0001150	97.05	gold quality
tibial nerve	UBERON:0001323	96.99	gold quality
lower esophagus	UBERON:0013473	96.87	gold quality
lower esophagus muscularis layer	UBERON:0035833	96.87	gold quality
heart left ventricle	UBERON:0002084	96.84	gold quality
metanephros cortex	UBERON:0010533	96.74	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	96.62	gold quality
cardiac ventricle	UBERON:0002082	96.61	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	96.46	gold quality
thyroid gland	UBERON:0002046	96.31	gold quality
body of stomach	UBERON:0001161	96.30	gold quality
lower esophagus mucosa	UBERON:0035834	96.19	gold quality
adenohypophysis	UBERON:0002196	96.18	gold quality
transverse colon	UBERON:0001157	96.16	gold quality
right atrium auricular region	UBERON:0006631	96.04	gold quality
upper lobe of left lung	UBERON:0008952	95.89	gold quality
right adrenal gland	UBERON:0001233	95.78	gold quality
mucosa of stomach	UBERON:0001199	95.75	gold quality
left uterine tube	UBERON:0001303	95.75	gold quality
left adrenal gland	UBERON:0001234	95.53	gold quality
esophagus	UBERON:0001043	95.34	gold quality
upper lobe of lung	UBERON:0008948	95.34	gold quality
left adrenal gland cortex	UBERON:0035825	95.34	gold quality
heart	UBERON:0000948	95.31	gold quality
spinal cord	UBERON:0002240	95.25	gold quality
pituitary gland	UBERON:0000007	95.24	gold quality
omental fat pad	UBERON:0010414	95.15	gold quality
cardiac atrium	UBERON:0002081	95.14	gold quality
peritoneum	UBERON:0002358	95.10	gold quality
muscle layer of sigmoid colon	UBERON:0035805	95.03	gold quality
adrenal cortex	UBERON:0001235	95.02	gold quality
right adrenal gland cortex	UBERON:0035827	94.97	gold quality
right lung	UBERON:0002167	94.91	gold quality
small intestine Peyer’s patch	UBERON:0003454	94.86	gold quality
lymph node	UBERON:0000029	94.74	gold quality
endocervix	UBERON:0000458	94.58	gold quality
adipose tissue of abdominal region	UBERON:0007808	94.45	gold quality
esophagus mucosa	UBERON:0002469	94.34	gold quality
adult mammalian kidney	UBERON:0000082	94.26	gold quality
amygdala	UBERON:0001876	94.26	gold quality
spleen	UBERON:0002106	94.25	gold quality
sigmoid colon	UBERON:0001159	94.22	gold quality
adrenal gland	UBERON:0002369	94.22	gold quality
colon	UBERON:0001155	94.16	gold quality
small intestine	UBERON:0002108	94.13	gold quality
fundus of stomach	UBERON:0001160	94.07	gold quality
stomach	UBERON:0000945	93.97	gold quality
caudate nucleus	UBERON:0001873	93.88	gold quality
cingulate cortex	UBERON:0003027	93.87	gold quality
anterior cingulate cortex	UBERON:0009835	93.86	gold quality
large intestine	UBERON:0000059	93.83	gold quality
putamen	UBERON:0001874	93.80	gold quality
nucleus accumbens	UBERON:0001882	93.79	gold quality
right frontal lobe	UBERON:0002810	93.66	gold quality
right hemisphere of cerebellum	UBERON:0014890	93.66	gold quality
ectocervix	UBERON:0012249	93.64	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	93.61	gold quality
middle frontal gyrus	UBERON:0002702	93.46	gold quality
intestine	UBERON:0000160	93.45	gold quality
minor salivary gland	UBERON:0001830	93.45	gold quality
duodenum	UBERON:0002114	93.38	gold quality
prostate gland	UBERON:0002367	93.23	gold quality
vermiform appendix	UBERON:0001154	93.17	gold quality
cerebellar hemisphere	UBERON:0002245	93.07	gold quality
body of uterus	UBERON:0009853	93.03	gold quality
right ovary	UBERON:0002118	93.01	gold quality
cerebellar cortex	UBERON:0002129	92.98	gold quality
paraflocculus	UBERON:0005351	92.93	gold quality
olfactory bulb	UBERON:0002264	92.90	silver quality
bone marrow cell	CL:0002092	92.83	gold quality
saliva-secreting gland	UBERON:0001044	92.79	gold quality
caecum	UBERON:0001153	92.77	gold quality
liver	UBERON:0002107	92.44	gold quality
leukocyte	CL:0000738	92.18	gold quality
blood	UBERON:0000178	92.17	gold quality
corpus epididymis	UBERON:0004359	92.17	gold quality
thymus	UBERON:0002370	92.07	gold quality
monocyte	CL:0000576	92.04	gold quality
mouth mucosa	UBERON:0003729	92.02	gold quality
cerebellum	UBERON:0002037	92.01	gold quality
prefrontal cortex	UBERON:0000451	91.99	gold quality
pancreas	UBERON:0001264	91.89	gold quality
left ovary	UBERON:0002119	91.80	gold quality

