PDCD5

Summary

PDCD5 (programmed cell death 5, HGNC:8764) is a protein-coding gene on chromosome 19q13.11, encoding Programmed cell death protein 5 (O14737). May function in the process of apoptosis. It is a selective cancer dependency (DepMap: 45.0% of cell lines).

This gene encodes a protein that is upregulated during apoptosis where it translocates rapidly from the cytoplasm to the nucleus. The encoded protein may be an important regulator of K(lysine) acetyltransferase 5 (a protein involved in transcription, DNA damage response and cell cycle control) by inhibiting its proteasome-dependent degradation. Pseudogenes have been identified on chromosomes 5 and 12

Source: NCBI Gene 9141 — RefSeq curated summary.

At a glance

• GWAS associations: 21
• Clinical variants (ClinVar): 26 total
• Druggable target: yes
• Cancer dependency (DepMap): dependent in 45.0% of screened cell lines
• MANE Select transcript: NM_004708

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:8764
Approved symbol	PDCD5
Name	programmed cell death 5
Location	19q13.11
Locus type	gene with protein product
Status	Approved
Aliases	TFAR19, MGC9294
Ensembl gene	ENSG00000105185
Ensembl biotype	protein_coding
OMIM	604583
Entrez	9141

Gene structure

Transcript identifiers

Ensembl transcripts: 12 — 9 protein_coding, 2 retained_intron, 1 nonsense_mediated_decay

ENST00000221784, ENST00000379316, ENST00000419343, ENST00000586035, ENST00000586316, ENST00000588622, ENST00000590247, ENST00000592786, ENST00000884500, ENST00000912659, ENST00000912660, ENST00000912661

RefSeq mRNA: 1 — MANE Select: NM_004708 NM_004708

CCDS: CCDS12423

Canonical transcript exons

ENST00000590247 — 6 exons

Exon	Start	End
ENSE00002747495	32581190	32581327
ENSE00003466331	32587253	32587453
ENSE00003480931	32586858	32586929
ENSE00003541929	32585816	32585907
ENSE00003703183	32584950	32585011
ENSE00003703838	32582195	32582232

Expression profiles

Bgee: expression breadth ubiquitous, 280 present calls, max score 99.07.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 197.7003 / max 1176.2429, expressed in 1827 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
175056	183.8310	1827
175057	11.9696	1635
175058	1.8997	779

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
right testis	UBERON:0004534	99.07	gold quality
left testis	UBERON:0004533	99.06	gold quality
body of pancreas	UBERON:0001150	98.57	gold quality
adenohypophysis	UBERON:0002196	98.55	gold quality
right atrium auricular region	UBERON:0006631	98.44	gold quality
lower esophagus	UBERON:0013473	98.44	gold quality
lower esophagus muscularis layer	UBERON:0035833	98.44	gold quality
left coronary artery	UBERON:0001626	98.35	gold quality
cortical plate	UBERON:0005343	98.34	gold quality
muscle layer of sigmoid colon	UBERON:0035805	98.32	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	98.32	gold quality
adrenal tissue	UBERON:0018303	98.30	gold quality
mucosa of stomach	UBERON:0001199	98.28	gold quality
apex of heart	UBERON:0002098	98.21	gold quality
anterior cingulate cortex	UBERON:0009835	98.15	gold quality
tibial artery	UBERON:0007610	98.12	gold quality
popliteal artery	UBERON:0002250	98.11	gold quality
left adrenal gland cortex	UBERON:0035825	98.10	gold quality
right coronary artery	UBERON:0001625	98.07	gold quality
descending thoracic aorta	UBERON:0002345	98.05	gold quality
left adrenal gland	UBERON:0001234	98.03	gold quality
tibial nerve	UBERON:0001323	98.03	gold quality
ascending aorta	UBERON:0001496	98.02	gold quality
thoracic aorta	UBERON:0001515	98.02	gold quality
right ovary	UBERON:0002118	98.01	gold quality
cingulate cortex	UBERON:0003027	98.00	gold quality
aorta	UBERON:0000947	97.99	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	97.98	gold quality
left ovary	UBERON:0002119	97.94	gold quality
gastrocnemius	UBERON:0001388	97.93	gold quality

Single-cell (SCXA)

Detected in 5 experiment(s), a significant marker in 5.

