PABIR1

gene
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Also known as MGC17347

Summary

PABIR1 (PP2A Aalpha (PPP2R1A) and B55A (PPP2R2A) interacting phosphatase regulator 1, HGNC:23490) is a protein-coding gene on chromosome 9q21.11, encoding PPP2R1A-PPP2R2A-interacting phosphatase regulator 1 (Q96E09). Acts as an inhibitor of serine/threonine-protein phosphatase 2A (PP2A) activity. It is a selective cancer dependency (DepMap: 21.5% of cell lines).

Enables protein phosphatase 2A binding activity and protein serine/threonine phosphatase inhibitor activity. Involved in mitotic G2/M transition checkpoint; positive regulation of cell growth; and positive regulation of proteasomal ubiquitin-dependent protein catabolic process. Located in cytoplasm and nuclear body.

Source: NCBI Gene 116224 — RefSeq curated summary.

At a glance

  • GWAS associations: 2
  • Clinical variants (ClinVar): 27 total
  • Cancer dependency (DepMap): dependent in 21.5% of screened cell lines
  • MANE Select transcript: NM_138333

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:23490
Approved symbolPABIR1
NamePP2A Aalpha (PPP2R1A) and B55A (PPP2R2A) interacting phosphatase regulator 1
Location9q21.11
Locus typegene with protein product
StatusApproved
AliasesMGC17347
Ensembl geneENSG00000187866
Ensembl biotypeprotein_coding
OMIM617249
Entrez116224

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000394264

RefSeq mRNA: 1 — MANE Select: NM_138333 NM_138333

CCDS: CCDS6623

Canonical transcript exons

ENST00000394264 — 1 exons

ExonStartEnd
ENSE000022400026878006568785566

Expression profiles

Bgee: expression breadth ubiquitous, 242 present calls, max score 94.50.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 19.1511 / max 126.0962, expressed in 1810 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter IDTPM avgSamples expressed
9680618.82481810
968080.232193
968070.094248

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
secondary oocyteCL:000065594.50gold quality
oocyteCL:000002391.63gold quality
epithelial cell of pancreasCL:000008391.63gold quality
tibialis anteriorUBERON:000138590.07silver quality
biceps brachiiUBERON:000150788.74gold quality
skeletal muscle tissue of biceps brachiiUBERON:000450288.44gold quality
deltoidUBERON:000147687.44silver quality
heart right ventricleUBERON:000208086.73gold quality
popliteal arteryUBERON:000225083.41gold quality
tibial arteryUBERON:000761083.38gold quality
pigmented layer of retinaUBERON:000178283.30gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047383.06gold quality
quadriceps femorisUBERON:000137782.79gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099182.73gold quality
vastus lateralisUBERON:000137982.71gold quality
right coronary arteryUBERON:000162582.67gold quality
descending thoracic aortaUBERON:000234582.62gold quality
skeletal muscle tissue of rectus abdominisUBERON:000451182.43gold quality
left coronary arteryUBERON:000162682.38gold quality
aortaUBERON:000094782.26gold quality
skeletal muscle tissueUBERON:000113481.77gold quality
esophagus squamous epitheliumUBERON:000692081.51gold quality
ileal mucosaUBERON:000033181.32gold quality
myocardiumUBERON:000234981.26silver quality
endothelial cellCL:000011581.24silver quality
coronary arteryUBERON:000162181.05gold quality
thoracic aortaUBERON:000151581.04gold quality
islet of LangerhansUBERON:000000680.90gold quality
ascending aortaUBERON:000149680.81gold quality
muscle tissueUBERON:000238580.80gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

ExperimentMarker?Max mean expression
E-ANND-3no0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

194 targeting PABIR1, 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-3924100.0072.092394
HSA-MIR-188-3P100.0068.761240
HSA-MIR-4533100.0069.482758
HSA-MIR-7110-3P100.0073.182486
HSA-MIR-574-5P100.0066.01989
HSA-MIR-1252-5P100.0069.802774
HSA-MIR-548C-3P99.9974.017587
HSA-MIR-450099.9972.722367
HSA-MIR-186-5P99.9970.833707
HSA-MIR-3667-3P99.9967.171636
HSA-LET-7A-5P99.9872.291790
HSA-LET-7B-5P99.9872.311790
HSA-LET-7C-5P99.9872.291790
HSA-LET-7E-5P99.9872.291790
HSA-LET-7F-5P99.9872.561784
HSA-LET-7G-5P99.9872.371784
HSA-LET-7I-5P99.9872.371788
HSA-MIR-98-5P99.9872.331787
HSA-MIR-480399.9871.993117
HSA-MIR-548N99.9871.944170
HSA-LET-7D-5P99.9671.761632
HSA-MIR-445899.9671.641650
HSA-MIR-4725-3P99.9669.532520
HSA-MIR-6780B-5P99.9669.602562
HSA-MIR-211099.9666.681930
HSA-MIR-590-3P99.9674.346478
HSA-MIR-548AA99.9670.643753
HSA-MIR-548AP-3P99.9670.643753
HSA-MIR-548T-3P99.9670.643753
HSA-MIR-6778-3P99.9667.292693

