PPP1CB

gene
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Also known as PP1CbetaPPP1CDPP1CdeltaPP1BPP-1BPP1betaPP1cMPPPP1beta

Summary

PPP1CB (protein phosphatase 1 catalytic subunit beta, HGNC:9282) is a protein-coding gene on chromosome 2p23.2, encoding Serine/threonine-protein phosphatase PP1-beta catalytic subunit (P62140). Protein phosphatase that associates with over 200 regulatory proteins to form highly specific holoenzymes which dephosphorylate hundreds of biological targets. It is a selective cancer dependency (DepMap: 89.6% of cell lines).

The protein encoded by this gene is one of the three catalytic subunits of protein phosphatase 1 (PP1). PP1 is a serine/threonine specific protein phosphatase known to be involved in the regulation of a variety of cellular processes, such as cell division, glycogen metabolism, muscle contractility, protein synthesis, and HIV-1 viral transcription. Mouse studies suggest that PP1 functions as a suppressor of learning and memory. Two alternatively spliced transcript variants encoding distinct isoforms have been observed.

Source: NCBI Gene 5500 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): Noonan syndrome-like disorder with loose anagen hair (Definitive, ClinGen) — +1 more curated relationship
  • GWAS associations: 8
  • Clinical variants (ClinVar): 366 total — 4 pathogenic, 8 likely-pathogenic
  • Phenotypes (HPO): 99
  • Druggable target: yes
  • Cancer dependency (DepMap): dependent in 89.6% of screened cell lines
  • Dosage sensitivity (ClinGen): haploinsufficiency no evidence, triplosensitivity no evidence
  • MANE Select transcript: NM_002709

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:9282
Approved symbolPPP1CB
Nameprotein phosphatase 1 catalytic subunit beta
Location2p23.2
Locus typegene with protein product
StatusApproved
AliasesPP1Cbeta, PPP1CD, PP1Cdelta, PP1B, PP-1B, PP1beta, PP1c, MP, PPP1beta
Ensembl geneENSG00000213639
Ensembl biotypeprotein_coding
OMIM600590
Entrez5500

Gene structure

Transcript identifiers

Ensembl transcripts: 34 — 28 protein_coding, 3 nonsense_mediated_decay, 2 protein_coding_CDS_not_defined, 1 retained_intron

ENST00000296122, ENST00000395366, ENST00000418910, ENST00000420282, ENST00000427786, ENST00000441461, ENST00000455580, ENST00000464273, ENST00000703171, ENST00000703172, ENST00000703173, ENST00000703174, ENST00000703175, ENST00000703176, ENST00000703177, ENST00000703183, ENST00000868409, ENST00000868410, ENST00000868411, ENST00000868412, ENST00000868413, ENST00000868414, ENST00000930106, ENST00000941104, ENST00000941105, ENST00000941106, ENST00000941107, ENST00000941108, ENST00000941109, ENST00000941110, ENST00000941111, ENST00000941112, ENST00000941113, ENST00000941114

RefSeq mRNA: 2 — MANE Select: NM_002709 NM_002709, NM_206876

CCDS: CCDS33169

Canonical transcript exons

ENST00000395366 — 8 exons

ExonStartEnd
ENSE000016231452878173828781842
ENSE000019069032879919928802940
ENSE000019323802875183028752176
ENSE000035126782877685128776982
ENSE000037866962878390728783978
ENSE000037897462877880928779039
ENSE000039882422878865828788809
ENSE000039882572879386328793997

Expression profiles

Bgee: expression breadth ubiquitous, 295 present calls, max score 99.17.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 77.1754 / max 868.3864, expressed in 1825 samples.

FANTOM5 promoters (10 alternative TSS)

Promoter IDTPM avgSamples expressed
1948545.85001796
1948232.54631810
1948430.18791812
194814.47241598
194804.08471495
194772.23401020
194781.3363797
194791.0931655
194870.6681337
194830.5526313

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
calcaneal tendonUBERON:000370199.17gold quality
amniotic fluidUBERON:000017399.11gold quality
buccal mucosa cellCL:000233699.10gold quality
ventricular zoneUBERON:000305399.03gold quality
descending thoracic aortaUBERON:000234598.98gold quality
tendonUBERON:000004398.91gold quality
lower esophagusUBERON:001347398.91gold quality
lower esophagus muscularis layerUBERON:003583398.91gold quality
popliteal arteryUBERON:000225098.90gold quality
tibial arteryUBERON:000761098.90gold quality
aortaUBERON:000094798.83gold quality
arteryUBERON:000163798.82gold quality
thoracic aortaUBERON:000151598.74gold quality
ascending aortaUBERON:000149698.73gold quality
ganglionic eminenceUBERON:000402398.73gold quality
caput epididymisUBERON:000435898.73gold quality
esophagogastric junction muscularis propriaUBERON:003584198.72gold quality
choroid plexus epitheliumUBERON:000391198.71gold quality
hindlimb stylopod muscleUBERON:000425298.67gold quality
mucosa of stomachUBERON:000119998.65gold quality
skeletal muscle tissue of rectus abdominisUBERON:000451198.61gold quality
parotid glandUBERON:000183198.60gold quality
muscle of legUBERON:000138398.58gold quality
cauda epididymisUBERON:000436098.56gold quality
gastrocnemiusUBERON:000138898.55gold quality
blood vessel layerUBERON:000479798.51gold quality
mucosa of paranasal sinusUBERON:000503098.51gold quality
left coronary arteryUBERON:000162698.45gold quality
esophagusUBERON:000104398.44gold quality
skeletal muscle organUBERON:001489298.44gold quality

Single-cell (SCXA)

Detected in 13 experiment(s), a significant marker in 7.

