PDRG1

Summary

PDRG1 (p53 and DNA damage regulated 1, HGNC:16119) is a protein-coding gene on chromosome 20q11.21, encoding p53 and DNA damage-regulated protein 1 (Q9NUG6). May play a role in chaperone-mediated protein folding. It is a common-essential gene (DepMap: required in 99.8% of cancer cell lines).

Predicted to enable unfolded protein binding activity. Predicted to be involved in protein stabilization. Part of RPAP3/R2TP/prefoldin-like complex.

Source: NCBI Gene 81572 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 13 total
• Cancer dependency (DepMap): dependent in 99.8% of screened cell lines (common-essential)
• MANE Select transcript: NM_030815

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:16119
Approved symbol	PDRG1
Name	p53 and DNA damage regulated 1
Location	20q11.21
Locus type	gene with protein product
Status	Approved
Aliases	dJ310O13.3
Ensembl gene	ENSG00000088356
Ensembl biotype	protein_coding
OMIM	610789
Entrez	81572

Gene structure

Transcript identifiers

Ensembl transcripts: 6 — 6 protein_coding

ENST00000202017, ENST00000902322, ENST00000902323, ENST00000902324, ENST00000902325, ENST00000918734

RefSeq mRNA: 1 — MANE Select: NM_030815 NM_030815

CCDS: CCDS13194

Canonical transcript exons

ENST00000202017 — 5 exons

Exon	Start	End
ENSE00000661137	31946496	31946576
ENSE00000661138	31948808	31948882
ENSE00000661139	31950312	31950387
ENSE00001109504	31944337	31945889
ENSE00001155739	31951875	31952046

Expression profiles

Bgee: expression breadth ubiquitous, 245 present calls, max score 92.24.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 20.1101 / max 185.4348, expressed in 1808 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
186887	18.9539	1805
186885	0.8152	460
186886	0.3409	183

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
pancreatic ductal cell	CL:0002079	92.24	silver quality
right testis	UBERON:0004534	92.22	gold quality
left testis	UBERON:0004533	91.97	gold quality
kidney epithelium	UBERON:0004819	91.68	silver quality
testis	UBERON:0000473	90.88	gold quality
cerebellar vermis	UBERON:0004720	89.43	gold quality
dorsal root ganglion	UBERON:0000044	89.36	gold quality
cerebellar hemisphere	UBERON:0002245	87.95	gold quality
cerebellar cortex	UBERON:0002129	87.92	gold quality
right hemisphere of cerebellum	UBERON:0014890	87.82	gold quality
cardiac muscle of right atrium	UBERON:0003379	87.60	gold quality
cerebellum	UBERON:0002037	87.47	gold quality
oocyte	CL:0000023	87.11	gold quality
trigeminal ganglion	UBERON:0001675	87.10	gold quality
left ventricle myocardium	UBERON:0006566	86.91	gold quality
deltoid	UBERON:0001476	86.78	silver quality
secondary oocyte	CL:0000655	86.46	gold quality
ileal mucosa	UBERON:0000331	85.92	gold quality
tibial nerve	UBERON:0001323	85.53	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	85.28	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	85.22	gold quality
mucosa of transverse colon	UBERON:0004991	85.15	gold quality
quadriceps femoris	UBERON:0001377	84.98	silver quality
prefrontal cortex	UBERON:0000451	84.80	gold quality
spinal cord	UBERON:0002240	84.78	gold quality
granulocyte	CL:0000094	84.68	gold quality
gastrocnemius	UBERON:0001388	84.54	gold quality
pons	UBERON:0000988	84.44	gold quality
adult organism	UBERON:0007023	84.38	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	84.18	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	8.26

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): POU2F1, TP53

miRNA regulators (miRDB)

