PDCD11

Summary

PDCD11 (programmed cell death 11, HGNC:13408) is a protein-coding gene on chromosome 10q24.33, encoding Protein RRP5 homolog (Q14690). Essential for the generation of mature 18S rRNA, specifically necessary for cleavages at sites A0, 1 and 2 of the 47S precursor. It is a common-essential gene (DepMap: required in 99.6% of cancer cell lines).

PDCD11 is a NF-kappa-B (NFKB1; 164011)-binding protein that colocalizes with U3 RNA (MIM 180710) in the nucleolus and is required for rRNA maturation and generation of 18S rRNA (Sweet et al., 2003 [PubMed 14624448]; Sweet et al., 2008 [PubMed 17654514]).

Source: NCBI Gene 22984 — RefSeq curated summary.

At a glance

• GWAS associations: 9
• Clinical variants (ClinVar): 306 total (top 10% of genes corpus-wide)
• GTEx eGene: eQTL in 43 tissues, sQTL in 18 (q < 0.05)
• Cancer dependency (DepMap): dependent in 99.6% of screened cell lines (common-essential)
• Constraint (gnomAD): pLI 0.00 (LoF-tolerant), LOEUF 0.57 (moderately constrained)
• MANE Select transcript: NM_014976
• Interaction hub: 3,207 STRING partners (top 2% of genes corpus-wide)
• Notable: 306 clinical variants but no curated precision-oncology (CIViC) evidence yet

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:13408
Approved symbol	PDCD11
Name	programmed cell death 11
Location	10q24.33
Locus type	gene with protein product
Status	Approved
Aliases	KIAA0185, ALG-4, RRP5, NFBP
Ensembl gene	ENSG00000148843
Ensembl biotype	protein_coding
OMIM	612333
Entrez	22984

Gene structure

Transcript identifiers

Ensembl transcripts: 26 — 16 protein_coding, 6 nonsense_mediated_decay, 4 retained_intron

MANE Select: ENST00000369797

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

ENST00000369797, ENST00000466959, ENST00000471061, ENST00000478543, ENST00000493610, ENST00000648051, ENST00000649849, ENST00000902786, ENST00000930107, ENST00000930108, ENST00000930109, ENST00000930110, ENST00000930111, ENST00000930112, ENST00000930113, ENST00000930114, ENST00000930115, ENST00000930116, ENST00000930117, ENST00000988499, ENST00001081549, ENST00001081550, ENST00001081551, ENST00001081552, ENST00001126814, ENST00001137419

RefSeq mRNA: 4 — MANE Select: NM_014976 NM_001411058, NM_001437420, NM_001437421, NM_014976

CCDS: CCDS31276, CCDS91342

Canonical transcript exons

ENST00000369797 — 36 exons

Exon	Start	End
ENSE00000987739	103405985	103406108
ENSE00000987740	103406609	103406790
ENSE00000987741	103409699	103409806
ENSE00000987742	103413116	103413322
ENSE00000987743	103413966	103414090
ENSE00000987744	103414270	103414330
ENSE00000987745	103415005	103415151
ENSE00000987746	103416491	103416742
ENSE00000987747	103417792	103417932
ENSE00000987749	103419538	103419708
ENSE00001025994	103444517	103444682
ENSE00001025995	103427329	103427391
ENSE00001025997	103418440	103418634
ENSE00001025998	103439746	103439868
ENSE00001026000	103443165	103443333
ENSE00001026002	103432129	103432234
ENSE00001026003	103443915	103444068
ENSE00001026005	103442213	103442460
ENSE00001026006	103441826	103441975
ENSE00001026007	103434248	103434350
ENSE00001026008	103438686	103438808
ENSE00001026009	103434798	103434975
ENSE00001026011	103440290	103440581
ENSE00001026012	103438015	103438071
ENSE00001026013	103424984	103425525
ENSE00001026014	103440734	103440850
ENSE00001026016	103433948	103434037
ENSE00001092404	103421348	103421567
ENSE00001092405	103423543	103423658
ENSE00001092406	103422988	103423137
ENSE00001450934	103445378	103446294
ENSE00003492214	103405022	103405183
ENSE00003505969	103398416	103398528
ENSE00003649254	103403118	103403285
ENSE00003683824	103400397	103400528
ENSE00003831406	103396626	103396730

Expression profiles

Bgee: expression breadth ubiquitous, 261 present calls, max score 90.92.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 31.6963 / max 270.0191, expressed in 1814 samples.