ExperimentMarker?Max mean expression
E-MTAB-8498yes14099.04
E-GEOD-111727yes6032.78
E-MTAB-10287yes44.11
E-GEOD-135922yes26.94
E-GEOD-134144yes11.19
E-HCAD-9yes5.45
E-CURD-97no11764.67
E-CURD-6no10867.14
E-GEOD-76312no7474.83
E-CURD-89no2696.07
E-MTAB-9154no627.41
E-MTAB-6524no307.68
E-ANND-3no0.00

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): GLI2, TEAD4

miRNA regulators (miRDB)

165 targeting PPP1CB, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-340-5P100.0072.504437
HSA-MIR-190A-3P100.0080.355520
HSA-MIR-4668-3P100.0068.742635
HSA-MIR-656-3P100.0072.152788
HSA-MIR-3613-3P100.0076.367965
HSA-MIR-429100.0073.442698
HSA-MIR-200B-3P100.0073.312693
HSA-MIR-200C-3P100.0073.352685
HSA-MIR-3646100.0073.565283
HSA-MIR-4776-3P100.0068.731340
HSA-MIR-1193100.0065.93529
HSA-MIR-4262100.0073.263931
HSA-MIR-548C-3P99.9974.017587
HSA-MIR-428299.9975.366408
HSA-MIR-371B-5P99.9975.344759
HSA-MIR-181A-5P99.9972.962995
HSA-MIR-181B-5P99.9972.972996
HSA-MIR-181C-5P99.9972.952996
HSA-MIR-181D-5P99.9973.042997
HSA-MIR-186-5P99.9970.833707
HSA-MIR-196A-1-3P99.9972.152772
HSA-MIR-4482-3P99.9872.503147
HSA-MIR-373-5P99.9875.364753
HSA-MIR-616-5P99.9875.584775
HSA-MIR-569699.9872.364487
HSA-MIR-520D-5P99.9873.344883
HSA-MIR-524-5P99.9873.434882
HSA-MIR-1185-1-3P99.9871.042593
HSA-MIR-1185-2-3P99.9871.042593
HSA-MIR-314899.9775.066478

Functional genomics

ClinGen dosage: haploinsufficiency 0 (no evidence), triplosensitivity 0 (no evidence). ClinGen Gene Dosage Map DepMap (CRISPR cell-line fitness): dependent in 89.6% of screened cell lines.

Literature-anchored findings (GeneRIF, showing 31)

  • In this study, we show that protein phosphatase-1 (PP1) inhibitor-3 (Inh3) is localized to the nucleoli and centrosomes in interphase HEK 293 cells. (PMID:16256067)
  • R16A at the membrane may mediate the PB signal to initiate CAR nuclear translocation, through a mechanism including its dimerization and inhibition of PP1beta activity. (PMID:18202305)
  • PP-1 ( PP-1alpha or PP-1beta ) acts as a major phosphatase to dephosphorylate AKT1 at Thr-450 and thus modulate its functions in regulating gene expression, cell survival and differentiation. (PMID:20186153)
  • mammalian Wdr82 functions in a variety of cellular processes; PTW/PP1 phosphatase complex (PNUTS, Tox4, Wdr82, PP1) has a role in the regulation of chromatin structure during the transition from mitosis into interphase (PMID:20516061)
  • serine/threonine protein phosphatase PP1beta is a physiological Nucleophosmin (NPM) phosphatase under both the genotoxic stress and growth conditions. (PMID:20962268)
  • Data suggest that double-thiophosphorylation of TIMAP has minor effect on its binding ability to PP1c, but considerably attenuates its inhibitory effect on the activity of PP1c. (PMID:21466834)
  • PPP1CB is over expressed in malignant melanoma. (PMID:21566537)
  • Protein phosphatase 1beta (PP1beta) is identified as a phosphatase for the cluster of phosphorylated threonines ((353)TTETQRT(359)) within the sst(2A) somatostatin receptor carboxyl terminus that mediates beta-arrestin binding using siRNA knock-down screening. (PMID:21795688)
  • Studies suggest that any change in substrate specificity of the spinophilin : PP1 holoenzyme complex was probably due to direct modification of a PP1 substrate binding surface. (PMID:22284538)
  • Studies indicate that the Ser/Thr phosphatases PP1 and PP2A are responsible for the dephosphorylation and activation of Rb proteins. (PMID:22299668)
  • Studies indicate that the diversity of the PP1 interactome and the properties of the PP1 binding code account for the exquisite specificity of PP1 in vivo. (PMID:22360570)
  • These findings provide evidence for the involvement of a particular PP1 complex, PPP1R12A/PP1cdelta, in insulin signaling. (PMID:22728334)
  • Interaction between protein phosphatase 1 beta and myosin phosphatase (MYPT)1 results in exclusion of Nkx2.5 from the cell nucleus. (PMID:23168335)
  • PPP1C isoforms have distinct contribution to the outside-in alphaIIbbeta3 signalling-dependent functions in HEK293 alphaIIbbeta3 cells. (PMID:23197154)
  • results indicate that SCN-iPS cells provide a useful disease model for SCN, and the activation of the Wnt3a/beta-catenin pathway may offer a novel therapy for SCN with ELANE mutation (PMID:23382248)
  • Findings show that PP1cbeta plays a role in endothelial cell migration through a mechanism involving the interplay of actin cytoskeleton proteins and focal adhesion molecules signaling. (PMID:25967976)
  • These results suggest a unique functional role for the PP1beta isoform in affecting cardiac contractile function (PMID:26334248)
  • Missense mutations in PPP1CB are associated with a phenotype resembling NS-LAH. Based on this phenotype and PPP1CB’s known role within the RAS/MAPK pathway, we think that this condition is a novel rasopathy, which may be provisionally termed “PPP1CB-related Noonan syndrome with loose anagen hair” (P-NS-LAH). (PMID:27264673)
  • this study shows a pivotal role for PP1 in impeding IRF7-mediated IFN-alpha production in host immune responses (PMID:27469204)
  • Our data suggest that our heterozygous de novo PPP1CB pathogenic variants are associated with syndromic intellectual disability. (PMID:27681385)
  • This report gives further support that this novel RASopathy-PPP1CB-related Noonan syndrome with loose anagen hair-shares great similarity to Noonan syndrome-like disorder with loose anagen hair, and expands the phenotypic spectrum by adding the cranial vault abnormality. (PMID:28211982)
  • PPP1CB mutation is associated with Noonan syndrome. (PMID:30368668)
  • Activating MRAS mutations cause Noonan syndrome associated with hypertrophic cardiomyopathy. (PMID:31108500)
  • The association of MYPT1 with PP1cbeta was profoundly reduced in the presence of excess TIMAP, leading to proteasomal MYPT1 degradation. (PMID:31315927)
  • our experiments support that PPP1CB and KPC2 together inhibit the activity of HOXA2 by activating its nuclear export, but favored HOXA2 de-ubiquitination and stabilization thereby establishing a store of HOXA2 in the cytoplasm. (PMID:31323436)
  • Integrative genomics analysis of eQTL and GWAS summary data identifies PPP1CB as a novel bone mineral density risk genes. (PMID:32266926)
  • A case report of Noonan syndrome-like disorder with loose anagen hair 2 treated with recombinant human growth hormone. (PMID:32476286)
  • Noonan syndrome with loose anagen hair with variants in the PPP1CB gene: First familial case reported. (PMID:33491856)
  • The expression and clinical prognostic value of protein phosphatase 1 catalytic subunit beta in pancreatic cancer. (PMID:34125004)
  • PP-1beta and PP-2Aalpha modulate cAMP response element-binding protein (CREB) functions in aging control and stress response through de-regulation of alphaB-crystallin gene and p300-p53 signaling axis. (PMID:34425033)
  • Histones Methyltransferase NSD3 Inhibits Lung Adenocarcinoma Glycolysis Through Interacting with PPP1CB to Decrease STAT3 Signaling Pathway. (PMID:39119928)