Single-cell (SCXA)

Detected in 4 experiment(s), a significant marker in 4.

Experiment	Marker?	Max mean expression
E-HCAD-6	yes	33.87
E-MTAB-6701	yes	18.19
E-HCAD-11	yes	18.03
E-ANND-3	no	0.00

HPA expression

RNA tissue specificity: Low tissue specificity

showing 60 of 76 HPA tissues / cells by nTPM:

Tissue / cell	Axis	nTPM	Protein (IHC)
Epididymis	tissue	80.8	not detected
Thyroid gland	tissue	66.6	not detected
Heart muscle	tissue	61.8	medium
Lymph node	tissue	60.6	low
Pituitary gland	tissue	59.0
Thymus	tissue	51.9
Adrenal gland	tissue	51.7	medium
Locus coeruleus	tissue	48.8
Tonsil	tissue	45.2	low
Spinal cord	tissue	45.0
Salivary gland	tissue	44.4	not detected
Hippocampus	tissue	44.0	not detected
Appendix	tissue	43.5	medium
Seminal vesicle	tissue	43.1	not detected
Nucleus accumbens	tissue	41.8
Colon	tissue	41.1	medium
Duodenum	tissue	40.3	medium
Vagina	tissue	38.9	not detected
Cervix	tissue	38.3	not detected
Small intestine	tissue	38.1	medium
Lung	tissue	37.6	not detected
Medulla oblongata	tissue	37.0
Corpus callosum	tissue	35.7
Thalamus	tissue	34.8
Superior colliculi	tissue	34.7
Spleen	tissue	34.3	not detected
Midbrain	tissue	33.8
Postcentral gyrus	tissue	33.7
Basal ganglia	tissue	33.5	not detected
Putamen	tissue	33.4
Pons	tissue	32.7
Hypothalamus	tissue	32.6
Stomach 1	tissue	32.5	not detected
Substantia nigra	tissue	32.0
Liver	tissue	31.8	not detected
Septum	tissue	31.5
Hippocampal formation	tissue	31.2
Pancreas	tissue	30.7	not detected
Choroid plexus	tissue	30.7
Fallopian tube	tissue	30.6	low
Bone marrow	tissue	30.3	not detected
Periaqueductal gray	tissue	30.0
Urinary bladder	tissue	29.8	not detected
Ventral forebrain	tissue	28.5
Smooth muscle	tissue	28.3	medium
Placenta	tissue	28.0	not detected
Cerebral cortex	tissue	27.2	not detected
Motor cortex	tissue	27.2
Cerebellum	tissue	26.4	not detected
Rectum	tissue	26.3	medium
Esophagus	tissue	26.2	not detected
Somatosensory cortex	tissue	26.2
Occipital cortex	tissue	26.2
Prostate	tissue	25.7	not detected
Gallbladder	tissue	25.6	not detected
Olfactory bulb	tissue	25.2
Prefrontal cortex	tissue	25.1
Adipose tissue	tissue	25.1	not detected
Retina	tissue	23.9
Entorhinal cortex	tissue	23.8

Brain sub-regions (HPA Brain Atlas): detected in 189; highest nTPM — Blood vessel (115.8), Area postrema (79.8), Inferior olive (73.1), Medial olivary nucleus (70.5), Nucleus gracilis (67.6).

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

Targeting CDK2AP2 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific).

