PDAP1

Summary

PDAP1 (PDGFA associated protein 1, HGNC:14634) is a protein-coding gene on chromosome 7q22.1, encoding 28 kDa heat- and acid-stable phosphoprotein (Q13442). Enhances PDGFA-stimulated cell growth in fibroblasts, but inhibits the mitogenic effect of PDGFB. It is a common-essential gene (DepMap: required in 95.2% of cancer cell lines).

The protein encoded by this gene is a phosphoprotein that may upregulate the PDGFA-stimulated growth of fibroblasts and also downregulate the mitogenicity of PDGFB. The encoded protein in rodents has been shown to bind PDGFA with a low affinity.

Source: NCBI Gene 11333 — RefSeq curated summary.

At a glance

• GWAS associations: 4
• Clinical variants (ClinVar): 21 total
• Druggable target: yes
• Cancer dependency (DepMap): dependent in 95.2% of screened cell lines (common-essential)
• MANE Select transcript: NM_014891

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:14634
Approved symbol	PDAP1
Name	PDGFA associated protein 1
Location	7q22.1
Locus type	gene with protein product
Status	Approved
Aliases	PAP1, PAP, HASPP28
Ensembl gene	ENSG00000106244
Ensembl biotype	protein_coding
OMIM	607075
Entrez	11333

Gene structure

Transcript identifiers

Ensembl transcripts: 11 — 8 protein_coding, 1 nonsense_mediated_decay, 1 retained_intron, 1 protein_coding_CDS_not_defined

ENST00000350498, ENST00000426447, ENST00000488214, ENST00000496335, ENST00000626285, ENST00000856632, ENST00000856633, ENST00000926895, ENST00000926896, ENST00000926897, ENST00000926898

RefSeq mRNA: 1 — MANE Select: NM_014891 NM_014891

CCDS: CCDS5662

Canonical transcript exons

ENST00000350498 — 6 exons

Exon	Start	End
ENSE00000708078	99403398	99403505
ENSE00000824720	99404862	99404953
ENSE00001104225	99394673	99396740
ENSE00001289631	99408536	99408597
ENSE00003470523	99397862	99398013
ENSE00003513823	99400303	99400424

Expression profiles

Bgee: expression breadth ubiquitous, 283 present calls, max score 98.51.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 101.9407 / max 997.1908, expressed in 1825 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
85101	100.4681	1825
85102	1.4726	1012

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
gastrocnemius	UBERON:0001388	98.51	gold quality
muscle of leg	UBERON:0001383	98.38	gold quality
mucosa of stomach	UBERON:0001199	97.99	gold quality
lower esophagus muscularis layer	UBERON:0035833	97.93	gold quality
lower esophagus	UBERON:0013473	97.92	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	97.85	gold quality
popliteal artery	UBERON:0002250	97.81	gold quality
tibial artery	UBERON:0007610	97.81	gold quality
sural nerve	UBERON:0015488	97.76	gold quality
muscle layer of sigmoid colon	UBERON:0035805	97.76	gold quality
thoracic aorta	UBERON:0001515	97.71	gold quality
ascending aorta	UBERON:0001496	97.70	gold quality
left coronary artery	UBERON:0001626	97.70	gold quality
aorta	UBERON:0000947	97.69	gold quality
hindlimb stylopod muscle	UBERON:0004252	97.68	gold quality
right coronary artery	UBERON:0001625	97.63	gold quality
descending thoracic aorta	UBERON:0002345	97.63	gold quality
cortical plate	UBERON:0005343	97.62	gold quality
ganglionic eminence	UBERON:0004023	97.60	gold quality
tibial nerve	UBERON:0001323	97.56	gold quality
skin of leg	UBERON:0001511	97.56	gold quality
stromal cell of endometrium	CL:0002255	97.55	gold quality
right atrium auricular region	UBERON:0006631	97.39	gold quality
monocyte	CL:0000576	97.37	gold quality
skin of abdomen	UBERON:0001416	97.37	gold quality
body of uterus	UBERON:0009853	97.36	gold quality
calcaneal tendon	UBERON:0003701	97.33	gold quality
ectocervix	UBERON:0012249	97.26	gold quality
minor salivary gland	UBERON:0001830	97.22	gold quality
left adrenal gland	UBERON:0001234	97.21	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	13.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

