PLPPR2

Summary

PLPPR2 (phospholipid phosphatase related 2, HGNC:29566) is a protein-coding gene on chromosome 19p13.2, encoding Phospholipid phosphatase-related protein type 2 (Q96GM1).

Predicted to enable phosphatidate phosphatase activity. Predicted to be involved in phospholipid dephosphorylation; phospholipid metabolic process; and signal transduction. Predicted to be located in membrane. Predicted to be active in plasma membrane.

Source: NCBI Gene 64748 — automated summary from GO annotations (Alliance of Genome Resources).

At a glance

• Clinical variants (ClinVar): 64 total
• GTEx eGene: eQTL in 31 tissues, sQTL in 26 (q < 0.05)
• Constraint (gnomAD): pLI 0.99 (loss-of-function intolerant), LOEUF 0.47 (moderately constrained)
• MANE Select transcript: NM_001393892
• Notable: 64 clinical variants but no curated precision-oncology (CIViC) evidence yet

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:29566
Approved symbol	PLPPR2
Name	phospholipid phosphatase related 2
Location	19p13.2
Locus type	gene with protein product
Status	Approved
Aliases	LPPR2, PRG-4
Ensembl gene	ENSG00000105520
Ensembl biotype	protein_coding
OMIM	619591
Entrez	64748

Gene structure

Transcript identifiers

Ensembl transcripts: 15 — 11 protein_coding, 3 retained_intron, 1 protein_coding_CDS_not_defined

MANE Select: ENST00000688289

Transcript support level (Ensembl TSL; 1 = fully mRNA-supported): TSL 1: 1, TSL 2: 3, TSL 3: 2, TSL 4: 2

ENST00000688289, ENST00000251473, ENST00000586380, ENST00000586431, ENST00000587801, ENST00000588196, ENST00000588360, ENST00000591329, ENST00000591608, ENST00000970837, ENST00000970838, ENST00000975297, ENST00000975298, ENST00001113349, ENST00001139147

RefSeq mRNA: 7 — MANE Select: NM_001393892 NM_001170635, NM_001393892, NM_001393893, NM_001393894, NM_001393895, NM_001393896, NM_022737

CCDS: CCDS12258, CCDS59352, CCDS92519

Canonical transcript exons

ENST00000688289 — 10 exons

Exon	Start	End
ENSE00000680511	11359532	11359720
ENSE00000680514	11359821	11359956
ENSE00001061222	11356802	11356976
ENSE00002209763	11364347	11365698
ENSE00002834936	11363713	11363835
ENSE00003509956	11362513	11362689
ENSE00003550449	11357660	11357739
ENSE00003586679	11361217	11361488
ENSE00003592863	11364161	11364212
ENSE00003935321	11355432	11355572

Expression profiles

Bgee: expression breadth ubiquitous, 246 present calls, max score 96.43.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 25.4766 / max 348.9528, expressed in 1743 samples.

Highest expression (Bgee): cortical plate, adenohypophysis, amygdala, frontal lobe, nucleus accumbens.

Genetic regulation across tissues (GTEx eQTL / sQTL)

PLPPR2 is an eGene in GTEx v10 — its expression is genetically regulated (eQTL) in 31 tissues and its splicing (sQTL) in 26 (q < 0.05). Strongest associations first; slope = normalized effect of the lead variant’s alternative allele.

showing 20 of 57 significant tissue × QTL associations:

Tissue	QTL	q-value	Slope	Lead variant
Muscle Skeletal	eqtl	2.3e-144	-0.76	19:11355475:T:C
Thyroid	eqtl	1.6e-54	-0.45	19:11355475:T:C
Heart Atrial Appendage	eqtl	9.5e-53	-0.51	19:11355475:T:C
Heart Left Ventricle	eqtl	2.7e-44	-0.43	19:11355475:T:C
Nerve Tibial	eqtl	2.4e-41	-0.34	19:11355475:T:C
Whole Blood	eqtl	1.1e-34	+0.21	19:11321225:G:A
Muscle Skeletal	sqtl	1.5e-31	-1.71	19:11358243:G:A
Testis	sqtl	8.7e-29	+0.84	19:11354453:C:T
Brain Cerebellum	sqtl	8.0e-24	-2.68	19:11358243:G:A
Brain Cerebellar Hemisphere	sqtl	2.7e-23	-2.55	19:11358243:G:A
Thyroid	sqtl	2.1e-22	-0.48	19:11355475:T:C
Brain Spinal cord cervical c-1	eqtl	4.2e-21	-0.71	19:11355475:T:C
Nerve Tibial	sqtl	4.6e-18	-0.44	19:11355475:T:C
Lung	sqtl	8.0e-16	+0.45	19:11348584:T:C
Brain Caudate basal ganglia	sqtl	2.3e-14	-1.65	19:11358243:G:A
Colon Sigmoid	sqtl	2.4e-14	+0.68	19:11354640:G:C
Testis	eqtl	2.0e-13	+0.30	19:11354640:G:C
Esophagus Muscularis	eqtl	8.4e-13	-0.25	19:11336355:A:C
Esophagus Muscularis	sqtl	8.0e-12	+0.49	19:11355475:T:C
Pituitary	sqtl	3.8e-11	+0.65	19:11355475:T:C

FANTOM5 promoters

3 alternative TSS:

Promoter ID	TPM avg	Samples expressed
173913	21.9297	1740
173914	3.4340	1237
173915	0.1129	35