Highest expression (Bgee): primordial germ cell in gonad, sural nerve, male germ line stem cell (sensu Vertebrata) in testis, testis, lower esophagus mucosa.

Genetic regulation across tissues (GTEx eQTL / sQTL)

PDCD11 is an eGene in GTEx v10 — its expression is genetically regulated (eQTL) in 43 tissues and its splicing (sQTL) in 18 (q < 0.05). Strongest associations first; slope = normalized effect of the lead variant’s alternative allele.

showing 20 of 61 significant tissue × QTL associations:

Tissue	QTL	q-value	Slope	Lead variant
Adipose Subcutaneous	eqtl	1.0e-25	+1.20	10:103266562:C:A
Nerve Tibial	eqtl	8.2e-25	+1.35	10:103247788:A:G
Thyroid	eqtl	2.7e-24	+1.25	10:103247788:A:G
Artery Aorta	eqtl	4.7e-22	+1.24	10:103247788:A:G
Skin Not Sun Exposed Suprapubic	eqtl	1.8e-21	+1.00	10:103247788:A:G
Skin Sun Exposed Lower leg	eqtl	1.1e-20	+0.90	10:103247788:A:G
Lung	eqtl	2.3e-20	+0.83	10:103247788:A:G
Colon Sigmoid	eqtl	1.8e-17	+1.52	10:103247788:A:G
Brain Cerebellar Hemisphere	eqtl	2.4e-15	+1.64	10:103247788:A:G
Breast Mammary Tissue	eqtl	4.1e-15	+1.07	10:103247788:A:G
Esophagus Muscularis	eqtl	3.7e-14	+1.14	10:103247788:A:G
Stomach	eqtl	1.6e-12	+1.14	10:103247788:A:G
Artery Tibial	eqtl	2.8e-12	+1.01	10:103329335:C:A
Adipose Visceral Omentum	eqtl	1.4e-11	+0.78	10:103247788:A:G
Colon Transverse	eqtl	5.3e-11	+0.90	10:103247788:A:G
Testis	eqtl	6.2e-10	+1.01	10:103327922:G:A
Esophagus Gastroesophageal Junction	eqtl	9.7e-10	+1.04	10:103327922:G:A
Artery Aorta	sqtl	1.2e-09	-2.40	10:103450469:G:GC
Heart Atrial Appendage	eqtl	3.6e-09	+0.76	10:103247788:A:G
Brain Cortex	eqtl	5.6e-09	+1.29	10:103309140:G:T

FANTOM5 promoters

2 alternative TSS:

Promoter ID	TPM avg	Samples expressed
106809	30.8141	1813
106810	0.8823	502

Top tissues by expression

showing 100 of 281 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	90.92	gold quality
sural nerve	UBERON:0015488	89.03	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	88.95	gold quality
left testis	UBERON:0004533	88.80	gold quality
right testis	UBERON:0004534	88.60	gold quality
testis	UBERON:0000473	87.88	gold quality
lower esophagus mucosa	UBERON:0035834	87.80	gold quality
tongue squamous epithelium	UBERON:0006919	87.75	gold quality
cervix squamous epithelium	UBERON:0006922	87.61	silver quality
mucosa of transverse colon	UBERON:0004991	86.21	gold quality
granulocyte	CL:0000094	86.17	gold quality
gastrocnemius	UBERON:0001388	85.91	gold quality
right uterine tube	UBERON:0001302	85.83	gold quality
muscle of leg	UBERON:0001383	85.52	gold quality
esophagus mucosa	UBERON:0002469	85.49	gold quality
stromal cell of endometrium	CL:0002255	85.47	gold quality
adrenal tissue	UBERON:0018303	85.44	gold quality
body of pancreas	UBERON:0001150	85.27	gold quality
tibialis anterior	UBERON:0001385	85.27	gold quality
ganglionic eminence	UBERON:0004023	85.17	gold quality
skin of leg	UBERON:0001511	85.10	gold quality
skin of abdomen	UBERON:0001416	84.98	gold quality
cortical plate	UBERON:0005343	84.93	gold quality
right ovary	UBERON:0002118	84.83	gold quality
embryo	UBERON:0000922	84.64	gold quality
pancreas	UBERON:0001264	84.42	gold quality
ventricular zone	UBERON:0003053	84.25	gold quality
left ovary	UBERON:0002119	84.11	gold quality
right lobe of liver	UBERON:0001114	84.08	gold quality
islet of Langerhans	UBERON:0000006	84.03	gold quality
body of uterus	UBERON:0009853	83.97	gold quality
spleen	UBERON:0002106	83.80	gold quality
left uterine tube	UBERON:0001303	83.69	gold quality
ectocervix	UBERON:0012249	83.69	gold quality
calcaneal tendon	UBERON:0003701	83.63	gold quality
lymph node	UBERON:0000029	83.59	gold quality
esophagus	UBERON:0001043	83.54	gold quality
zone of skin	UBERON:0000014	83.52	gold quality
ovary	UBERON:0000992	83.17	gold quality
apex of heart	UBERON:0002098	83.01	gold quality
vagina	UBERON:0000996	82.78	gold quality
tibial nerve	UBERON:0001323	82.69	gold quality
left adrenal gland cortex	UBERON:0035825	82.66	gold quality
upper lobe of left lung	UBERON:0008952	82.65	gold quality
muscle organ	UBERON:0001630	82.61	gold quality
metanephros cortex	UBERON:0010533	82.57	gold quality
smooth muscle tissue	UBERON:0001135	82.52	gold quality
uterine cervix	UBERON:0000002	82.39	gold quality
left adrenal gland	UBERON:0001234	82.36	gold quality
endocervix	UBERON:0000458	82.28	gold quality
peritoneum	UBERON:0002358	82.28	gold quality
omental fat pad	UBERON:0010414	82.27	gold quality
mucosa of stomach	UBERON:0001199	82.26	gold quality
transverse colon	UBERON:0001157	82.23	gold quality
adrenal gland	UBERON:0002369	82.17	gold quality
upper lobe of lung	UBERON:0008948	82.14	gold quality
adrenal cortex	UBERON:0001235	82.07	gold quality
right adrenal gland	UBERON:0001233	81.98	gold quality
ileal mucosa	UBERON:0000331	81.97	gold quality
right lobe of thyroid gland	UBERON:0001119	81.97	gold quality
adenohypophysis	UBERON:0002196	81.95	gold quality
hindlimb stylopod muscle	UBERON:0004252	81.76	gold quality
vermiform appendix	UBERON:0001154	81.75	gold quality
body of stomach	UBERON:0001161	81.73	gold quality
adipose tissue of abdominal region	UBERON:0007808	81.64	gold quality
muscle layer of sigmoid colon	UBERON:0035805	81.62	gold quality
fallopian tube	UBERON:0003889	81.61	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	81.58	gold quality
lower esophagus	UBERON:0013473	81.56	gold quality
lower esophagus muscularis layer	UBERON:0035833	81.55	gold quality
right adrenal gland cortex	UBERON:0035827	81.42	gold quality
tendon	UBERON:0000043	81.39	gold quality
heart left ventricle	UBERON:0002084	81.34	gold quality
tonsil	UBERON:0002372	81.32	gold quality
stomach	UBERON:0000945	81.28	gold quality
minor salivary gland	UBERON:0001830	81.27	gold quality
left lobe of thyroid gland	UBERON:0001120	81.26	gold quality
caecum	UBERON:0001153	81.19	gold quality
small intestine Peyer’s patch	UBERON:0003454	81.12	gold quality
oviduct epithelium	UBERON:0004804	81.12	gold quality
right hemisphere of cerebellum	UBERON:0014890	81.09	gold quality
cardiac ventricle	UBERON:0002082	81.02	gold quality
mouth mucosa	UBERON:0003729	80.99	gold quality
leukocyte	CL:0000738	80.94	gold quality
thyroid gland	UBERON:0002046	80.94	gold quality
female reproductive system	UBERON:0000474	80.93	gold quality
cerebellar hemisphere	UBERON:0002245	80.91	gold quality
rectum	UBERON:0001052	80.85	gold quality
myometrium	UBERON:0001296	80.85	gold quality
cerebellar cortex	UBERON:0002129	80.83	gold quality
liver	UBERON:0002107	80.82	gold quality
endothelial cell	CL:0000115	80.81	gold quality
left coronary artery	UBERON:0001626	80.79	gold quality
pituitary gland	UBERON:0000007	80.77	gold quality
right atrium auricular region	UBERON:0006631	80.72	gold quality
monocyte	CL:0000576	80.69	gold quality
mononuclear cell	CL:0000842	80.58	gold quality
colon	UBERON:0001155	80.53	gold quality
coronary artery	UBERON:0001621	80.44	gold quality
uterus	UBERON:0000995	80.43	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	6.40