125 targeting PDAP1, 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-4262	100.00	73.26	3931
HSA-MIR-4673	100.00	66.64	1490
HSA-MIR-3120-5P	100.00	65.56	965
HSA-LET-7A-3P	100.00	74.03	3932
HSA-LET-7B-3P	100.00	74.08	3913
HSA-LET-7F-1-3P	100.00	74.02	3928
HSA-MIR-98-3P	100.00	74.08	3907
HSA-MIR-4533	100.00	69.48	2758
HSA-MIR-181A-5P	99.99	72.96	2995
HSA-MIR-181B-5P	99.99	72.97	2996
HSA-MIR-181C-5P	99.99	72.95	2996
HSA-MIR-181D-5P	99.99	73.04	2997
HSA-MIR-150-5P	99.99	66.69	1976
HSA-MIR-4645-5P	99.98	65.81	1284
HSA-MIR-12136	99.98	72.81	5713
HSA-MIR-5696	99.98	72.36	4487
HSA-MIR-548N	99.98	71.94	4170
HSA-MIR-548P	99.98	72.25	3784
HSA-MIR-6888-3P	99.97	65.95	1170
HSA-MIR-4666A-3P	99.96	71.71	3434
HSA-MIR-6778-3P	99.96	67.29	2693
HSA-MIR-548AJ-3P	99.96	73.38	5345
HSA-MIR-548X-3P	99.96	73.38	5345
HSA-MIR-185-3P	99.95	67.01	1743
HSA-MIR-545-3P	99.95	70.74	2783
HSA-MIR-381-3P	99.93	71.87	2854
HSA-MIR-300	99.92	71.76	2856
HSA-MIR-15A-5P	99.90	72.80	2787
HSA-MIR-15B-5P	99.90	72.78	2798
HSA-MIR-16-5P	99.90	72.80	2780

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 95.2% of screened cell lines, common-essential.

Literature-anchored findings (GeneRIF, showing 3)

• PDAP-1 as an effecter of PDGF signaling in glioma cells (PMID:27448842)
• AG1024+U0126 acted synergistically to downregulate “synergy” genes, especially STAT6 and PDAP1, which displayed significant expression codependency and a common expression pattern linked with other key “synergy” genes, supporting their predicted role in an STAT6-ERK-nuclear factor kappa beta (NF-kappaB) network. Daunorubicin and PDAP1 loss were synergistic, so PDAP1 is important for the response to this anthracycline. (PMID:29656114)
• RFX transcription factors control a miR-150/PDAP1 axis that restrains the proliferation of human T cells. (PMID:35143476)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	pdap1b	ENSDARG00000002967
mus_musculus	Pdap1	ENSMUSG00000029623
rattus_norvegicus	Pdap1	ENSRNOG00000000990
drosophila_melanogaster	CG11444	FBGN0029715
drosophila_melanogaster	CG4438	FBGN0032115

Protein

Protein identifiers

28 kDa heat- and acid-stable phosphoprotein — Q13442 (reviewed: Q13442)

Alternative names: PDGF-associated protein, PDGFA-associated protein 1

All UniProt accessions (2): Q13442, F8WBW6

UniProt curated annotations — full annotation on UniProt →

Function. Enhances PDGFA-stimulated cell growth in fibroblasts, but inhibits the mitogenic effect of PDGFB.

Similarity. Belongs to the PDAP1 family.

RefSeq proteins (1): NP_055706* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR019380	Casein_kinase_sb_PP28	Domain
IPR039876	HAP28	Family

Pfam: PF10252

UniProt features (27 total): modified residue 11, sequence conflict 7, compositionally biased region 5, region of interest 2, chain 1, cross-link 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q13442-F1	77.09	0.32

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 (12): 57, 60, 63, 70, 126, 132, 164, 176, 178, 52, 18, 19

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-6798695	Neutrophil degranulation

MSigDB gene sets: 223 (showing top): MORF_MTA1, REACTOME_INNATE_IMMUNE_SYSTEM, GOCC_SECRETORY_GRANULE, GCANCTGNY_MYOD_Q6, MORF_UBE2I, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, DACOSTA_UV_RESPONSE_VIA_ERCC3_UP, CAGCTG_AP4_Q5, CEBPB_01, MONNIER_POSTRADIATION_TUMOR_ESCAPE_UP, MARTINEZ_RB1_TARGETS_UP, MODULE_120, MORF_SKP1A, CEBP_Q2, MORF_RAF1

