PDCD2L

Summary

PDCD2L (programmed cell death 2 like, HGNC:28194) is a protein-coding gene on chromosome 19q13.11, encoding uS5 assembly chaperone PDCD2L (Q9BRP1). May function as a chaperone for ribosomal protein uS5; its function appears redundant to PDCD2.

Predicted to be involved in apoptotic process. Located in membrane.

Source: NCBI Gene 84306 — automated summary from GO annotations (Alliance of Genome Resources).

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 80 total
• Expression (HPA): Tissue enhanced — highest in frontal cortex, skeletal muscle, caudate putamen
• GTEx eGene: eQTL in 7 tissues, sQTL in 0 (q < 0.05)
• ChEMBL bioactivity: 1 clinical-phase molecule tested; no curated mechanism-of-action drug
• Constraint (gnomAD): pLI 0.00 (LoF-tolerant), LOEUF 1.37 (unconstrained)
• MANE Select transcript: NM_032346
• Notable: 80 clinical variants but no curated precision-oncology (CIViC) evidence yet

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:28194
Approved symbol	PDCD2L
Name	programmed cell death 2 like
Location	19q13.11
Locus type	gene with protein product
Status	Approved
Aliases	MGC13096
Ensembl gene	ENSG00000126249
Ensembl biotype	protein_coding
OMIM	615661
Entrez	84306

Gene structure

Transcript identifiers

Ensembl transcripts: 17 — 8 protein_coding, 6 nonsense_mediated_decay, 3 retained_intron

MANE Select: ENST00000246535

Transcript support level (Ensembl TSL; 1 = fully mRNA-supported): TSL 1: 1, TSL 2: 2, TSL 3: 1, TSL 5: 1

ENST00000246535, ENST00000585821, ENST00000587065, ENST00000587385, ENST00000589589, ENST00001001598, ENST00001001599, ENST00001022242, ENST00001084884, ENST00001084885, ENST00001084886, ENST00001084887, ENST00001084888, ENST00001084889, ENST00001084890, ENST00001095592, ENST00001137246

RefSeq mRNA: 2 — MANE Select: NM_032346 NM_001353433, NM_032346

CCDS: CCDS12438

Canonical transcript exons

ENST00000246535 — 7 exons

Exon	Start	End
ENSE00000862680	34404399	34404538
ENSE00002759398	34425990	34426168
ENSE00003476662	34404649	34404815
ENSE00003570416	34413737	34413847
ENSE00003595430	34404930	34404990
ENSE00003624432	34421519	34421667
ENSE00003625680	34409161	34409510

Expression profiles

Bgee: expression breadth ubiquitous, 242 present calls, max score 95.42.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 16.7753 / max 203.1966, expressed in 1749 samples.

Highest expression (Bgee): primordial germ cell in gonad, male germ line stem cell (sensu Vertebrata) in testis, hindlimb stylopod muscle, oocyte, gastrocnemius.

Genetic regulation across tissues (GTEx eQTL / sQTL)

PDCD2L is an eGene in GTEx v10 — its expression is genetically regulated (eQTL) in 7 tissues and its splicing (sQTL) in 0 (q < 0.05). Strongest associations first; slope = normalized effect of the lead variant’s alternative allele.

7 significant tissue × QTL associations:

Tissue	QTL	q-value	Slope	Lead variant
Cells EBV-transformed lymphocytes	eqtl	9.5e-05	+0.68	19:34306517:T:A
Breast Mammary Tissue	eqtl	1.8e-03	+0.18	19:33938754:C:T
Pituitary	eqtl	1.3e-02	-1.34	19:34051639:G:A
Spleen	eqtl	1.8e-02	-0.35	19:34749120:T:G
Brain Nucleus accumbens basal ganglia	eqtl	3.9e-02	-0.69	19:34811172:T:C
Cells Cultured fibroblasts	eqtl	4.2e-02	+0.18	19:33851543:C:T
Brain Spinal cord cervical c-1	eqtl	4.5e-02	+0.97	19:33941348:G:C

FANTOM5 promoters

3 alternative TSS:

Promoter ID	TPM avg	Samples expressed
175143	16.0567	1745
175142	0.6644	283
175141	0.0542	16