44 targeting PDRG1, 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-4789-3P	99.99	70.75	2484
HSA-MIR-454-3P	99.91	74.01	1925
HSA-MIR-498-3P	99.91	71.27	1114
HSA-MIR-106A-5P	99.90	73.94	2683
HSA-MIR-130A-3P	99.90	73.31	1861
HSA-MIR-130B-3P	99.90	73.27	1850
HSA-MIR-301A-3P	99.90	73.15	1839
HSA-MIR-301B-3P	99.90	73.19	1836
HSA-MIR-3666	99.90	73.24	1833
HSA-MIR-4295	99.90	73.11	1838
HSA-MIR-17-5P	99.89	73.83	2665
HSA-MIR-106B-5P	99.88	74.72	2795
HSA-MIR-20A-5P	99.88	74.76	2769
HSA-MIR-20B-5P	99.88	74.01	2621
HSA-MIR-519D-3P	99.88	73.97	2607
HSA-MIR-526B-3P	99.88	74.06	2587
HSA-MIR-93-5P	99.88	73.98	2606
HSA-MIR-519A-3P	99.67	71.67	1868
HSA-MIR-519B-3P	99.67	71.67	1868
HSA-MIR-519C-3P	99.67	71.67	1870
HSA-MIR-4690-5P	99.65	66.24	813
HSA-MIR-330-3P	99.41	69.95	2521
HSA-MIR-4667-3P	99.26	65.45	1608
HSA-MIR-6510-5P	99.14	66.59	1081
HSA-MIR-4758-3P	99.12	63.96	869
HSA-MIR-3619-5P	99.00	68.87	2308
HSA-MIR-214-3P	98.71	68.12	2128
HSA-MIR-761	98.71	68.07	2051
HSA-MIR-6761-5P	98.71	68.03	1504

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 99.8% of screened cell lines, common-essential.

Literature-anchored findings (GeneRIF, showing 8)

• Cloning and characterization of a novel gene PDRG that is differentially regulated by p53 and ultraviolet radiation (PMID:14562055)
• Is part of an RNA polymerase II-associated complex with possible chaperone activity. (PMID:19450687)
• PDRG1 expression is increased in multiple human malignancies suggesting it to be a high-value novel tumor marker that could play a role in cancer development and/or progression. (PMID:21193842)
• It was found that PDRG1 could promote radio-resistance that involved the ATM-p53 signaling pathway in lung cancer cells. (PMID:27610824)
• Specific PDRG1 gene silencing may inhibit the growth and metastasis of gastric cancer cells through the activation of ATM/p53 pathway. (PMID:31383535)
• PDRG1 association with the Wnt signaling pathway in esophageal cancer cells.PDRG1 may promote proliferation while inhibiting apoptosis and chemotherapy sensitivity in esophageal cancer cells. (PMID:31882431)
• PDRG1 predicts a poor prognosis and facilitates the proliferation and metastasis of colorectal cancer. (PMID:34780783)
• PDRG1 promotes the proliferation and migration of GBM cells by the MEK/ERK/CD44 pathway. (PMID:34812552)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	pdrg1	ENSDARG00000045017
mus_musculus	Pdrg1	ENSMUSG00000027472
rattus_norvegicus	Pdrg1	ENSRNOG00000008845
drosophila_melanogaster	Pdrg1	FBGN0033467
caenorhabditis_elegans		WBGENE00045407

Protein

Protein identifiers

p53 and DNA damage-regulated protein 1 — Q9NUG6 (reviewed: Q9NUG6)

All UniProt accessions (2): Q9NUG6, A0A384NKN4

UniProt curated annotations — full annotation on UniProt →

Function. May play a role in chaperone-mediated protein folding.

Subunit / interactions. Component of the PAQosome complex which is responsible for the biogenesis of several protein complexes and which consists of R2TP complex members RUVBL1, RUVBL2, RPAP3 and PIH1D1, URI complex members PFDN2, PFDN6, PDRG1, UXT and URI1 as well as ASDURF, POLR2E and DNAAF10/WDR92.

Subcellular location. Cytoplasm.

Tissue specificity. Predominantly expressed in normal testis and exhibits reduced but detectable expression in other organs.

Induction. By UV irradiation and repressed by p53/TP53.

Similarity. Belongs to the prefoldin subunit beta family.

