PDCD7

Summary

PDCD7 (programmed cell death 7, HGNC:8767) is a protein-coding gene on chromosome 15q22.31, encoding Programmed cell death protein 7 (Q8N8D1). Promotes apoptosis when overexpressed. It is a selective cancer dependency (DepMap: 83.7% of cell lines).

This gene encodes a 59 kDa protein that is associated with the U11 small nuclear ribonucleoprotein (snRNP), which is a component of the minor U12-type spliceosome responsible for catalyzing pre-mRNA splicing of U12-type introns.

Source: NCBI Gene 10081 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 59 total
• Cancer dependency (DepMap): dependent in 83.7% of screened cell lines
• MANE Select transcript: NM_005707

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:8767
Approved symbol	PDCD7
Name	programmed cell death 7
Location	15q22.31
Locus type	gene with protein product
Status	Approved
Aliases	HES18, ES18, 59K
Ensembl gene	ENSG00000090470
Ensembl biotype	protein_coding
OMIM	608138
Entrez	10081

Gene structure

Transcript identifiers

Ensembl transcripts: 3 — 2 protein_coding, 1 retained_intron

ENST00000204549, ENST00000559051, ENST00000560313

RefSeq mRNA: 1 — MANE Select: NM_005707 NM_005707

CCDS: CCDS10201

Canonical transcript exons

ENST00000204549 — 5 exons

Exon	Start	End
ENSE00000449898	65119376	65119463
ENSE00000693634	65129032	65129170
ENSE00001211778	65117379	65118840
ENSE00001211785	65132912	65133808
ENSE00001301782	65119718	65119954

Expression profiles

Bgee: expression breadth ubiquitous, 258 present calls, max score 97.45.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 22.6552 / max 160.2454, expressed in 1811 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter ID	TPM avg	Samples expressed
150528	18.3591	1800
150529	1.7587	1064
150526	1.7555	1148
150525	0.7550	508
150527	0.0270	4

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
secondary oocyte	CL:0000655	97.45	gold quality
buccal mucosa cell	CL:0002336	95.58	gold quality
nipple	UBERON:0002030	93.65	gold quality
kidney epithelium	UBERON:0004819	93.27	gold quality
superior surface of tongue	UBERON:0007371	93.00	gold quality
oocyte	CL:0000023	92.67	gold quality
tendon of biceps brachii	UBERON:0008188	92.43	gold quality
thymus	UBERON:0002370	92.31	gold quality
lateral globus pallidus	UBERON:0002476	91.76	gold quality
nasal cavity epithelium	UBERON:0005384	91.68	silver quality
cauda epididymis	UBERON:0004360	91.58	gold quality
medulla oblongata	UBERON:0001896	91.48	gold quality
caput epididymis	UBERON:0004358	91.48	gold quality
pharyngeal mucosa	UBERON:0000355	91.44	gold quality
layer of synovial tissue	UBERON:0007616	91.41	gold quality
trigeminal ganglion	UBERON:0001675	91.36	gold quality
ventral tegmental area	UBERON:0002691	91.28	gold quality
inferior vagus X ganglion	UBERON:0005363	91.22	gold quality
superior vestibular nucleus	UBERON:0007227	91.15	gold quality
superficial temporal artery	UBERON:0001614	91.02	gold quality
epithelial cell of pancreas	CL:0000083	90.95	gold quality
oral cavity	UBERON:0000167	90.94	gold quality
saphenous vein	UBERON:0007318	90.87	gold quality
trachea	UBERON:0003126	90.71	gold quality
substantia nigra pars reticulata	UBERON:0001966	90.65	gold quality
adult organism	UBERON:0007023	90.61	gold quality
dorsal plus ventral thalamus	UBERON:0001897	90.56	gold quality
substantia nigra pars compacta	UBERON:0001965	90.54	gold quality
cerebellar vermis	UBERON:0004720	90.47	gold quality
renal medulla	UBERON:0000362	90.45	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	4.76