Experiment	Marker?	Max mean expression
E-MTAB-8381	yes	3938.53
E-GEOD-134144	yes	27.62
E-ANND-3	yes	13.26
E-CURD-112	yes	10.09
E-MTAB-9067	yes	9.98

Regulation

Is transcription factor: yes

Downstream targets (CollecTRI)

1 targets.

Target	Regulation
FOXP3	Activation

Upstream regulators (CollecTRI, top): CTNNB1, DNMT1, KLF9, NFKB, NR0B2, RELA

miRNA regulators (miRDB)

31 targeting PDCD5, 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-548AN	99.97	70.91	2817
HSA-MIR-3910	99.95	71.13	2227
HSA-MIR-548AB	99.95	71.31	3488
HSA-MIR-559	99.95	72.28	3609
HSA-MIR-548A-5P	99.94	71.27	3482
HSA-MIR-548AD-5P	99.94	71.23	3502
HSA-MIR-548AE-5P	99.94	71.23	3502
HSA-MIR-548AK	99.94	71.24	3488
HSA-MIR-548AM-5P	99.94	71.24	3488
HSA-MIR-548AP-5P	99.94	71.14	3489
HSA-MIR-548AQ-5P	99.94	71.34	3426
HSA-MIR-548AR-5P	99.94	71.28	3515
HSA-MIR-548AS-5P	99.94	71.22	3482
HSA-MIR-548AU-5P	99.94	71.24	3488
HSA-MIR-548AY-5P	99.94	71.23	3502
HSA-MIR-548B-5P	99.94	71.23	3502
HSA-MIR-548BB-5P	99.94	71.27	3509
HSA-MIR-548C-5P	99.94	71.24	3488
HSA-MIR-548D-5P	99.94	71.23	3502
HSA-MIR-548H-5P	99.94	71.24	3488
HSA-MIR-548I	99.94	71.25	3481
HSA-MIR-548J-5P	99.94	71.14	3489
HSA-MIR-548O-5P	99.94	71.24	3488
HSA-MIR-548W	99.94	71.24	3488
HSA-MIR-548Y	99.94	71.28	3514
HSA-MIR-4307	99.82	70.45	3374
HSA-MIR-3680-3P	99.75	72.51	3095
HSA-MIR-4677-3P	99.49	67.91	1246
HSA-MIR-148A-5P	99.30	68.27	1141
HSA-MIR-3973	99.20	69.19	1990

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 45.0% of screened cell lines.

Literature-anchored findings (GeneRIF, showing 40)