RefSeq proteins (1): NP_110442* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR002777	PFD_beta-like	Family
IPR030482	PDRG1	Family

Pfam: PF01920

UniProt features (1 total): chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9NUG6-F1	92.16	0.78

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 117 (showing top): RODRIGUES_THYROID_CARCINOMA_ANAPLASTIC_UP, LFA1_Q6, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_UP, GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_UP, GOBP_PROTEIN_MATURATION, GROSS_HYPOXIA_VIA_ELK3_UP, GOBP_PROTEIN_STABILIZATION, GROSS_HYPOXIA_VIA_ELK3_ONLY_DN, GOBP_PROTEIN_FOLDING, GOBP_REGULATION_OF_PROTEIN_STABILITY, DODD_NASOPHARYNGEAL_CARCINOMA_UP, P300_01, chr20q11, GAVIN_FOXP3_TARGETS_CLUSTER_T7, WGTTNNNNNAAA_UNKNOWN

GO Biological Process (2): protein folding (GO:0006457), protein stabilization (GO:0050821)

GO Molecular Function (2): obsolete unfolded protein binding (GO:0051082), protein binding (GO:0005515)

GO Cellular Component (4): cytoplasm (GO:0005737), prefoldin complex (GO:0016272), protein folding chaperone complex (GO:0101031), RPAP3/R2TP/prefoldin-like complex (GO:1990062)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
protein-containing complex	2
cellular process	1
protein maturation	1
regulation of protein stability	1
binding	1
intracellular anatomical structure	1
cellular anatomical structure	1
intracellular protein-containing complex	1

Protein interactions and networks

STRING

712 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
PDRG1	PFDN2	Q9UHV9	996
PDRG1	PFDN6	O15212	995
PDRG1	UXT	Q9UBK9	995
PDRG1	DNAAF10	Q96MX6	984
PDRG1	POLR2E	P19388	950
PDRG1	RPAP3	Q9H6T3	857
PDRG1	ASDURF	L0R819	793
PDRG1	URI1	O94763	755
PDRG1	PIH1D1	Q9NWS0	734
PDRG1	RUVBL2	Q9Y230	671
PDRG1	RUVBL1	P82276	663
PDRG1	PFDN5	Q99471	601
PDRG1	TP53	P04637	547
PDRG1	SURF6	O75683	508
PDRG1	SH3BP4	Q9P0V3	495

IntAct

127 interactions, top by confidence:

A	B	Type	Score
PARD6A	PRKCI	psi-mi:“MI:0914”(association)	0.950
POLR2E	POLR3A	psi-mi:“MI:0914”(association)	0.870
RUVBL1	ZNHIT1	psi-mi:“MI:0914”(association)	0.860
PPP1CC	CCDC85C	psi-mi:“MI:0914”(association)	0.740
PPP1CC	CCDC85C	psi-mi:“MI:2364”(proximity)	0.740
PFDN2	PDRG1	psi-mi:“MI:0915”(physical association)	0.740
PFDN4	PFDN6	psi-mi:“MI:0914”(association)	0.730
POLR2E	MED19	psi-mi:“MI:0914”(association)	0.730
RPRD1B	POLR2D	psi-mi:“MI:0914”(association)	0.730
POLR2G	RECQL5	psi-mi:“MI:0914”(association)	0.730
PPP1CA	CCDC85C	psi-mi:“MI:0914”(association)	0.670
PPP1CA	CCDC85C	psi-mi:“MI:2364”(proximity)	0.670
PFDN2	POLR3A	psi-mi:“MI:0914”(association)	0.670
RUVBL1	POLR3A	psi-mi:“MI:0914”(association)	0.640
VBP1	PFDN6	psi-mi:“MI:0914”(association)	0.640
PFDN1	PFDN6	psi-mi:“MI:0914”(association)	0.640
DDB2	CCT5	psi-mi:“MI:0914”(association)	0.640
POLR2L	POLR3A	psi-mi:“MI:0914”(association)	0.640

