PPP2R2C

gene
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Also known as PR52IMYPNOMGC33570PR55GB55gamma

Summary

PPP2R2C (protein phosphatase 2 regulatory subunit Bgamma, HGNC:9306) is a protein-coding gene on chromosome 4p16.1, encoding Serine/threonine-protein phosphatase 2A 55 kDa regulatory subunit B gamma isoform (Q9Y2T4). The B regulatory subunit might modulate substrate selectivity and catalytic activity, and might also direct the localization of the catalytic enzyme to a particular subcellular compartment.

The product of this gene belongs to the phosphatase 2 regulatory subunit B family. Protein phosphatase 2 is one of the four major Ser/Thr phosphatases, and it is implicated in the negative control of cell growth and division. It consists of a common heteromeric core enzyme, which is composed of a catalytic subunit and a constant regulatory subunit, that associates with a variety of regulatory subunits. The B regulatory subunit might modulate substrate selectivity and catalytic activity. This gene encodes a gamma isoform of the regulatory subunit B55 subfamily. Alternatively spliced transcript variants encoding different isoforms have been identified.

Source: NCBI Gene 5522 — RefSeq curated summary.

At a glance

  • GWAS associations: 5
  • Clinical variants (ClinVar): 53 total
  • MANE Select transcript: NM_020416

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:9306
Approved symbolPPP2R2C
Nameprotein phosphatase 2 regulatory subunit Bgamma
Location4p16.1
Locus typegene with protein product
StatusApproved
AliasesPR52, IMYPNO, MGC33570, PR55G, B55gamma
Ensembl geneENSG00000074211
Ensembl biotypeprotein_coding
OMIM605997
Entrez5522

Gene structure

Transcript identifiers

Ensembl transcripts: 9 — 5 protein_coding, 2 protein_coding_CDS_not_defined, 1 nonsense_mediated_decay, 1 retained_intron

ENST00000314348, ENST00000335585, ENST00000382599, ENST00000506140, ENST00000507028, ENST00000507294, ENST00000509917, ENST00000513943, ENST00000515571

RefSeq mRNA: 6 — MANE Select: NM_020416 NM_001206994, NM_001206995, NM_001206996, NM_001363388, NM_020416, NM_181876

CCDS: CCDS3387, CCDS3388, CCDS56304, CCDS56305

Canonical transcript exons

ENST00000382599 — 9 exons

ExonStartEnd
ENSE0000070104163292626329353
ENSE0000070111463335626333731
ENSE0000149274564721606472614
ENSE0000208433963205816323593
ENSE0000350450363478466348010
ENSE0000353375863758196375931
ENSE0000357645963784076378572
ENSE0000361407563725236372700
ENSE0000363681563809976381094

Expression profiles

Bgee: expression breadth ubiquitous, 208 present calls, max score 99.07.

FANTOM5 (CAGE): breadth broad, TPM avg 7.8880 / max 262.1373, expressed in 517 samples.

FANTOM5 promoters (22 alternative TSS)

Promoter IDTPM avgSamples expressed
512514.1049419
512491.1469281
512610.5866112
512480.5712135
512470.211278
512530.187362
512620.178463
512460.170992
512540.150357
512520.140981

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
middle temporal gyrusUBERON:000277199.07gold quality
Brodmann (1909) area 46UBERON:000648398.87gold quality
superior frontal gyrusUBERON:000266198.61gold quality
parietal lobeUBERON:000187298.57gold quality
postcentral gyrusUBERON:000258198.55gold quality
occipital lobeUBERON:000202198.30gold quality
Brodmann (1909) area 23UBERON:001355498.30gold quality
entorhinal cortexUBERON:000272898.28gold quality
primary visual cortexUBERON:000243698.14gold quality
prefrontal cortexUBERON:000045198.09gold quality
inferior vagus X ganglionUBERON:000536398.06gold quality
frontal cortexUBERON:000187097.97gold quality
ponsUBERON:000098897.86gold quality
medial globus pallidusUBERON:000247797.81gold quality
lateral nuclear group of thalamusUBERON:000273697.75gold quality
globus pallidusUBERON:000187597.74gold quality
temporal lobeUBERON:000187197.66gold quality
dorsolateral prefrontal cortexUBERON:000983497.66gold quality
right frontal lobeUBERON:000281097.60gold quality
caudate nucleusUBERON:000187397.57gold quality
nucleus accumbensUBERON:000188297.53gold quality
putamenUBERON:000187497.51gold quality
lateral globus pallidusUBERON:000247697.42gold quality
superior vestibular nucleusUBERON:000722797.37gold quality
substantia nigra pars reticulataUBERON:000196697.30gold quality
substantia nigra pars compactaUBERON:000196597.27gold quality
ventral tegmental areaUBERON:000269197.23gold quality
medulla oblongataUBERON:000189697.21gold quality
Brodmann (1909) area 9UBERON:001354097.21gold quality
C1 segment of cervical spinal cordUBERON:000646997.20gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-ANND-3yes4.49
E-GEOD-124858no1.29