HPA expression

RNA tissue specificity: Low tissue specificity

showing 60 of 77 HPA tissues / cells by nTPM:

Tissue / cell	Axis	nTPM	Protein (IHC)
Skin 1	tissue	14.6	medium
Testis	tissue	13.9	medium
Thymus	tissue	11.1
Choroid plexus	tissue	11.0
Tonsil	tissue	11.0	medium
Nucleus accumbens	tissue	10.7
Locus coeruleus	tissue	10.7
Postcentral gyrus	tissue	10.4
Lymph node	tissue	10.3	low
Pancreas	tissue	9.9	medium
Skeletal muscle	tissue	9.5	low
Hippocampus	tissue	9.5	high
Appendix	tissue	9.4	medium
Urinary bladder	tissue	9.2	medium
Breast	tissue	8.8	medium
Smooth muscle	tissue	8.5	low
Fallopian tube	tissue	8.4	medium
Ovary	tissue	8.2	low
Vagina	tissue	8.1	low
Spleen	tissue	8.1	low
Corpus callosum	tissue	8.1
Parathyroid gland	tissue	8.0	medium
Esophagus	tissue	7.9	medium
Endometrium 1	tissue	7.8	not detected
Tongue	tissue	7.6
Rectum	tissue	7.5	medium
Adipose tissue	tissue	7.1	not detected
Placenta	tissue	7.1	medium
Bone marrow	tissue	7.1	high
Superior colliculi	tissue	6.9
Colon	tissue	6.8	medium
Spinal cord	tissue	6.7
Substantia nigra	tissue	6.5
Midbrain	tissue	6.3
Medulla oblongata	tissue	6.3
Pituitary gland	tissue	6.1
Thalamus	tissue	6.1
Cerebellum	tissue	6.1	high
Liver	tissue	6.1	low
Cervix	tissue	6.0	low
Stomach 1	tissue	6.0	medium
Prostate	tissue	6.0	not detected
Seminal vesicle	tissue	5.9	medium
Salivary gland	tissue	5.9	low
Hypothalamus	tissue	5.8
Thyroid gland	tissue	5.8	low
Retina	tissue	5.7
Pons	tissue	5.7
Lung	tissue	5.7	medium
Caudate putamen	tissue	5.7
Epididymis	tissue	5.5	medium
Duodenum	tissue	5.5	medium
Hippocampal formation	tissue	5.5
Periaqueductal gray	tissue	5.5
Frontal cortex	tissue	5.4
Septum	tissue	5.4
Putamen	tissue	5.3
Cerebral cortex	tissue	5.2	high
Small intestine	tissue	5.2	medium
Ventral forebrain	tissue	5.2

Brain sub-regions (HPA Brain Atlas): detected in 192; highest nTPM — Anterior thalamic nucleus, ventral (12.7), Parieto-temporal junction (white matter) (11.5), Ventromedial nucleus (11.5), Arcuate nucleus (11.4), Piriform cortex (11.3).

Regulation

Is transcription factor: yes

Downstream targets (CollecTRI)

1 targets:

Target	Regulation
FASLG	Unknown

Functional genomics

gnomAD constraint: pLI 1.07e-07, LOEUF 0.573, missense Z 2.1 — population loss-of-function intolerance (pLI ≥ 0.9 = LoF-intolerant; lower LOEUF = more constrained). gnomAD

Regional missense constraint (gnomAD RMC): no regional variation along ENST00000369797 — one region, missense o/e 0.91. DepMap (CRISPR cell-line fitness): dependent in 99.6% of screened cell lines, common-essential.