BioGRID (181): PDRG1 (Affinity Capture-MS), PDRG1 (Affinity Capture-MS), PDRG1 (Affinity Capture-MS), PDRG1 (Affinity Capture-MS), PDRG1 (Affinity Capture-MS), PDRG1 (Affinity Capture-MS), PDRG1 (Affinity Capture-MS), PDRG1 (Affinity Capture-MS), PDRG1 (Affinity Capture-MS), ACY1 (Co-fractionation), URI1 (Co-fractionation), PDRG1 (Proximity Label-MS), PDRG1 (Proximity Label-MS), PDRG1 (Affinity Capture-MS), PDRG1 (Affinity Capture-MS)

ESM2 similar proteins: A0A1D5P556, A1A5P5, A7RX34, A7T0W1, A8WVJ9, A8XPL7, O18054, O94307, P40005, P46988, P48363, P57741, P59048, P61758, P61759, Q09305, Q0VIA1, Q10143, Q148L7, Q17827, Q21993, Q2KI89, Q2TBX2, Q3ZCF2, Q4R6W4, Q54JS0, Q54LS2, Q54ND3, Q5R629, Q5R6P5, Q5RCG9, Q5RFA9, Q61SU8, Q642A0, Q6CKH5, Q6DJ25, Q6GKV1, Q6IP67, Q8SYD0, Q9BTT4

Diamond homologs: P59048, Q148L7, Q5RFA9, Q642A0, Q9NUG6

SIGNOR signaling

1 interactions.

A	Effect	B	Mechanism
PDRG1	“form complex”	“URI1 prefoldin co-chaperone”	binding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 111 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
FGFR2 mutant receptor activation	8	83.4×	6e-13
RNA Polymerase III Chain Elongation	9	78.2×	7e-14
Signaling by FGFR2 IIIa TM	8	65.9×	5e-12
RNA Polymerase III Transcription Termination	9	61.2×	6e-13
RNA Polymerase III Transcription Initiation From Type 2 Promoter	10	57.9×	7e-14
RNA Polymerase III Transcription Initiation From Type 1 Promoter	10	55.9×	7e-14
RNA Polymerase III Transcription Initiation From Type 3 Promoter	10	55.9×	7e-14
Telomere Maintenance	11	55.5×	1e-14

GO biological processes:

GO term	Partners	Fold	FDR
protein dephosphorylation	5	11.6×	5e-03
protein folding	10	10.8×	5e-06
protein stabilization	15	10.4×	6e-09
transcription by RNA polymerase II	9	6.6×	8e-04

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	6
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

914 predictions. Top by Δscore:

Variant	Effect	Δscore
20:31945890:C:CC	acceptor_gain	1.0000
20:31946491:AATAC:A	donor_loss	1.0000
20:31946492:ATACC:A	donor_loss	1.0000
20:31946493:TACCT:T	donor_loss	1.0000
20:31946575:ATCTG:A	acceptor_loss	1.0000
20:31946576:TCTGA:T	acceptor_loss	1.0000
20:31946577:C:A	acceptor_loss	1.0000
20:31946577:C:CC	acceptor_gain	1.0000
20:31946578:T:A	acceptor_loss	1.0000
20:31946585:A:AC	acceptor_gain	1.0000
20:31948802:CCTTA:C	donor_loss	1.0000
20:31948803:CTTAC:C	donor_loss	1.0000
20:31948804:TTAC:T	donor_loss	1.0000
20:31948805:TACC:T	donor_loss	1.0000
20:31948806:A:AC	donor_gain	1.0000
20:31948806:AC:A	donor_gain	1.0000
20:31948806:ACCTT:A	donor_loss	1.0000
20:31948807:C:CC	donor_gain	1.0000
20:31948807:CC:C	donor_gain	1.0000
20:31948878:ATCTT:A	acceptor_gain	1.0000
20:31948879:TCTT:T	acceptor_loss	1.0000
20:31948880:CTT:C	acceptor_gain	1.0000
20:31948880:CTTC:C	acceptor_loss	1.0000
20:31948881:TT:T	acceptor_gain	1.0000
20:31948881:TTCTG:T	acceptor_loss	1.0000
20:31948882:TC:T	acceptor_loss	1.0000
20:31948883:C:CC	acceptor_gain	1.0000
20:31948883:CTGA:C	acceptor_loss	1.0000
20:31948884:T:G	acceptor_loss	1.0000
20:31950305:AACTT:A	donor_loss	1.0000