• Results imply that the PDCD5 gene may be a target gene under the control of some important apoptosis-related transcriptional factors during the cell apoptosis. (PMID:15033527)
• The effects of the secondary structure of PDCD5 on its tertiary structure and function are reported. (PMID:16083422)
• Data show that the number of apoptotic cells in renal tubuli with lupus nephritis correlated negatively with the intensity of PDCD5 expression. (PMID:16083554)
• -27G/-11A SNP is associated with reduced PDCD5 promoter activity and increased susceptibility to chronic myelogenous leukemia. (PMID:16361542)
• Could play an important role in regulation of apoptotic processes in gastric cancer cells and gastric tumors. (PMID:16547588)
• PDCD5 may be involved in the pathogenesis of rheumatoid arthritis. (PMID:17468978)
• PDCD5 expression in bone marrow nucleated cells in untreated acute myeloid leukemia patients is lower than in normal controls. (PMID:17605845)
• exogenous PDCD5 expression enhances the chemosensitivity of K562 leukemia cells to either low or high doses of idarubicin in vitro, resulting in increased apoptosis. (PMID:18401719)
• Reduced expression of PDCD5 is associated with high-grade astrocytic gliomas (PMID:18695908)
• Overexpression of PDCD5 could enhance apoptosis of rheumatoid arthritis fibroblast-like synoviocytes induced by triptolide. (PMID:19088824)
• PDCD5 contributes to maintaining a basal pool of Tip60 and its HAT activity (PMID:19308289)
• Studies of structure-function relationship of PDCD5 by multidimensional NMR methods and flow cytometer and fluorescence microscopey. (PMID:19358820)
• these results suggest a functional link between the CK2 phosphorylation and the apoptotic potential of PDCD5. (PMID:19616514)
• PDCDS was highly expressed in some ragged red fibers in patients with limb-girdle type mitochondrial myopathy and chronic progressive external ophthalmoplegia. (PMID:19957502)
• protein overexpression enhance apoptosis in triptolide-induced synoviocytes of rheumatoid arthritis patients (PMID:20047520)
• By downregulating apoptosis, low PDCD5 expression may play an important role in the occurrence and development of PAROSTATIC NEOPLASM. (PMID:20120772)
• Abnormal expression of pdcd5 may be involved in the pathogenesis of multiple myeloma. (PMID:20561417)
• Downregulated expression of programmed cell death 5 is associated with chondrosarcoma. (PMID:20872801)
• Lost or reduced PDCD5 expression may contribute to the pathogenesis of human serous cystadenocarcinomas. (PMID:21165576)
• This study is the first providing evidence that PDCD5 plays an important role in cardiac remodeling. (PMID:22253891)
• The effect of recombinant human PDCD5 was also investigated and shown to sensitize cells to DNA damage by promoting caspase-3 activity. (PMID:22261045)
• the PDCD5 binding site on p53 is localized within residues 41-56 of p53 TAD2 subdomain while p53 binds preferentially to the positively charged surface region around the C-terminals of helices alpha3 and alpha5 and the N-terminal of helix alpha4 of PDCD5 (PMID:22372375)
• PDCD5 promotes chemosensitivity by activating the mitochondria-related apoptotic pathway. (PMID:22688731)
• PDCD5 participates in the inflammatory process of asthmatic airway. Its abnormal expression may be associated with the uncontrolled state of asthmatics. (PMID:22883196)
• PDCD5 may contribute to maintain a basal pool of p53 proteins in unstressed conditions, but upon DNA damage it functions as a co-activator of p53 to regulate transcription and cell cycle arrest. (PMID:22914926)
• results suggest that PDCD5 expression plays a significant role in the malignant progression of human gastrointestinal stromal tumors and may be a key inhibitory factor (PMID:22965478)
• Insulin-like growth factor 1 down-regulates programmed cell death 5 in osteoarthritis chondrocytes. (PMID:23322062)
• Plasma and synovial fluid PDCD5 expression levels are inversely associated with TNF-alpha and disease activity in patients with rheumatoid arthritis. (PMID:23327497)
• Data indicate that the expressions of genes PDCD5 and TIMP2 were consistent with their DNA methylation profiles. (PMID:23369618)
• a correlation between increased levels of PDCD5 in serum and liver disease progression and indicate the potential utility of serum PDCD5 as a biomarker for monitoring liver injury. (PMID:23656249)
• Transgenic PDCD5 plays an antitumor role with increased expression, suppressing skin cancer development. (PMID:23688867)
• PDCD5 could be considered as a reliable marker of favorable prognosis of HCC patients (PMID:23807738)
• We confirmed that PDCD5 overexpression stimulated the promoter activities of KLF9 by luciferase reporter assays. (PMID:24173774)
• The expression of PDCD5 and its protein were shown to be reduced in laryngeal squamous cell carcinoma. The functional importance of PDCD5 as a regulating agent in cell apoptosis suggests that it may play a key role in tumour pathogenesis and development. (PMID:24265335)
• PDCD5 is necessary and sufficient for NF-kappaB p65 mediated apoptosis (PMID:24343129)
• PDCD5 bound the apical domain of the CCTbeta subunit, projecting above the folding cavity without entering it. Like PDCD5, beta-tubulin also interacts with the CCTbeta apical domain, but a second site is found at the sensor loop deep within the folding cavity. (PMID:24375412)
• our study describes a new mechanism for p53 stabilization through PDCD5 upon hypoxia or pVHL loss, and reveals new clinical potential for the treatment of pathobiological disorders linked to hypoxic stress (PMID:24469044)
• Authors identified DNAJB1 as a negative regulator of PDCD5-mediated apoptosis and found that the apoptosis network of PDCD5 regulates cancer cell death. (PMID:25444898)
• Findings have uncovered an apoptotic signaling cascade linking PDCD5, OTUD5, and p53 during genotoxic stress responses. (PMID:25499082)
• These findings uncovered an apoptotic signaling cascade linking YAF2, PDCD5, and TP53 during genotoxic stress responses. (PMID:25603536)