Top tissues by expression

showing 100 of 252 tissues by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	95.42	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	90.84	gold quality
hindlimb stylopod muscle	UBERON:0004252	89.61	gold quality
oocyte	CL:0000023	88.24	gold quality
gastrocnemius	UBERON:0001388	88.11	gold quality
muscle of leg	UBERON:0001383	88.07	gold quality
tibialis anterior	UBERON:0001385	87.45	silver quality
cortical plate	UBERON:0005343	85.91	gold quality
deltoid	UBERON:0001476	84.36	gold quality
quadriceps femoris	UBERON:0001377	84.25	gold quality
left ventricle myocardium	UBERON:0006566	84.16	silver quality
skeletal muscle tissue	UBERON:0001134	83.48	gold quality
prefrontal cortex	UBERON:0000451	83.25	gold quality
right testis	UBERON:0004534	83.20	gold quality
muscle tissue	UBERON:0002385	83.16	gold quality
apex of heart	UBERON:0002098	82.97	gold quality
ventricular zone	UBERON:0003053	82.97	gold quality
ganglionic eminence	UBERON:0004023	82.97	gold quality
vastus lateralis	UBERON:0001379	82.95	gold quality
left testis	UBERON:0004533	82.85	gold quality
testis	UBERON:0000473	82.76	gold quality
cerebellar cortex	UBERON:0002129	81.86	gold quality
cerebellar hemisphere	UBERON:0002245	81.81	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	81.56	gold quality
Brodmann (1909) area 9	UBERON:0013540	81.20	gold quality
mucosa of transverse colon	UBERON:0004991	81.11	gold quality
body of pancreas	UBERON:0001150	81.08	gold quality
cerebellum	UBERON:0002037	80.94	gold quality
right hemisphere of cerebellum	UBERON:0014890	80.93	gold quality
secondary oocyte	CL:0000655	80.85	gold quality
calcaneal tendon	UBERON:0003701	80.82	gold quality
biceps brachii	UBERON:0001507	80.44	gold quality
anterior cingulate cortex	UBERON:0009835	80.29	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	80.08	gold quality
heart left ventricle	UBERON:0002084	79.90	gold quality
right frontal lobe	UBERON:0002810	79.80	gold quality
neocortex	UBERON:0001950	79.75	gold quality
islet of Langerhans	UBERON:0000006	79.67	gold quality
frontal cortex	UBERON:0001870	79.58	gold quality
pancreas	UBERON:0001264	79.53	gold quality
cardiac ventricle	UBERON:0002082	79.38	gold quality
caudate nucleus	UBERON:0001873	79.35	gold quality
hypothalamus	UBERON:0001898	79.29	gold quality
right adrenal gland	UBERON:0001233	79.07	gold quality
putamen	UBERON:0001874	78.98	gold quality
stromal cell of endometrium	CL:0002255	78.90	gold quality
right adrenal gland cortex	UBERON:0035827	78.78	gold quality
nucleus accumbens	UBERON:0001882	78.77	gold quality
amygdala	UBERON:0001876	78.75	gold quality
popliteal artery	UBERON:0002250	78.54	gold quality
tibial artery	UBERON:0007610	78.53	gold quality
adenohypophysis	UBERON:0002196	78.43	gold quality
cerebral cortex	UBERON:0000956	78.39	gold quality
body of stomach	UBERON:0001161	78.30	gold quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	78.17	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	78.10	gold quality
forebrain	UBERON:0001890	77.96	gold quality
brain	UBERON:0000955	77.95	gold quality
left adrenal gland	UBERON:0001234	77.92	gold quality
heart	UBERON:0000948	77.87	gold quality
tendon	UBERON:0000043	77.85	gold quality
left adrenal gland cortex	UBERON:0035825	77.75	gold quality
pituitary gland	UBERON:0000007	77.59	gold quality
granulocyte	CL:0000094	77.57	gold quality
adrenal gland	UBERON:0002369	77.41	gold quality
aorta	UBERON:0000947	77.20	gold quality
left coronary artery	UBERON:0001626	77.06	gold quality
muscle layer of sigmoid colon	UBERON:0035805	77.04	gold quality
lymph node	UBERON:0000029	77.01	gold quality
right coronary artery	UBERON:0001625	76.90	gold quality
adrenal cortex	UBERON:0001235	76.89	gold quality
primary visual cortex	UBERON:0002436	76.84	gold quality
cardiac atrium	UBERON:0002081	76.71	gold quality
spinal cord	UBERON:0002240	76.67	gold quality
right atrium auricular region	UBERON:0006631	76.64	gold quality
lower esophagus mucosa	UBERON:0035834	76.61	gold quality
stomach	UBERON:0000945	76.58	gold quality
ovary	UBERON:0000992	76.54	gold quality
right ovary	UBERON:0002118	76.48	gold quality
left uterine tube	UBERON:0001303	76.46	gold quality
coronary artery	UBERON:0001621	76.26	gold quality
esophagus mucosa	UBERON:0002469	76.26	gold quality
body of uterus	UBERON:0009853	76.24	gold quality
right lobe of liver	UBERON:0001114	76.23	gold quality
esophagus	UBERON:0001043	76.09	gold quality
spleen	UBERON:0002106	75.97	gold quality
lower esophagus	UBERON:0013473	75.92	gold quality
lower esophagus muscularis layer	UBERON:0035833	75.91	gold quality
adrenal tissue	UBERON:0018303	75.77	gold quality
corpus callosum	UBERON:0002336	75.76	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	75.68	gold quality
Ammon’s horn	UBERON:0001954	75.67	gold quality
left ovary	UBERON:0002119	75.66	gold quality
thoracic aorta	UBERON:0001515	75.61	gold quality
ascending aorta	UBERON:0001496	75.55	gold quality
ileal mucosa	UBERON:0000331	75.38	gold quality
ectocervix	UBERON:0012249	75.32	gold quality
anatomical system	UBERON:0000467	75.27	gold quality
multicellular organism	UBERON:0000468	75.14	gold quality
material anatomical entity	UBERON:0000465	75.13	gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-MTAB-7249	yes	11.13
E-MTAB-7303	no	938.23
E-ANND-3	no	2.61