AlphaMissense

879 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
20:31950353:C:G	R41P	0.995
20:31946510:A:G	L102P	0.990
20:31950377:A:G	L33P	0.990
20:31946531:A:G	L95P	0.987
20:31946564:A:G	L84P	0.987
20:31945862:A:G	L116S	0.985
20:31946502:C:G	A105P	0.983
20:31946573:T:G	Q81P	0.981
20:31950364:C:A	R37S	0.981
20:31950364:C:G	R37S	0.981
20:31945872:C:G	G113R	0.980
20:31948851:A:C	F65L	0.980
20:31948851:A:T	F65L	0.980
20:31948852:A:G	F65S	0.980
20:31948853:A:G	F65L	0.980
20:31950344:A:G	L44P	0.980
20:31951904:C:G	A20P	0.980
20:31948870:A:T	V59D	0.978
20:31950348:C:G	G43R	0.978
20:31951903:G:T	A20D	0.978
20:31946540:C:G	R92P	0.975
20:31948861:C:A	G62V	0.973
20:31950339:C:G	A46P	0.973
20:31950354:G:C	R41G	0.973
20:31951924:A:G	L13P	0.973
20:31950335:A:G	L47P	0.972
20:31950347:C:T	G43D	0.972
20:31946543:A:G	L91P	0.968
20:31951891:A:G	L24P	0.967
20:31945853:A:T	L119H	0.966

dbSNP variants (sampled 300 via entrez): RS1000030839 (20:31952053 G>A), RS1000175146 (20:31947896 A>G), RS1000199095 (20:31943928 G>A), RS1000200999 (20:31953150 A>C), RS1000360235 (20:31949605 A>G), RS1000458580 (20:31947640 A>C), RS1000509425 (20:31949336 C>A), RS1000634054 (20:31948667 A>C), RS1000688065 (20:31948371 T>C), RS1000790529 (20:31949161 C>G), RS1001815065 (20:31951213 C>T), RS1002188327 (20:31950982 C>A,T), RS1002704865 (20:31944660 T>G), RS1002805296 (20:31951960 A>G), RS1002991506 (20:31945504 T>C)

Disease associations

OMIM: gene MIM:610789 | 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

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

Chemical	Actions (top 5)	PubMed papers
Cisplatin	decreases expression, increases expression, affects cotreatment	2
Cadmium Chloride	increases abundance, increases expression	2
aristolochic acid I	increases expression	1
ginger extract	decreases expression, increases abundance	1
bisphenol A	decreases expression	1
glycidyl methacrylate	increases expression	1
sodium arsenite	increases expression	1
butyraldehyde	increases expression	1
potassium chromate(VI)	affects cotreatment, increases expression	1
epigallocatechin gallate	affects cotreatment, increases expression	1
pentanal	increases expression	1
di-n-butylphosphoric acid	affects expression	1
perfluorooctane sulfonic acid	decreases expression	1
abrine	increases expression	1
(4-amino-1,4-dihydro-3-(2-pyridyl)-5-thioxo-1,2,4-triazole)copper(II)	increases expression	1
jinfukang	affects cotreatment, decreases expression	1
PCI 5002	affects cotreatment, increases expression	1
Sunitinib	decreases expression	1
Benzo(a)pyrene	decreases methylation	1
Cadmium	increases abundance, increases expression	1
Copper	affects binding, decreases expression	1
Dimethyl Sulfoxide	increases expression	1
Disulfiram	decreases expression, affects binding	1
Doxorubicin	increases expression	1
Enzyme Inhibitors	increases O-linked glycosylation, decreases activity	1
Methyl Methanesulfonate	increases expression	1
Oils, Volatile	decreases expression, increases abundance	1
Rotenone	decreases expression	1
Smoke	decreases expression	1
Thiram	increases expression	1

Clinical trials (associated diseases)

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