27 miRNAs:

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-6870-5P	99.99	68.55	2115
HSA-MIR-4723-5P	99.97	68.70	2034
HSA-MIR-5698	99.97	68.49	2029
HSA-MIR-7111-5P	99.97	68.48	2062
HSA-MIR-6768-5P	99.92	67.36	1942
HSA-MIR-4493	99.90	66.48	977
HSA-MIR-4671-3P	99.88	72.46	1045
HSA-MIR-4447	99.85	67.81	2900
HSA-MIR-548F-5P	99.78	71.02	3093
HSA-MIR-4516	99.61	67.78	3390
HSA-MIR-671-5P	99.52	67.11	1277
HSA-MIR-4441	99.49	66.56	3216
HSA-MIR-519D-5P	99.41	69.30	2057
HSA-MIR-4254	99.11	65.15	1315
HSA-MIR-5703	99.10	67.09	2053
HSA-MIR-4434	99.10	67.01	1984
HSA-MIR-4270	99.02	66.26	1987
HSA-MIR-3194-3P	98.83	66.22	1167
HSA-MIR-5000-3P	98.79	65.63	1251
HSA-MIR-3945	98.68	64.21	553
HSA-MIR-6840-3P	98.68	65.95	1923
HSA-MIR-6754-5P	98.60	65.54	1627
HSA-MIR-6878-5P	98.49	67.91	2142
HSA-MIR-4436A	98.05	64.83	1140
HSA-MIR-4446-3P	97.91	64.29	991
HSA-MIR-4761-3P	96.27	66.26	524
HSA-MIR-4743-5P	88.08	64.31	91

Functional genomics

gnomAD constraint: pLI 0.979, LOEUF 0.41, missense Z 0.73 — population loss-of-function intolerance (pLI ≥ 0.9 = LoF-intolerant; lower LOEUF = more constrained). gnomAD

Regional missense constraint (gnomAD)

ENST00000301488 splits into 2 regions with different missense tolerance; 0 are missense-constrained. Missense variants in a constrained region (low observed/expected) are more likely to be pathogenic. gnomAD

Region (GRCh38)	Missense obs / exp	o/e	Constrained
11:67,506,948–67,507,462	31 / 76.0	0.41	no
11:67,507,463–67,508,082	98 / 99.7	0.98	no

Literature-anchored findings (GeneRIF, showing 3)

• antitumor effects of DOC-1R may be mediated by negatively regulating G1 phase progression and G1/S transition through inhibiting CDK2 expression and activation (PMID:23781148)
• Our findings suggest that alteration of p16, p14, p27, p21, and p53 status may contribute to carcinogenesis and the clinical behavior of HPV-negative adenocarcinoma of the uterine cervix (PMID:25675191)
• Novel circular RNA hsa_circ_0036683 suppresses proliferation and migration by mediating the miR-4664-3p/CDK2AP2 axis in non-small cell lung cancer. (PMID:39113208)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	cdk2ap2	ENSDARG00000103145
mus_musculus	Cdk2ap2	ENSMUSG00000024856
rattus_norvegicus	Cdk2ap2	ENSRNOG00000018391
drosophila_melanogaster	CDK2AP1	FBGN0030269
caenorhabditis_elegans		WBGENE00012807

Paralogs (1): CDK2AP1 (ENSG00000111328)

Mouse-model phenotypes

Observed phenotypes of the mouse ortholog (MGI:1098779) from MGI (Alliance of Genome Resources) — knockout/mutant phenotypes, ranked by annotation count. 4 distinct phenotype terms.

Mouse phenotype (MP)	Records
cataract	1
hyperactivity	1
increased vertical activity	1
decreased mean corpuscular hemoglobin	1

Additional cross-species homologs

Sequence homologs in species beyond Ensembl Compara’s model organisms, by Diamond local protein alignment (% sequence identity; best hit per species). Lower-identity rows are more distant homologs. The matched accessions’ gene symbols aren’t in biobtree yet, so each row shows the UniProt accession.

Organism	UniProt	Identity	Method
Mesocricetus auratus	P49119	100.0%	Diamond
Bos taurus	Q58CN7	95.3%	Diamond

Genomic neighbors (locus context)

Genes flanking this one on the chromosome (NCBI/Entrez gene neighborhood). Positional context only — some neighbors share regulatory elements (bidirectional promoters, antisense/overlapping transcripts), but chromosomal adjacency is not itself a functional relationship (see Interactions for that).