Most-dependent cell lines (DepMap gene-effect, lower = stronger; ≤ −0.5 shown): BICR 6 (-2.691), SNU-886 (-2.603), NCI-H460 (-2.493), HCC-95 (-2.468), Du4475 (-2.302), HCC-461 (-2.246), G-402 (-2.242), CH-157MN (-2.237), LU99 (-2.178), Panc 05.04 (-2.162), CJM (-2.155), HuH-7 (-2.152), S-117 (-2.151), U-87 MG (-2.133), SNU-840 (-2.117).

Literature-anchored findings (GeneRIF, showing 3)

• Evidence is presented for involvement of PDCD11 in processing of ribosomal RNA. (PMID:17654514)
• The 50S U3 snoRNP is an small subunit assembly intermediate that is likely recruited to the pre-rRNA through the RNA-binding proteins nucleolin and RRP5.[RRP5, DBP4] (PMID:19332556)
• data provide no evidence for the contribution of rare PDCD11 variations to the risk of schizophrenia in the Japanese population. (PMID:28657695)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	pdcd11	ENSDARG00000052480
mus_musculus	Pdcd11	ENSMUSG00000025047
rattus_norvegicus	Pdcd11	ENSRNOG00000020304
drosophila_melanogaster	Rrp5	FBGN0039182
caenorhabditis_elegans		WBGENE00002850

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
Bos taurus	A7MB10	83.4%	Diamond
Staphylococcus saprophyticus subsp. saprophyticus ATCC 15305 = NCTC 7292	Q49XT0	81.7%	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
CALHM2	protein-coding	51063
TAF5	protein-coding	6877
PCGF6	protein-coding	84108
ATP5MK	protein-coding	84833
MIR1307	ncRNA	100302174
INA	protein-coding	9118
NEURL1-AS1	ncRNA	102724341
CALHM3	protein-coding	119395
CALHM1	protein-coding	255022
NEURL1	protein-coding	9148

Protein

Protein identifiers

Protein RRP5 homolog — Q14690 (reviewed: Q14690)

Alternative names: NF-kappa-B-binding protein, Programmed cell death protein 11

All UniProt accessions (3): Q14690, A0A3B3IUD7, S4R3Q4

UniProt curated annotations — full annotation on UniProt →

Function. Essential for the generation of mature 18S rRNA, specifically necessary for cleavages at sites A0, 1 and 2 of the 47S precursor. Directly interacts with U3 snoRNA. Involved in the biogenesis of rRNA.

Subunit / interactions. Interacts with NF-kappa-B p50/NFKB1 and NF-kappa-B p65/RELA.

Subcellular location. Nucleus. Nucleolus.

RefSeq proteins (4): NP_001397987, NP_001424349, NP_001424350, NP_055791* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR003029	S1_domain	Domain
IPR003107	HAT	Repeat
IPR008847	Suf	Domain
IPR011990	TPR-like_helical_dom_sf	Homologous_superfamily
IPR012340	NA-bd_OB-fold	Homologous_superfamily
IPR045209	Rrp5	Family
IPR048058	Rrp5_S1_rpt_hs11_sc8	Domain
IPR048059	Rrp5_S1_rpt_hs1_sc1	Domain
IPR057302	Rrp5_S1	Domain

Pfam: PF00575, PF05843, PF23459

UniProt features (52 total): domain 12, modified residue 8, sequence variant 7, strand 6, repeat 4, region of interest 4, compositionally biased region 4, cross-link 2, initiator methionine 1, chain 1, sequence conflict 1, turn 1, helix 1

Structure

Experimental structures (PDB)

1 structures by resolution:

PDB	Title	Method	Resolution (Å)
1WI5	Solution structure of the S1 RNA binding domain from human hypothetical protein BAA11502	SOLUTION NMR

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q14690-F1	74.40	0.18

Human Protein Atlas

Protein class: Predicted intracellular proteins, Plasma proteins, Essential proteins