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): MYCN

miRNA regulators (miRDB)

110 targeting PPP2R2C, 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-8485100.0077.574731
HSA-MIR-200B-3P100.0073.312693
HSA-MIR-200C-3P100.0073.352685
HSA-MIR-429100.0073.442698
HSA-MIR-4262100.0073.263931
HSA-MIR-3613-3P100.0076.367965
HSA-MIR-4713-3P100.0065.92505
HSA-MIR-513B-5P99.9969.962150
HSA-MIR-480399.9871.993117
HSA-MIR-302C-5P99.9772.563642
HSA-MIR-314899.9775.066478
HSA-MIR-55999.9572.283609
HSA-MIR-548AB99.9571.313488
HSA-MIR-548A-5P99.9471.273482
HSA-MIR-548AD-5P99.9471.233502
HSA-MIR-548AE-5P99.9471.233502
HSA-MIR-548AK99.9471.243488
HSA-MIR-548AM-5P99.9471.243488
HSA-MIR-548AP-5P99.9471.143489
HSA-MIR-548AQ-5P99.9471.343426
HSA-MIR-548AR-5P99.9471.283515
HSA-MIR-548AS-5P99.9471.223482
HSA-MIR-548AU-5P99.9471.243488
HSA-MIR-548AY-5P99.9471.233502
HSA-MIR-548B-5P99.9471.233502
HSA-MIR-548BB-5P99.9471.273509
HSA-MIR-548C-5P99.9471.243488
HSA-MIR-548D-5P99.9471.233502
HSA-MIR-548H-5P99.9471.243488
HSA-MIR-548I99.9471.253481

Literature-anchored findings (GeneRIF, showing 9)

  • specific PP2A complexes involved in human cell transformation (PMID:14998489)
  • novel mechanism of c-SRC regulation whereby in response to stress c-SRC activity is regulated, at least in part, through loss of the interaction with its inhibitor, PR55gamma (PMID:18069897)
  • encoding a subunit of proteinphosphatase 2A with a unique expression pattern in brain and a role in synaptic plasticity (PMID:20601260)
  • evidence suggests that allelic variation in PPP2R2C may be associated with a variety of personality traits and ADHD per se. (PMID:22664926)
  • These findings provide insights into mechanisms by which prostate cancers resist AR-pathway suppression and support inhibiting PPP2R2C complexes. (PMID:23493267)
  • PPP2R2C is a potential tumor suppressor gene in human brain cancers. (PMID:24126060)
  • miR-1301 promoted prostate cancer proliferation by inhibiting PPP2R2C. (PMID:27261573)
  • B55gamma is induced by glucocorticoid receptor in human primary BM-MSCs during differentiation to osteoblast and is required for osteoblast morphogenesis. (PMID:28805158)
  • High genetic risk scores of SLIT3, PLEKHA5 and PPP2R2C variants increase susceptibility to increased insulin resistance by 50% and its risk may be exacerbated by consuming more than 10 cups coffee/week or 220 mg caffeine/day. (PMID:30454882)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_rerioppp2r2caENSDARG00000056797
danio_rerioppp2r2cbENSDARG00000062277
mus_musculusPpp2r2cENSMUSG00000029120
rattus_norvegicusPpp2r2cENSRNOG00000058202
caenorhabditis_eleganssur-6WBGENE00006352

Paralogs (3): PPP2R2B (ENSG00000156475), PPP2R2D (ENSG00000175470), PPP2R2A (ENSG00000221914)

Protein

Protein identifiers

Serine/threonine-protein phosphatase 2A 55 kDa regulatory subunit B gamma isoformQ9Y2T4 (reviewed: Q9Y2T4)

Alternative names: IMYPNO1, PP2A subunit B isoform B55-gamma, PP2A subunit B isoform PR55-gamma, PP2A subunit B isoform R2-gamma, PP2A subunit B isoform gamma

All UniProt accessions (2): Q9Y2T4, D6R943

UniProt curated annotations — full annotation on UniProt →

Function. The B regulatory subunit might modulate substrate selectivity and catalytic activity, and might also direct the localization of the catalytic enzyme to a particular subcellular compartment.