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 21.5% of screened cell lines.

Literature-anchored findings (GeneRIF, showing 6)

  • identify FAM122A as a new endogenous PP2A inhibitor (PMID:27588481)
  • FAM122A promotes acute myeloid leukemia cell growth through inhibiting PP2A activity and sustaining MYC expression. (PMID:32354864)
  • FAM122A Inhibits Erythroid Differentiation through GATA1. (PMID:32763160)
  • FAM122A maintains DNA stability possibly through the regulation of topoisomerase IIalpha expression. (PMID:32866497)
  • FAM122A is required for hematopoietic stem cell function. (PMID:33262527)
  • FAM122A ensures cell cycle interphase progression and checkpoint control by inhibiting B55alpha/PP2A through helical motifs. (PMID:38982062)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_reriopabir2ENSDARG00000036500
mus_musculusPabir1ENSMUSG00000074922
rattus_norvegicusPabir1ENSRNOG00000051051
drosophila_melanogasterCG4497FBGN0031895
caenorhabditis_elegansWBGENE00018518

Paralogs (2): PABIR3 (ENSG00000156500), PABIR2 (ENSG00000156504)

Protein

Protein identifiers

PPP2R1A-PPP2R2A-interacting phosphatase regulator 1Q96E09 (reviewed: Q96E09)

Alternative names: PABIR family member 1

All UniProt accessions (1): Q96E09

UniProt curated annotations — full annotation on UniProt →

Function. Acts as an inhibitor of serine/threonine-protein phosphatase 2A (PP2A) activity. Inhibits PP2A activity by blocking the substrate binding site on PPP2R2A and the active site of PPP2CA. Potentiates ubiquitin-mediated proteasomal degradation of serine/threonine-protein phosphatase 2A catalytic subunit alpha (PPP2CA). Inhibits PP2A-mediated dephosphorylation of WEE1, promoting ubiquitin-mediated proteolysis of WEE1, thereby releasing G2/M checkpoint.

Subunit / interactions. Interacts with PPP2CA and PPP2R1A. Interacts (via its N-terminus) with PPP2R2A; the interaction is direct and this interaction inhibits PP2A activity. The CHEK1-mediated Ser-37 phosphorylated form interacts with 14-3-3 proteins.

Subcellular location. Nucleus. Cytoplasm.

Post-translational modifications. CHEK1-mediated phosphorylation at Ser-37 negatively regulates its ability to inhibit serine/threonine-protein phosphatase 2A (PP2A) activity. Phosphorylation leads to its release from the PP2A complex and its sequestration by 14-3-3 proteins in the cytoplasm resulting in its inability to translocate to the nucleus, where it otherwise inhibits PP2A.

Similarity. Belongs to the FAM122 family.

RefSeq proteins (1): NP_612206* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR026716PBIR1/2/3Family

UniProt features (33 total): modified residue 15, mutagenesis site 7, compositionally biased region 4, region of interest 3, helix 2, chain 1, cross-link 1

Structure

Experimental structures (PDB)

3 structures.

PDBMethodResolution (Å)
8TWEELECTRON MICROSCOPY2.55
8TWIELECTRON MICROSCOPY2.69
8SO0ELECTRON MICROSCOPY2.8

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q96E09-F160.540.08

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 (16): 45, 47, 48, 62, 76, 143, 147, 149, 187, 189, 267, 270, 276, 89, 35, 37

Mutagenesis-validated functional residues (7):

PositionPhenotype
37loss of phosphorylation and interaction with 14-3-3 proteins. enhanced interaction with ppp2r2a.
84–85impairs interaction with ppp2r2a and reduces the inhibition of pp2a activity by pabir1/fam122a.
88–89impairs interaction with ppp2r2a and reduces the inhibition of pp2a activity by pabir1/fam122a.
91impairs interaction with ppp2r2a and reduces the inhibition of pp2a activity by pabir1/fam122a.
92impairs interaction with ppp2r2a and reduces the inhibition of pp2a activity by pabir1/fam122a.
105reduces the inhibition of pp2a activity by pabir1/fam122a.
107reduces the inhibition of pp2a activity by pabir1/fam122a.