Cross-species orthologs

6 orthologs

Organism	Symbol	Gene ID
danio_rerio	pdcd5	ENSDARG00000026072
mus_musculus	Pdcd5	ENSMUSG00000030417
rattus_norvegicus		ENSRNOG00000067430
rattus_norvegicus	Pdcd5l1	ENSRNOG00000078933
drosophila_melanogaster	PDCD-5	FBGN0036580
caenorhabditis_elegans	D2005.3	WBGENE00008398

Protein

Protein identifiers

Programmed cell death protein 5 — O14737 (reviewed: O14737)

Alternative names: TF-1 cell apoptosis-related protein 19

All UniProt accessions (5): K7EQA1, K7ESJ4, O14737, Q3HM38, X6R2P6

UniProt curated annotations — full annotation on UniProt →

Function. May function in the process of apoptosis.

Tissue specificity. Widely expressed. Highest levels in heart, testis, kidney, pituitary gland, adrenal gland and placenta.

Induction. Activated in cells undergoing apoptosis.

Similarity. Belongs to the PDCD5 family.

Isoforms (2)

UniProt ID	Names	Canonical?
O14737-1	1	yes
O14737-2	2

RefSeq proteins (1): NP_004699* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR002836	PDCD5-like	Family
IPR036883	PDCD5-like_sf	Homologous_superfamily

Pfam: PF01984

UniProt features (15 total): helix 5, modified residue 4, initiator methionine 1, chain 1, strand 1, region of interest 1, splice variant 1, sequence conflict 1

Structure

Experimental structures (PDB)

3 structures.

PDB	Method	Resolution (Å)
1YYB	SOLUTION NMR
2CRU	SOLUTION NMR
2K6B	SOLUTION NMR

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-O14737-F1	75.13	0.05

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 (4): 2, 51, 63, 119

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 147 (showing top): HONMA_DOCETAXEL_RESISTANCE, RODRIGUES_THYROID_CARCINOMA_POORLY_DIFFERENTIATED_UP, STARK_PREFRONTAL_CORTEX_22Q11_DELETION_DN, DARWICHE_SKIN_TUMOR_PROMOTER_UP, DARWICHE_PAPILLOMA_RISK_LOW_UP, DARWICHE_PAPILLOMA_RISK_HIGH_UP, KYNG_DNA_DAMAGE_DN, DARWICHE_SQUAMOUS_CELL_CARCINOMA_UP, GOBP_PROTEIN_MATURATION, KYNG_ENVIRONMENTAL_STRESS_RESPONSE_NOT_BY_GAMMA_IN_WS, MILI_PSEUDOPODIA_HAPTOTAXIS_UP, GOBP_RESPONSE_TO_TRANSFORMING_GROWTH_FACTOR_BETA, YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_13, GOBP_PROTEIN_FOLDING, GARY_CD5_TARGETS_DN

GO Biological Process (6): apoptotic process (GO:0006915), positive regulation of gene expression (GO:0010628), regulation of apoptotic process (GO:0042981), positive regulation of apoptotic process (GO:0043065), cellular response to transforming growth factor beta stimulus (GO:0071560), negative regulation of protein folding (GO:1903333)

