CDKN2D

Summary

CDKN2D (cyclin dependent kinase inhibitor 2D, HGNC:1790) is a protein-coding gene on chromosome 19p13.2, encoding Cyclin-dependent kinase 4 inhibitor D (P55273). Interacts strongly with CDK4 and CDK6 and inhibits them.

The protein encoded by this gene is a member of the INK4 family of cyclin-dependent kinase inhibitors. This protein has been shown to form a stable complex with CDK4 or CDK6, and prevent the activation of the CDK kinases, thus function as a cell growth regulator that controls cell cycle G1 progression. The abundance of the transcript of this gene was found to oscillate in a cell-cycle dependent manner with the lowest expression at mid G1 and a maximal expression during S phase. The negative regulation of the cell cycle involved in this protein was shown to participate in repressing neuronal proliferation, as well as spermatogenesis. Two alternatively spliced variants of this gene, which encode an identical protein, have been reported.

Source: NCBI Gene 1032 — RefSeq curated summary.

At a glance

• GWAS associations: 11
• Clinical variants (ClinVar): 15 total
• MANE Select transcript: NM_001800

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:1790
Approved symbol	CDKN2D
Name	cyclin dependent kinase inhibitor 2D
Location	19p13.2
Locus type	gene with protein product
Status	Approved
Aliases	INK4D, p19
Ensembl gene	ENSG00000129355
Ensembl biotype	protein_coding
OMIM	600927
Entrez	1032

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 2 protein_coding

ENST00000335766, ENST00000393599

RefSeq mRNA: 2 — MANE Select: NM_001800 NM_001800, NM_079421

CCDS: CCDS12244

Canonical transcript exons

ENST00000393599 — 2 exons

Exon	Start	End
ENSE00000888297	10566460	10567417
ENSE00001515998	10568513	10568979

Expression profiles

Bgee: expression breadth ubiquitous, 200 present calls, max score 97.97.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 7.6772 / max 385.2168, expressed in 1485 samples.

FANTOM5 promoters (6 alternative TSS)

Promoter ID	TPM avg	Samples expressed
179158	2.5154	859
179154	2.4434	461
179156	1.3439	529
179157	0.9763	351
179155	0.3263	116
179159	0.0719	29

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
monocyte	CL:0000576	97.97	gold quality
cortical plate	UBERON:0005343	97.69	gold quality
mononuclear cell	CL:0000842	97.53	gold quality
leukocyte	CL:0000738	97.43	gold quality
granulocyte	CL:0000094	96.79	gold quality
right frontal lobe	UBERON:0002810	96.46	gold quality
cingulate cortex	UBERON:0003027	96.41	gold quality
anterior cingulate cortex	UBERON:0009835	96.41	gold quality
prefrontal cortex	UBERON:0000451	95.86	gold quality
amygdala	UBERON:0001876	94.57	gold quality
nucleus accumbens	UBERON:0001882	94.45	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	94.30	gold quality
caudate nucleus	UBERON:0001873	94.08	gold quality
blood	UBERON:0000178	94.00	gold quality
Brodmann (1909) area 9	UBERON:0013540	93.78	gold quality
neocortex	UBERON:0001950	93.30	gold quality
frontal cortex	UBERON:0001870	93.12	gold quality
putamen	UBERON:0001874	92.80	gold quality
cerebellar hemisphere	UBERON:0002245	92.26	gold quality
right hemisphere of cerebellum	UBERON:0014890	92.19	gold quality
cerebellar cortex	UBERON:0002129	92.15	gold quality
cerebral cortex	UBERON:0000956	91.57	gold quality
telencephalon	UBERON:0001893	91.27	gold quality
ganglionic eminence	UBERON:0004023	91.23	gold quality
Brodmann (1909) area 10	UBERON:0013541	91.16	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	91.15	gold quality
frontal pole	UBERON:0002795	90.57	gold quality
cerebellum	UBERON:0002037	90.52	gold quality
bone marrow	UBERON:0002371	90.37	gold quality
hypothalamus	UBERON:0001898	90.23	gold quality

Single-cell (SCXA)

Detected in 6 experiment(s), a significant marker in 6.