Cross-species orthologs

8 orthologs

OrganismSymbolGene ID
danio_rerioppp1cbENSDARG00000044153
danio_rerioppp1cblENSDARG00000102012
mus_musculusPpp1cbENSMUSG00000014956
rattus_norvegicusPpp1cbENSRNOG00000004612
rattus_norvegicusENSRNOG00000069573
rattus_norvegicusENSRNOG00000084581
drosophila_melanogasterflwFBGN0000711
caenorhabditis_elegansWBGENE00001747

Paralogs (12): PPP5C (ENSG00000011485), PPEF1 (ENSG00000086717), PPP2CB (ENSG00000104695), PPP3CB (ENSG00000107758), PPP2CA (ENSG00000113575), PPP6C (ENSG00000119414), PPP3CC (ENSG00000120910), PPP3CA (ENSG00000138814), PPP4C (ENSG00000149923), PPEF2 (ENSG00000156194), PPP1CA (ENSG00000172531), PPP1CC (ENSG00000186298)

Protein

Protein identifiers

Serine/threonine-protein phosphatase PP1-beta catalytic subunitP62140 (reviewed: P62140)

All UniProt accessions (10): A0A8V8TQ71, A0A8V8TR83, A0A8V8TRH9, B4DJ75, C9J9S3, C9JP48, P62140, F8WE71, H0Y3Y6, V9HW04

UniProt curated annotations — full annotation on UniProt →

Function. Protein phosphatase that associates with over 200 regulatory proteins to form highly specific holoenzymes which dephosphorylate hundreds of biological targets. Protein phosphatase (PP1) is essential for cell division, it participates in the regulation of glycogen metabolism, muscle contractility and protein synthesis. Involved in regulation of ionic conductances and long-term synaptic plasticity. Component of the PTW/PP1 phosphatase complex, which plays a role in the control of chromatin structure and cell cycle progression during the transition from mitosis into interphase. In balance with CSNK1D and CSNK1E, determines the circadian period length, through the regulation of the speed and rhythmicity of PER1 and PER2 phosphorylation. May dephosphorylate CSNK1D and CSNK1E. Dephosphorylates the ‘Ser-418’ residue of FOXP3 in regulatory T-cells (Treg) from patients with rheumatoid arthritis, thereby inactivating FOXP3 and rendering Treg cells functionally defective. Core component of the SHOC2-MRAS-PP1c (SMP) holophosphatase complex that regulates the MAPK pathway activation. The SMP complex specifically dephosphorylates the inhibitory phosphorylation at ‘Ser-259’ of RAF1 kinase, ‘Ser-365’ of BRAF kinase and ‘Ser-214’ of ARAF kinase, stimulating their kinase activities. The SMP complex enhances the dephosphorylation activity and substrate specificity of PP1c.

Subunit / interactions. PP1 comprises a catalytic subunit, PPP1CA, PPP1CB or PPP1CC, which is folded into its native form by inhibitor 2 and glycogen synthetase kinase 3, and then complexed to one or several targeting or regulatory subunits. The targeting or regulatory subunits determine the substrate specificity of PP1. PPP1R12A, PPP1R12B and PPP1R12C mediate binding to myosin. PPP1R3A (in skeletal muscle), PPP1R3B (in liver), PPP1R3C, PPP1R3D and PPP1R3F (in brain) mediate binding to glycogen. Part of a complex containing PPP1R15B, PP1 and NCK1/2. Interacts with PPP1R7 and PPP1R12C. PPP1R15A and PPP1R15B mediate binding to EIF2S1. Interacts with PPP1R16B. Component of the PTW/PP1 phosphatase complex, composed of PPP1R10/PNUTS, TOX4, WDR82, and PPP1CA or PPP1CB or PPP1CC. Interacts with PPP1R8. Interacts with TRIM28; the interaction is weak. Interacts with PPP1R12A and NUAK1; the interaction is direct. Interacts with FOXP3. Interacts with RRP1B. Interacts with SERPINE1. Interacts with LZTR1. Component of the SHOC2-MRAS-PP1c (SMP) complex consisting of SHOC2, GTP-bound M-Ras/MRAS and the catalytic subunit of protein phosphatase 1 (either PPP1CA, PPP1CB or PPP1CC). SHOC2 and PP1c preferably bind M-Ras/MRAS, but they also bind K-Ras/KRAS, N-Ras/NRAS and H-Ras/HRAS; these interactions are GTP-dependent and both SHOC2 and PP1c are required to form a stable complex. Interacts with SHOC2 in the absence of Ras GTPases.