Top tissues by expression

showing 100 of 278 tissues by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
cortical plate	UBERON:0005343	96.43	gold quality
adenohypophysis	UBERON:0002196	96.26	gold quality
amygdala	UBERON:0001876	95.98	gold quality
right frontal lobe	UBERON:0002810	95.98	gold quality
nucleus accumbens	UBERON:0001882	95.51	gold quality
anterior cingulate cortex	UBERON:0009835	95.51	gold quality
pituitary gland	UBERON:0000007	95.50	gold quality
cingulate cortex	UBERON:0003027	95.49	gold quality
stromal cell of endometrium	CL:0002255	95.36	gold quality
Ammon’s horn	UBERON:0001954	94.52	gold quality
right hemisphere of cerebellum	UBERON:0014890	94.28	gold quality
hypothalamus	UBERON:0001898	93.92	gold quality
prefrontal cortex	UBERON:0000451	93.77	gold quality
lower esophagus muscularis layer	UBERON:0035833	93.67	gold quality
lower esophagus	UBERON:0013473	93.65	gold quality
frontal cortex	UBERON:0001870	93.47	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	93.46	gold quality
left uterine tube	UBERON:0001303	93.35	gold quality
cerebellar hemisphere	UBERON:0002245	93.32	gold quality
temporal lobe	UBERON:0001871	93.30	gold quality
neocortex	UBERON:0001950	93.30	gold quality
cerebellar cortex	UBERON:0002129	93.28	gold quality
caudate nucleus	UBERON:0001873	93.25	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	93.03	gold quality
forebrain	UBERON:0001890	93.00	gold quality
Brodmann (1909) area 9	UBERON:0013540	92.98	gold quality
cerebral cortex	UBERON:0000956	92.89	gold quality
CA1 field of hippocampus	UBERON:0003881	92.82	gold quality
telencephalon	UBERON:0001893	92.80	gold quality
putamen	UBERON:0001874	92.49	gold quality
mucosa of stomach	UBERON:0001199	92.44	gold quality
brain	UBERON:0000955	92.40	gold quality
cerebellum	UBERON:0002037	92.35	gold quality
postcentral gyrus	UBERON:0002581	92.35	gold quality
granulocyte	CL:0000094	92.33	gold quality
right ovary	UBERON:0002118	92.20	gold quality
muscle layer of sigmoid colon	UBERON:0035805	92.03	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	91.95	gold quality
endocervix	UBERON:0000458	91.82	gold quality
left adrenal gland cortex	UBERON:0035825	91.74	gold quality
parietal lobe	UBERON:0001872	91.58	gold quality
left ovary	UBERON:0002119	91.55	gold quality
superior frontal gyrus	UBERON:0002661	91.46	gold quality
left adrenal gland	UBERON:0001234	91.45	gold quality
ascending aorta	UBERON:0001496	91.44	gold quality
thoracic aorta	UBERON:0001515	91.43	gold quality
right adrenal gland cortex	UBERON:0035827	91.40	gold quality
right coronary artery	UBERON:0001625	91.34	gold quality
right adrenal gland	UBERON:0001233	91.33	gold quality
blood	UBERON:0000178	91.24	gold quality
spinal cord	UBERON:0002240	91.24	gold quality
adrenal cortex	UBERON:0001235	91.09	gold quality
body of uterus	UBERON:0009853	90.95	gold quality
aorta	UBERON:0000947	90.85	gold quality
monocyte	CL:0000576	90.82	gold quality
entorhinal cortex	UBERON:0002728	90.82	gold quality
cerebellar vermis	UBERON:0004720	90.80	silver quality
leukocyte	CL:0000738	90.78	gold quality
mononuclear cell	CL:0000842	90.74	gold quality
right atrium auricular region	UBERON:0006631	90.54	gold quality
apex of heart	UBERON:0002098	90.53	gold quality
ectocervix	UBERON:0012249	90.52	gold quality
popliteal artery	UBERON:0002250	90.51	gold quality
tibial artery	UBERON:0007610	90.51	gold quality
descending thoracic aorta	UBERON:0002345	90.33	gold quality
left coronary artery	UBERON:0001626	90.11	gold quality
coronary artery	UBERON:0001621	89.89	gold quality
type B pancreatic cell	CL:0000169	89.88	gold quality
cardiac atrium	UBERON:0002081	89.81	gold quality
olfactory bulb	UBERON:0002264	89.51	gold quality
tibial nerve	UBERON:0001323	89.49	gold quality
right uterine tube	UBERON:0001302	89.41	gold quality
right lung	UBERON:0002167	89.31	gold quality
gastrocnemius	UBERON:0001388	89.22	gold quality
adrenal gland	UBERON:0002369	89.20	gold quality
upper lobe of left lung	UBERON:0008952	88.44	gold quality
fundus of stomach	UBERON:0001160	88.39	gold quality
hindlimb stylopod muscle	UBERON:0004252	88.33	gold quality
substantia nigra	UBERON:0002038	88.17	gold quality
right lobe of thyroid gland	UBERON:0001119	88.15	gold quality
body of stomach	UBERON:0001161	88.06	gold quality
muscle of leg	UBERON:0001383	88.03	gold quality
lower esophagus mucosa	UBERON:0035834	88.02	gold quality
midbrain	UBERON:0001891	87.91	gold quality
vena cava	UBERON:0004087	87.91	silver quality
left lobe of thyroid gland	UBERON:0001120	87.89	gold quality
ganglionic eminence	UBERON:0004023	87.83	gold quality
decidua	UBERON:0002450	87.78	gold quality
esophagus	UBERON:0001043	87.55	gold quality
prostate gland	UBERON:0002367	87.51	gold quality
skin of leg	UBERON:0001511	87.43	gold quality
Brodmann (1909) area 46	UBERON:0006483	87.36	gold quality
orbitofrontal cortex	UBERON:0004167	87.32	gold quality
upper lobe of lung	UBERON:0008948	87.20	gold quality
spleen	UBERON:0002106	87.04	gold quality
metanephros cortex	UBERON:0010533	87.04	gold quality
omental fat pad	UBERON:0010414	86.93	gold quality
peritoneum	UBERON:0002358	86.92	gold quality
skin of abdomen	UBERON:0001416	86.84	gold quality
minor salivary gland	UBERON:0001830	86.76	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 2.

Experiment	Marker?	Max mean expression
E-GEOD-93593	yes	15.28
E-ANND-3	yes	6.23

HPA expression

RNA tissue specificity: Tissue enhanced

showing 60 of 80 HPA tissues / cells by nTPM:

Tissue / cell	Axis	nTPM	Protein (IHC)
Hippocampal formation	tissue	201.4
Hippocampus	tissue	187.5	high
Amygdala	tissue	111.9
Frontal cortex	tissue	93.0
Cerebral cortex	tissue	89.1	high
Temporal cortex	tissue	89.1
Prefrontal cortex	tissue	88.6
Insular cortex	tissue	84.5
Nucleus accumbens	tissue	80.0
Septum	tissue	79.9
Motor cortex	tissue	79.6
Entorhinal cortex	tissue	78.0
Locus coeruleus	tissue	76.6
Hypothalamus	tissue	75.8
Retrosplenial and cingulate cortex	tissue	74.0
Retrosplenial cortex	tissue	67.6
Somatosensory cortex	tissue	67.0
Postcentral gyrus	tissue	66.3
Ventral forebrain	tissue	61.6
Occipital cortex	tissue	57.9
Caudate putamen	tissue	56.5
Basal ganglia	tissue	56.1	high
Pituitary gland	tissue	51.4
Pons	tissue	50.9
Thalamus	tissue	48.7
Substantia nigra	tissue	46.1
Olfactory bulb	tissue	46.1
Putamen	tissue	42.2
Periaqueductal gray	tissue	39.9
Midbrain	tissue	38.9
Cerebellum	tissue	37.1	medium
Superior colliculi	tissue	34.2
Medulla oblongata	tissue	30.3
Choroid plexus	tissue	29.0
Skeletal muscle	tissue	24.3	low
Spinal cord	tissue	22.9
Vagina	tissue	18.2	medium
Prostate	tissue	16.4	high
Corpus callosum	tissue	15.8
Skin 1	tissue	15.3	medium
Smooth muscle	tissue	15.3	not detected
Adrenal gland	tissue	15.0	high
Bone marrow	tissue	14.9	medium
Ovary	tissue	13.6	high
Seminal vesicle	tissue	12.7	low
Gallbladder	tissue	12.4	high
Parathyroid gland	tissue	12.2	medium
Salivary gland	tissue	12.0	high
Cervix	tissue	11.7	high
Pancreas	tissue	11.6	high
Endometrium 1	tissue	11.2	high
Adipose tissue	tissue	10.7	not detected
Placenta	tissue	10.4	high
Spleen	tissue	10.3	low
Heart muscle	tissue	9.9	not detected
Urinary bladder	tissue	9.8	high
Appendix	tissue	9.8	high
Retina	tissue	9.7
Lung	tissue	9.0	low
Stomach 1	tissue	8.1	high

Brain sub-regions (HPA Brain Atlas): detected in 192; highest nTPM — Hippocampus, CA3 (211.1), Hippocampus, CA1 (207.1), Dorsal hippocampus (201.4), Ventral hippocampus (182.4), Dentate gyrus (178.5).

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

Targeting PLPPR2 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific).

showing 30 of 78 miRNAs:

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-6748-5P	100.00	65.81	1057
HSA-MIR-6870-5P	99.99	68.55	2115
HSA-MIR-4723-5P	99.97	68.70	2034
HSA-MIR-5698	99.97	68.49	2029
HSA-MIR-7111-5P	99.97	68.48	2062
HSA-MIR-6825-5P	99.96	69.81	3431
HSA-MIR-96-5P	99.95	72.80	2140
HSA-MIR-185-3P	99.95	67.01	1743
HSA-MIR-6721-5P	99.93	68.92	2981
HSA-MIR-12133	99.92	71.82	2006
HSA-MIR-1271-5P	99.91	71.99	1972
HSA-MIR-4728-5P	99.85	69.39	4718
HSA-MIR-765	99.84	68.24	2442
HSA-MIR-6785-5P	99.82	68.68	4428
HSA-MIR-149-3P	99.72	68.22	3963
HSA-MIR-6752-3P	99.72	66.71	1587
HSA-MIR-6883-5P	99.69	68.05	3785
HSA-MIR-4470	99.66	69.35	1767
HSA-MIR-1287-3P	99.63	66.93	492
HSA-MIR-1827	99.63	68.57	3265
HSA-MIR-7150	99.62	66.80	1322
HSA-MIR-24-3P	99.59	69.97	1934
HSA-MIR-486-3P	99.51	66.82	1901
HSA-MIR-3128	99.50	67.85	1258
HSA-MIR-1207-5P	99.49	69.11	2983
HSA-MIR-4688	99.48	64.68	828
HSA-MIR-6743-5P	99.48	63.60	721
HSA-MIR-6722-3P	99.45	67.62	1919
HSA-MIR-183-5P	99.31	72.27	1164
HSA-MIR-5589-3P	99.29	68.30	1443

Functional genomics

gnomAD constraint: pLI 0.993, LOEUF 0.473, missense Z 1.86 — population loss-of-function intolerance (pLI ≥ 0.9 = LoF-intolerant; lower LOEUF = more constrained). gnomAD

Regional missense constraint (gnomAD RMC): no regional variation along ENST00000688289 — one region, missense o/e 0.78.