HPA expression

RNA tissue specificity: Tissue enhanced

showing 60 of 79 HPA tissues / cells by nTPM:

Tissue / cell	Axis	nTPM	Protein (IHC)
Frontal cortex	tissue	18.3
Skeletal muscle	tissue	17.8	low
Caudate putamen	tissue	16.0
Testis	tissue	8.8	high
Tongue	tissue	8.5
Pituitary gland	tissue	5.6
Heart muscle	tissue	5.3	medium
Salivary gland	tissue	5.2	medium
Spinal cord	tissue	5.2
Corpus callosum	tissue	5.2
Medulla oblongata	tissue	5.1
Putamen	tissue	5.0
Midbrain	tissue	5.0
Superior colliculi	tissue	4.9
Thalamus	tissue	4.8
Hippocampal formation	tissue	4.6
Cerebral cortex	tissue	4.5	medium
Basal ganglia	tissue	4.5	high
Tonsil	tissue	4.5	high
Somatosensory cortex	tissue	4.5
Lymph node	tissue	4.4	high
Pancreas	tissue	4.4	medium
Substantia nigra	tissue	4.3
Skin 1	tissue	4.2	medium
Prefrontal cortex	tissue	4.1
Stomach 1	tissue	4.1	high
Pons	tissue	4.1
Septum	tissue	4.1
Ovary	tissue	4.0	high
Motor cortex	tissue	4.0
Ventral forebrain	tissue	4.0
Temporal cortex	tissue	4.0
Retrosplenial and cingulate cortex	tissue	3.9
Occipital cortex	tissue	3.9
Vagina	tissue	3.7	not detected
Hypothalamus	tissue	3.7
Entorhinal cortex	tissue	3.7
Periaqueductal gray	tissue	3.7
Fallopian tube	tissue	3.7	high
Retrosplenial cortex	tissue	3.7
Seminal vesicle	tissue	3.6	medium
Adipose tissue	tissue	3.6	low
Nucleus accumbens	tissue	3.5
Cerebellum	tissue	3.5	medium
Postcentral gyrus	tissue	3.5
Olfactory bulb	tissue	3.4
Insular cortex	tissue	3.4
Breast	tissue	3.3	high
Amygdala	tissue	3.3
Spleen	tissue	3.3	high
Liver	tissue	3.3	medium
Hippocampus	tissue	3.3	medium
Rectum	tissue	3.2	high
Urinary bladder	tissue	3.2	medium
Adrenal gland	tissue	3.2	high
Esophagus	tissue	3.0	low
Locus coeruleus	tissue	3.0
Smooth muscle	tissue	2.9	medium
Colon	tissue	2.9	medium
Bone marrow	tissue	2.9	medium

Brain sub-regions (HPA Brain Atlas): detected in 192; highest nTPM — Blood vessel (6.2), Occipital cortex (white matter) (5.8), Arcuate nucleus (5.5), Corpus callosum, genu (white matter) (5.4), Corpus callosum, splenium (white matter) (5.2).