GO Molecular Function (5): DNA binding (GO:0003677), heparin binding (GO:0008201), acetyltransferase activator activity (GO:0010698), beta-tubulin binding (GO:0048487), protein binding (GO:0005515)

GO Cellular Component (4): nucleus (GO:0005634), cytoplasm (GO:0005737), cytosol (GO:0005829), extracellular exosome (GO:0070062)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
apoptotic process	2
cellular anatomical structure	2
programmed cell death	1
apoptotic signaling pathway	1
execution phase of apoptosis	1
gene expression	1
regulation of gene expression	1
positive regulation of macromolecule biosynthetic process	1
regulation of programmed cell death	1
regulation of apoptotic process	1
positive regulation of programmed cell death	1
cellular response to growth factor stimulus	1
response to transforming growth factor beta	1
protein folding	1
negative regulation of cellular process	1
regulation of protein folding	1
nucleic acid binding	1
glycosaminoglycan binding	1
sulfur compound binding	1
enzyme activator activity	1
acetyltransferase activity	1
tubulin binding	1
binding	1
intracellular membrane-bounded organelle	1
intracellular anatomical structure	1
cytoplasm	1
extracellular vesicle	1

Protein interactions and networks

STRING

2470 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
PDCD5	KAT5	Q92993	727
PDCD5	YAF2	Q8IY57	593
PDCD5	CSF2	P04141	588
PDCD5	PDCD6IP	Q8WUM4	465
PDCD5	MTHFSD	Q2M296	434
PDCD5	SPESP1	Q6UW49	424
PDCD5	DEF8	Q6ZN54	419
PDCD5	TCP1	P17987	417
PDCD5	OTUD5	Q96G74	415
PDCD5	TMBIM6	P55061	405
PDCD5	ZPBP	Q9BS86	398
PDCD5	OSTF1	Q92882	376
PDCD5	KCNMB1	P78475	372
PDCD5	TP53	P04637	368
PDCD5	EXOG	Q9Y2C4	353
PDCD5	PDCD2	Q16342	353

IntAct

87 interactions, top by confidence:

A	B	Type	Score
CFTR	ESYT2	psi-mi:“MI:2364”(proximity)	0.710
CCT2	PPP6C	psi-mi:“MI:0914”(association)	0.640
CCT3	TXNDC9	psi-mi:“MI:0914”(association)	0.640
PDCD5	TRIM35	psi-mi:“MI:0915”(physical association)	0.560
PDCD5	PICK1	psi-mi:“MI:0915”(physical association)	0.560
PDCD5	RAD18	psi-mi:“MI:0915”(physical association)	0.560
Cct3	PDCD5	psi-mi:“MI:0915”(physical association)	0.560
Cct7	PDCD5	psi-mi:“MI:0915”(physical association)	0.560
CCT3	PDCD5	psi-mi:“MI:0914”(association)	0.530
CCT6A	TXNDC9	psi-mi:“MI:0914”(association)	0.530
TUBA1A	TUBAL3	psi-mi:“MI:0914”(association)	0.420
NUDT3	PDCD5	psi-mi:“MI:0915”(physical association)	0.370
UBE2D3	PDCD5	psi-mi:“MI:0915”(physical association)	0.370
KDM1A	PDCD5	psi-mi:“MI:0915”(physical association)	0.370
OTUB1	EPM2A	psi-mi:“MI:0914”(association)	0.350
Cct4	ARHGAP32	psi-mi:“MI:0914”(association)	0.350
Cct2	OSBPL9	psi-mi:“MI:0914”(association)	0.350
Cct7	DTL	psi-mi:“MI:0914”(association)	0.350
Cct4		psi-mi:“MI:0914”(association)	0.350
Cct3	PFDN1	psi-mi:“MI:0914”(association)	0.350
Cct8	DTL	psi-mi:“MI:0914”(association)	0.350
PHOSPHO1	DDX39A	psi-mi:“MI:0914”(association)	0.350
FBXW8	PDCD5	psi-mi:“MI:0914”(association)	0.350
TUBG1	PDCD5	psi-mi:“MI:0914”(association)	0.350
PRNP	CARNS1	psi-mi:“MI:0914”(association)	0.350
TCEAL1	PDCD5	psi-mi:“MI:0914”(association)	0.350
HDAC1	HIGD1C	psi-mi:“MI:0914”(association)	0.350