Subunit / interactions. PP2A consists of a common heterodimeric core enzyme, composed of a 36 kDa catalytic subunit (subunit C) and a 65 kDa constant regulatory subunit (PR65 or subunit A), that associates with a variety of regulatory subunits. Proteins that associate with the core dimer include three families of regulatory subunits B (the R2/B/PR55/B55, R3/B’’/PR72/PR130/PR59 and R5/B’/B56 families), the 48 kDa variable regulatory subunit, viral proteins, and cell signaling molecules. Interacts with IER5.

Similarity. Belongs to the phosphatase 2A regulatory subunit B family.

Isoforms (4)

UniProt IDNamesCanonical?
Q9Y2T4-11yes
Q9Y2T4-22
Q9Y2T4-33
Q9Y2T4-44

RefSeq proteins (6): NP_001193923, NP_001193924, NP_001193925, NP_001350317, NP_065149, NP_870991 (=MANE)

Domains & families (InterPro)

IDNameType
IPR000009PP2A_PR55Family
IPR001680WD40_rptRepeat
IPR015943WD40/YVTN_repeat-like_dom_sfHomologous_superfamily
IPR018067PP2A_PR55_CSConserved_site
IPR036322WD40_repeat_dom_sfHomologous_superfamily

UniProt features (14 total): repeat 7, splice variant 3, sequence conflict 3, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9Y2T4-F189.530.75

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 96 (showing top): RNGTGGGC_UNKNOWN, AP1_01, PEREZ_TP63_TARGETS, TATTATA_MIR374, KEGG_TIGHT_JUNCTION, HANN_RESISTANCE_TO_BCL2_INHIBITOR_UP, ATGTTAA_MIR302C, WANG_ESOPHAGUS_CANCER_VS_NORMAL_DN, chr4p16, TGANTCA_AP1_C, NRF2_Q4, FUJII_YBX1_TARGETS_DN, PEREZ_TP53_AND_TP63_TARGETS, HAND1E47_01, ACEVEDO_METHYLATED_IN_LIVER_CANCER_DN

GO Biological Process (0):

GO Molecular Function (2): protein phosphatase regulator activity (GO:0019888), protein binding (GO:0005515)

GO Cellular Component (2): protein phosphatase type 2A complex (GO:0000159), cytosol (GO:0005829)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
phosphoprotein phosphatase activity1
phosphatase regulator activity1
protein phosphatase binding1
binding1
protein serine/threonine phosphatase complex1
cytoplasm1
cellular anatomical structure1

Protein interactions and networks

STRING

2004 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
PPP2R2CPPP2R1BP30154874
PPP2R2CPPP2R5CQ13362722
PPP2R2CPPP2R3BQ9Y5P8719
PPP2R2CPPP2CAP05323712
PPP2R2CPPP2R3CQ969Q6687
PPP2R2CPPP2R1AP30153678
PPP2R2CPPP2R5AQ15172644
PPP2R2CSTRNO43815633
PPP2R2CPPP2R5BQ15173612
PPP2R2CPPP2R3AQ06190568
PPP2R2CPPP2R5DQ14738510
PPP2R2CMINK1Q8N4C8508
PPP2R2CPPP2R5EQ16537495
PPP2R2CPTPAQ15257491
PPP2R2CHMX1Q9NP08458

IntAct

22 interactions, top by confidence:

ABTypeScore
PPP2R2CPPP2R1Apsi-mi:“MI:0914”(association)0.730
SERTAD4PPP2R1Apsi-mi:“MI:0914”(association)0.730
PPP2R2CPPP2CApsi-mi:“MI:0915”(physical association)0.710
PPP2CAPPP2R2Cpsi-mi:“MI:0914”(association)0.710
PPP2R2CTCP1psi-mi:“MI:0914”(association)0.640
PPP2R2Creppsi-mi:“MI:0915”(physical association)0.550
PPP2R2DBAG2psi-mi:“MI:0914”(association)0.350
PPP2R2AS100A8psi-mi:“MI:0914”(association)0.350
PPP2R2CBAG2psi-mi:“MI:0914”(association)0.350
SLX4SMAPpsi-mi:“MI:0914”(association)0.350
Mpsi-mi:“MI:0914”(association)0.350
repPRDX5psi-mi:“MI:0914”(association)0.350
S100A2PLEKHG3psi-mi:“MI:0914”(association)0.350
SMAD9VSIG8psi-mi:“MI:0914”(association)0.350
ZNF114PPP2R1Bpsi-mi:“MI:0914”(association)0.350
SERTAD2PPP2R1Bpsi-mi:“MI:0914”(association)0.350
PABIR1PPP2R1Bpsi-mi:“MI:0914”(association)0.350
CBLL2COL1A1psi-mi:“MI:0914”(association)0.350
PPP2R2CPLEKHG3psi-mi:“MI:0914”(association)0.350
PPP2R1Apsi-mi:“MI:0914”(association)0.350