Symbol	Type	Entrez
GPR152	protein-coding	390212
CABP4	protein-coding	57010
TMEM134	protein-coding	80194
AIP	protein-coding	9049
PITPNM1	protein-coding	9600
NDUFV1-DT	ncRNA	100505621
GSTP1	protein-coding	2950
CABP2	protein-coding	51475
MIR6752	ncRNA	102465450
NDUFV1	protein-coding	4723

Protein

Protein identifiers

Cyclin-dependent kinase 2-associated protein 2 — O75956 (reviewed: O75956)

Alternative names: DOC-1-related protein

All UniProt accessions (4): O75956, E9PKR4, E9PQJ3, Q6IAV4

UniProt curated annotations — full annotation on UniProt →

Function. Acts as a component of the histone deacetylase NuRD complex which participates in the remodeling of chromatin. Inhibits cell cycle G1/S phase transition by repressing CDK2 expression and activation; represses CDK2 activation by inhibiting its interaction with cyclin E and A. Plays a role in regulating the self-renewal of embryonic stem cells (ESCs) and in maintaining cell survival during terminal differentiation of ESCs. Regulates microtubule organization of metaphase II oocytes.

Subunit / interactions. Component of the nucleosome remodeling and deacetylase (NuRD) repressor complex, composed of core proteins MTA1, MTA2, MTA3, RBBP4, RBBP7, HDAC1, HDAC2, MBD2, MBD3, and peripherally associated proteins CDK2AP1, CDK2AP2, GATAD2A, GATAD2B, CHD3, CHD4 and CHD5. The exact stoichiometry of the NuRD complex is unknown, and some subunits such as MBD2 and MBD3, GATAD2A and GATAD2B, and CHD3, CHD4 and CHD5 define mutually exclusive NuRD complexes. Interacts with CDK2AP1. Interacts with CDK2. Interacts with MAPK1.

Subcellular location. Cytoplasm. Nucleus.

Tissue specificity. Ubiquitous.

Post-translational modifications. Phosphorylated by MAPK1 and CDK2.

Similarity. Belongs to the CDK2AP family.

RefSeq proteins (2): NP_001258778, NP_005842* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR017266	DOC_1/2	Family

Pfam: PF09806

UniProt features (8 total): helix 3, region of interest 2, chain 1, compositionally biased region 1, strand 1

Structure

Experimental structures (PDB)

1 structures by resolution:

PDB	Title	Method	Resolution (Å)
2M1L	Solution NMR Structure of Cyclin-dependent kinase 2-associated protein 2 (CDK2AP2 …	SOLUTION NMR

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-O75956-F1	75.81	0.38

Human Protein Atlas

Protein class: Predicted intracellular proteins

Protein evidence: Evidence at protein level

Subcellular location (HPA, imaging): nucleoplasm

Antibody reliability (HPA): IH uncertain · IF approved

Function

Pathways and Gene Ontology

Reactome pathways

2 curated (TAS) of 2; 0 disease pathways. Curated-first; evidence = TAS (manually curated) vs IEA (electronic inference).

2 pathways:

ID	Pathway	Evidence
R-HSA-9940951	Interaction of NuRD complexes with transcription factors	curated
R-HSA-9937850	NuRD complex assembly	curated

MSigDB gene sets: 231 (showing top): ATF_B, YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_10, YAGI_AML_WITH_INV_16_TRANSLOCATION, GOBP_REGULATION_OF_MICROTUBULE_BASED_PROCESS, TGCGCANK_UNKNOWN, ENK_UV_RESPONSE_KERATINOCYTE_UP, GCANCTGNY_MYOD_Q6, GOBP_CELL_CYCLE_PHASE_TRANSITION, ACEVEDO_NORMAL_TISSUE_ADJACENT_TO_LIVER_TUMOR_DN, AREB6_01, CREBP1_Q2, ACTGCAG_MIR173P, chr11q13, CREB_Q4, GOBP_STEM_CELL_DIVISION

GO Biological Process (3): regulation of microtubule cytoskeleton organization (GO:0070507), regulation of stem cell division (GO:2000035), negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)

GO Molecular Function (2): protein binding (GO:0005515), kinase activity (GO:0016301)