GO Biological Process (1): signal transduction (GO:0007165)

GO Molecular Function (2): RNA binding (GO:0003723), protein binding (GO:0005515)

GO Cellular Component (4): extracellular region (GO:0005576), cytosol (GO:0005829), plasma membrane (GO:0005886), ficolin-1-rich granule lumen (GO:1904813)

Reactome top-level categories

Rollup of top-1 pathways:

Category	Pathways
Innate Immune System	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	2
cell communication	1
cellular process	1
signaling	1
regulation of cellular process	1
cellular response to stimulus	1
nucleic acid binding	1
binding	1
cytoplasm	1
membrane	1
cell periphery	1
intracellular organelle lumen	1
ficolin-1-rich granule	1

Protein interactions and networks

STRING

900 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
PDAP1	PDGFA	P04085	849
PDAP1	PDGFB	P01127	653
PDAP1	C8orf88	P0DMB2	468
PDAP1	RFX8	Q6ZV50	463
PDAP1	SAXO5	Q8NA69	431
PDAP1	RMND1	Q9NWS8	427
PDAP1	CAPZA2	P47755	418
PDAP1	ZSCAN29	Q8IWY8	408
PDAP1	RCN2	Q14257	398
PDAP1	OR5I1	Q13606	393
PDAP1	KCTD6	Q8NC69	391
PDAP1	DTYMK	P23919	389
PDAP1	NDUFB7	P17568	378
PDAP1	CDC42EP4	Q9H3Q1	378
PDAP1	OR4D6	Q8NGJ1	365

IntAct

50 interactions, top by confidence:

A	B	Type	Score
MED4	MED19	psi-mi:“MI:0914”(association)	0.900
PELI1	PDAP1	psi-mi:“MI:0915”(physical association)	0.560
PDAP1	PELI1	psi-mi:“MI:0915”(physical association)	0.560
PDAP1	KLHL36	psi-mi:“MI:0915”(physical association)	0.500
	PDAP1	psi-mi:“MI:0407”(direct interaction)	0.440
PDAP1	CSNK2A1	psi-mi:“MI:0217”(phosphorylation reaction)	0.440
	GNAT3	psi-mi:“MI:0915”(physical association)	0.400
PDAP1	FZD7	psi-mi:“MI:0915”(physical association)	0.370
RPL10	RPS6	psi-mi:“MI:0914”(association)	0.350
Xpo1	IFT56	psi-mi:“MI:0914”(association)	0.350
LIN37	RPLP1	psi-mi:“MI:0914”(association)	0.350
LIN54	HDAC3	psi-mi:“MI:0914”(association)	0.350
		psi-mi:“MI:0914”(association)	0.350
MAPT	MEX3A	psi-mi:“MI:0914”(association)	0.350
MAPT	C11orf98	psi-mi:“MI:0914”(association)	0.350
MAPT	POTEF	psi-mi:“MI:0914”(association)	0.350
APP	ESYT2	psi-mi:“MI:0914”(association)	0.350
PRNP	CARNS1	psi-mi:“MI:0914”(association)	0.350
PRNP	WDR91	psi-mi:“MI:0914”(association)	0.350
CD74		psi-mi:“MI:0914”(association)	0.350
DDX60	G6PD	psi-mi:“MI:0914”(association)	0.350
MAB21L2	PTBP1	psi-mi:“MI:0914”(association)	0.350
MAP2K3	USP9Y	psi-mi:“MI:0914”(association)	0.350
DISC1	AGRN	psi-mi:“MI:0914”(association)	0.350
PAK4	MCM5	psi-mi:“MI:0914”(association)	0.350
BMI1	HMGB1P1	psi-mi:“MI:0914”(association)	0.350
EGFR	ACADVL	psi-mi:“MI:0914”(association)	0.350
MAPT	SHTN1	psi-mi:“MI:0914”(association)	0.350