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 225 (showing top): GSE18804_BRAIN_VS_COLON_TUMORAL_MACROPHAGE_UP, AGGAAGC_MIR5163P, GOBP_REGULATION_OF_PROTEASOMAL_UBIQUITIN_DEPENDENT_PROTEIN_CATABOLIC_PROCESS, TGCGCANK_UNKNOWN, GOZGIT_ESR1_TARGETS_DN, GOBP_CELL_CYCLE_PHASE_TRANSITION, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_DN, GOBP_GROWTH, GOBP_POSITIVE_REGULATION_OF_PROTEIN_CATABOLIC_PROCESS, GOBP_MACROMOLECULE_CATABOLIC_PROCESS, IVANOVA_HEMATOPOIESIS_LATE_PROGENITOR, GGAMTNNNNNTCCY_UNKNOWN, GOBP_MITOTIC_G2_M_TRANSITION_CHECKPOINT, GOBP_REGULATION_OF_CELL_CYCLE_G2_M_PHASE_TRANSITION

GO Biological Process (3): positive regulation of cell growth (GO:0030307), positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436), mitotic G2/M transition checkpoint (GO:0044818)

GO Molecular Function (4): protein phosphatase inhibitor activity (GO:0004864), protein serine/threonine phosphatase inhibitor activity (GO:0004865), protein phosphatase 2A binding (GO:0051721), protein binding (GO:0005515)

GO Cellular Component (4): nucleus (GO:0005634), nucleoplasm (GO:0005654), cytoplasm (GO:0005737), nuclear body (GO:0016604)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure2
regulation of cell growth1
cell growth1
positive regulation of growth1
positive regulation of cellular process1
regulation of proteasomal ubiquitin-dependent protein catabolic process1
proteasome-mediated ubiquitin-dependent protein catabolic process1
positive regulation of proteasomal protein catabolic process1
positive regulation of ubiquitin-dependent protein catabolic process1
mitotic cell cycle checkpoint signaling1
negative regulation of G2/M transition of mitotic cell cycle1
phosphoprotein phosphatase activity1
phosphatase inhibitor activity1
protein phosphatase regulator activity1
protein serine/threonine phosphatase activity1
protein phosphatase inhibitor activity1
protein phosphatase binding1
binding1
intracellular membrane-bounded organelle1
nuclear lumen1
intracellular anatomical structure1
nucleoplasm1
intracellular membraneless organelle1

Protein interactions and networks

STRING

250 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
PABIR1OGFOD1Q8N543607
PABIR1PIP5K1BP78518478
PABIR1INTS15Q96N11446
PABIR1ZFYVE19Q96K21446
PABIR1PRKAG2Q9UGJ0402
PABIR1ENSAO43768398
PABIR1CIP2AQ8TCG1380
PABIR1UBE2Q2Q8WVN8325
PABIR1NAIF1Q69YI7325
PABIR1PHTF2Q8N3S3323
PABIR1NKAPLQ5M9Q1322
PABIR1DCUN1D4Q92564318
PABIR1ADGRF2PQ8IZF7317
PABIR1ARPP19P56211310
PABIR1MIGA1Q8NAN2310

IntAct

57 interactions, top by confidence:

ABTypeScore
PPP2R1APPP2R2Apsi-mi:“MI:0915”(physical association)0.970
PPP2R2APPP2R1Apsi-mi:“MI:0915”(physical association)0.970
PABIR1PPP2R1Apsi-mi:“MI:0914”(association)0.880
PPP2R1ASTRNpsi-mi:“MI:0914”(association)0.880
PPP2R2APABIR1psi-mi:“MI:0407”(direct interaction)0.820
PABIR1PPP2R2Apsi-mi:“MI:0407”(direct interaction)0.820
PPP2R2CPPP2R1Apsi-mi:“MI:0914”(association)0.730
POLR3GLPOLR3Apsi-mi:“MI:0914”(association)0.730
PPP2R2DYEATS4psi-mi:“MI:0914”(association)0.730
YWHAGBLTP3Bpsi-mi:“MI:2364”(proximity)0.640
PPP2R2AARPP19psi-mi:“MI:0407”(direct interaction)0.630
YWHAHPLEKHG3psi-mi:“MI:0914”(association)0.610
YWHAHBLTP3Bpsi-mi:“MI:2364”(proximity)0.570
PPP2R2ARBL1psi-mi:“MI:0915”(physical association)0.540
PPP2R1AENSApsi-mi:“MI:0914”(association)0.530
PABIR1TERF2IPpsi-mi:“MI:0915”(physical association)0.510
PABIR1psi-mi:“MI:0203”(dephosphorylation reaction)0.440
PKMPABIR1psi-mi:“MI:0217”(phosphorylation reaction)0.440
Ppp2r1aCCHCR1psi-mi:“MI:0914”(association)0.350
KIF11ILVBLpsi-mi:“MI:0914”(association)0.350
PPP2R1AINTS2psi-mi:“MI:0914”(association)0.350
Ppp2r2aPPP2R1Apsi-mi:“MI:0914”(association)0.350

BioGRID (65): FAM122A (Affinity Capture-MS), KLHL15 (Affinity Capture-MS), PPP2R1A (Affinity Capture-MS), PPP3CA (Affinity Capture-MS), FAM122B (Affinity Capture-MS), PPP2R2D (Affinity Capture-MS), PPP2R2A (Affinity Capture-MS), PPP3R1 (Affinity Capture-MS), RCAN1 (Affinity Capture-MS), FAM122A (Affinity Capture-MS), FAM122A (Affinity Capture-MS), FAM122A (Affinity Capture-MS), FAM122A (Affinity Capture-MS), FAM122A (Affinity Capture-MS), FAM122A (Affinity Capture-MS)

ESM2 similar proteins: A2AQ25, A4IGU9, A7E300, A8E4V2, B5DF41, B5DGK1, F1N4M2, O15079, O55003, O60238, O60516, Q0IHF8, Q0P5A7, Q12983, Q13541, Q14DQ1, Q1LWL8, Q3B7T9, Q3T013, Q3UN70, Q3ZCB6, Q5PR01, Q5XG16, Q5XKK7, Q5ZLN7, Q60876, Q62622, Q62739, Q63744, Q68EF0, Q68FF7, Q6AYT4, Q6PBI2, Q6PFP3, Q6ZNC4, Q7Z309, Q80U23, Q80VV3, Q8AVU0, Q8LD26

Diamond homologs: Q5ZLN7, Q6AYT4, Q6NZE7, Q6P4D5, Q7Z309, Q96E09, Q9DB52

SIGNOR signaling

2 interactions.

AEffectBMechanism
PABIR1“down-regulates activity”PPP2R2Abinding
CHEK1“down-regulates activity”PABIR1phosphorylation

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 47 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
Activation of BAD and translocation to mitochondria7152.3×9e-13
Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex7134.3×2e-12
SARS-CoV-1 targets host intracellular signalling and regulatory pathways7134.3×2e-12
Activation of BH3-only proteins799.3×2e-11
RHO GTPases activate PKNs763.4×4e-10
Intrinsic Pathway for Apoptosis758.6×7e-10
FOXO-mediated transcription657.6×2e-08
RAF activation548.0×6e-07

GO biological processes:

GO termPartnersFoldFDR
protein targeting544.7×1e-05
mitotic cell cycle722.8×6e-06
intracellular protein localization717.9×1e-05

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance26
Likely benign0
Benign1

Top pathogenic / likely-pathogenic (0)

SpliceAI

184 predictions. Top by Δscore:

VariantEffectΔscore
9:68781019:GTC:Gdonor_gain0.9600
9:68781020:TCT:Tdonor_gain0.9600
9:68781021:C:Gdonor_gain0.9600
9:68781025:G:GGdonor_gain0.9000
9:68780947:C:Adonor_gain0.8800
9:68781021:C:CGdonor_gain0.8700
9:68781024:A:AGdonor_gain0.8700
9:68780652:GTTTT:Gdonor_gain0.8500
9:68780945:G:GGdonor_gain0.8500
9:68781029:T:Gdonor_gain0.8500
9:68780290:C:CAacceptor_gain0.8300
9:68780623:G:Tdonor_gain0.8300
9:68780944:A:AGdonor_gain0.8200
9:68780623:G:GTdonor_gain0.8000
9:68780657:G:GGdonor_gain0.8000
9:68780942:A:Tdonor_gain0.7800
9:68780501:A:Gdonor_gain0.7700
9:68781028:A:AGdonor_gain0.7400
9:68780520:A:Tdonor_gain0.7200
9:68780932:C:Gdonor_gain0.7200
9:68781505:T:Adonor_gain0.7100
9:68780653:TTTT:Tdonor_gain0.7000
9:68780654:TTTG:Tdonor_loss0.6400
9:68780655:TTG:Tdonor_loss0.6400
9:68780656:TG:Tdonor_loss0.6400
9:68780657:G:GCdonor_loss0.6400
9:68780658:TAA:Tdonor_loss0.6400
9:68780659:A:ACdonor_loss0.6400
9:68780660:AGTAG:Adonor_loss0.6400
9:68780661:G:Cdonor_loss0.6400

AlphaMissense

1882 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
9:68780633:T:CF157L0.999
9:68780635:T:AF157L0.999
9:68780635:T:GF157L0.999
9:68780776:A:CR204S0.999
9:68780776:A:TR204S0.999
9:68780265:G:TR34M0.998
9:68780427:T:CI88T0.998
9:68780427:T:GI88S0.998
9:68780478:G:CR105P0.998
9:68780273:A:CS37R0.997
9:68780275:C:AS37R0.997
9:68780275:C:GS37R0.997
9:68780513:T:AW117R0.997
9:68780513:T:CW117R0.997
9:68780607:C:AP148H0.997
9:68780773:A:CK203N0.997
9:68780773:A:TK203N0.997
9:68780775:G:CR204T0.997
9:68780286:T:CI41T0.996
9:68780431:A:CK89N0.996
9:68780431:A:TK89N0.996
9:68780460:G:CR99P0.996
9:68780492:G:CA110P0.996
9:68780606:C:TP148S0.996
9:68780626:G:CK154N0.996
9:68780626:G:TK154N0.996
9:68780753:A:CS197R0.996
9:68780755:T:AS197R0.996
9:68780755:T:GS197R0.996
9:68780771:A:GK203E0.995

dbSNP variants (sampled 300 via entrez): RS1000762651 (9:68778099 T>C), RS1000779266 (9:68781319 ATAAC>A), RS1001186345 (9:68782324 A>G), RS1001818969 (9:68781922 C>T), RS1001883948 (9:68783237 T>C), RS1001916520 (9:68782833 ATCT>A), RS1001995024 (9:68785002 G>T), RS1002799471 (9:68781162 G>T), RS1002877105 (9:68779597 G>C), RS1003177627 (9:68781610 A>G,T), RS1003556675 (9:68784749 A>G), RS1004130584 (9:68778441 AC>A), RS1004440950 (9:68783022 T>A), RS1004807206 (9:68784185 A>G), RS1004856248 (9:68779111 G>A)

Disease associations

OMIM: gene MIM:617249 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

2 associations (top):

StudyTraitp-value
GCST000649_28Chronic kidney disease8.000000e-14
GCST007876_57Estimated glomerular filtration rate7.000000e-31

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

23 total (human), top 23 by PubMed support.

ChemicalActions (top 5)PubMed papers
Valproic Acidincreases expression2
3-((6-(2-methoxyphenyl)pyrimidin-4-yl)amino)phenyl)methane sulfonamidedecreases expression1
GSK-J4decreases expression1
FR900359affects phosphorylation1
triphenyl phosphateaffects expression1
kojic acidincreases expression1
coumarinincreases phosphorylation1
di-n-butylphosphoric acidaffects expression1
cylindrospermopsinincreases expression1
Sunitinibincreases expression1
Leflunomideincreases expression1
Acetaminophenincreases expression1
Atrazinedecreases expression1
Caffeineaffects phosphorylation1
Doxorubicindecreases expression1
Quercetinaffects phosphorylation1
Urethanedecreases expression1
Vanadatesdecreases expression1
Aflatoxin B1decreases methylation1
Antirheumatic Agentsincreases expression1
Copper Sulfatedecreases expression1
Lactic Aciddecreases expression1
Genisteinincreases expression1

Cellosaurus cell lines

2 cell lines: 2 cancer cell line

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

CellosaurusNameCategorySex
CVCL_SM82HAP1 FAM122A (-) 1Cancer cell lineMale
CVCL_XN63HAP1 FAM122A (-) 2Cancer cell lineMale

Clinical trials (associated diseases)

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

No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.