GO Cellular Component (4): nucleus (GO:0005634), cytoplasm (GO:0005737), microtubule (GO:0005874), NuRD complex (GO:0016581)

Reactome top-level categories

2 top-level categories:

Category	Pathways
CHD3, CHD4, CHD5 subfamily	1
NuRD complex assembly	1

GO top-level categories

19 GO namespaces:

Category	Terms
microtubule cytoskeleton organization	1
regulation of microtubule-based process	1
regulation of cytoskeleton organization	1
stem cell division	1
regulation of cell division	1
G1/S transition of mitotic cell cycle	1
negative regulation of mitotic cell cycle phase transition	1
negative regulation of cell cycle G1/S phase transition	1
regulation of G1/S transition of mitotic cell cycle	1
binding	1
transferase activity, transferring phosphorus-containing groups	1
intracellular membrane-bounded organelle	1
intracellular anatomical structure	1
cellular anatomical structure	1
microtubule cytoskeleton	1
polymeric cytoskeletal fiber	1
histone deacetylase complex	1
transcription regulator complex	1
CHD-type complex	1

Experimentally-supported GO annotations

GO terms backed by direct experimental evidence (ECO experimental codes) — 3 of 9 annotations. The rest are phylogenetic / computational / electronic (IEA).

3 experimentally-supported GO terms:

GO term	NS	Evidence
negative regulation of G1/S transition of mitotic cell cycle	BP	mutant phenotype
NuRD complex	CC	direct assay
nucleus	CC	direct assay

Protein interactions and networks

STRING

showing 15 of 512 interactions by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CDK2AP2	GARS1	P41250	432
CDK2AP2	TMEM217	Q8N7C4	431
CDK2AP2	ZMYND8	Q9ULU4	416
CDK2AP2	CCDC86	Q9H6F5	404
CDK2AP2	MANF	P55145	402
CDK2AP2	CDC26	Q8NHZ8	388
CDK2AP2	ARHGAP15	Q53QZ3	368
CDK2AP2	ZFP14	Q9HCL3	367
CDK2AP2	ATP2B4	P23634	367
CDK2AP2	LIN28B	Q6ZN17	365
CDK2AP2	ERLIN2	O94905	364
CDK2AP2	BTBD16	Q32M84	362
CDK2AP2	SPATA17	Q96L03	349
CDK2AP2	GADD45GIP1	Q8TAE8	317
CDK2AP2	AURKAIP1	Q9NWT8	313

IntAct

Human interaction partners of CDK2AP2 in IntAct, one row per partner (best MIscore; records = supporting IntAct interaction records).

15 partners by confidence:

Partner	Interaction type	MIscore	Records
MRFAP1L1	physical association	0.560	3
A2M	physical association	0.370	1
DBN1	physical association	0.370	1
EED	physical association	0.370	1
EEF1G	physical association	0.370	1
HSF4	physical association	0.370	1
IKZF1	physical association	0.370	1
MBTPS1	physical association	0.370	1
PYCR1	physical association	0.370	1
RCC1	physical association	0.370	1
RPLP1	physical association	0.370	1
TRA2A	physical association	0.370	1
YIF1A	physical association	0.370	1
ZBTB48	physical association	0.370	1
MTA3	association	0.350	1

BioGRID (55 interactions; top human partners by supporting records): CDK2AP1 (Two-hybrid; 4 records), CHD4 (Affinity Capture-MS; 3 records), HDAC2 (Affinity Capture-MS; 2 records), MRFAP1L1 (Two-hybrid; 2 records), A2M (Two-hybrid), APP (Reconstituted Complex), BCAR1 (Affinity Capture-MS), BCL11A (Affinity Capture-MS), CBL (Affinity Capture-MS), CHD3 (Affinity Capture-MS), CHD5 (Affinity Capture-MS), DBN1 (Two-hybrid), DDX39A (Affinity Capture-RNA), EED (Two-hybrid), EEF1G (Two-hybrid)

Disease & clinical

Genetic variants

Variant evidence for CDK2AP2: 19 ClinVar records (0 pathogenic / likely pathogenic).