Experiment	Marker?	Max mean expression
E-HCAD-5	yes	42.94
E-HCAD-6	yes	34.09
E-MTAB-9221	yes	17.45
E-HCAD-10	yes	16.63
E-HCAD-1	yes	6.02
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): DNMT3A, E2F1, FOXO1, FOXO3, MSX1, PAX6, SP1, SP3, STAT3

miRNA regulators (miRDB)

18 targeting CDKN2D, 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-6721-5P	99.93	68.92	2981
HSA-MIR-362-3P	99.91	66.38	1267
HSA-MIR-329-3P	99.91	66.56	1234
HSA-MIR-3121-3P	99.82	71.96	3630
HSA-MIR-4422	99.72	72.07	2908
HSA-MIR-4649-3P	99.56	66.90	1783
HSA-MIR-8064	99.45	66.92	875
HSA-MIR-4506	99.34	67.47	526
HSA-MIR-449B-3P	99.20	67.24	1047
HSA-MIR-6794-3P	98.76	66.99	894
HSA-MIR-5197-3P	98.71	67.05	1905
HSA-MIR-2115-5P	98.66	68.07	1191
HSA-MIR-3135B	98.61	65.33	1470
HSA-MIR-4463	98.56	66.05	1071
HSA-MIR-1248	98.47	67.54	1314
HSA-MIR-4722-5P	98.46	66.34	1611
HSA-MIR-4433B-3P	97.22	63.62	663
HSA-MIR-3197	94.02	63.47	85

Literature-anchored findings (GeneRIF, showing 32)