Subcellular location. Cytoplasm. Nucleus. Nucleoplasm. Nucleolus.

Disease relevance. Noonan syndrome-like disorder with loose anagen hair 2 (NSLH2) [MIM:617506] A syndrome characterized by Noonan dysmorphic features such as macrocephaly, high forehead, hypertelorism, palpebral ptosis, low-set and posteriorly rotated ears, short and webbed neck, pectus anomalies, in association with pluckable, sparse, thin and slow-growing hair. The disease is caused by variants affecting the gene represented in this entry.

Activity regulation. Inhibited by the toxins okadaic acid, tautomycin and microcystin Leu-Arg. The phosphatase activity of the PPP1R15A-PP1 complex toward EIF2S1 is specifically inhibited by Salubrinal, a drug that protects cells from endoplasmic reticulum stress.

Cofactor. Binds 2 manganese ions per subunit.

Induction. Up-regulated in synovial fluid mononuclear cells and peripheral blood mononuclear cells from patients with rheumatoid arthritis.

Similarity. Belongs to the PPP phosphatase family. PP-1 subfamily.

RefSeq proteins (2): NP_002700, NP_996759 (=MANE)

Domains & families (InterPro)

IDNameType
IPR004843Calcineurin-like_PHPDomain
IPR006186Ser/Thr-sp_prot-phosphataseDomain
IPR029052Metallo-depent_PP-likeHomologous_superfamily
IPR031675STPPase_NDomain
IPR050341PP1_catalytic_subunitFamily

Pfam: PF00149, PF16891

Enzyme classification (BRENDA):

  • EC 3.1.3.16 — protein-serine/threonine phosphatase (BRENDA: 92 organisms, 641 substrates, 468 inhibitors, 127 Km, 67 kcat entries)

Substrate kinetics (BRENDA)

59 substrates with measured Km, best-characterized 15. Km ranges are aggregated across organisms/conditions.

SubstrateKm (mM)Measurements
6,8-DIFLUORO-4-METHYLUMBELLIFERYL PHOSPHATE0.023–0.86222
4-NITROPHENYL PHOSPHATE0.0028–12.713
P-NITROPHENYL PHOSPHATE3–20011
RRAPTVA0.058–1.9544
PHOSPHOCASEIN0.0001–0.0023
PHOSPHOHISTONE0.0023–0.07233
PHOSPHORYLATED MYOSIN LIGHT CHAIN PEPTIDE0.01–0.113
PHOSPHOSERINE-MYELIN BASIC PROTEIN0.0004–0.0223
DLDVPIPGRFDRRVSVAAE0.0006–0.01382
DLDVPIPGRFDRRVY(P)VAAE0.0025–0.0232
PHOSPHORYLASE A0.004–0.0212
RRA(PT)VA0.0536–0.3082
80S-RIBOSOME0.00271
AAAPTVA0.2061
AGPALSPVPPV0.3571

Catalyzed reactions (Rhea), 4 shown:

  • O-phospho-L-seryl-[myosin light chain] + H2O = L-seryl-[myosin light chain] + phosphate (RHEA:12849)
  • O-phospho-L-seryl-[protein] + H2O = L-seryl-[protein] + phosphate (RHEA:20629)
  • O-phospho-L-threonyl-[protein] + H2O = L-threonyl-[protein] + phosphate (RHEA:47004)
  • O-phospho-L-threonyl-[myosin light chain] + H2O = L-threonyl-[myosin light chain] + phosphate (RHEA:53988)

UniProt features (20 total): binding site 7, sequence variant 6, modified residue 2, initiator methionine 1, chain 1, sequence conflict 1, region of interest 1, active site 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-P62140-F191.910.87

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Catalytic / active sites (1): 124 (proton donor)

Ligand- & substrate-binding residues (7): 247; 63; 65; 91; 91; 123; 172

Post-translational modifications (2): 2, 316

Function

Pathways and Gene Ontology

Reactome pathways

13 pathways

IDPathway
R-HSA-163560Triglyceride catabolism
R-HSA-2173788Downregulation of TGF-beta receptor signaling
R-HSA-2565942Regulation of PLK1 Activity at G2/M Transition
R-HSA-5625740RHO GTPases activate PKNs
R-HSA-5625900RHO GTPases activate CIT
R-HSA-5627117RHO GTPases Activate ROCKs
R-HSA-5627123RHO GTPases activate PAKs
R-HSA-5673000RAF activation
R-HSA-9726840SHOC2 M1731 mutant abolishes MRAS complex function
R-HSA-9726842Gain-of-function MRAS complexes activate RAF signaling
R-HSA-9770562mRNA Polyadenylation
R-HSA-9828806Maturation of hRSV A proteins
R-HSA-9931530Phosphorylation and nuclear translocation of the CRY:PER:kinase complex

MSigDB gene sets: 522 (showing top): GOBP_CIRCADIAN_RHYTHM, REACTOME_TRIGLYCERIDE_CATABOLISM, BERENJENO_ROCK_SIGNALING_NOT_VIA_RHOA_DN, MOOTHA_GLYCOGEN_METABOLISM, REACTOME_SIGNALING_BY_TGF_BETA_RECEPTOR_COMPLEX, HNF3ALPHA_Q6, MODULE_255, GOBP_PHOTOPERIODISM, TTTGTAG_MIR520D, YANG_BREAST_CANCER_ESR1_LASER_DN, GOBP_REGULATION_OF_SMALL_GTPASE_MEDIATED_SIGNAL_TRANSDUCTION, TGACCTY_ERR1_Q2, GOBP_CIRCADIAN_REGULATION_OF_GENE_EXPRESSION, HNF1_Q6, FOXO1_01

GO Biological Process (9): MAPK cascade (GO:0000165), glycogen metabolic process (GO:0005977), protein dephosphorylation (GO:0006470), regulation of cell adhesion (GO:0030155), circadian regulation of gene expression (GO:0032922), regulation of circadian rhythm (GO:0042752), entrainment of circadian clock by photoperiod (GO:0043153), cell division (GO:0051301), rhythmic process (GO:0048511)