Regulation

Is transcription factor: no

Functional genomics

gnomAD constraint: pLI 9.5e-12, LOEUF 1.37, missense Z -0.323 — population loss-of-function intolerance (pLI ≥ 0.9 = LoF-intolerant; lower LOEUF = more constrained). gnomAD

Regional missense constraint (gnomAD RMC): no regional variation along ENST00000246535 — one region, missense o/e 1.04.

Literature-anchored findings (GeneRIF, showing 4)

• To study the role of PDCD2_C domain in apoptosis, the cDNAs of two isoforms of PDCD2 and MGC13096 were cloned. PDCD2 (NM_002598) was over expressed when endothelial cells treated with leukotriene D4 or natural killer cells were activated by IL-2. (PMID:16311922)
• MGC13096 over-expression restrained proliferation of HEK293T cells. DNA/flow cytometry analysis showed that the over-expression of MGC13096 severely delays cell cycle progression at S phase. (PMID:17393540)
• Overexpression of PDCD2-like gene attenutates TNF-alpha release in Daudi cells (PMID:18486760)
• Findings uncover the existence of an extra-ribosomal complex consisting of PDCD2L, RPS2, and PRMT3 and support a role for PDCD2L in the late maturation of 40S ribosomal subunits. (PMID:27697862)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	pdcd2l	ENSDARG00000002754
mus_musculus	Pdcd2l	ENSMUSG00000002635
rattus_norvegicus	Pdcd2l	ENSRNOG00000021119
drosophila_melanogaster	trus	FBGN0038055

Paralogs (2): ZMYND12 (ENSG00000066185), PDCD2 (ENSG00000071994)

Mouse-model phenotypes

Observed phenotypes of the mouse ortholog (MGI:1915329) from MGI (Alliance of Genome Resources) — knockout/mutant phenotypes, ranked by annotation count. 2 distinct phenotype terms.

Mouse phenotype (MP)	Records
prenatal lethality, complete penetrance	1
embryonic lethality during organogenesis, incomplete penetrance	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
Gallus gallus	Q5ZID2	49.9%	Diamond
Schizosaccharomyces pombe 972h-	P87156	39.2%	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
WTIP	protein-coding	126374
UBA2	protein-coding	10054
GPI	protein-coding	2821
GARRE1	protein-coding	9710
LSM14A	protein-coding	26065

Protein

Protein identifiers

uS5 assembly chaperone PDCD2L — Q9BRP1 (reviewed: Q9BRP1)

Alternative names: Programmed cell death protein 2-like

All UniProt accessions (2): Q9BRP1, U3KQL1

UniProt curated annotations — full annotation on UniProt →

Function. May function as a chaperone for ribosomal protein uS5; its function appears redundant to PDCD2.

Subunit / interactions. Interacts with the 40S ribosomal protein RPS2/uS5; for putative chaperone function of PDC2L.

Subcellular location. Nucleus. Nucleolus. Cytoplasm. Cytosol.

Tissue specificity. Higher expression in lung, colon, mammary gland, cervix, stomach and small intestine.

Similarity. Belongs to the TSR4 family.

RefSeq proteins (2): NP_001340362, NP_115722* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR007320	PDCD2_C	Domain
IPR052815	PDCD2-like_regulator	Family

Pfam: PF04194

UniProt features (6 total): modified residue 3, initiator methionine 1, chain 1, short sequence motif 1

Structure

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9BRP1-F1	75.93	0.40

Human Protein Atlas

Protein class: Predicted intracellular proteins, Cancer-related genes, Mutated cancer genes

Protein evidence: Evidence at protein level

Subcellular location (HPA, imaging): mitochondria

Antibody reliability (HPA): IH approved · IF approved

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 (3)

Type	Positions
N-acetylalanine	2
Phosphoserine	20
Phosphothreonine	22

Function

Pathways and Gene Ontology

Reactome pathways

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

MSigDB gene sets: 77 (showing top): MODULE_255, MODULE_317, WEI_MYCN_TARGETS_WITH_E_BOX, MARZEC_IL2_SIGNALING_UP, GRADE_COLON_AND_RECTAL_CANCER_UP, NUYTTEN_EZH2_TARGETS_DN, YGCGYRCGC_UNKNOWN, MODULE_69, KRIEG_KDM3A_TARGETS_NOT_HYPOXIA, MODULE_37, STK33_DN, STK33_SKM_DN, NRF1_Q6, GSE13547_WT_VS_ZFX_KO_BCELL_ANTI_IGM_STIM_2H_DN, GSE13547_CTRL_VS_ANTI_IGM_STIM_BCELL_2H_DN