Protein evidence: Evidence at protein level

Subcellular location (HPA, imaging): nucleoli rim; vesicles

Antibody reliability (HPA): IH approved · IF supported

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 (10)

Type	Positions
N-acetylalanine	2
Phosphoserine	7, 438, 1360, 1362, 1476, 1493, 1498
Glycyl lysine isopeptide (lys-gly) (interchain with g-cter in sumo1)	1030
Glycyl lysine isopeptide (lys-gly) (interchain with g-cter in sumo2)	1416

Function

Pathways and Gene Ontology

Reactome pathways

1 curated (TAS) of 5; 0 disease pathways. Curated-first; evidence = TAS (manually curated) vs IEA (electronic inference).

5 pathways:

ID	Pathway	Evidence
R-HSA-6791226	Major pathway of rRNA processing in the nucleolus and cytosol	curated
R-HSA-8953854	Metabolism of RNA	—
R-HSA-6790901	rRNA modification in the nucleus and cytosol	electronic
R-HSA-72312	rRNA processing	—
R-HSA-8868773	rRNA processing in the nucleus and cytosol	—

MSigDB gene sets: 89 (showing top): GOBP_RIBOSOME_BIOGENESIS, MONNIER_POSTRADIATION_TUMOR_ESCAPE_UP, CAGCAGG_MIR370, MARZEC_IL2_SIGNALING_UP, LAU_APOPTOSIS_CDKN2A_UP, GOBP_RIBONUCLEOPROTEIN_COMPLEX_BIOGENESIS, REACTOME_METABOLISM_OF_RNA, GOCC_PRERIBOSOME, GOCC_SMALL_SUBUNIT_PROCESSOME, GOCC_NUCLEOLUS, GOCC_RIBONUCLEOPROTEIN_COMPLEX, COLDREN_GEFITINIB_RESISTANCE_UP, GOMF_NF_KAPPAB_BINDING, GOMF_TRANSCRIPTION_FACTOR_BINDING, KRIGE_RESPONSE_TO_TOSEDOSTAT_6HR_DN

GO Biological Process (2): rRNA processing (GO:0006364), RNA processing (GO:0006396)

GO Molecular Function (4): RNA binding (GO:0003723), NF-kappaB binding (GO:0051059), nucleic acid binding (GO:0003676), protein binding (GO:0005515)

GO Cellular Component (5): nucleus (GO:0005634), nucleoplasm (GO:0005654), nucleolus (GO:0005730), cytosol (GO:0005829), small-subunit processome (GO:0032040)

Reactome top-level categories

3 top-level categories:

Category	Pathways
rRNA processing in the nucleus and cytosol	2
Metabolism of RNA	1
rRNA processing	1

GO top-level categories

18 GO namespaces:

Category	Terms
binding	2
nuclear lumen	2
cellular anatomical structure	2
RNA processing	1
rRNA metabolic process	1
ribosome biogenesis	1
gene expression	1
RNA biosynthetic process	1
primary metabolic process	1
nucleic acid binding	1
RNA polymerase II-specific DNA-binding transcription factor binding	1
intracellular membrane-bounded organelle	1
intracellular membraneless organelle	1
cytoplasm	1
nucleolus	1
preribosome	1
t-UTP complex	1
nuclear protein-containing complex	1

Experimentally-supported GO annotations

GO terms backed by direct experimental evidence (ECO experimental codes) — 4 of 11 annotations. The rest are phylogenetic / computational / electronic (IEA).

4 experimentally-supported GO terms:

GO term	NS	Evidence
nucleolus	CC	direct assay
nucleus	CC	direct assay
NF-kappaB binding	MF	physical interaction
RNA binding	MF	high-throughput assay

Protein interactions and networks

STRING

showing 15 of 3,207 interactions by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
PDCD11	NOL6	Q9H6R4	870
PDCD11	UTP20	O75691	868
PDCD11	PWP2	Q15269	867
PDCD11	HEATR1	Q9H583	865
PDCD11	KRR1	Q13601	849
PDCD11	NOP14	P78316	839
PDCD11	RRP9	O43818	827
PDCD11	MPHOSPH10	O00566	824
PDCD11	UTP18	Q9Y5J1	817
PDCD11	FBL	P22087	816
PDCD11	UTP15	Q8TED0	801
PDCD11	DDX52	Q9Y2R4	800
PDCD11	EMG1	Q92979	795
PDCD11	UTP6	Q9NYH9	789
PDCD11	WDR46	O15213	789

IntAct

Human interaction partners of PDCD11 in IntAct, one row per partner (best MIscore; records = supporting IntAct interaction records).