BioGRID (177): CCT3 (Affinity Capture-MS), CCT6A (Affinity Capture-MS), CCT2 (Affinity Capture-MS), CCT7 (Affinity Capture-MS), POLR3A (Affinity Capture-MS), SIK2 (Affinity Capture-MS), TCP1 (Affinity Capture-MS), IQGAP1 (Affinity Capture-MS), PPP2R1B (Affinity Capture-MS), PPP2R1A (Affinity Capture-MS), STRN (Affinity Capture-MS), STRN3 (Affinity Capture-MS), STRN4 (Affinity Capture-MS), PPP2R2B (Affinity Capture-MS), ZCCHC8 (Affinity Capture-MS)

ESM2 similar proteins: A1L3L9, A2X2K3, B0R0D7, B6VA23, O35142, O55029, P35606, P36876, P36877, P50410, P54614, P56932, P63150, P63151, P97888, Q00005, Q00006, Q0D2F4, Q0E2P1, Q29090, Q38821, Q39247, Q4R4I8, Q4R7Z4, Q4R8L3, Q5E9Q7, Q5R4A2, Q5R664, Q5Z8Z7, Q5ZIY5, Q66LE6, Q6AY57, Q6DIY3, Q6NY64, Q6P1F6, Q6QEF8, Q6ZWR4, Q7ZWU5, Q7ZX64, Q80W47

Diamond homologs: A1L3L9, A2X2K3, B6VA23, G5EDR3, P36872, P36876, P36877, P50410, P53031, P54614, P56932, P63150, P63151, P97888, Q00005, Q00006, Q00362, Q0D2F4, Q0E2P1, Q12702, Q29090, Q38821, Q39247, Q4R7Z4, Q4R8L3, Q54Q99, Q5E9Q7, Q5R4A2, Q5Z8Z7, Q5ZIY5, Q66LE6, Q6DIY3, Q6NY64, Q6P1F6, Q6ZWR4, Q7ZX64, Q8BG02, Q925E7, Q95LP0, Q9Y2T4

SIGNOR signaling

1 interactions.

AEffectBMechanism
PPP2R2C“down-regulates activity”SRCbinding

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance39
Likely benign0
Benign2

Top pathogenic / likely-pathogenic (0)

SpliceAI

2546 predictions. Top by Δscore:

VariantEffectΔscore
4:6323589:TGACG:Tacceptor_gain1.0000
4:6323592:CG:Cacceptor_gain1.0000
4:6323594:C:CCacceptor_gain1.0000
4:6329256:GCTTA:Gdonor_loss1.0000
4:6329257:CTTA:Cdonor_loss1.0000
4:6329258:TTACC:Tdonor_loss1.0000
4:6329259:TAC:Tdonor_loss1.0000
4:6329260:A:ACdonor_gain1.0000
4:6329260:A:Cdonor_loss1.0000
4:6329261:C:CCdonor_gain1.0000
4:6333727:AAAGA:Aacceptor_gain1.0000
4:6333728:AAGA:Aacceptor_gain1.0000
4:6333729:AGA:Aacceptor_gain1.0000
4:6333729:AGAC:Aacceptor_loss1.0000
4:6333730:GA:Gacceptor_gain1.0000
4:6333731:AC:Aacceptor_loss1.0000
4:6333732:C:CCacceptor_gain1.0000
4:6333733:T:Cacceptor_loss1.0000
4:6347844:A:ACdonor_gain1.0000
4:6347844:ACG:Adonor_gain1.0000
4:6347845:C:CCdonor_gain1.0000
4:6347845:CG:Cdonor_gain1.0000
4:6347845:CGC:Cdonor_gain1.0000
4:6372521:A:ACdonor_gain1.0000
4:6372522:C:CCdonor_gain1.0000
4:6372525:AAGCT:Adonor_gain1.0000
4:6372529:T:TAdonor_gain1.0000
4:6375817:A:ATdonor_loss1.0000
4:6375818:CCTG:Cdonor_gain1.0000
4:6375927:TTTAT:Tacceptor_gain1.0000