GO Molecular Function (9): protein serine/threonine phosphatase activity (GO:0004722), phosphatase activity (GO:0016791), myosin phosphatase activity (GO:0017018), protein kinase binding (GO:0019901), metal ion binding (GO:0046872), myosin-light-chain-phosphatase activity (GO:0050115), phosphoprotein phosphatase activity (GO:0004721), protein binding (GO:0005515), hydrolase activity (GO:0016787)

GO Cellular Component (9): nucleus (GO:0005634), nucleoplasm (GO:0005654), nucleolus (GO:0005730), cytoplasm (GO:0005737), cytosol (GO:0005829), focal adhesion (GO:0005925), extracellular exosome (GO:0070062), PTW/PP1 phosphatase complex (GO:0072357), chromosome, telomeric region (GO:0000781)

Reactome top-level categories

Rollup of top-9 pathways:

CategoryPathways
RHO GTPase Effectors4
Signaling by MRAS-complex mutants2
Triglyceride metabolism1
TGF-beta receptor signaling activates SMADs1
G2/M Transition1
RAF/MAP kinase cascade1
mRNA 3’-end processing1
Respiratory syncytial virus (RSV) genome replication, transcription and translation1
Circadian clock1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure3
circadian rhythm2
phosphoprotein phosphatase activity2
nuclear lumen2
intracellular signaling cassette1
energy reserve metabolic process1
glucan metabolic process1
dephosphorylation1
protein modification process1
cell adhesion1
regulation of cellular process1
regulation of gene expression1
regulation of biological process1
photoperiodism1
entrainment of circadian clock1
cellular process1
biological_process1
phosphoric ester hydrolase activity1
protein serine/threonine phosphatase activity1
kinase binding1
cation binding1
phosphatase activity1
catalytic activity, acting on a protein1
binding1
catalytic activity1
intracellular membrane-bounded organelle1
intracellular membraneless organelle1
intracellular anatomical structure1
cytoplasm1
cell-substrate junction1
extracellular vesicle1
protein phosphatase type 1 complex1
chromosomal region1

Protein interactions and networks

STRING

0 interactions, top by confidence (×1000):

IntAct

332 interactions, top by confidence:

ABTypeScore
PPP1CBSH2D4Apsi-mi:“MI:0915”(physical association)0.960
SH2D4APPP1CBpsi-mi:“MI:0915”(physical association)0.960
PPP1CBPPP1R7psi-mi:“MI:0915”(physical association)0.930
PPP1R11PPP1CBpsi-mi:“MI:0915”(physical association)0.920
PPP1R16APPP1CBpsi-mi:“MI:0915”(physical association)0.830
PPP1CBPPP1R16Apsi-mi:“MI:0915”(physical association)0.830
PPP1CBPPP1R16Bpsi-mi:“MI:0915”(physical association)0.790
PPP1R16BPPP1CBpsi-mi:“MI:0915”(physical association)0.790
PPP1CBPPP1R3Cpsi-mi:“MI:0915”(physical association)0.780
PPP1R3CPPP1CBpsi-mi:“MI:0915”(physical association)0.780
PPP1CBCCDC85Cpsi-mi:“MI:0914”(association)0.750
PPP1CBCCDC85Cpsi-mi:“MI:2364”(proximity)0.750
CSRNP2PPP1CBpsi-mi:“MI:0915”(physical association)0.740
PPP1CBCSRNP2psi-mi:“MI:0915”(physical association)0.740
PPP1CBPPP1R2Bpsi-mi:“MI:0915”(physical association)0.720

BioGRID (712): PPP1R3C (Two-hybrid), TP53BP2 (Two-hybrid), SH2D4A (Two-hybrid), CSRNP2 (Two-hybrid), PPP1R16A (Two-hybrid), PPP1R2P3 (Two-hybrid), PPP1CB (Affinity Capture-MS), AKT1 (Affinity Capture-Western), PPP1CB (Affinity Capture-Western), PPP1CB (Affinity Capture-MS), PPP1CB (Affinity Capture-MS), PPP1CB (Two-hybrid), PPP1CB (Two-hybrid), PPP1CB (Two-hybrid), RORC (Two-hybrid)

ESM2 similar proteins: A2YEB4, A3C4N5, O00743, O02658, O04856, O04857, O04860, O04951, P0C5D7, P20604, P23696, P23778, P36614, P36874, P48462, P48481, P48482, P48485, P48486, P48487, P48529, P48578, P48580, P61292, P62140, P62141, P62142, P62143, P62207, P91420, Q06009, Q07098, Q07099, Q07100, Q0DBD3, Q27497, Q3SWW9, Q5I085, Q5R740, Q61JR3

Diamond homologs: A0C1E4, A0CCD2, A6H772, A8XE00, A9JRC7, B0XUR7, G5EGK8, O02658, O04856, O04857, O04858, O15757, O76932, O82733, O82734, P11084, P11493, P11611, P11612, P12982, P13681, P20654, P22198, P23696, P23733, P23734, P23777, P23880, P26570, P30366, P32598, P32945, P33329, P36873, P36874, P48458, P48459, P48461, P48462, P48463

SIGNOR signaling

18 interactions.