BioGRID (141): OTUD5 (Affinity Capture-Western), TP53 (Affinity Capture-Western), PDCD5 (Affinity Capture-Western), PDCD5 (Co-localization), OTUD5 (Two-hybrid), OTUD5 (Reconstituted Complex), STMN1 (Co-fractionation), PDCD5 (Proximity Label-MS), PDCD5 (Affinity Capture-MS), PDCD5 (Affinity Capture-MS), PDCD5 (Affinity Capture-MS), PDCD5 (Affinity Capture-MS), PDCD5 (Affinity Capture-MS), YAF2 (Affinity Capture-Western), ARRDC5 (Affinity Capture-Western)

ESM2 similar proteins: A0JN61, B5FZ63, O14737, O43242, O82197, P02643, P13412, P27768, P48788, P49205, P50502, P50503, P56812, Q06364, Q08AG7, Q15691, Q2HJH9, Q3ZBD9, Q3ZBJ0, Q4QQV8, Q5R7Z5, Q5RBR3, Q5RBT0, Q5RF31, Q5SRX1, Q5XGW6, Q5XGY9, Q5ZHP5, Q5ZLF0, Q61166, Q66HR2, Q6DD52, Q6GL11, Q6IQ73, Q6PBL0, Q6ZVM7, Q7ZVC4, Q8K396, Q8NFI4, Q99L47

Diamond homologs: A0B9G7, A0RYF8, A1RRN7, A1RXF0, A2STJ1, A3CWZ8, A4G031, A4WLS5, A5UL35, A6UVQ4, A6VIE7, A7I9J0, B0R6V4, B1YAF2, B6YWX7, B8GEU2, C3MR75, C3MXG4, C3MZB0, C3N7D0, C3NGA4, C4KII8, C5A636, C6A1U6, O14737, O27652, O28211, O58787, P56812, P56813, Q05E29, Q0W5G9, Q12ZJ1, Q18DQ4, Q2FTJ7, Q2NGR0, Q3INK4, Q46FA5, Q4J8U0, Q54YS0

SIGNOR signaling

2 interactions.

A	Effect	B	Mechanism
CSNK2A1	up-regulates	PDCD5	phosphorylation
PPEF1	“down-regulates quantity by destabilization”	PDCD5	dephosphorylation

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 97 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
Formation of tubulin folding intermediates by CCT/TriC	11	67.4×	9e-16
Cooperation of Prefoldin and TriC/CCT in actin and tubulin folding	11	65.0×	9e-16
Prefoldin mediated transfer of substrate to CCT/TriC	10	57.1×	8e-14
Chaperonin-mediated protein folding	11	47.9×	3e-14
Protein folding	11	41.4×	1e-13
BBSome-mediated cargo-targeting to cilium	5	36.0×	8e-06
Activation of AMPK downstream of NMDARs	6	33.1×	9e-07
Cargo trafficking to the periciliary membrane	9	32.4×	4e-10

GO biological processes:

GO term	Partners	Fold	FDR
positive regulation of telomere maintenance via telomerase	7	57.6×	5e-09
binding of sperm to zona pellucida	6	28.4×	9e-06
cytoplasmic microtubule organization	5	19.3×	5e-04
microtubule cytoskeleton organization	9	12.3×	9e-06
protein folding	9	10.4×	2e-05
mitotic cell cycle	6	9.0×	4e-03
protein stabilization	10	7.5×	8e-05

Disease & clinical

Clinical variants and AI predictions

ClinVar

26 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	2

Top pathogenic / likely-pathogenic (0)

SpliceAI

944 predictions. Top by Δscore:

Variant	Effect	Δscore
19:32581325:GGG:G	donor_gain	1.0000
19:32581325:GGGGT:G	donor_loss	1.0000
19:32581326:GGG:G	donor_gain	1.0000
19:32581326:GGGT:G	donor_loss	1.0000
19:32581328:GT:G	donor_loss	1.0000
19:32585010:GT:G	donor_gain	1.0000
19:32585012:G:GG	donor_gain	1.0000
19:32585815:GTAA:G	acceptor_gain	1.0000
19:32586846:T:TA	acceptor_gain	1.0000
19:32586930:G:GG	donor_gain	1.0000
19:32586987:T:G	donor_gain	1.0000
19:32587251:A:AG	acceptor_gain	1.0000
19:32587252:G:GA	acceptor_gain	1.0000
19:32581283:GCGC:G	donor_gain	0.9900
19:32581324:CGGG:C	donor_gain	0.9900
19:32581325:GGGG:G	donor_gain	0.9900
19:32581326:GG:G	donor_gain	0.9900
19:32581327:GG:G	donor_gain	0.9900
19:32581328:G:GG	donor_gain	0.9900
19:32581329:T:G	donor_loss	0.9900
19:32582193:A:AG	acceptor_gain	0.9900
19:32582193:AG:A	acceptor_gain	0.9900
19:32582194:G:GG	acceptor_gain	0.9900
19:32582194:GG:G	acceptor_gain	0.9900
19:32582228:CACAG:C	donor_loss	0.9900
19:32582229:ACAG:A	donor_loss	0.9900
19:32582230:CAG:C	donor_loss	0.9900
19:32582231:AG:A	donor_loss	0.9900
19:32582232:GGTAT:G	donor_loss	0.9900
19:32582233:GT:G	donor_loss	0.9900

AlphaMissense

823 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:32586874:T:C	L92S	0.993
19:32585000:C:A	A52D	0.992
19:32586886:T:C	L96P	0.991
19:32587253:T:C	F111L	0.991
19:32587255:C:A	F111L	0.991
19:32587255:C:G	F111L	0.991
19:32585870:T:C	L74P	0.989
19:32585003:G:C	R53P	0.988
19:32585870:T:A	L74H	0.988
19:32586886:T:A	L96H	0.987
19:32587261:A:C	R113S	0.987
19:32587261:A:T	R113S	0.987
19:32585009:G:T	R55M	0.986
19:32585816:T:C	L56S	0.986
19:32585881:G:C	A78P	0.984
19:32585825:T:C	L59S	0.982
19:32585005:G:C	A54P	0.981
19:32585858:T:A	V70E	0.981
19:32581290:G:T	R10M	0.979
19:32585010:G:C	R55S	0.979
19:32585010:G:T	R55S	0.979
19:32587254:T:C	F111S	0.979
19:32587264:A:C	R114S	0.978
19:32587264:A:T	R114S	0.978
19:32584976:T:C	L44S	0.977
19:32584985:T:A	V47D	0.977
19:32585891:G:T	G81V	0.976
19:32581291:G:C	R10S	0.973
19:32581291:G:T	R10S	0.973
19:32581300:G:C	R13S	0.973

dbSNP variants (sampled 300 via entrez): RS1000053061 (19:32583687 T>G), RS1000357277 (19:32581013 C>A,T), RS1000396744 (19:32583429 A>C,G), RS1000704140 (19:32581526 G>A), RS1000767747 (19:32583097 G>C), RS1000810026 (19:32581917 A>T), RS1001482006 (19:32579719 G>A), RS1001567945 (19:32580410 G>A), RS1001742695 (19:32579320 G>A), RS1002041414 (19:32584747 G>A), RS1002245411 (19:32579385 G>A), RS1002477622 (19:32584934 T>C), RS1002731475 (19:32587604 C>T), RS1002824183 (19:32581987 A>G), RS1003160784 (19:32583416 A>G)

Disease associations

OMIM: gene MIM:604583 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

21 associations (top):