Cross-species orthologs

13 orthologs

Organism	Symbol	Gene ID
danio_rerio	plppr2b	ENSDARG00000044600
danio_rerio	plppr2a	ENSDARG00000101478
mus_musculus	Plppr2	ENSMUSG00000040563
rattus_norvegicus	Plppr2	ENSRNOG00000012164
drosophila_melanogaster	wun	FBGN0016078
drosophila_melanogaster	laza	FBGN0037163
drosophila_melanogaster	CG11438	FBGN0037164
drosophila_melanogaster	CG11437	FBGN0037165
drosophila_melanogaster	CG11426	FBGN0037166
drosophila_melanogaster	CG11425	FBGN0037167
drosophila_melanogaster	CG12746	FBGN0037341
drosophila_melanogaster	wun2	FBGN0041087
caenorhabditis_elegans		WBGENE00018756

Paralogs (9): PLPP1 (ENSG00000067113), PLPPR5 (ENSG00000117598), PLPPR4 (ENSG00000117600), PLPPR3 (ENSG00000129951), PLPP2 (ENSG00000141934), PLPP5 (ENSG00000147535), PLPPR1 (ENSG00000148123), PLPP3 (ENSG00000162407), PLPP4 (ENSG00000203805)

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
Xenopus tropicalis	A4II83	88.6%	Diamond
Xenopus laevis	Q6GM05	84.8%	Diamond
Bos taurus	Q29RT8	78.2%	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
CCDC159	protein-coding	126075
EPOR	protein-coding	2057
RGL3	protein-coding	57139
SWSAP1	protein-coding	126074
TSPAN16	protein-coding	26526
TMEM205	protein-coding	374882
RAB3D	protein-coding	9545
TSPAN16-AS1	ncRNA	105372274
ODAD3	protein-coding	115948
PRKCSH	protein-coding	5589

Protein

Protein identifiers

Phospholipid phosphatase-related protein type 2 — Q96GM1 (reviewed: Q96GM1)

Alternative names: Inactive phospholipid phosphatase PLPPR2, Lipid phosphate phosphatase-related protein type 2, Plasticity-related gene 4 protein

All UniProt accessions (4): A0A8I5KWF3, K7EMX8, K7EQF7, Q96GM1

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Membrane.

Similarity. Belongs to the PA-phosphatase related phosphoesterase family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q96GM1-1	1	yes
Q96GM1-2	2

RefSeq proteins (7): NP_001164106, NP_001380821, NP_001380822, NP_001380823, NP_001380824, NP_001380825, NP_073574 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000326	PAP2/HPO	Domain
IPR036938	PAP2/HPO_sf	Homologous_superfamily
IPR043216	PAP-like	Family

Pfam: PF01569

Enzyme classification (BRENDA)

• EC 3.1.3.4 — phosphatidate phosphatase (BRENDA: 31 organisms, 190 substrates, 196 inhibitors, 44 Km, 3 kcat entries)

Substrate kinetics (BRENDA)

10 substrates with measured Km, best-characterized 10. Km ranges are aggregated across organisms/conditions.

Substrate	Km (mM)	Measurements
PHOSPHATIDIC ACID	0.0054–1.2	17
LYSOPHOSPHATIDATE	0.046–0.179	3
PHOSPHATIDATE	0.284–0.369	3
SPHINGOSINE-1-PHOSPHATE	0.028–0.26	3
CERAMIDE-1-PHOSPHATE	0.022–0.052	2
DIACYLGLYCEROL DIPHOSPHATE	0.041–0.104	2
LYSOPHOSPHATIDIC ACID	0.295–0.58	2
1,2-DIACYL-SN-GLYCEROL-3-PHOSPHATE	0.5954	1
2-(4,4-DIFLUORO-5,7-DIMETHYL-4-BORA-3A,4A-DIAZA-	0.024	1
DIOCTANOYL PHOSPHATIDIC ACID	1.4	1

UniProt features (17 total): transmembrane region 6, modified residue 2, splice variant 2, sequence conflict 2, chain 1, glycosylation site 1, sequence variant 1, region of interest 1, compositionally biased region 1

Structure

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q96GM1-F1	79.10	0.49

Human Protein Atlas

Protein class: Metabolic proteins, Predicted membrane proteins, Predicted intracellular proteins

Protein evidence: Evidence at protein level

Subcellular location (HPA, imaging): nucleoplasm

Antibody reliability (HPA): IH approved · IF uncertain

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 (2)

Type	Positions
Phosphoserine	312, 299

Glycosylation sites (1)

Type	Positions
N-linked (glcnac…) asparagine	165

Function

Pathways and Gene Ontology

Reactome pathways

1 curated (TAS) of 5; 0 disease pathways. Curated-first; evidence = TAS (manually curated) vs IEA (electronic inference).