AEffectBMechanism
PPP1CBup-regulatesNF2dephosphorylation
PPP1CBdown-regulatesAKT1dephosphorylation
PPP1CBup-regulatesIKZF1dephosphorylation
PPP1CB“down-regulates activity”AXIN1dephosphorylation
PPP1CB“down-regulates activity”TP53dephosphorylation
PPP1CB“up-regulates activity”NOS3dephosphorylation
PPP1CB“down-regulates activity”AKTdephosphorylation
PPP1CB“up-regulates quantity by stabilization”MDM2dephosphorylation
PPP1CB“down-regulates activity”AKT1dephosphorylation
PPP1R1B“down-regulates activity”PPP1CBbinding
PPP1CBunknownAHCYL1dephosphorylation
PPP1CB“up-regulates activity”CASP2dephosphorylation
PPP1R14A“down-regulates activity”PPP1CBbinding
PPP1R14B“down-regulates activity”PPP1CBbinding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 118 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:

PathwayPartnersFoldFDR
Mitotic G1 phase and G1/S transition515.3×6e-04
MITF-M-dependent gene expression515.1×6e-04
EML4 and NUDC in mitotic spindle formation812.4×2e-05
Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal611.7×4e-04
Resolution of Sister Chromatid Cohesion811.5×3e-05
RHO GTPase Effectors1011.3×4e-06
Regulation of TP53 Activity511.1×2e-03
RHO GTPases Activate Formins810.4×5e-05

GO biological processes:

GO termPartnersFoldFDR
glycogen metabolic process527.4×7e-04
G1/S transition of mitotic cell cycle612.5×3e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic4
Likely pathogenic8
Uncertain significance95
Likely benign220
Benign18

Top pathogenic / likely-pathogenic (12)

Variant IDHGVSClassification
254648NM_002709.3(PPP1CB):c.146C>G (p.Pro49Arg)Pathogenic
254651NM_002709.3(PPP1CB):c.548A>T (p.Glu183Val)Pathogenic
254652NM_002709.3(PPP1CB):c.548A>C (p.Glu183Ala)Pathogenic
4282429NM_002709.3(PPP1CB):c.569G>A (p.Arg190Lys)Pathogenic
1727054NM_002709.3(PPP1CB):c.493G>C (p.Asp165His)Likely pathogenic
2231503NM_002709.3(PPP1CB):c.755A>G (p.Asp252Gly)Likely pathogenic
254649NM_002709.3(PPP1CB):c.754G>T (p.Asp252Tyr)Likely pathogenic
254653NM_002709.3(PPP1CB):c.820G>A (p.Glu274Lys)Likely pathogenic
3256555NM_002709.3(PPP1CB):c.493G>A (p.Asp165Asn)Likely pathogenic
4075297NM_002709.3(PPP1CB):c.515A>G (p.His172Arg)Likely pathogenic
427633NM_002709.3(PPP1CB):c.166G>C (p.Ala56Pro)Likely pathogenic
546861NM_002709.3(PPP1CB):c.255C>A (p.Asn85Lys)Likely pathogenic

SpliceAI

1533 predictions. Top by Δscore:

VariantEffectΔscore
2:28751857:G:GTdonor_gain1.0000
2:28752172:GGAGG:Gdonor_gain1.0000
2:28752173:GAGG:Gdonor_gain1.0000
2:28752173:GAGGG:Gdonor_gain1.0000
2:28752175:GG:Gdonor_gain1.0000
2:28752176:GG:Gdonor_gain1.0000
2:28752177:G:Adonor_loss1.0000
2:28752178:T:Gdonor_loss1.0000
2:28776841:C:Aacceptor_gain1.0000
2:28776845:T:TAacceptor_gain1.0000
2:28776846:GTCA:Gacceptor_loss1.0000
2:28776848:CAG:Cacceptor_loss1.0000
2:28776849:A:AGacceptor_gain1.0000
2:28776849:A:ATacceptor_loss1.0000
2:28776849:AGTAC:Aacceptor_gain1.0000
2:28776850:G:GTacceptor_gain1.0000
2:28776850:GT:Gacceptor_gain1.0000
2:28776850:GTA:Gacceptor_gain1.0000
2:28776850:GTAC:Gacceptor_gain1.0000
2:28776850:GTACG:Gacceptor_gain1.0000
2:28776852:ACGAG:Aacceptor_gain1.0000
2:28776961:G:GTdonor_gain1.0000
2:28776980:GTG:Gdonor_gain1.0000
2:28776983:G:Cdonor_loss1.0000
2:28776983:G:GGdonor_gain1.0000
2:28776984:T:Adonor_loss1.0000
2:28778803:TTTTA:Tacceptor_loss1.0000
2:28778804:TTTAG:Tacceptor_loss1.0000
2:28778805:TTAG:Tacceptor_loss1.0000
2:28778808:G:GTacceptor_loss1.0000

AlphaMissense

2136 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
2:28776982:G:AG62R1.000
2:28776982:G:CG62R1.000
2:28778809:G:AG62E1.000
2:28778809:G:TG62V1.000
2:28778811:G:CD63H1.000
2:28778812:A:CD63A1.000
2:28778812:A:GD63G1.000
2:28778812:A:TD63V1.000
2:28778813:T:AD63E1.000
2:28778813:T:GD63E1.000
2:28778817:C:AH65N1.000
2:28778817:C:GH65D1.000
2:28778819:T:AH65Q1.000
2:28778819:T:GH65Q1.000
2:28778820:G:AG66R1.000
2:28778820:G:CG66R1.000
2:28778821:G:AG66E1.000
2:28778821:G:TG66V1.000
2:28778884:T:AL87H1.000
2:28778884:T:CL87P1.000
2:28778892:G:AG90R1.000
2:28778892:G:CG90R1.000
2:28778893:G:AG90E1.000
2:28778893:G:TG90V1.000
2:28778895:G:CD91H1.000
2:28778896:A:CD91A1.000
2:28778896:A:GD91G1.000
2:28778896:A:TD91V1.000
2:28778897:T:AD91E1.000
2:28778897:T:GD91E1.000

dbSNP variants (sampled 300 via entrez): RS1000022162 (2:28773012 A>G), RS1000087650 (2:28766834 C>A), RS1000112033 (2:28788158 T>TG), RS1000190200 (2:28760743 A>G), RS1000193450 (2:28771119 T>A,G), RS1000219865 (2:28760974 C>T), RS1000283818 (2:28800443 G>A), RS1000335883 (2:28793566 A>C,T), RS1000374327 (2:28754573 CA>C), RS1000411380 (2:28760042 C>A), RS1000459962 (2:28766651 T>A), RS1000478203 (2:28749659 T>C,G), RS1000511063 (2:28750008 A>G), RS1000547592 (2:28787874 C>G,T), RS1000644011 (2:28783088 C>A)

Disease associations

OMIM: gene MIM:600590 | disease phenotypes: MIM:617506, MIM:220200, MIM:163950, MIM:607721

GenCC curated gene-disease

DiseaseClassificationInheritance
Noonan syndrome-like disorder with loose anagen hairDefinitiveAutosomal dominant
Noonan syndrome-like disorder with loose anagen hair 2DefinitiveAutosomal dominant

ClinGen Gene-Disease Validity (1)

Expert-panel classifications — Definitive > Strong > Moderate > Limited > Disputed > Refuted.

