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): 22 total
• Expression (HPA): Low tissue specificity — highest in spinal cord, ventral spinal cord, midbrain
• GTEx eGene: eQTL in 9 tissues, sQTL in 3 (q < 0.05)
• Cancer dependency (DepMap): dependent in 95.2% of screened cell lines (common-essential)
• Constraint (gnomAD): pLI 0.00 (LoF-tolerant), LOEUF 0.93 (unconstrained)
• 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: 38 — 23 protein_coding, 13 nonsense_mediated_decay, 1 retained_intron, 1 protein_coding_CDS_not_defined

MANE Select: ENST00000350498

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

ENST00000350498, ENST00000426447, ENST00000488214, ENST00000496335, ENST00000626285, ENST00000856632, ENST00000856633, ENST00000926895, ENST00000926896, ENST00000926897, ENST00000926898, ENST00000977178, ENST00000977179, ENST00000977180, ENST00001030474, ENST00001030476, ENST00001030478, ENST00001030482, ENST00001086401, ENST00001086402, ENST00001086403, ENST00001086405, ENST00001086409, ENST00001086415, ENST00001086416, ENST00001086417, ENST00001086418, ENST00001086419, ENST00001091001, ENST00001091002, ENST00001091003, ENST00001091004, ENST00001091005, ENST00001091006, ENST00001091007, ENST00001113624, ENST00001128066, ENST00001142155

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.

Highest expression (Bgee): gastrocnemius, muscle of leg, mucosa of stomach, lower esophagus muscularis layer, lower esophagus.

Genetic regulation across tissues (GTEx eQTL / sQTL)

PDAP1 is an eGene in GTEx v10 — its expression is genetically regulated (eQTL) in 9 tissues and its splicing (sQTL) in 3 (q < 0.05). Strongest associations first; slope = normalized effect of the lead variant’s alternative allele.

12 significant tissue × QTL associations:

Tissue	QTL	q-value	Slope	Lead variant
Testis	sqtl	4.8e-18	-0.87	7:99383134:C:T
Skin Sun Exposed Lower leg	sqtl	7.8e-07	-1.06	7:99439732:G:A
Testis	eqtl	9.4e-03	-0.23	7:98983889:C:A
Cells Cultured fibroblasts	eqtl	1.3e-02	-0.07	7:99427277:C:T
Colon Sigmoid	eqtl	1.5e-02	-0.11	7:99260544:T:C
Whole Blood	eqtl	1.8e-02	-0.10	7:99387773:A:G
Nerve Tibial	eqtl	2.4e-02	+0.07	7:100002782:A:T
Skin Not Sun Exposed Suprapubic	eqtl	3.3e-02	+0.31	7:99166594:T:C
Skin Sun Exposed Lower leg	eqtl	4.2e-02	+0.21	7:98989800:C:A
Thyroid	sqtl	4.3e-02	+0.38	7:99384417:CT:C
Heart Left Ventricle	eqtl	4.3e-02	+0.09	7:98443657:T:C
Artery Tibial	eqtl	4.9e-02	-0.12	7:99094891:G:A

FANTOM5 promoters

2 alternative TSS:

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

Top tissues by expression

showing 100 of 291 tissues 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
endometrium epithelium	UBERON:0004811	97.21	gold quality
left ovary	UBERON:0002119	97.19	gold quality
right lung	UBERON:0002167	97.19	gold quality
esophagus	UBERON:0001043	97.15	gold quality
right ovary	UBERON:0002118	97.15	gold quality
right adrenal gland	UBERON:0001233	97.13	gold quality
left uterine tube	UBERON:0001303	97.13	gold quality
upper lobe of left lung	UBERON:0008952	97.13	gold quality
right adrenal gland cortex	UBERON:0035827	97.10	gold quality
left lobe of thyroid gland	UBERON:0001120	97.08	gold quality
left adrenal gland cortex	UBERON:0035825	97.08	gold quality
right lobe of thyroid gland	UBERON:0001119	97.07	gold quality
body of pancreas	UBERON:0001150	97.04	gold quality
body of stomach	UBERON:0001161	97.04	gold quality
mucosa of transverse colon	UBERON:0004991	97.01	gold quality
endocervix	UBERON:0000458	96.97	gold quality
ventricular zone	UBERON:0003053	96.95	gold quality
mononuclear cell	CL:0000842	96.91	gold quality
transverse colon	UBERON:0001157	96.91	gold quality
coronary artery	UBERON:0001621	96.90	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	96.90	gold quality
leukocyte	CL:0000738	96.79	gold quality
small intestine Peyer’s patch	UBERON:0003454	96.76	gold quality
metanephros cortex	UBERON:0010533	96.68	gold quality
granulocyte	CL:0000094	96.66	gold quality
gall bladder	UBERON:0002110	96.63	gold quality
apex of heart	UBERON:0002098	96.61	gold quality
right frontal lobe	UBERON:0002810	96.59	gold quality
esophagus mucosa	UBERON:0002469	96.56	gold quality
omental fat pad	UBERON:0010414	96.54	gold quality
peritoneum	UBERON:0002358	96.52	gold quality
muscle organ	UBERON:0001630	96.51	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	96.51	gold quality
rectum	UBERON:0001052	96.47	gold quality
islet of Langerhans	UBERON:0000006	96.41	gold quality
gluteal muscle	UBERON:0002000	96.40	gold quality
adenohypophysis	UBERON:0002196	96.34	gold quality
cardiac atrium	UBERON:0002081	96.26	gold quality
cingulate cortex	UBERON:0003027	96.26	gold quality
anterior cingulate cortex	UBERON:0009835	96.25	gold quality
right hemisphere of cerebellum	UBERON:0014890	96.20	gold quality
heart left ventricle	UBERON:0002084	96.19	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	96.19	gold quality
smooth muscle tissue	UBERON:0001135	96.16	gold quality
triceps brachii	UBERON:0001509	96.15	gold quality
cerebellar hemisphere	UBERON:0002245	96.15	gold quality
adrenal gland	UBERON:0002369	96.13	gold quality
lower esophagus mucosa	UBERON:0035834	96.11	gold quality
cerebellar cortex	UBERON:0002129	96.08	gold quality
adrenal cortex	UBERON:0001235	96.07	gold quality
upper lobe of lung	UBERON:0008948	96.04	gold quality
thyroid gland	UBERON:0002046	95.99	gold quality
prefrontal cortex	UBERON:0000451	95.93	gold quality
cardiac ventricle	UBERON:0002082	95.87	gold quality
stomach	UBERON:0000945	95.63	gold quality
small intestine	UBERON:0002108	95.60	gold quality
heart	UBERON:0000948	95.55	gold quality
sigmoid colon	UBERON:0001159	95.40	gold quality
spleen	UBERON:0002106	95.40	gold quality
amygdala	UBERON:0001876	95.33	gold quality
left testis	UBERON:0004533	95.33	gold quality
right testis	UBERON:0004534	95.29	gold quality
right uterine tube	UBERON:0001302	95.26	gold quality
pancreas	UBERON:0001264	95.21	gold quality
adipose tissue of abdominal region	UBERON:0007808	95.20	gold quality
tendon	UBERON:0000043	95.19	gold quality
saliva-secreting gland	UBERON:0001044	95.16	gold quality
spinal cord	UBERON:0002240	95.15	gold quality
embryo	UBERON:0000922	95.12	gold quality
cerebellum	UBERON:0002037	95.03	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

HPA expression

RNA tissue specificity: Low tissue specificity

showing 60 of 80 HPA tissues / cells by nTPM:

Tissue / cell	Axis	nTPM	Protein (IHC)
Spinal cord	tissue	118.2
Midbrain	tissue	111.9
Thalamus	tissue	108.5
Hippocampal formation	tissue	107.7
Pons	tissue	106.2
Corpus callosum	tissue	105.2
Medulla oblongata	tissue	104.7
Superior colliculi	tissue	104.2
Cerebral cortex	tissue	102.8	medium
Motor cortex	tissue	102.8
Somatosensory cortex	tissue	99.7
Prefrontal cortex	tissue	98.5
Substantia nigra	tissue	98.5
Skeletal muscle	tissue	98.3	high
Occipital cortex	tissue	96.1
Putamen	tissue	94.4
Retrosplenial and cingulate cortex	tissue	91.6
Entorhinal cortex	tissue	91.4
Periaqueductal gray	tissue	91.1
Temporal cortex	tissue	90.2
Hypothalamus	tissue	88.9
Retrosplenial cortex	tissue	86.3
Insular cortex	tissue	85.7
Septum	tissue	84.6
Basal ganglia	tissue	83.6	low
Amygdala	tissue	83.6
Ventral forebrain	tissue	81.7
Olfactory bulb	tissue	79.1
Cerebellum	tissue	76.3	high
Tongue	tissue	55.8
Frontal cortex	tissue	45.6
Caudate putamen	tissue	38.3
Locus coeruleus	tissue	32.4
Hippocampus	tissue	27.6	medium
Choroid plexus	tissue	27.3
Postcentral gyrus	tissue	27.3
Heart muscle	tissue	24.4	medium
Nucleus accumbens	tissue	24.4
Vagina	tissue	24.2	medium
Thymus	tissue	23.8
Ovary	tissue	22.8	high
Adipose tissue	tissue	22.2	low
Bone marrow	tissue	21.8	medium
Appendix	tissue	21.3	high
Retina	tissue	21.2
Parathyroid gland	tissue	21.2	medium
Tonsil	tissue	21.0	high
Pituitary gland	tissue	20.7
Seminal vesicle	tissue	19.7	medium
Smooth muscle	tissue	19.7	medium
Urinary bladder	tissue	19.0	medium
Colon	tissue	18.6	high
Salivary gland	tissue	18.4	medium
Placenta	tissue	18.1	medium
Skin 1	tissue	18.0	high
Lymph node	tissue	17.7	high
Liver	tissue	17.7	medium
Prostate	tissue	17.6	medium
Adrenal gland	tissue	17.6	high
Stomach 1	tissue	17.4	medium