5 pathways:

ID	Pathway	Evidence
R-HSA-419408	Lysosphingolipid and LPA receptors	curated
R-HSA-373076	Class A/1 (Rhodopsin-like receptors)	—
R-HSA-500792	GPCR ligand binding	—
R-HSA-162582	Signal Transduction	—
R-HSA-372790	Signaling by GPCR	—

MSigDB gene sets: 123 (showing top): GOBP_LIPID_MODIFICATION, GOBP_PHOSPHOLIPID_METABOLIC_PROCESS, GOBP_PHOSPHOLIPID_DEPHOSPHORYLATION, GOBP_ORGANOPHOSPHATE_METABOLIC_PROCESS, TGACCTY_ERR1_Q2, SHEDDEN_LUNG_CANCER_GOOD_SURVIVAL_A5, GOBP_LIPID_METABOLIC_PROCESS, HELLER_HDAC_TARGETS_SILENCED_BY_METHYLATION_UP, HFH1_01, GOBP_DEPHOSPHORYLATION, DOUGLAS_BMI1_TARGETS_UP, OCT1_B, SAGIV_CD24_TARGETS_DN, LEIN_LOCALIZED_TO_PROXIMAL_DENDRITES, CTGAGCC_MIR24

GO Biological Process (3): phospholipid metabolic process (GO:0006644), signal transduction (GO:0007165), phospholipid dephosphorylation (GO:0046839)

GO Molecular Function (2): phosphatidate phosphatase activity (GO:0008195), protein binding (GO:0005515)

GO Cellular Component (2): plasma membrane (GO:0005886), membrane (GO:0016020)

Reactome top-level categories

4 top-level categories:

Category	Pathways
Class A/1 (Rhodopsin-like receptors)	1
Signal Transduction	1
GPCR ligand binding	1
Signaling by GPCR	1

GO top-level categories

14 GO namespaces:

Category	Terms
lipid metabolic process	1
organophosphate metabolic process	1
cell communication	1
cellular process	1
signaling	1
regulation of cellular process	1
cellular response to stimulus	1
dephosphorylation	1
lipid modification	1
lipid phosphatase activity	1
binding	1
membrane	1
cell periphery	1
cellular anatomical structure	1

Protein interactions and networks

STRING

showing 15 of 846 interactions by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
PLPPR2	DGAT2L6	Q6ZPD8	426
PLPPR2	PLPP6	Q8IY26	399
PLPPR2	SWSAP1	Q6NVH7	385
PLPPR2	ORMDL2	Q53FV1	384
PLPPR2	MBOAT2	Q6ZWT7	383
PLPPR2	CCDC159	P0C7I6	379
PLPPR2	INPP5A	Q14642	369
PLPPR2	CHKB	Q9Y259	352
PLPPR2	TMEM51	Q9NW97	350
PLPPR2	E5RHQ9	E5RHQ9	346
PLPPR2	DOLPP1	Q86YN1	343
PLPPR2	SPTSSB	Q8NFR3	332
PLPPR2	PLCD4	Q9BRC7	330
PLPPR2	GSG1L	Q6UXU4	330
PLPPR2	GPAT2	Q6NUI2	326

IntAct

Human interaction partners of PLPPR2 in IntAct, one row per partner (best MIscore; records = supporting IntAct interaction records).