• protein folding and stability (PMID:11786024)
• The human p19(INK4d) gene is under the control of TATA-less promoter and the Sp1 binding site is involved in the transcription. (PMID:12062451)
• Deletions in the CDKN2D locus and hypermethylation in the CDKN2D promoter region plays a role in ovarian granulosa cell tumorogenesis. (PMID:12203782)
• Inhibitor shows antitumor effect on glioma cells. (PMID:12698196)
• p19(INK4d) in addition to p21(WAF1/Cip1) is an important molecular target of HDAC inhibitors inducing growth arrest (PMID:15107822)
• In addition to its role as cell cycle inhibitor, p19INK4d is involved in maintenance of DNA integrity and, therefore, would contribute to cancer prevention. (PMID:15750620)
• Data suggest that the graded stability and the facile unfolding of repeats 1 and 2 is a prerequisite for the down-regulation of the inhibitory activity of p19(INK4d) during the cell-cycle. (PMID:17804013)
• p19(INK4D) knockdown led to a moderate increase (31.7% +/- 5%) in the mean ploidy of megakaryocytes suggesting a role of p19(INK4D) in the endomitotic arrest. (PMID:18276842)
• The study shows that mimicking the phosphorylation site of p19INK4d by a glutamate substitution at position 76 dramatically decreases the stability of the native but not an intermediate state. (PMID:19063602)
• Results show that overexpression of CDK4, cyclin D1, and Rb proteins, and loss of expression of proteins p16, p27, and p19 were statistically significant in NPC tissues compared with non-cancerous NPE (P<0.05) by real-time RT-PCR and tissue microarray. (PMID:19430707)
• p19INK4d is transcriptionally regulated by E2F1 through two response elements present in the p19INK4d promoter. (PMID:21765927)
• expression of p19INK4D may be an effective predictor of clinical behavior in hepatocellular carcinoma, and therefore, a new prognostic marker (PMID:21901251)
• E2F1 is involved in the induction of p19INK4d following UV irradiation (PMID:22476863)
• CDK2 and PKA mediated-sequential phosphorylation is critical for p19INK4d function in the DNA damage response to ensure cell survival. (PMID:22558186)
• Up-regulation of CDKN2D during in-vitro passages of human amniotic fluid-derived mesenchymal stromal cells may indicate the begging of early senescence process in a p53-independent mechanism. (PMID:22747700)
• PTB plays as a negative regulator in H1299 cell proliferation at least by inducing p19(Ink4d) expression at transcriptional and post-transcriptional levels. (PMID:23536791)
• P19(INK4d) expression is a poor prognostic factor in ovarian cancer patients. (PMID:24022213)
• Mutations in CDKN2D is associated with sporadic parathyroid adenoma. (PMID:24127162)
• CDKN2D-WDFY2 fusion could be an important molecular signature for understanding and classifying sub-lineages among heterogeneous high-grade serous ovarian carcinomas. (PMID:24675677)
• p19-INK4d inhibits neuroblastoma cell growth, induces differentiation and is hypermethylated and downregulated in MYCN-amplified neuroblastomas. (PMID:25104850)
• Data indicate that upon oxidative DNA damage, cyclin-dependent kinase inhibitor p19INK4d strongly binds to and relaxes chromatin. (PMID:25204969)
• CDKN2D repression by PML/RARalpha disrupts both cell proliferation and differentiation in the pathogenesis of acute promyelocytic leukemia. (PMID:25275592)
• MiR-451 inhibited the proliferation of esophageal squamous cell carcinoma cells by targeting CDKN2D and MAP3K1 expression. (PMID:26019450)
• p19 may play an important role in the ototoxic effects of cisplatin and is probably involved in the pathogenesis of hearing loss. (PMID:26722409)
• p19(INK4D) is one of the key mediators of miR-125b activity during the onset of megakaryocyte polyploidization. (PMID:27763644)
• We unexpectedly found that p19INK4d plays an important role in human terminal erythropoiesis (PMID:27879259)
• p19(INK4d) plays an active role during human tooth development along with MSX1 and MSX2 (PMID:28933666)
• he results support the concept that P19ink4d may play an important role in the pathogenesis and development of noise induced hearing loss. (PMID:30808142)
• p19INK4d: More than Just a Cyclin-Dependent Kinase Inhibitor. (PMID:31400265)
• p19(INK4d) inhibits proliferation and enhances imatinib efficacy through BCR-ABL signaling pathway in chronic myeloid leukemia. (PMID:32711219)
• Identification of Cdk8 and Cdkn2d as New Prame-Target Genes in 2C-like Embryonic Stem Cells. (PMID:36292630)
• Deregulation of the p19/CDK4/CDK6 axis in Jak2[V617F] megakaryocytes accelerates the development of myelofibrosis. (PMID:38378843)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	cdkn2d	ENSDARG00000094176
mus_musculus	Cdkn2d	ENSMUSG00000096472
rattus_norvegicus	Cdkn2d	ENSRNOG00000064248

Paralogs (2): CDKN2C (ENSG00000123080), ANKRD39 (ENSG00000213337)

Protein

Protein identifiers

Cyclin-dependent kinase 4 inhibitor D — P55273 (reviewed: P55273)

Alternative names: p19-INK4d

All UniProt accessions (1): P55273

UniProt curated annotations — full annotation on UniProt →

Function. Interacts strongly with CDK4 and CDK6 and inhibits them.

Subunit / interactions. Interacts with CDK6.

Subcellular location. Nucleus. Cytoplasm.

Similarity. Belongs to the CDKN2 cyclin-dependent kinase inhibitor family.

RefSeq proteins (2): NP_001791, NP_524145 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR002110	Ankyrin_rpt	Repeat
IPR036770	Ankyrin_rpt-contain_sf	Homologous_superfamily
IPR050776	Ank_Repeat/CDKN_Inhibitor	Family

Pfam: PF12796

UniProt features (17 total): helix 10, repeat 4, chain 1, modified residue 1, sequence conflict 1

Structure

Experimental structures (PDB)

2 structures.