Brain sub-regions (HPA Brain Atlas): detected in 192; highest nTPM — Ventral spinal cord (118.2), Dorsal hippocampus (107.7), White matter (105.2), Dorsal spinal cord (102.9), Ventral hippocampus (96.5).

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

Targeting PDAP1 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific).

showing 30 of 125 miRNAs:

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

gnomAD constraint: pLI 0.00355, LOEUF 0.934, missense Z 1.72 — population loss-of-function intolerance (pLI ≥ 0.9 = LoF-intolerant; lower LOEUF = more constrained). gnomAD

Regional missense constraint (gnomAD RMC): no regional variation along ENST00000350498 — one region, missense o/e 0.65. DepMap (CRISPR cell-line fitness): dependent in 95.2% of screened cell lines, common-essential.

Most-dependent cell lines (DepMap gene-effect, lower = stronger; ≤ −0.5 shown): SNU-840 (-2.517), F-36P (-2.248), GSU (-2.14), KELLY (-2.095), MFE-280 (-2.05), AsPC-1 (-1.975), B-CPAP (-1.856), NCI-H82 (-1.828), IMR-32 (-1.747), KARPAS-422 (-1.734), NMC-G1 (-1.731), SNU-685 (-1.729), RD-ES (-1.721), OCI-LY-19 (-1.72), NB-4 (-1.718).

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

Mouse-model phenotypes

Observed phenotypes of the mouse ortholog (MGI:2448536) from MGI (Alliance of Genome Resources) — knockout/mutant phenotypes, ranked by annotation count. 7 distinct phenotype terms.

Mouse phenotype (MP)	Records
abnormal B cell physiology	1
abnormal somatic hypermutation frequency	1
abnormal class switch recombination	1
abnormal mitochondrial physiology	1
decreased germinal center B cell number	1
decreased mature B cell number	1
increased B cell apoptosis	1

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
Dictyostelium discoideum	Q556U5	46.5%	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
ARPC1A	protein-coding	10552
MIR12119	ncRNA	113219453
MYH16	protein-coding	84176
BUD31	protein-coding	8896
ARPC1B	protein-coding	10095
KPNA7	protein-coding	402569
SMURF1	protein-coding	57154
ATP5MF-PTCD1	protein-coding	100526740
PTCD1	protein-coding	26024
CPSF4	protein-coding	10898
ATP5MF	protein-coding	9551

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): F8WBW6, Q13442

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

Predicted structure (AlphaFold)

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

Human Protein Atlas

Protein class: Predicted intracellular proteins, Plasma proteins, Cancer-related genes, Mutated cancer genes, Essential proteins

Protein evidence: Evidence at protein level

Subcellular location (HPA, imaging): cytosol; plasma membrane

Antibody reliability (HPA): IH approved · IF enhanced

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)

Type	Positions
Phosphoserine	57, 60, 63, 176, 178, 19
Phosphotyrosine	70
N6-methyllysine	126
N6-acetyllysine	132, 164
Glycyl lysine isopeptide (lys-gly) (interchain with g-cter in sumo2)	52
Phosphothreonine	18

Function

Pathways and Gene Ontology

Reactome pathways

1 curated (TAS) of 3; 0 disease pathways. Curated-first; evidence = TAS (manually curated) vs IEA (electronic inference).

3 pathways:

ID	Pathway	Evidence
R-HSA-6798695	Neutrophil degranulation	curated
R-HSA-168256	Immune System	—
R-HSA-168249	Innate Immune System	—

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

2 top-level categories:

Category	Pathways
Innate Immune System	1
Immune System	1

GO top-level categories

13 GO namespaces:

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

Experimentally-supported GO annotations

GO terms backed by direct experimental evidence (ECO experimental codes) — 3 of 7 annotations. The rest are phylogenetic / computational / electronic (IEA).