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

55 targeting PDCD7, 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-4425	100.00	67.59	1049
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-3662	99.99	73.82	5684
HSA-MIR-3148	99.97	75.06	6478
HSA-MIR-5688	99.96	73.23	4504
HSA-MIR-495-3P	99.96	72.81	4197
HSA-MIR-6778-3P	99.96	67.29	2693
HSA-MIR-548AA	99.96	70.64	3753
HSA-MIR-548AP-3P	99.96	70.64	3753
HSA-MIR-548T-3P	99.96	70.64	3753
HSA-MIR-3912-5P	99.95	66.11	925
HSA-MIR-9983-3P	99.94	71.48	3631
HSA-MIR-7-1-3P	99.91	71.53	4384
HSA-MIR-7-2-3P	99.91	71.40	4394
HSA-MIR-129-5P	99.88	70.26	3273
HSA-MIR-548D-3P	99.87	70.67	4362
HSA-MIR-182-5P	99.87	74.03	2589
HSA-MIR-548BB-3P	99.86	70.58	4354
HSA-MIR-548AC	99.84	70.77	4351
HSA-MIR-548H-3P	99.84	70.80	4349
HSA-MIR-548Z	99.84	70.80	4349
HSA-MIR-6875-3P	99.82	70.26	2983
HSA-MIR-4802-3P	99.72	70.13	1273
HSA-MIR-7157-5P	99.66	69.33	1829
HSA-MIR-9851-3P	99.63	69.68	1110
HSA-MIR-497-3P	99.61	69.71	1990
HSA-MIR-4310	99.59	68.84	2527
HSA-MIR-3120-3P	99.54	70.28	2669
HSA-MIR-377-3P	99.37	70.18	1905

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 83.7% of screened cell lines.

Literature-anchored findings (GeneRIF, showing 4)

• PDCD7, Ang2 and FIS1 may indicate a more aggressive form and poor prognosis of acute myeloid leukemia. (PMID:24416201)
• Downregulation of both PDCD7 and E-cad and high levels miR-134 expression was observed in OSCC tumor tissues. (PMID:29971778)
• FIS1 and PDCD7 expression are considered independent risk factors and should be integrated into the current acute myeloid leukemia stratification system (PMID:30555023)
• Polymerase acidic subunit of H9N2 polymerase complex induces cell apoptosis by binding to PDCD 7 in A549 cells. (PMID:33849599)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	pdcd7	ENSDARG00000038976
mus_musculus	Pdcd7	ENSMUSG00000041837
rattus_norvegicus	Pdcd7	ENSRNOG00000014340

Paralogs (23): C1QTNF3 (ENSG00000082196), COL19A1 (ENSG00000082293), COL10A1 (ENSG00000123500), C1QL1 (ENSG00000131094), C1QTNF6 (ENSG00000133466), C1QL2 (ENSG00000144119), COL8A1 (ENSG00000144810), C1QTNF2 (ENSG00000145861), C1QC (ENSG00000159189), C1QTNF7 (ENSG00000163145), C1QL3 (ENSG00000165985), COL8A2 (ENSG00000171812), C1QTNF4 (ENSG00000172247), C1QB (ENSG00000173369), C1QA (ENSG00000173372), C1QTNF1 (ENSG00000173918), ADIPOQ (ENSG00000181092), OTOL1 (ENSG00000182447), C1QTNF8 (ENSG00000184471), C1QL4 (ENSG00000186897), C1QTNF9B (ENSG00000205863), C1QTNF5 (ENSG00000223953), C1QTNF9 (ENSG00000240654)

Protein

Protein identifiers

Programmed cell death protein 7 — Q8N8D1 (reviewed: Q8N8D1)

Alternative names: ES18

All UniProt accessions (3): Q8N8D1, H3BT73, Q6IEG3

UniProt curated annotations — full annotation on UniProt →

Function. Promotes apoptosis when overexpressed.

Subunit / interactions. Interacts with RBM40. Component of the U11/U12 snRNPs that are part of the U12-type spliceosome.

Subcellular location. Nucleus.

RefSeq proteins (1): NP_005698* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR031974	PDCD7	Family
IPR052831	Apoptosis_promoter	Family

Pfam: PF16021

UniProt features (19 total): helix 8, compositionally biased region 4, coiled-coil region 2, sequence conflict 2, chain 1, region of interest 1, turn 1

Structure

Experimental structures (PDB)

5 structures.