DiseaseClassificationInheritance
Noonan syndrome-like disorder with loose anagen hairDefinitiveAD

Mondo (6): Noonan syndrome-like disorder with loose anagen hair 2 (MONDO:0054588), Dandy-Walker syndrome (MONDO:0009072), Noonan syndrome (MONDO:0018997), RASopathy (MONDO:0021060), Noonan syndrome-like disorder with loose anagen hair (MONDO:0011899), intellectual disability (MONDO:0001071)

Orphanet (5): Isolated Dandy-Walker malformation (Orphanet:217), RASopathy (Orphanet:536391), Noonan syndrome (Orphanet:648), Noonan syndrome-like disorder with loose anagen hair (Orphanet:2701), NON RARE IN EUROPE: Unexplained intellectual disability (Orphanet:319658)

HPO phenotypes

99 total (30 of 99 shown, HPO-id order):

HPOTerm
HP:0000006Autosomal dominant inheritance
HP:0000028Cryptorchidism
HP:0000174Abnormal palate morphology
HP:0000179Thick lower lip vermilion
HP:0000193Bifid uvula
HP:0000207Triangular mouth
HP:0000218High palate
HP:0000219Thin upper lip vermilion
HP:0000233Thin vermilion border
HP:0000238Hydrocephalus
HP:0000256Macrocephaly
HP:0000286Epicanthus
HP:0000316Hypertelorism
HP:0000319Smooth philtrum
HP:0000329Facial hemangioma
HP:0000341Narrow forehead
HP:0000343Long philtrum
HP:0000348High forehead
HP:0000358Posteriorly rotated ears
HP:0000365Hearing impairment
HP:0000369Low-set ears
HP:0000391Thickened helices
HP:0000396Overfolded helix
HP:0000400Macrotia
HP:0000430Underdeveloped nasal alae
HP:0000445Wide nose
HP:0000463Anteverted nares
HP:0000465Webbed neck
HP:0000470Short neck
HP:0000475Broad neck

GWAS associations

8 associations (top):

StudyTraitp-value
GCST002783_312Body mass index9.000000e-07
GCST006090_1Excessive sweating2.000000e-11
GCST006288_419Heel bone mineral density4.000000e-08
GCST006288_569Heel bone mineral density1.000000e-11
GCST006979_916Heel bone mineral density1.000000e-21
GCST007656_7Chronic obstructive pulmonary disease or resting heart rate (pleiotropy)9.000000e-12
GCST008523_1Pure non-grapefruit juice consumption2.000000e-07
GCST008758_32Pre-treatment viral load in HIV-1 infection4.000000e-19

EFO canonical traits (4, from GWAS)

EFO IDTrait name
EFO:0004340body mass index
EFO:0009270heel bone mineral density
EFO:0010095non-grapefruit juice consumption measurement
EFO:0010125viral load

MeSH disease descriptors (4)

DescriptorNameTree numbers
D003616Dandy-Walker SyndromeC10.228.140.252.300; C10.228.140.602.500; C10.500.205; C16.131.666.205
D008607Intellectual DisabilityC10.597.606.360; C23.888.592.604.646; F01.700.687; F03.625.539
D009634Noonan SyndromeC05.660.207.690; C14.240.400.787; C14.280.400.787; C16.131.240.400.784; C16.131.621.207.690; C17.300.690
C564342Noonan-Like Syndrome With Loose Anagen Hair (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL4546 (SINGLE PROTEIN)

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
Arsenic Trioxidedecreases expression, increases expression3
Valproic Aciddecreases methylation, affects expression, decreases expression3
bisphenol Aincreases expression, affects cotreatment2
Air Pollutantsdecreases expression, increases abundance2
Benzeneincreases expression2
Rotenonedecreases expression, increases expression2
Smokeincreases abundance, decreases expression2
Tobacco Smoke Pollutionaffects expression, increases expression2
Cadmium Chlorideincreases abundance, increases expression2
Particulate Matterdecreases expression, increases abundance2
aristolochic acid Iincreases expression, decreases expression1
FR900359increases phosphorylation1
bisphenol Fincreases expression1
moringindecreases expression1
dicrotophosdecreases expression1
methylmercuric chloridedecreases expression1
oxybenzoneincreases expression1
triphenyl phosphateaffects expression1
pyrogallol 1,3-dimethyl etheraffects cotreatment, affects localization, decreases expression1
mono-(2-ethylhexyl)phthalateincreases expression1
tris(1,3-dichloro-2-propyl)phosphatedecreases expression1
sodium arseniteincreases expression1
tamibarotenedecreases expression1
perfluorooctane sulfonic aciddecreases expression1
deguelinincreases expression1
4-chloro-N-((4-(1,1-dimethylethyl)phenyl)methyl)-3-ethyl-1-methyl-1H-pyrazole-5-carboxamideincreases expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, increases expression1
pyrimidifenincreases expression1
nutlin 3increases secretion, affects cotreatment1
bisphenol Bincreases expression1

ChEMBL screening assays

9 unique, capped per target: 9 binding

Representative assays (with source publication via chembl_document):

Assay IDTypeDescriptionSource paper
CHEMBL4221651BindingBinding affinity to full length recombinant human N-terminal His6-tagged PP1cdelta expressed in Escherichia coli M15 assessed as inhibition of protein interaction with GST-tagged MYPT1 at 10 to 50 uM by surface plasmon resonance methodAralkyl selenoglycosides and related selenosugars in acetylated form activate protein phosphatase-1 and -2A. — Bioorg Med Chem