BioGRID (134): PDAP1 (Affinity Capture-MS), PDAP1 (Co-fractionation), RBM8A (Co-fractionation), PDAP1 (Affinity Capture-MS), PDAP1 (Proximity Label-MS), PDAP1 (Proximity Label-MS), PDAP1 (Affinity Capture-MS), PDAP1 (Affinity Capture-MS), PDAP1 (Affinity Capture-MS), PDAP1 (Affinity Capture-MS), PDAP1 (Affinity Capture-MS), PDAP1 (Affinity Capture-MS), PDAP1 (Proximity Label-MS), PDAP1 (Affinity Capture-MS), PDAP1 (Affinity Capture-RNA)

ESM2 similar proteins: A0A024R1R8, A1A4Q4, A1CMP1, A2R091, A3N0X3, A5DF06, A6R5Z3, A6S6B0, A6ZWL1, A7F9B8, B0BPQ7, B3GXV7, H3BMG3, O31573, P25886, P47915, Q02642, Q05AK9, Q05AX4, Q06DK3, Q0ULD0, Q13442, Q1DI23, Q1HRV4, Q20588, Q28GR1, Q32KU9, Q32LJ0, Q3E764, Q3UHX2, Q4KLG3, Q4P9Y9, Q4SUE2, Q55F75, Q5ASI4, Q5RCI9, Q60QR6, Q62785, Q66654, Q6C2F3

Diamond homologs: Q13442, Q3UHX2, Q556U5, Q62785

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 62 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
Peptide chain elongation	5	14.8×	2e-03
Viral mRNA Translation	5	14.8×	2e-03
PELO:HBS1L and ABCE1 dissociate a ribosome on a non-stop mRNA	5	14.6×	2e-03
Selenocysteine synthesis	5	14.0×	2e-03
Eukaryotic Translation Termination	5	14.0×	2e-03
Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC)	5	13.7×	2e-03
ZNF598 and the Ribosome-associated Quality Trigger (RQT) complex dissociate a ribosome stalled on a no-go mRNA	5	13.7×	2e-03
Formation of a pool of free 40S subunits	5	13.0×	2e-03

GO biological processes:

GO term	Partners	Fold	FDR
cytoplasmic translation	6	19.5×	4e-04

Disease & clinical

Clinical variants and AI predictions

ClinVar

21 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

1439 predictions. Top by Δscore:

Variant	Effect	Δscore
7:99392273:G:GT	donor_gain	1.0000
7:99392873:TCAGG:T	donor_loss	1.0000
7:99392874:CAG:C	donor_loss	1.0000
7:99392875:AGGTG:A	donor_loss	1.0000
7:99392877:G:A	donor_loss	1.0000
7:99392877:G:GG	donor_gain	1.0000
7:99392878:T:A	donor_loss	1.0000
7:99394023:TTGCA:T	acceptor_loss	1.0000
7:99394024:T:TA	acceptor_gain	1.0000
7:99394024:TGCA:T	acceptor_loss	1.0000
7:99394025:GCAGC:G	acceptor_loss	1.0000
7:99394026:CAGCC:C	acceptor_loss	1.0000
7:99394027:A:AG	acceptor_gain	1.0000
7:99394028:G:GG	acceptor_gain	1.0000
7:99394028:GC:G	acceptor_gain	1.0000
7:99394028:GCC:G	acceptor_gain	1.0000
7:99394028:GCCA:G	acceptor_gain	1.0000
7:99397876:T:TA	donor_gain	1.0000
7:99398012:CT:C	acceptor_gain	1.0000
7:99400310:T:A	donor_gain	1.0000
7:99400420:TTTTG:T	acceptor_gain	1.0000
7:99400422:TTG:T	acceptor_gain	1.0000
7:99400423:TG:T	acceptor_gain	1.0000
7:99400425:C:CC	acceptor_gain	1.0000
7:99403394:GTACC:G	donor_loss	1.0000
7:99403395:TA:T	donor_loss	1.0000
7:99403396:A:AT	donor_loss	1.0000
7:99403397:CC:C	donor_loss	1.0000
7:99408537:T:TA	donor_gain	1.0000
7:99392274:A:T	donor_gain	0.9900