PDB	Method	Resolution (Å)
1BD8	X-RAY DIFFRACTION	1.8
1BI8	X-RAY DIFFRACTION	2.8

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-P55273-F1	95.91	0.93

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 (1): 1

Function

Pathways and Gene Ontology

Reactome pathways

11 pathways

ID	Pathway
R-HSA-2559580	Oxidative Stress Induced Senescence
R-HSA-2559582	Senescence-Associated Secretory Phenotype (SASP)
R-HSA-2559585	Oncogene Induced Senescence
R-HSA-69231	Cyclin D associated events in G1
R-HSA-1640170	Cell Cycle
R-HSA-2262752	Cellular responses to stress
R-HSA-2559583	Cellular Senescence
R-HSA-453279	Mitotic G1 phase and G1/S transition
R-HSA-69236	G1 Phase
R-HSA-69278	Cell Cycle, Mitotic
R-HSA-8953897	Cellular responses to stimuli

MSigDB gene sets: 309 (showing top): GOBP_SENSORY_PERCEPTION_OF_MECHANICAL_STIMULUS, GOBP_NEGATIVE_REGULATION_OF_CELL_GROWTH, GOBP_CELL_CYCLE_PHASE_TRANSITION, RIZ_ERYTHROID_DIFFERENTIATION_CCNE1, GOBP_GROWTH, IVANOVA_HEMATOPOIESIS_MATURE_CELL, THEILGAARD_NEUTROPHIL_AT_SKIN_WOUND_DN, GOBP_NEGATIVE_REGULATION_OF_INTRINSIC_APOPTOTIC_SIGNALING_PATHWAY_IN_RESPONSE_TO_DNA_DAMAGE, GOBP_NEGATIVE_REGULATION_OF_INTRACELLULAR_SIGNAL_TRANSDUCTION, GOBP_NEGATIVE_REGULATION_OF_INTRINSIC_APOPTOTIC_SIGNALING_PATHWAY, GOBP_NEGATIVE_REGULATION_OF_CELL_CYCLE_PROCESS, GOBP_APOPTOTIC_SIGNALING_PATHWAY, GOBP_NEGATIVE_REGULATION_OF_CELL_CYCLE, FISCHER_G2_M_CELL_CYCLE, GOBP_REGULATION_OF_CELL_CYCLE

GO Biological Process (13): DNA synthesis involved in DNA repair (GO:0000731), sensory perception of sound (GO:0007605), negative regulation of cell population proliferation (GO:0008285), response to UV (GO:0009411), negative regulation of cell growth (GO:0030308), response to retinoic acid (GO:0032526), response to vitamin D (GO:0033280), autophagic cell death (GO:0048102), negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902230), regulation of G1/S transition of mitotic cell cycle (GO:2000045), negative regulation of G1/S transition of mitotic cell cycle (GO:2000134), regulation of cell cycle G1/S phase transition (GO:1902806), negative regulation of cell cycle G1/S phase transition (GO:1902807)

GO Molecular Function (3): cyclin-dependent protein serine/threonine kinase inhibitor activity (GO:0004861), protein kinase binding (GO:0019901), protein binding (GO:0005515)

GO Cellular Component (5): nucleus (GO:0005634), nucleoplasm (GO:0005654), cytoplasm (GO:0005737), cytosol (GO:0005829), cyclin D2-CDK4 complex (GO:0097129)

Reactome top-level categories

Rollup of top-7 pathways:

Category	Pathways
Cellular Senescence	3
G1 Phase	1
Cellular responses to stimuli	1
Cellular responses to stress	1
Cell Cycle, Mitotic	1
Mitotic G1 phase and G1/S transition	1
Cell Cycle	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	3
negative regulation of cellular process	2
response to lipid	2
response to oxygen-containing compound	2
G1/S transition of mitotic cell cycle	2
regulation of cell cycle G1/S phase transition	2
cell cycle G1/S phase transition	2
DNA repair	1
DNA biosynthetic process	1
sensory perception of mechanical stimulus	1
cell population proliferation	1
regulation of cell population proliferation	1
response to light stimulus	1
regulation of cell growth	1
cell growth	1
negative regulation of growth	1
response to vitamin	1
programmed cell death	1
macroautophagy	1
intrinsic apoptotic signaling pathway in response to DNA damage	1
regulation of intrinsic apoptotic signaling pathway in response to DNA damage	1
negative regulation of intrinsic apoptotic signaling pathway	1
regulation of mitotic cell cycle phase transition	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
regulation of cell cycle phase transition	1
negative regulation of cell cycle phase transition	1
cyclin-dependent protein serine/threonine kinase activity	1
cyclin-dependent protein serine/threonine kinase regulator activity	1
protein serine/threonine kinase inhibitor activity	1
kinase binding	1
binding	1
intracellular membrane-bounded organelle	1
nuclear lumen	1
intracellular anatomical structure	1
cytoplasm	1
cyclin-dependent protein kinase holoenzyme complex	1