PDB	Method	Resolution (Å)
9GCM	ELECTRON MICROSCOPY	3.1
9GC0	ELECTRON MICROSCOPY	3.2
8Y6O	ELECTRON MICROSCOPY	3.38
8R7N	ELECTRON MICROSCOPY	3.4
9GBW	ELECTRON MICROSCOPY	3.5

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8N8D1-F1	77.68	0.41

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-72165	mRNA Splicing - Minor Pathway

MSigDB gene sets: 112 (showing top): GOBP_RESPONSE_TO_CORTICOSTEROID, MARTINEZ_RB1_TARGETS_DN, REACTOME_PROCESSING_OF_CAPPED_INTRON_CONTAINING_PRE_MRNA, GOBP_PROTEIN_RNA_COMPLEX_ORGANIZATION, GOBP_RNA_SPLICING, AGGAGTG_MIR483, GOBP_RESPONSE_TO_STEROID_HORMONE, GOBP_RESPONSE_TO_HORMONE, REACTOME_MRNA_SPLICING, GOBP_RESPONSE_TO_LIPID, ACEVEDO_LIVER_CANCER_UP, GOBP_RIBONUCLEOPROTEIN_COMPLEX_BIOGENESIS, REACTOME_METABOLISM_OF_RNA, GOCC_PRECATALYTIC_SPLICEOSOME, GOCC_SPLICEOSOMAL_COMPLEX

GO Biological Process (3): apoptotic process (GO:0006915), RNA splicing (GO:0008380), response to glucocorticoid (GO:0051384)

GO Molecular Function (0):

GO Cellular Component (3): nucleoplasm (GO:0005654), U12-type spliceosomal complex (GO:0005689), nucleus (GO:0005634)

Reactome top-level categories

Rollup of top-1 pathways:

Category	Pathways
mRNA Splicing	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
programmed cell death	1
apoptotic signaling pathway	1
execution phase of apoptosis	1
RNA processing	1
response to corticosteroid	1
nuclear lumen	1
cellular anatomical structure	1
spliceosomal complex	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

1120 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
PDCD7	SNRNP35	Q16560	711
PDCD7	SNRNP48	Q6IEG0	643
PDCD7	SNRNP25	Q9BV90	619
PDCD7	DDX5	P17844	472
PDCD7	CEP85	Q6P2H3	470
PDCD7	PDCD6	O75340	462
PDCD7	HNRNPR	O43390	454
PDCD7	RNPC3	Q96LT9	444
PDCD7	SRSF2	Q01130	439
PDCD7	PRKACA	P17612	436
PDCD7	PRKACB	P22694	436
PDCD7	PRKACG	P22612	429
PDCD7	PDCD4	Q53EL6	426
PDCD7	SRSF1	Q07955	419
PDCD7	PDCD1	Q15116	385

IntAct

55 interactions, top by confidence:

A	B	Type	Score
SNRPF	GEMIN2	psi-mi:“MI:0914”(association)	0.910
ODAD1	HGS	psi-mi:“MI:0914”(association)	0.850
SNRPE	GEMIN2	psi-mi:“MI:0914”(association)	0.770
ZRSR2	SF3B1	psi-mi:“MI:0914”(association)	0.730
SNRPG	GEMIN2	psi-mi:“MI:0914”(association)	0.710
SNRPB	PRMT5	psi-mi:“MI:0914”(association)	0.670
ZCRB1	SF3B1	psi-mi:“MI:0914”(association)	0.640
SNRPE	PRMT5	psi-mi:“MI:0914”(association)	0.530
SNRPN	PRMT5	psi-mi:“MI:0914”(association)	0.530
ZCRB1	DKC1	psi-mi:“MI:0914”(association)	0.530
ZMAT5	DENND4B	psi-mi:“MI:0914”(association)	0.530
SNRPE	SNRPGP15	psi-mi:“MI:0914”(association)	0.530
SNRPF	SNRPGP15	psi-mi:“MI:0914”(association)	0.530
NUP62	RGPD8	psi-mi:“MI:0914”(association)	0.530
PDCD7	EIF3J	psi-mi:“MI:0915”(physical association)	0.400
PDCD7	H2BC9	psi-mi:“MI:0915”(physical association)	0.400
PDCD7	PRPF40A	psi-mi:“MI:0915”(physical association)	0.370
MARK2	WDR46	psi-mi:“MI:0914”(association)	0.350
Nrip3	ILVBL	psi-mi:“MI:0914”(association)	0.350
RPL10	RPS6	psi-mi:“MI:0914”(association)	0.350
Myh9	GOSR1	psi-mi:“MI:0914”(association)	0.350
Fbxo21	ESYT2	psi-mi:“MI:0914”(association)	0.350
ESR1	ESYT2	psi-mi:“MI:0914”(association)	0.350