AlphaMissense

3019 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
4:6323342:A:GL435P1.000
4:6323357:G:TA430D1.000
4:6323363:G:TA428D1.000
4:6323388:A:GW420R1.000
4:6323388:A:TW420R1.000
4:6323516:G:TA377D1.000
4:6323574:A:CY358D1.000
4:6323574:A:GY358H1.000
4:6323579:C:AG356V1.000
4:6323579:C:TG356E1.000
4:6323580:C:AG356W1.000
4:6323580:C:GG356R1.000
4:6323580:C:TG356R1.000
4:6329288:A:CF342L1.000
4:6329288:A:TF342L1.000
4:6329290:A:GF342L1.000
4:6329295:T:AD340V1.000
4:6329296:C:GD340H1.000
4:6329297:G:CF339L1.000
4:6329297:G:TF339L1.000
4:6329298:A:CF339C1.000
4:6329298:A:GF339S1.000
4:6329299:A:CF339V1.000
4:6329299:A:GF339L1.000
4:6329299:A:TF339I1.000
4:6329301:A:TI338N1.000
4:6329307:T:AD336V1.000
4:6329308:C:GD336H1.000
4:6329317:A:GY333H1.000
4:6329319:A:GL332P1.000

dbSNP variants (sampled 300 via entrez): RS10000024 (4:6423539 A>G), RS1000014818 (4:6470834 G>A), RS1000020151 (4:6371575 T>C), RS1000023460 (4:6461736 T>C), RS1000055518 (4:6357437 C>A,T), RS1000065825 (4:6549586 C>G,T), RS1000073588 (4:6499537 A>T), RS1000096133 (4:6535455 C>A,T), RS1000119446 (4:6408430 G>C), RS10001231 (4:6332552 C>G,T), RS1000124714 (4:6363653 G>A), RS1000130401 (4:6541776 C>G), RS1000139383 (4:6408245 C>T), RS10001583 (4:6523803 T>A,C,G), RS1000167815 (4:6516242 G>A)

Disease associations

OMIM: gene MIM:605997 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

5 associations (top):

StudyTraitp-value
GCST000478_2Type 2 diabetes1.000000e-08
GCST002709_27Electroencephalogram traits9.000000e-06
GCST004134_15Multiple keratinocyte cancers5.000000e-06
GCST008513_7Health literacy2.000000e-06
GCST009391_1718Metabolite levels7.000000e-06

EFO canonical traits (3, from GWAS)

EFO IDTrait name
EFO:0004357electroencephalogram measurement
EFO:0010104health literacy measurement
EFO:0010341cholesteryl ester 16:0 measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
Valproic Acidaffects cotreatment, increases expression, affects expression, increases methylation9
sodium arsenitedecreases expression, increases abundance, increases expression5
Estradiolaffects cotreatment, increases expression3
bisphenol Aaffects cotreatment, decreases methylation, increases expression2
entinostatincreases expression, affects cotreatment2
Benzo(a)pyreneaffects methylation, increases methylation2
Copperaffects binding, increases expression, affects cotreatment, decreases expression2
Aflatoxin B1increases methylation2
aristolochic acid Idecreases expression1
OTX015decreases expression1
bisphenol Faffects cotreatment, increases methylation1
mivebresibdecreases expression1
dicrotophosincreases expression1
methylmercuric chlorideincreases expression1
testosterone undecanoateaffects cotreatment, increases expression1
trichostatin Aincreases expression1
arsenitedecreases expression, increases abundance1
11-nor-delta(9)-tetrahydrocannabinol-9-carboxylic acidaffects methylation, increases abundance1
benzo(e)pyreneincreases methylation1
aflatoxin B2affects methylation1
cupric chlorideincreases expression1
beta-methylcholineaffects expression1
2,4-decadienalaffects response to substance1
CGP 52608affects binding, increases reaction1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, increases expression1
erucylphospho-N,N,N-trimethylpropylammoniumincreases expression1
abrinedecreases expression1
dorsomorphinaffects cotreatment, increases expression1
bisphenol Saffects methylation1
apatinibaffects cotreatment, increases expression1

Cellosaurus cell lines

1 cell lines: 1 cancer cell line

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

CellosaurusNameCategorySex
CVCL_TF97HAP1 PPP2R2C (-)Cancer cell lineMale

Clinical trials (associated diseases)

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

  • Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): squamous cell carcinoma