Protein interactions and networks

STRING

1374 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CDKN2D	CDK4	P11802	997
CDKN2D	CDK6	Q00534	997
CDKN2D	CDKN1B	P46527	852
CDKN2D	CDK2	P24941	838
CDKN2D	CCNL2	Q96S94	819
CDKN2D	CCND3	P30281	771
CDKN2D	CDKN1C	P49918	764
CDKN2D	CDKN1A	P38936	718
CDKN2D	SLC44A2	Q8IWA5	671
CDKN2D	CCND2	P30279	653
CDKN2D	CIB1	Q99828	622
CDKN2D	CCNA2	P20248	575
CDKN2D	CCND1	P24385	548
CDKN2D	CCNA1	P78396	528
CDKN2D	MYCN	P04198	522

IntAct

232 interactions, top by confidence:

A	B	Type	Score
CDKN2D	CDK4	psi-mi:“MI:0915”(physical association)	0.970
CDK4	CDKN2D	psi-mi:“MI:0915”(physical association)	0.970
CDK6	CDKN2D	psi-mi:“MI:0915”(physical association)	0.960
CDKN2D	CDK6	psi-mi:“MI:0407”(direct interaction)	0.960
CDKN2D	CDK6	psi-mi:“MI:0915”(physical association)	0.960
HSD17B14	CDKN2D	psi-mi:“MI:0915”(physical association)	0.790
CDKN2D	HSD17B14	psi-mi:“MI:0915”(physical association)	0.790

BioGRID (113): CDKN2D (Two-hybrid), CDKN2D (Two-hybrid), NR4A1 (Two-hybrid), NR4A2 (Two-hybrid), IKZF3 (Two-hybrid), HSD17B14 (Two-hybrid), C1orf94 (Two-hybrid), INCA1 (Two-hybrid), CDKN2D (Affinity Capture-MS), CDKN2D (Affinity Capture-MS), CDKN2D (Two-hybrid), TBC1D17 (Two-hybrid), IKZF3 (Two-hybrid), C1orf94 (Two-hybrid), CDKN2D (Two-hybrid)

ESM2 similar proteins: A1VWK8, A4XWX9, A5EBX1, A6TGV0, B0U229, B1JBS6, B2I7N1, B2ULE2, B5XXZ1, B8DN19, C0ZLE1, C1B7S7, D5H7Z5, L7N653, O83515, O87455, P31759, P49990, P55273, P55610, P56644, P63400, P71229, P9WQI6, P9WQI7, Q0AEJ6, Q0SAG7, Q13IW3, Q13XV3, Q1DFT5, Q1I610, Q1QHC7, Q29RV0, Q2NR08, Q3KHC9, Q48F46, Q4WGU1, Q4ZWU3, Q50864, Q50899

Diamond homologs: F1M5M3, O77617, P42771, P42772, P42773, P51480, P55271, P55272, P55273, Q29RV0, Q2KJD8, Q38998, Q60772, Q60773, Q91ZU1, Q9R0Z3, Q18297, Q28FJ2, Q6ZVH7, Q5R4M7, Q69ZR2, Q9NWX5, Q9ULT8, Q9VL06, A0A084B9Z8, Q25338, Q5ZLC8, Q8BTI7, Q8NB46, Q9J5I7, P53356, Q14161, Q3SX00, Q5R8C8, Q66H91, Q68FF6, Q76K24, Q86W74, Q8BTZ5, Q9JLQ2

SIGNOR signaling

7 interactions.