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	12
Likely benign	2
Benign	2

SpliceAI

Top 10 splice-impact sites by Δscore (adjacent positions with the same effect merged into one range; 24 predictions of 195):

Position(s)	Effect	Δscore	Sites
11:67507363–67507364	donor_loss	1.0000	5
11:67507498–67507500	acceptor_gain	1.0000	2
11:67507499	acceptor_loss	1.0000
11:67507505	acceptor_gain	1.0000
11:67507690–67507691	acceptor_loss	0.9900	6
11:67507694	acceptor_gain	0.9900
11:67507697	acceptor_gain	0.9900
11:67507999–67508000	donor_loss	0.9900	5
11:67507498	acceptor_gain	0.9800
11:67507499	acceptor_loss	0.9800

AlphaMissense

497 missense substitutions predicted likely pathogenic (of 795 scored), across 100 residues. Top 20 hotspot residues, ranked by the number of likely-pathogenic substitutions (of those reachable by a single-nucleotide change), then by mean score:

Residue	Likely-pathogenic substitutions	Mean am_pathogenicity	Max am_pathogenicity
M84	9	0.919	1.000
M99	9	0.892	0.993
S95	8	0.991	1.000
H108	8	0.989	1.000
D50	8	0.963	0.995
F48	8	0.846	0.967
E100	7	0.997	1.000
C116	7	0.996	1.000
E115	7	0.993	0.999
E119	7	0.993	0.999
E121	7	0.989	0.999
I106	7	0.987	1.000
S97	7	0.959	0.999
K103	7	0.958	1.000
E82	7	0.956	0.996
I88	7	0.953	1.000
I107	7	0.934	0.999
F51	7	0.931	0.974
E83	7	0.926	0.999
E87	7	0.915	0.999

HPA cancer prognostics

RNA cancer specificity: Low cancer specificity

Human Protein Atlas survival analysis — favorable = higher expression predicts better survival.

1 prognostic cancer types:

Cancer	Prognostic	p-value
Liver Hepatocellular Carcinoma (TCGA)	unfavorable	0.000245

Disease associations

OMIM: gene MIM:620061 | disease phenotypes:

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL6010 (SINGLE PROTEIN)

PharmGKB: 1 entry (CPIC guideline: no)

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Cyclosporine	increases expression	4
bisphenol A	affects expression, decreases expression	2
sodium arsenite	affects cotreatment, decreases expression, increases abundance, increases expression	2
Benzo(a)pyrene	affects methylation, decreases expression	2
Cisplatin	decreases expression, increases expression	2
Nickel	increases expression	2
Smoke	decreases expression, increases abundance, increases expression	2
Tetrachlorodibenzodioxin	increases expression	2
Tunicamycin	increases expression	2
Valproic Acid	affects expression, increases expression	2
Cadmium Chloride	decreases expression, increases abundance, increases expression	2
Thapsigargin	increases expression	2
dicrotophos	increases expression	1
beauvericin	decreases expression	1
methyleugenol	decreases expression	1
arsenite	affects binding, increases reaction	1
manganese chloride	affects cotreatment, decreases expression, increases abundance	1
2,3-bis(3’-hydroxybenzyl)butyrolactone	affects cotreatment, increases expression	1
di-n-butylphosphoric acid	affects expression	1
perfluorooctane sulfonic acid	increases expression	1
CGP 52608	increases reaction, affects binding	1
perfluoro-n-nonanoic acid	decreases expression	1
abrine	decreases expression	1
(4-amino-1,4-dihydro-3-(2-pyridyl)-5-thioxo-1,2,4-triazole)copper(II)	increases expression	1
licochalcone B	increases expression	1
Resveratrol	affects cotreatment, decreases expression	1
Temozolomide	decreases expression	1
Zoledronic Acid	increases expression, affects cotreatment	1
Fluvastatin	increases expression, affects cotreatment	1
Air Pollutants	increases abundance, increases expression	1

ChEMBL screening assays

2 unique, capped per target: 2 binding

Representative assays (with source publication via chembl_document):

Assay ID	Type	Description	Source paper
CHEMBL966739	Binding	Inhibition of Cdk2	Identification of genotype-correlated sensitivity to selective kinase inhibitors by using high-throughput tumor cell line profiling. — *Proc Natl Acad Sci U S A*

Clinical trials (associated diseases)

Via MONDO — disease-level, not drug-specific.

Predicted chemistry — Sugi Predict

The predicted patent-compound landscape for CDK2AP2 across ~30M SureChEMBL compounds — explore on Sugi Predict.