BioGRID (79): PDCD7 (Affinity Capture-MS), PDCD7 (Affinity Capture-MS), PDCD7 (Affinity Capture-MS), PDCD7 (Affinity Capture-MS), PDCD7 (Affinity Capture-MS), PDCD7 (Affinity Capture-MS), PDCD7 (Affinity Capture-MS), PDCD7 (Affinity Capture-MS), PDCD7 (Affinity Capture-MS), PDCD7 (Affinity Capture-MS), PDCD7 (Affinity Capture-MS), PDCD7 (Affinity Capture-MS), PDCD7 (Affinity Capture-MS), PDCD7 (Affinity Capture-MS), PDCD7 (Affinity Capture-MS)

ESM2 similar proteins: A0AUP1, A5D8V7, B0BM24, D3ZND0, D6REC4, O60826, P86182, Q15051, Q1RM03, Q1RM35, Q1RMI8, Q2YD98, Q3TVW5, Q494V2, Q499E4, Q4R8V8, Q571B6, Q5BK43, Q5R694, Q5RE49, Q5REX6, Q5SPX1, Q5XIA0, Q62036, Q6NVC9, Q6P5U8, Q7T0Y4, Q7Z4T9, Q8BP00, Q8C2K1, Q8C9J3, Q8CB59, Q8IYY4, Q8N8D1, Q8NCU4, Q8TF30, Q8VDI1, Q95JM8, Q95KD7, Q95LR0

Diamond homologs: Q8N8D1, Q9WTY1

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 50 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

Pathway	Partners	Fold	FDR
Metabolism of non-coding RNA	6	105.7×	3e-10
mRNA Splicing - Minor Pathway	11	68.4×	6e-16
snRNP Assembly	8	47.0×	1e-10
SARS-CoV-2 modulates host translation machinery	7	43.5×	3e-09
CHD1 and CHD2 subfamily	12	36.2×	2e-14
mRNA Splicing	11	33.5×	5e-13
mRNA Polyadenylation	13	31.7×	6e-15
RNA Polymerase II Transcription Termination	5	30.5×	8e-06

GO biological processes:

GO term	Partners	Fold	FDR
U2-type prespliceosome assembly	8	116.1×	2e-13
spliceosomal snRNP assembly	7	94.6×	4e-11
spliceosomal complex assembly	5	70.0×	3e-07
mRNA splicing, via spliceosome	14	29.8×	3e-15
RNA splicing	13	26.7×	1e-13
mRNA processing	6	11.0×	6e-04

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

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

Top pathogenic / likely-pathogenic (0)

SpliceAI

511 predictions. Top by Δscore:

Variant	Effect	Δscore
15:65119459:CTCAT:C	acceptor_gain	1.0000
15:65119952:CCC:C	acceptor_gain	1.0000
15:65119953:CCC:C	acceptor_gain	1.0000
15:65129027:GTTAC:G	donor_loss	1.0000
15:65129028:TTA:T	donor_loss	1.0000
15:65129029:TA:T	donor_loss	1.0000
15:65129030:A:AC	donor_gain	1.0000
15:65129031:C:CC	donor_gain	1.0000
15:65129031:CCTTT:C	donor_gain	1.0000
15:65129035:T:A	donor_gain	1.0000
15:65129053:T:A	donor_gain	1.0000
15:65129166:TGCTC:T	acceptor_gain	1.0000
15:65129168:CTC:C	acceptor_gain	1.0000
15:65129169:TC:T	acceptor_gain	1.0000
15:65129170:CC:C	acceptor_gain	1.0000
15:65129171:C:CC	acceptor_gain	1.0000
15:65132911:CCCG:C	donor_gain	1.0000
15:65132931:T:TA	donor_gain	1.0000
15:65119463:TCT:T	acceptor_loss	0.9900
15:65119465:T:A	acceptor_loss	0.9900
15:65119816:T:TA	donor_gain	0.9900
15:65129030:AC:A	donor_gain	0.9900
15:65129031:CC:C	donor_gain	0.9900
15:65129171:C:T	acceptor_gain	0.9900
15:65132944:TC:T	donor_gain	0.9900
15:65119460:TCAT:T	acceptor_gain	0.9800
15:65119461:CAT:C	acceptor_gain	0.9800
15:65119461:CATC:C	acceptor_gain	0.9800
15:65119464:C:CC	acceptor_gain	0.9800
15:65119953:CC:C	acceptor_gain	0.9800