A	Effect	B	Mechanism
FOXO1	“up-regulates quantity by expression”	CDKN2D	“transcriptional regulation”
CDK2	up-regulates	CDKN2D	phosphorylation
PRKCA	up-regulates	CDKN2D	phosphorylation
FOXO	“up-regulates quantity by expression”	CDKN2D	“transcriptional regulation”
DNMT3A	“down-regulates quantity by repression”	CDKN2D	“transcriptional regulation”

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	14
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

430 predictions. Top by Δscore:

Variant	Effect	Δscore
19:10568509:TCACC:T	donor_loss	1.0000
19:10568511:A:AC	donor_gain	1.0000
19:10568511:A:AT	donor_loss	1.0000
19:10568512:C:CC	donor_gain	1.0000
19:10568512:CCTG:C	donor_gain	1.0000
19:10567414:TGAC:T	acceptor_gain	0.9900
19:10567418:C:CC	acceptor_gain	0.9900
19:10567418:C:T	acceptor_loss	0.9900
19:10567422:G:C	acceptor_gain	0.9900
19:10568945:AC:A	donor_gain	0.9900
19:10568946:CC:C	donor_gain	0.9900
19:10567420:G:GC	acceptor_gain	0.9800
19:10568528:G:A	donor_gain	0.9800
19:10568945:ACCCT:A	donor_gain	0.9800
19:10568946:CCCTC:C	donor_gain	0.9800
19:10568946:CCCT:C	donor_gain	0.9600
19:10567420:G:C	acceptor_gain	0.9500
19:10567413:ATGAC:A	acceptor_gain	0.9400
19:10567422:G:GC	acceptor_gain	0.9400
19:10568939:TAAC:T	donor_loss	0.9300
19:10568940:AACT:A	donor_loss	0.9300
19:10568941:ACTC:A	donor_loss	0.9300
19:10568942:CT:C	donor_loss	0.9300
19:10568943:T:TA	donor_loss	0.9300
19:10568944:CACCC:C	donor_loss	0.9300
19:10568945:A:T	donor_loss	0.9300
19:10568946:C:CA	donor_loss	0.9300
19:10568950:C:A	donor_gain	0.9300
19:10567415:GAC:G	acceptor_gain	0.9200
19:10567956:T:TA	donor_gain	0.9000

AlphaMissense

1066 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:10567314:G:T	A82D	0.994
19:10567380:A:G	L60P	0.994
19:10567218:G:T	A114E	0.990
19:10567215:A:T	V115D	0.989
19:10567377:A:G	L61P	0.989
19:10568537:G:C	N39K	0.989
19:10568537:G:T	N39K	0.989
19:10567315:C:G	A82P	0.987
19:10567318:C:G	A81P	0.985
19:10567317:G:T	A81E	0.984
19:10567230:G:C	P110R	0.983
19:10567191:A:T	V123D	0.982
19:10567326:A:T	V78D	0.982
19:10567347:T:A	D71V	0.981
19:10568520:G:T	A45E	0.981
19:10568538:T:A	N39I	0.981
19:10567290:A:G	L90P	0.980
19:10567122:G:T	A146E	0.978
19:10567182:A:G	L126P	0.978
19:10567123:C:G	A146P	0.977
19:10567406:A:C	F51L	0.977
19:10567406:A:T	F51L	0.977
19:10567408:A:G	F51L	0.977
19:10567219:C:G	A114P	0.975
19:10567230:G:T	P110Q	0.975
19:10567281:A:G	L93P	0.975
19:10567305:C:A	G85V	0.974
19:10567305:C:T	G85E	0.973
19:10567348:C:G	D71H	0.973
19:10568529:C:A	G42V	0.972

dbSNP variants (sampled 300 via entrez): RS1000006425 (19:10566701 CGGCCAA>C), RS1000122204 (19:10570041 G>C), RS1000445138 (19:10568792 C>G,T), RS1000577364 (19:10570212 T>C), RS1000809294 (19:10570238 C>T), RS1001954645 (19:10570657 G>C), RS1002016291 (19:10569205 C>A,T), RS1002364752 (19:10570932 A>C), RS1002614231 (19:10568049 T>C), RS1002995597 (19:10566750 T>G), RS1003253400 (19:10567918 C>A), RS1003332777 (19:10566405 C>T), RS1003736503 (19:10568237 A>G), RS1005006968 (19:10569530 T>C), RS1005341780 (19:10569284 G>A)