AlphaMissense

1180 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
7:99397900:C:G	R150P	1.000
7:99397912:A:T	I146N	1.000
7:99397919:C:G	A144P	1.000
7:99397921:A:G	L143P	1.000
7:99397921:A:T	L143Q	1.000
7:99397930:A:G	L140P	1.000
7:99397937:C:G	A138P	1.000
7:99397951:G:A	T133I	1.000
7:99397957:C:T	G131E	1.000
7:99397958:C:A	G131W	1.000
7:99397967:G:C	H128D	1.000
7:99400303:C:G	R112P	1.000
7:99400312:C:A	R109M	1.000
7:99400383:G:C	N85K	1.000
7:99400383:G:T	N85K	1.000
7:99397892:C:G	A153P	0.999
7:99397900:C:A	R150L	0.999
7:99397901:G:A	R150W	0.999
7:99397901:G:C	R150G	0.999
7:99397903:T:G	Q149P	0.999
7:99397909:C:G	R147P	0.999
7:99397912:A:C	I146S	0.999
7:99397924:C:G	R142P	0.999
7:99397925:G:C	R142G	0.999
7:99397928:C:G	A141P	0.999
7:99397932:G:C	D139E	0.999
7:99397932:G:T	D139E	0.999
7:99397933:T:A	D139V	0.999
7:99397933:T:C	D139G	0.999
7:99397933:T:G	D139A	0.999

dbSNP variants (sampled 300 via entrez): RS1000305397 (7:99399234 C>T), RS1000375588 (7:99410460 G>A), RS1000515755 (7:99403526 C>A,G,T), RS1000581038 (7:99397611 T>C), RS1000698508 (7:99409159 C>G,T), RS1000914097 (7:99405782 C>A,G), RS1001035010 (7:99397799 G>A), RS1001323756 (7:99406202 T>C), RS1001519394 (7:99394924 A>G), RS1001737405 (7:99401044 T>C), RS1001863380 (7:99407704 C>A), RS1002299647 (7:99396621 AC>A), RS1002329777 (7:99408489 C>A,G,T), RS1002566018 (7:99396328 C>T), RS1002652226 (7:99406739 ACT>A)

Disease associations

OMIM: gene MIM:607075 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

4 associations (top):

Study	Trait	p-value
GCST004730_2	Facial emotion recognition (sad faces)	3.000000e-06
GCST006249_21	Serum metabolite levels	4.000000e-11
GCST006249_46	Serum metabolite levels	4.000000e-21
GCST90002397_305	Mean spheric corpuscular volume	3.000000e-13

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0008329	facial emotion recognition measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL6067112 (SINGLE PROTEIN)

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Fluorouracil	decreases expression, increases expression	3
bisphenol A	decreases expression	2
Aflatoxin B1	affects cotreatment, decreases expression	2
aristolochic acid I	decreases expression	1
FR900359	affects phosphorylation	1
triphenyl phosphate	affects expression	1
pyrogallol 1,3-dimethyl ether	affects cotreatment, decreases expression, affects localization, increases expression	1
sodium arsenite	decreases expression	1
butyraldehyde	decreases expression	1
ochratoxin A	decreases expression	1
quinoline	decreases expression	1
di-n-butylphosphoric acid	affects expression	1
CGP 52608	affects binding, increases reaction	1
bisphenol AF	increases expression	1
Air Pollutants	increases abundance, increases expression	1
Caffeine	affects phosphorylation	1
Choline	affects expression	1
Doxorubicin	increases expression	1
Ethyl Methanesulfonate	decreases expression	1
Formaldehyde	decreases expression	1
Furaldehyde	decreases expression, affects cotreatment	1
Ivermectin	decreases expression	1
Methyl Methanesulfonate	decreases expression	1
Perfume	increases expression	1
Progesterone	increases expression	1
Ribonucleotides	affects binding	1
Rifampin	decreases expression	1
Smoke	decreases expression	1
Sodium Chloride	affects cotreatment, decreases expression, affects localization, increases expression	1
Tobacco Smoke Pollution	affects 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
CHEMBL5651992	Binding	Binding affinity to human PDAP1 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

1 cell lines: 1 transformed cell line

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

Cellosaurus	Name	Category	Sex
CVCL_B3DM	Abcam HEK293T PDAP1 KO	Transformed cell line	Female

Clinical trials (associated diseases)

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