24 partners by confidence:

Partner	Interaction type	MIscore	Records
ARL13B	physical association	0.560	3
CD79A	physical association	0.560	3
CIAO2A	physical association	0.560	3
CISD2	physical association	0.560	3
CLDN5	physical association	0.560	3
CLDN9	physical association	0.560	3
CREB3L1	physical association	0.560	3
GYPC	physical association	0.560	3
KIR2DL3	physical association	0.560	3
LYPD5	physical association	0.560	3
MARCHF2	physical association	0.560	3
SCN3B	physical association	0.560	3
SIGLEC12	physical association	0.560	3
SLC19A3	physical association	0.560	3
SMAGP	physical association	0.560	3
SSMEM1	physical association	0.560	3
STX12	physical association	0.560	3
TMED9	physical association	0.560	3
TMEM237	physical association	0.560	3
UBE2J1	physical association	0.560	3
VSIR	physical association	0.560	3
METAP2	association	0.530	2
BCL2L1	association	0.350	1
SEC24D	association	0.350	1

Disease & clinical

Genetic variants

Variant evidence for PLPPR2: 64 ClinVar records (0 pathogenic / likely pathogenic).

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	51
Likely benign	6
Benign	0

SpliceAI

Top 10 splice-impact sites by Δscore (adjacent positions with the same effect merged into one range; 28 predictions of 1,119):

Position(s)	Effect	Δscore	Sites
19:11359505	acceptor_gain	1.0000
19:11359519	acceptor_gain	1.0000
19:11359721–11359722	donor_loss	1.0000	5
19:11362690–11362691	donor_loss	1.0000	5
19:11363711–11363712	acceptor_loss	1.0000	6
19:11363821	donor_gain	1.0000
19:11355573–11355574	donor_loss	0.9900	6
19:11359500	acceptor_gain	0.9900
19:11359513	acceptor_gain	0.9900
19:11359518	acceptor_gain	0.9900

AlphaMissense

800 missense substitutions predicted likely pathogenic (of 2,845 scored), across 210 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
F158	8	0.974	0.999
F205	8	0.974	0.996
D265	8	0.972	0.993
F288	8	0.964	0.995
F135	8	0.934	0.989
F49	8	0.927	0.995
F143	8	0.921	0.975
F279	8	0.912	0.989
F42	8	0.902	0.985
F18	8	0.841	0.957
D53	8	0.799	0.959
H262	8	0.777	0.883
C162	7	0.991	0.996
C51	7	0.987	0.995
C191	7	0.968	0.985
F129	7	0.952	0.989
F184	7	0.948	0.985
C171	7	0.947	0.976
E90	7	0.922	0.966
F270	7	0.915	0.969

HPA cancer prognostics

RNA cancer specificity: Low cancer specificity

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

1 prognostic cancer types:

Cancer	Prognostic	p-value
Kidney Chromophobe (TCGA)	unfavorable	2.92e-06

Disease associations

OMIM: gene MIM:619591 | disease phenotypes:

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (CPIC guideline: no)

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	decreases expression, affects cotreatment, increases abundance, increases expression	3
bisphenol A	affects cotreatment, increases methylation, increases expression	2
Arsenic	increases abundance, increases expression, decreases expression, affects cotreatment	2
Valproic Acid	increases expression, increases methylation	2
aristolochic acid I	increases expression	1
bisphenol F	affects cotreatment, increases expression	1
triphenyl phosphate	affects expression	1
o,p’-DDT	increases expression	1
manganese chloride	affects cotreatment, increases abundance, increases expression	1
benzo(e)pyrene	increases methylation	1
aflatoxin B2	increases methylation	1
di-n-butylphosphoric acid	affects expression	1
(+)-JQ1 compound	increases expression	1
4-(4-((5-(4,5-dimethyl-2-nitrophenyl)-2-furanyl)methylene)-4,5-dihydro-3-methyl-5-oxo-1H-pyrazol-1-yl)benzoic acid	decreases expression	1
Resveratrol	increases expression	1
Sunitinib	decreases expression	1
Fulvestrant	affects cotreatment, increases methylation	1
Acetaminophen	increases expression	1
Air Pollutants	affects expression, increases abundance	1
Atrazine	increases expression	1
Dexamethasone	affects cotreatment, increases expression	1
Diazinon	increases methylation	1
Doxorubicin	decreases expression	1
Indomethacin	affects cotreatment, increases expression	1
Manganese	affects cotreatment, increases abundance, increases expression	1
Methapyrilene	increases methylation	1
Ozone	affects expression, increases abundance	1
Smoke	decreases expression	1
Tobacco Smoke Pollution	decreases expression	1
Urethane	increases expression	1

Clinical trials (associated diseases)

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