Disease associations

OMIM: gene MIM:600927 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

11 associations (top):

Study	Trait	p-value
GCST90002389_390	Lymphocyte percentage of white cells	5.000000e-13
GCST90002390_520	Mean corpuscular hemoglobin	4.000000e-18
GCST90002390_521	Mean corpuscular hemoglobin	7.000000e-17
GCST90002392_59	Mean corpuscular volume	2.000000e-27
GCST90002392_60	Mean corpuscular volume	2.000000e-19
GCST90002396_17	Mean reticulocyte volume	1.000000e-15
GCST90002397_182	Mean spheric corpuscular volume	3.000000e-22
GCST90002403_276	Red blood cell count	5.000000e-12
GCST90002403_277	Red blood cell count	5.000000e-09
GCST90002404_558	Red cell distribution width	3.000000e-21
GCST90002404_559	Red cell distribution width	5.000000e-15

EFO canonical traits (5, from GWAS)

EFO ID	Trait name
EFO:0007993	lymphocyte percentage of leukocytes
EFO:0004527	mean corpuscular hemoglobin
EFO:0010701	mean reticulocyte volume
EFO:0004305	erythrocyte count
EFO:0009188	Red cell distribution width

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
(+)-JQ1 compound	decreases expression, increases expression	3
Arsenic Trioxide	affects cotreatment, increases expression	3
Estradiol	increases expression, decreases expression, affects cotreatment	3
Hydrogen Peroxide	affects expression, decreases expression	3
Cadmium Chloride	decreases expression, increases expression	3
bisphenol A	increases expression, affects cotreatment	2
methylselenic acid	affects expression, increases expression	2
Decitabine	increases expression	2
Acetaminophen	increases expression	2
Calcitriol	decreases expression, increases expression, affects cotreatment	2
Phenylmercuric Acetate	affects cotreatment, increases expression	2
Tobacco Smoke Pollution	affects expression, decreases expression	2
Tretinoin	affects cotreatment, increases expression	2
aristolochic acid I	increases expression	1
alpha phellandrene	increases expression	1
triphenyl phosphate	affects expression	1
testosterone undecanoate	affects cotreatment, increases expression	1
ethyl-p-hydroxybenzoate	increases expression	1
3,3’-diindolylmethane	increases expression	1
tris(1,3-dichloro-2-propyl)phosphate	decreases expression	1
sodium arsenite	increases expression	1
potassium chromate(VI)	increases expression	1
4-hydroxy-2-nonenal	decreases expression	1
nickel sulfate	increases expression	1
avobenzone	increases expression	1
gardenoside	affects binding, decreases reaction, increases expression	1
chromium hexavalent ion	increases expression	1
2-(4-morpholinyl)-8-phenyl-4H-1-benzopyran-4-one	affects expression, affects reaction	1
CGP 52608	affects binding, increases reaction	1
perfluoro-n-nonanoic acid	increases expression	1

Cellosaurus cell lines

14 cell lines: 10 cancer cell line, 3 embryonic stem cell, 1 transformed cell line

First 10 cell lines (id-ordered, not curated):

Cellosaurus	Name	Category	Sex
CVCL_3768	OV-90	Cancer cell line	Female
CVCL_4Z23	OV90C-A	Cancer cell line	Female
CVCL_4Z24	OV90C-D	Cancer cell line	Female
CVCL_4Z25	OV90D-6	Cancer cell line	Female
CVCL_4Z26	OV90D-7	Cancer cell line	Female
CVCL_4Z27	OV90P-3	Cancer cell line	Female
CVCL_4Z28	OV90P-7	Cancer cell line	Female
CVCL_A0M8	SEES3-1V human CDKN2D, clone1	Embryonic stem cell	Male
CVCL_A0M9	SEES3-1V human CDKN2D, clone2	Embryonic stem cell	Male
CVCL_A0N0	SEES3-1V human CDKN2D, clone3	Embryonic stem cell	Male

Clinical trials (associated diseases)

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