GO Biological Process (2): apoptotic process (GO:0006915), ribosome biogenesis (GO:0042254)

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

GO Cellular Component (4): nucleolus (GO:0005730), cytosol (GO:0005829), membrane (GO:0016020), cytoplasm (GO:0005737)

GO top-level categories

10 GO namespaces:

Category	Terms
cellular anatomical structure	3
programmed cell death	1
apoptotic signaling pathway	1
execution phase of apoptosis	1
ribonucleoprotein complex biogenesis	1
binding	1
nuclear lumen	1
intracellular membraneless organelle	1
cytoplasm	1
intracellular anatomical structure	1

Experimentally-supported GO annotations

GO terms backed by direct experimental evidence (ECO experimental codes) — 1 of 7 annotations. The rest are phylogenetic / computational / electronic (IEA).

1 experimentally-supported GO terms:

GO term	NS	Evidence
membrane	CC	high-throughput assay

Protein interactions and networks

STRING

showing 15 of 584 interactions by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
PDCD2L	PRMT3	O60678	605
PDCD2L	ZNF277	Q9NRM2	599
PDCD2L	GGN	Q86UU5	578
PDCD2L	BYSL	Q13895	481
PDCD2L	PABPN1	Q86U42	431
PDCD2L	RPS2	P15880	428
PDCD2L	RPL4	P36578	413
PDCD2L	PNO1	Q9NRX1	371
PDCD2L	WTIP	A6NIX2	370
PDCD2L	HSD17B2	P37059	366
PDCD2L	CCDC73	Q6ZRK6	364
PDCD2L	PERP	Q96FX8	357
PDCD2L	IQCF6	A8MYZ5	346
PDCD2L	EDRF1	Q3B7T1	342
PDCD2L	LSM14A	Q8ND56	325

IntAct

Human interaction partners of PDCD2L in IntAct, one row per partner (best MIscore; records = supporting IntAct interaction records).

7 partners by confidence:

Partner	Interaction type	MIscore	Records
ITGB1BP2	physical association	0.690	2
BRAF	physical association	0.600	4
SMAD4	proximity	0.270	4
FBXW7	proximity	0.270	3
EGFR	proximity	0.270	1
SMARCA4	proximity	0.270	1
DISC1	physical association	0.000	1

BioGRID (106 interactions; top human partners by supporting records): ITGB1BP2 (Affinity Capture-MS; 5 records), RPS2 (Affinity Capture-MS; 4 records), BMX (Affinity Capture-MS; 3 records), NAP1L5 (Affinity Capture-MS; 3 records), OTUD5 (Affinity Capture-MS; 3 records), PCBP3 (Affinity Capture-MS; 3 records), PRMT3 (Affinity Capture-MS; 3 records), SLX4IP (Affinity Capture-MS; 3 records), AHCYL2 (Affinity Capture-MS; 2 records), ARHGAP22 (Affinity Capture-MS; 2 records), ARIH1 (Affinity Capture-MS; 2 records), GPBP1L1 (Affinity Capture-MS; 2 records), GPR156 (Affinity Capture-MS; 2 records), GRAMD1B (Affinity Capture-MS; 2 records), KANK4 (Affinity Capture-MS; 2 records)

Disease & clinical

Genetic variants

Variant evidence for PDCD2L: 80 ClinVar records (0 pathogenic / likely pathogenic); 1 GWAS association.

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	61
Likely benign	4
Benign	0

SpliceAI

Top 10 splice-impact sites by Δscore (adjacent positions with the same effect merged into one range; 37 predictions of 486):

Position(s)	Effect	Δscore	Sites
19:34404524	donor_gain	1.0000
19:34413735–34413736	acceptor_loss	1.0000	6
19:34421517–34421518	acceptor_loss	1.0000	5
19:34421668–34421669	donor_loss	1.0000	5
19:34404520	donor_gain	0.9900
19:34404539–34404540	donor_loss	0.9900	6
19:34413848–34413849	donor_loss	0.9900	5
19:34421518	acceptor_loss	0.9900
19:34421642	donor_gain	0.9900
19:34404647–34404648	acceptor_loss	0.9800	6