Clinical trials (associated diseases)

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

TrialPhaseStatusTitle
NCT05657860PHASE4COMPLETEDGuanfacine Extended Release for the Reduction of Aggression and Self-injurious Behavior Associated With Prader-Willi Syndrome
NCT05744479PHASE4RECRUITINGMetformin for Antipsychotic-induced Weight Gain in Adults With Intellectual Disability
NCT06107829PHASE4WITHDRAWNValbenazine Treatment of Tardive Dyskinesia in Adults With Intellectual/Developmental Disabilities
NCT06997198PHASE4NOT_YET_RECRUITINGDeutetrabenazine Treatment for Tardive Dyskinesia in Intellectual/Developmental Disabilities
NCT00452725PHASE3COMPLETEDEffect of MAXOMAT ® on the Growth of Small Children to NOONAN’s Syndrome
NCT01529840PHASE3COMPLETEDSomatropin Effect on Linear Growth and Final Height in Subjects With Noonan Syndrome
NCT01529944PHASE3COMPLETEDGenetic Testing of Noonan Subjects Previously Treated With Norditropin®. An Extension to Trial GHNOO-1658
NCT01927861PHASE3COMPLETEDInvestigating the Long-term Efficacy and Safety of Two Doses of NN-220 (Somatropin) in Short Stature Due to Noonan Syndrome
NCT02713945PHASE3COMPLETEDTreatment With HMG-COA Reductase Inhibitor of Growth and Bone Abnormalities in Children With Noonan Syndrome
NCT05723835PHASE3ACTIVE_NOT_RECRUITINGA Research Study Looking at How Safe Somapacitan is and How Well it Works in Children Who Need Help to Grow - REAL 9
NCT02270736PHASE3COMPLETEDClinical Study to Investigate the Efficacy and Safety of NT 201 Compared to Placebo in the Treatment of Chronic Troublesome Drooling Associated With Neurological Disorders and/or Intellectual Disability
NCT00351221PHASE2TERMINATEDResearch Study Using Recombinant Human Insulin-Like Growth Factor-1/Recombinant Human Insulin-Like Growth Factor Binding Protein-3 for Children With Noonan Syndrome
NCT06555237PHASE2RECRUITINGMEK Inhibitors for the Treatment of Hypertrophic Cardiomyopathy in Patients With RASopathies
NCT06668805PHASE2RECRUITINGA Study of Vosoritide in Children With Noonan Syndrome With Inadequate Growth During or After Human Growth Hormone Treatment
NCT02304302PHASE2COMPLETEDDown Syndrome Memantine Follow-up Study
NCT03862950PHASE2COMPLETEDA Trial of Metformin in Individuals With Fragile X Syndrome (Met)
NCT04529226PHASE2UNKNOWNStudy to Compare Clozapine vs Treatment as Usual in People With Intellectual Disability & Treatment-resistant Psychosis
NCT04821856PHASE2COMPLETEDEvaluation of the Effectiveness of Cannabidiol in Treating Severe Behavioural Problems in Children and Adolescents With Intellectual Disability
NCT05273320PHASE1COMPLETEDClinical Trial of Nabilone for Aggression in Adults With Intellectual and Developmental Disabilities
NCT05301361PHASE1ENROLLING_BY_INVITATIONSensitivity of the NIH Toolbox to Stimulant Treatment in Intellectual Disabilities
NCT06016764PHASE1COMPLETEDUse of MRI and cTBS for Catatonia in Autism
NCT06586827PHASE1COMPLETEDImpact of Competency-Based Training and Technical Assistance Employment Outcomes of Individuals With ID/DD
NCT07531940PHASE1NOT_YET_RECRUITINGEscalating Doses of Memantine in Down Syndrome (MEDS-123)
NCT00960128Not specifiedCOMPLETEDObservational Prospective Study on Patients Treated With Norditropin®
NCT02486731Not specifiedCOMPLETEDHormonal Sensitivity in Patients With Noonan and LEOPARD Syndromes
NCT03435627Not specifiedCOMPLETEDPost Marketing Surveillance on Long-term Use With Norditropin® (Short Stature Due to Noonan Syndrome)
NCT04395495Not specifiedRECRUITINGRASopathy Biorepository
NCT04463316Not specifiedRECRUITINGGROWing Up With Rare GENEtic Syndromes
NCT04888936Not specifiedRECRUITINGClinical, Genetic, and Epidemiologic Study of Children and Adults With RASopathies
NCT05202210Not specifiedRECRUITINGConstitution of a Biological Collection to Study the Pathophysiology in Noonan Syndrome
NCT05308927Not specifiedENROLLING_BY_INVITATIONFrench Registry of Children Treated With Norditropin® for Short Stature Associated With Noonan Syndrome
NCT05361811Not specifiedRECRUITINGAcceptance and Commitment Therapy for Caregivers of Children With a RASopathy: An Internal Pilot Feasibility Study and Follow-up Randomized Controlled Trial
NCT05761314Not specifiedRECRUITINGSolid Tumors in RASopathies
NCT06267807Not specifiedCOMPLETEDLymphatic Phenotype in Noonan Syndrome Spectrum Disorders
NCT06331117Not specifiedUNKNOWNEffect of RAS/MAPK Pathway Hyperactivation on Growth’ and Bone’ Profile of the RASopathies
NCT06355622Not specifiedUNKNOWNPrevalence and Characterization of Pain in RASopathies
NCT06550635Not specifiedCOMPLETEDJoint and Hematologic Disorders of Noonan Syndrome: French Descriptive Cross-sectional Study
NCT06938542Not specifiedENROLLING_BY_INVITATIONPalliative Care Needs of Children With Rare Diseases and Their Families
NCT07259135Not specifiedNOT_YET_RECRUITINGLink Between Abnormal Bleeding and Coagulation Disorders in Noonan Syndromes
NCT07336394Not specifiedRECRUITINGPrecision Diagnosis and Risk Stratification of Rare Cardiomyopathies Based on Novel Cardiac Magnetic Resonance Techniques