20 partners by confidence:

Partner	Interaction type	MIscore	Records
NFKB1	physical association	0.510	2
EPRS1	physical association	0.400	1
H1-5	physical association	0.400	1
HMGN2	physical association	0.400	1
LMNA	physical association	0.400	1
LRRC71	physical association	0.400	1
NOL7	physical association	0.400	1
PKN2	physical association	0.400	1
PPM1A	physical association	0.400	1
RELA	physical association	0.400	1
SGPL1	physical association	0.400	1
TTC21A	physical association	0.400	1
TTC28	physical association	0.400	1
ZC3H13	physical association	0.400	1
ERBB2	physical association	0.370	1
ARL13B	association	0.350	1
RPP40	association	0.350	1
ZSCAN31	association	0.350	1
MYC	physical association	0.000	1
S100A8	physical association	0.000	1

BioGRID (456 interactions; top human partners by supporting records): MYC (Affinity Capture-MS; 4 records), NPM1 (Affinity Capture-MS; 4 records), FBL (Affinity Capture-MS; 3 records), IFI16 (Affinity Capture-MS; 3 records), RPS6 (Proximity Label-MS; 3 records), ANLN (Affinity Capture-MS; 2 records), CDC42 (Cross-Linking-MS (XL-MS); 2 records), FGF3 (Affinity Capture-MS; 2 records), FGF8 (Affinity Capture-MS; 2 records), GRSF1 (Proximity Label-MS; 2 records), H2AFY2 (Affinity Capture-MS; 2 records), LMNA (Proximity Label-MS; 2 records), MECP2 (Affinity Capture-MS; 2 records), MTDH (Protein-RNA; 2 records), PDS5A (Affinity Capture-MS; 2 records)

Disease & clinical

Genetic variants

Variant evidence for PDCD11: 306 ClinVar records (0 pathogenic / likely pathogenic); 9 GWAS associations.

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	245
Likely benign	15
Benign	0

SpliceAI

Top 10 splice-impact sites by Δscore (adjacent positions with the same effect merged into one range; 37 predictions of 3,165):

Position(s)	Effect	Δscore	Sites
10:103398406–103398407	acceptor_gain	1.0000	2
10:103398414–103398415	acceptor_loss	1.0000	3
10:103398415	acceptor_gain	1.0000
10:103398529	donor_loss	1.0000
10:103403116–103403117	acceptor_loss	1.0000	5
10:103403286–103403287	donor_loss	1.0000	4
10:103405020–103405021	acceptor_loss	1.0000	5
10:103405184–103405185	donor_loss	1.0000	5
10:103405983–103405984	acceptor_loss	1.0000	6
10:103406109–103406110	donor_loss	1.0000	5

AlphaMissense

2,543 missense substitutions predicted likely pathogenic (of 12,241 scored), across 815 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
D1796	8	0.944	0.978
F1835	8	0.925	0.983
D671	8	0.922	0.973
F8	8	0.921	0.990
D1803	8	0.903	0.965
N960	8	0.897	0.990
F1651	8	0.896	0.990
F748	8	0.895	0.979
F1818	8	0.884	0.969
F561	8	0.876	0.984
M1626	8	0.871	0.990
F33	8	0.841	0.963
F1784	8	0.839	0.974
F1834	8	0.803	0.969
D1312	8	0.793	0.904
M1831	8	0.779	0.945
F864	8	0.771	0.947
W1622	7	0.985	0.999
W1661	7	0.970	0.998
W1798	7	0.970	0.998

HPA cancer prognostics

RNA cancer specificity: Low cancer specificity

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

4 prognostic cancer types:

Cancer	Prognostic	p-value
Glioblastoma Multiforme (validation)	favorable	1.09e-05
Liver Hepatocellular Carcinoma (TCGA)	unfavorable	0.000306
Kidney Chromophobe (TCGA)	unfavorable	0.000893
Lung Adenocarcinoma (validation)	unfavorable	0.000957

Disease associations

OMIM: gene MIM:612333 | disease phenotypes:

GWAS associations

9 associations:

Study	Trait	p-value
GCST002539_77	Schizophrenia	6e-19
GCST90000025_585	Appendicular lean mass	2e-14
GCST004521_123	Autism spectrum disorder or schizophrenia	4e-14
GCST008058_263	Estimated glomerular filtration rate	1e-13
GCST002149_2	Schizophrenia	4e-13
GCST008059_188	Estimated glomerular filtration rate	1e-10
GCST003013_17	White matter hyperintensity burden	2e-9
GCST003013_3	White matter hyperintensity burden	3e-8
GCST008361_2	Response to cognitive-behavioural therapy in major depressive disorder	2e-6

EFO canonical traits (from GWAS)

3 canonical traits:

EFO ID	Trait name
EFO:0005665	white matter hyperintensity measurement
EFO:0007820	cognitive behavioural therapy
EFO:0004980	appendicular lean mass

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL6067274 (SINGLE PROTEIN)

PharmGKB: 1 entry (CPIC guideline: no)

Binding affinities (BindingDB)

1 measured of 1 human assays (2 total across all organisms); most potent 1 below. Values come from heterogeneous assays and are not directly comparable.

Ligand	Measure	Value
CHEMBL5653589	KD	1440 nM

ChEMBL bioactivities

4 potent at pChembl≥5 of 4 total, top 4 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChembl	Type	Value	Unit	Molecule
7.47	Kd	33.94	nM	CHEMBL3752910
7.47	ED50	33.94	nM	CHEMBL3752910
7.14	Kd	71.72	nM	CHEMBL5653589
7.14	ED50	71.72	nM	CHEMBL5653589

PubChem BioAssay actives

2 with measured affinity, of 4 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	2148952: Binding affinity to human PDCD11 incubated for 45 mins by Kinobead based pull down assay	kd	0.0339	uM
4-methyl-3-[(2-methyl-6-pyridin-3-ylpyrazolo[3,4-d]pyrimidin-4-yl)amino]-N-[3-(trifluoromethyl)phenyl]benzamide	2148952: Binding affinity to human PDCD11 incubated for 45 mins by Kinobead based pull down assay	kd	0.0717	uM

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
bisphenol A	affects cotreatment, increases methylation, decreases expression	2
sodium arsenite	decreases expression, affects cotreatment, increases abundance, increases expression	2
Estradiol	increases expression	2
aristolochic acid I	increases expression	1
FR900359	decreases phosphorylation	1
TAK-243	decreases sumoylation	1
dicrotophos	increases expression	1
beauvericin	decreases expression	1
triphenyl phosphate	affects expression	1
coumarin	decreases phosphorylation	1
di-n-butylphosphoric acid	affects expression	1
CGP 52608	affects binding, increases reaction	1
motexafin gadolinium	decreases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
bisphenol S	affects expression	1
LDN 193189	affects cotreatment, decreases expression	1
Fulvestrant	affects cotreatment, increases methylation	1
Arsenic	affects cotreatment, increases abundance, increases expression	1
Atrazine	decreases expression	1
Cadmium	increases abundance, increases expression	1
Caffeine	decreases phosphorylation	1
Cannabidiol	increases expression	1
Cisplatin	decreases expression	1
Clozapine	increases expression	1
Enzyme Inhibitors	decreases activity, increases O-linked glycosylation	1
Ivermectin	decreases expression	1
Methyl Methanesulfonate	decreases expression	1
Nickel	increases expression	1
Ribonucleotides	affects binding	1
Tretinoin	decreases expression	1

ChEMBL screening assays

1 unique, capped per target: 1 binding

Representative assays (with source publication via chembl_document):

Assay ID	Type	Description	Source paper
CHEMBL5651994	Binding	Binding affinity to human PDCD11 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 PDCD11 across ~30M SureChEMBL compounds — explore on Sugi Predict.