AlphaMissense

3063 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
15:65118833:A:G	W448R	0.999
15:65118833:A:T	W448R	0.999
15:65119837:A:G	M376T	0.999
15:65119846:A:G	L373P	0.999
15:65119846:A:T	L373H	0.999
15:65129054:C:A	R329S	0.999
15:65129054:C:G	R329S	0.999
15:65129055:C:A	R329M	0.999
15:65129055:C:G	R329T	0.999
15:65129064:C:A	R326M	0.999
15:65129064:C:G	R326T	0.999
15:65129067:A:G	L325S	0.999
15:65118743:A:G	W478R	0.998
15:65118743:A:T	W478R	0.998
15:65118831:C:A	W448C	0.998
15:65118831:C:G	W448C	0.998
15:65119376:C:A	R445M	0.998
15:65119837:A:C	M376R	0.998
15:65119837:A:T	M376K	0.998
15:65119857:T:A	E369D	0.998
15:65119857:T:G	E369D	0.998
15:65129058:A:G	L328P	0.998
15:65129148:G:T	A298D	0.998
15:65129160:A:G	L294P	0.998
15:65118776:A:G	W467R	0.997
15:65118776:A:T	W467R	0.997
15:65119858:T:A	E369V	0.997
15:65119900:A:G	L355P	0.997
15:65119920:A:C	F348L	0.997
15:65119920:A:T	F348L	0.997

dbSNP variants (sampled 300 via entrez): RS1000071942 (15:65135277 G>A), RS1000171767 (15:65130526 C>T), RS1000318788 (15:65135498 T>C), RS1000509230 (15:65131839 C>G,T), RS1000578352 (15:65117782 G>A), RS1000623822 (15:65131547 G>A,C), RS1000894341 (15:65119945 G>A), RS1000905079 (15:65130401 G>A,C,T), RS1001119988 (15:65125688 T>A), RS1001205799 (15:65123959 T>C), RS1001469321 (15:65119498 C>T), RS1001570884 (15:65118913 T>G), RS1001583771 (15:65119300 T>C), RS1001634366 (15:65130863 AGCT>A), RS1001897326 (15:65126582 T>C)

Disease associations

OMIM: gene MIM:608138 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects expression, decreases expression	3
Phenylmercuric Acetate	affects cotreatment, decreases expression	2
Cadmium Chloride	decreases expression, increases expression	2
bisphenol F	affects cotreatment, decreases expression	1
TAK-243	increases sumoylation	1
triphenyl phosphate	affects expression	1
uranyl acetate	affects expression	1
bisphenol A	increases expression	1
o,p’-DDT	increases expression	1
beta-methylcholine	affects expression	1
di-n-butylphosphoric acid	affects expression	1
chloropicrin	increases expression	1
2-palmitoylglycerol	increases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
abrine	increases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
bisphenol S	affects cotreatment, decreases expression	1
Resveratrol	increases expression	1
Sunitinib	increases expression	1
Leflunomide	decreases expression	1
Benzo(a)pyrene	affects methylation	1
Cocaine	increases expression	1
Dexamethasone	affects cotreatment, decreases expression	1
Indomethacin	affects cotreatment, decreases expression	1
Methotrexate	increases expression	1
Silver	decreases expression	1
Thiram	decreases expression	1
Uranium	affects expression	1
Zearalenone	increases expression	1
1-Methyl-3-isobutylxanthine	decreases expression, affects cotreatment	1

Clinical trials (associated diseases)

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