AlphaMissense

525 missense substitutions predicted likely pathogenic (of 2,357 scored), across 129 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
D351	8	0.852	0.941
D353	8	0.716	0.856
F253	7	0.970	0.992
C329	7	0.960	0.983
E299	7	0.957	0.984
F298	7	0.936	0.975
F321	7	0.933	0.990
C289	7	0.923	0.969
R266	7	0.916	0.986
M303	7	0.915	0.970
C333	7	0.904	0.935
Q301	7	0.894	0.975
F78	7	0.893	0.940
E344	7	0.882	0.963
W93	7	0.880	0.977
C292	7	0.876	0.932
F250	7	0.873	0.978
W334	7	0.853	0.954
C49	7	0.828	0.909
W130	7	0.819	0.931

HPA cancer prognostics

RNA cancer specificity: Low cancer specificity

Disease associations

OMIM: gene MIM:615661 | disease phenotypes:

GWAS associations

1 association:

Study	Trait	p-value
GCST010796_2274	Electrocardiogram morphology (amplitude at temporal datapoints)	4e-8

EFO canonical traits (from GWAS)

1 canonical traits:

EFO ID	Trait name
EFO:0004327	electrocardiography

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL5725169 (SINGLE PROTEIN)

Molecules with ChEMBL bioactivity

Phase ≥1, by development phase (incl. off-target/promiscuous compounds). Patent mentions across the top 20 by phase: 1,601 (via chembl_molecule»patent_compound — counts attach to the compound, not the gene–compound relationship, so off-target/promiscuous molecules can dominate).

1 molecule by phase:

Molecule	Name	Phase	Patents
CHEMBL1232461	MOLIBRESIB	2	1,601

PharmGKB: 1 entry (CPIC guideline: no)

ChEMBL bioactivities

3 potent at pChembl≥5 of 3 total, top 3 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChembl	Type	Value	Unit	Molecule
5.36	Kd	4322	nM	CHEMBL3752910
5.35	ED50	4491	nM	CHEMBL3752910
5.00	IC50	1e+04	nM	MOLIBRESIB

PubChem BioAssay actives

2 with measured affinity, of 8 total; 2 most potent distinct compounds. Largely complementary to BindingDB; screening values are coarse (µM, 4 dp), so sub-nM hits tie at the floor.

Compound	Assay	Type	Value	Unit
4-methyl-3-[(1-methyl-6-pyridin-3-ylpyrazolo[3,4-d]pyrimidin-4-yl)amino]-N-[3-(trifluoromethyl)phenyl]benzamide	2149906: Binding affinity to human PDCD2L incubated for 45 mins by Kinobead based pull down assay	kd	4.3216	uM
2-[(4S)-6-(4-chlorophenyl)-8-methoxy-1-methyl-4H-[1,2,4]triazolo[4,3-a][1,4]benzodiazepin-4-yl]-N-ethylacetamide	2178930: Inhibition of PDCD2L (unknown origin) incubated for 1 hr by colloidal coomassie staining based LC-MS/MS analysis	ic50	10.0000	uM

CTD chemical–gene interactions

25 total (human), top 25 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	decreases expression, increases abundance, increases expression	2
Arsenic	affects methylation, increases abundance, increases expression	2
Valproic Acid	affects expression, decreases expression	2
beauvericin	increases expression	1
beta-methylcholine	affects expression	1
di-n-butylphosphoric acid	affects expression	1
4-phenylbutyric acid	decreases expression	1
cylindrospermopsin	increases expression	1
jinfukang	increases expression	1
Temozolomide	increases expression	1
Sunitinib	increases expression	1
Cadmium	increases expression	1
Estradiol	increases expression	1
Ethyl Methanesulfonate	decreases expression	1
Formaldehyde	decreases expression	1
Ivermectin	decreases expression	1
Methyl Methanesulfonate	decreases expression	1
Nickel	increases expression	1
Phenobarbital	affects expression	1
Thiram	decreases expression	1
Tretinoin	decreases expression	1
Urethane	decreases expression	1
Cyclosporine	increases expression	1
Aflatoxin B1	increases expression	1
Copper Sulfate	increases expression	1

ChEMBL screening assays

7 unique, capped per target: 7 binding

Representative assays (with source publication via chembl_document):

Assay ID	Type	Description	Source paper
CHEMBL5652948	Binding	Binding affinity to human PDCD2L incubated for 45 mins by Kinobead based pull down assay	NVP-BHG712: Effects of Regioisomers on the Affinity and Selectivity toward the EPHrin Family. — *ChemMedChem*

Clinical trials (associated diseases)

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

Predicted chemistry — Sugi Predict

The predicted patent-compound landscape for PDCD2L across ~30M SureChEMBL compounds — explore on Sugi Predict.