3 experimentally-supported GO terms:

GO term	NS	Evidence
cytosol	CC	direct assay
plasma membrane	CC	direct assay
RNA binding	MF	high-throughput assay

Protein interactions and networks

STRING

showing 15 of 1,372 interactions by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
PDAP1	PDGFA	P04085	773
PDAP1	PDGFB	P01127	642
PDAP1	C8orf88	P0DMB2	499
PDAP1	RFX8	Q6ZV50	458
PDAP1	KCTD6	Q8NC69	434
PDAP1	CDC42EP4	Q9H3Q1	433
PDAP1	RCN2	Q14257	427
PDAP1	ZSCAN29	Q8IWY8	398
PDAP1	RMND1	Q9NWS8	393
PDAP1	OR5I1	Q13606	382
PDAP1	DPY19L4	Q7Z388	380
PDAP1	RBM7	Q9Y580	371
PDAP1	CAPZA2	P47755	370
PDAP1	TBCK	Q8TEA7	366
PDAP1	ZFYVE21	Q9BQ24	346

IntAct

Human interaction partners of PDAP1 in IntAct, one row per partner (best MIscore; records = supporting IntAct interaction records).

4 partners by confidence:

Partner	Interaction type	MIscore	Records
PELI1	physical association	0.560	3
KLHL36	physical association	0.500	1
CSNK2A1	phosphorylation reaction	0.440	1
FZD7	physical association	0.370	1

BioGRID (142 interactions; top human partners by supporting records): EIF1AX (Cross-Linking-MS (XL-MS); 2 records), HSPA1A (Proximity Label-MS; 2 records), LMNA (Co-fractionation; 2 records), RPS11 (Affinity Capture-MS; 2 records), ABCE1 (Cross-Linking-MS (XL-MS)), APP (Reconstituted Complex), ASAP2 (Co-fractionation), ASUN (Co-fractionation), BAD (Proximity Label-MS), BAG1 (Co-fractionation), BAP1 (Affinity Capture-MS), BICD2 (Proximity Label-MS), CD74 (Affinity Capture-MS), CDH1 (Proximity Label-MS), CEBPA (Protein-peptide)

Disease & clinical

Genetic variants

Variant evidence for PDAP1: 22 ClinVar records (0 pathogenic / likely pathogenic); 4 GWAS associations.

ClinVar

22 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

SpliceAI

Top 10 splice-impact sites by Δscore (adjacent positions with the same effect merged into one range; 33 predictions of 503):

Position(s)	Effect	Δscore	Sites
7:99397870	donor_gain	1.0000
7:99400310	donor_gain	1.0000
7:99403396–99403397	donor_loss	1.0000	5
7:99397860–99397861	donor_loss	0.9900	5
7:99397865	donor_gain	0.9900
7:99398014–99398016	acceptor_gain	0.9900	2
7:99398014–99398015	acceptor_loss	0.9900	5
7:99400301–99400302	donor_loss	0.9900	6
7:99400425–99400426	acceptor_loss	0.9900	6
7:99400300	donor_loss	0.9800

AlphaMissense

559 missense substitutions predicted likely pathogenic (of 1,180 scored), across 118 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
D139	8	0.999	0.999
N85	8	0.998	1.000
H128	8	0.993	1.000
N87	8	0.982	0.998
R109	7	0.994	1.000
R15	7	0.969	0.998
E113	7	0.969	0.989
E111	7	0.963	0.994
I81	7	0.958	0.998
M127	7	0.939	0.981
M125	7	0.920	0.979
E114	7	0.903	0.991
H10	7	0.884	0.987
I23	7	0.883	0.997
E22	7	0.879	0.974
Q118	7	0.840	0.999
E151	7	0.760	0.929
E122	7	0.729	0.956
G131	6	0.999	1.000
I146	6	0.996	1.000

HPA cancer prognostics

RNA cancer specificity: Low cancer specificity

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

5 prognostic cancer types:

Cancer	Prognostic	p-value
Liver Hepatocellular Carcinoma (validation)	unfavorable	2.06e-06
Kidney Chromophobe (TCGA)	unfavorable	4.71e-05
Liver Hepatocellular Carcinoma (TCGA)	unfavorable	0.000172
Pancreatic Adenocarcinoma (validation)	unfavorable	0.000204
Kidney Renal Clear Cell Carcinoma (TCGA)	unfavorable	0.000211

Disease associations

OMIM: gene MIM:607075 | disease phenotypes:

GWAS associations

4 associations:

Study	Trait	p-value
GCST006249_62	Serum metabolite levels	4e-21
GCST90002397_330	Mean spheric corpuscular volume	3e-13
GCST006249_11	Serum metabolite levels	4e-11
GCST004730_2	Facial emotion recognition (sad faces)	3e-6

EFO canonical traits (from GWAS)

1 canonical traits:

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 (CPIC guideline: no)

Binding affinities (BindingDB)

1 measured of 1 human assays (1 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

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	affects cotreatment, decreases expression	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)

Via MONDO — disease-level, not drug-specific.

Predicted chemistry — Sugi Predict

The predicted patent-compound landscape for PDAP1 across ~30M SureChEMBL compounds — explore on Sugi Predict.