Study	Trait	p-value
GCST001850_7	Major depressive disorder	7.000000e-07
GCST004599_148	Mean platelet volume	3.000000e-09
GCST004602_270	Mean corpuscular volume	2.000000e-17
GCST004621_162	Red cell distribution width	3.000000e-10
GCST004630_63	Mean corpuscular hemoglobin	1.000000e-17
GCST004630_64	Mean corpuscular hemoglobin	4.000000e-22
GCST009391_1644	Metabolite levels	8.000000e-06
GCST011956_116	Systemic lupus erythematosus	5.000000e-10
GCST90002387_49	Immature fraction of reticulocytes	3.000000e-19
GCST90002390_649	Mean corpuscular hemoglobin	3.000000e-15
GCST90002390_688	Mean corpuscular hemoglobin	4.000000e-27
GCST90002391_113	Mean corpuscular hemoglobin concentration	1.000000e-11
GCST90002392_89	Mean corpuscular volume	3.000000e-21
GCST90002392_90	Mean corpuscular volume	2.000000e-21
GCST90002395_408	Mean platelet volume	6.000000e-30
GCST90002396_30	Mean reticulocyte volume	7.000000e-13
GCST90002396_31	Mean reticulocyte volume	1.000000e-14
GCST90002397_199	Mean spheric corpuscular volume	9.000000e-14
GCST90002397_200	Mean spheric corpuscular volume	1.000000e-17
GCST90002402_556	Platelet count	2.000000e-17
GCST90002404_525	Red cell distribution width	1.000000e-25

EFO canonical traits (6, from GWAS)

EFO ID	Trait name
EFO:0009188	Red cell distribution width
EFO:0004527	mean corpuscular hemoglobin
EFO:0007787	plasma betaine measurement
EFO:0004528	mean corpuscular hemoglobin concentration
EFO:0010701	mean reticulocyte volume
EFO:0004309	platelet count

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL6066424 (SINGLE PROTEIN)

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	decreases expression	4
bisphenol A	decreases expression, increases expression	3
sodium arsenite	decreases expression, affects cotreatment, increases abundance, increases expression	3
arsenite	increases methylation, affects binding, increases reaction	2
beauvericin	increases expression	1
deoxynivalenol	increases expression	1
pyrogallol 1,3-dimethyl ether	affects cotreatment, decreases expression, affects localization, increases expression	1
cobaltous chloride	decreases expression	1
manganese chloride	affects cotreatment, increases abundance, increases expression	1
potassium chromate(VI)	affects cotreatment, decreases expression	1
epigallocatechin gallate	decreases expression, affects cotreatment	1
avobenzone	increases expression	1
pentabromodiphenyl ether	increases expression	1
CGP 52608	affects binding, increases reaction	1
pluronic block copolymer p85	affects cotreatment, increases expression	1
motexafin gadolinium	decreases expression, affects cotreatment	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	increases expression, affects cotreatment	1
10’(Z),13’(E),15’(E)-heptadecatrienylhydroquinone	increases expression	1
bisphenol B	increases expression	1
quinocetone	decreases expression, increases expression	1
2,2’,4,4’-tetrabromodiphenyl ether	increases expression	1
LDN 193189	affects cotreatment, increases expression	1
Resveratrol	affects cotreatment, increases expression	1
Arsenic Trioxide	increases expression	1
Vorinostat	increases expression	1
Arsenic	increases abundance, increases expression, affects cotreatment	1
Atrazine	increases expression	1
Calcitriol	decreases expression	1
Cisplatin	increases response to substance	1
Demecolcine	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
CHEMBL5651996	Binding	Binding affinity to human PDCD5 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

Cellosaurus cell lines

3 cell lines: 2 cancer cell line, 1 transformed cell line

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

Cellosaurus	Name	Category	Sex
CVCL_D9MF	Ubigene HEK293 PDCD5 KO	Transformed cell line	Female
CVCL_TC62	HAP1 PDCD5 (-) 1	Cancer cell line	Male
CVCL_XR46	HAP1 PDCD5 (-) 2	Cancer cell line	Male

Clinical trials (associated diseases)

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