PPP2R1B

protein phosphatase 2 scaffold subunit Abeta, the group of Armadillo like helical domain containing|Protein phosphatase 2 scaffold subunits|STRIPAK complex

Basic information

Region (hg38): 11:111726907-111766389

Links

ENSG00000137713 ∙ NCBI:5519 ∙ OMIM:603113 ∙ HGNC:9303 ∙ Uniprot:P30154 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PPP2R1B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PPP2R1B gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1		1
missense			28	5	1	34
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding				1		1
Total	0	0	28	7	1

Variants in PPP2R1B

This is a list of pathogenic ClinVar variants found in the PPP2R1B region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
11-111726958-T-C		PPP2R1B-related disorder	Likely benign (Sep 17, 2019)
11-111726969-T-A		PPP2R1B-related disorder	Likely benign (Jun 01, 2022)
11-111727038-C-T		not specified	Likely benign (Jan 08, 2024)
11-111727039-G-A		not specified	Uncertain significance (Feb 14, 2023)
11-111737492-T-A		PPP2R1B-related disorder	Benign/Likely benign (Nov 01, 2022)
11-111737534-C-G		PPP2R1B-related disorder	Benign (Nov 18, 2019)
11-111742059-T-C		PPP2R1B-related disorder	Likely benign (Jul 20, 2022)
11-111742068-G-C		not specified	Uncertain significance (Mar 16, 2022)
11-111742079-T-C		not specified	Uncertain significance (May 07, 2024)
11-111742515-A-C		PPP2R1B-related disorder	Likely benign (Jan 06, 2020)
11-111742589-T-C		not specified	Uncertain significance (Jul 22, 2022)
11-111742628-T-A		not specified	Uncertain significance (Aug 17, 2021)
11-111742643-T-A		not specified	Uncertain significance (Jun 03, 2022)
11-111743383-C-T		not specified	Uncertain significance (Nov 29, 2023)
11-111743423-T-C		not specified	Uncertain significance (Nov 03, 2023)
11-111743450-T-C		not specified	Uncertain significance (Jul 14, 2021)
11-111743482-T-G		not specified	Uncertain significance (Jun 30, 2023)
11-111743527-T-C		not specified	Uncertain significance (Sep 17, 2021)
11-111752301-T-C		not specified	Uncertain significance (Aug 09, 2021)
11-111752319-C-T		not specified	Uncertain significance (Jan 04, 2022)
11-111752323-C-T		not specified	Uncertain significance (Oct 12, 2021)
11-111753448-C-T		not specified	Uncertain significance (Mar 06, 2023)
11-111753522-A-G		not specified	Uncertain significance (Jan 10, 2023)
11-111753543-G-A		not specified	Uncertain significance (Aug 01, 2022)
11-111754509-G-A		not specified	Uncertain significance (Jul 26, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PPP2R1B	protein_coding	protein_coding	ENST00000311129	16	39520

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.00e-15	0.239	125467	2	279	125748	0.00112

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.07	311	369	0.843	0.0000194	4323
Missense in Polyphen		67	99.621	0.67255		1027
Synonymous	0.589	125	134	0.935	0.00000665	1340
Loss of Function	1.26	27	35.0	0.771	0.00000179	420

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00185	0.00185
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.000218	0.000217
Finnish	0.000601	0.000554
European (Non-Finnish)	0.00139	0.00136
Middle Eastern	0.000218	0.000217
South Asian	0.00132	0.00131
Other	0.00215	0.00196

dbNSFP

Source: dbNSFP

• Function: FUNCTION: The PR65 subunit of protein phosphatase 2A serves as a scaffolding molecule to coordinate the assembly of the catalytic subunit and a variable regulatory B subunit.
• Pathway: PI3K-Akt signaling pathway - Homo sapiens (human);TGF-beta signaling pathway - Homo sapiens (human);Dopaminergic synapse - Homo sapiens (human);Oocyte meiosis - Homo sapiens (human);Long-term depression - Homo sapiens (human);Tight junction - Homo sapiens (human);mRNA surveillance pathway - Homo sapiens (human);AMPK signaling pathway - Homo sapiens (human);Adrenergic signaling in cardiomyocytes - Homo sapiens (human);Hippo signaling pathway - Homo sapiens (human);Chagas disease (American trypanosomiasis) - Homo sapiens (human);Sphingolipid signaling pathway - Homo sapiens (human);Hepatitis C - Homo sapiens (human);Human papillomavirus infection - Homo sapiens (human);Focal Adhesion-PI3K-Akt-mTOR-signaling pathway;Wnt Signaling Pathway and Pluripotency;PI3K-Akt Signaling Pathway;Glycogen Metabolism;Signaling by GPCR;Degradation of beta-catenin by the destruction complex;RAF activation;Toll Like Receptor 7/8 (TLR7/8) Cascade;Interleukin-17 signaling;Signaling by WNT;Signal Transduction;Gene expression (Transcription);Inhibition of replication initiation of damaged DNA by RB1/E2F1;Signaling by Interleukins;Generic Transcription Pathway;Metabolism of carbohydrates;Cytokine Signaling in Immune system;Toll Like Receptor 9 (TLR9) Cascade;PP2A-mediated dephosphorylation of key metabolic factors;GPCR Dopamine D1like receptor;MyD88 cascade initiated on plasma membrane;Toll Like Receptor 10 (TLR10) Cascade;Toll Like Receptor 3 (TLR3) Cascade;Toll Like Receptor 5 (TLR5) Cascade;Toll-Like Receptors Cascades;CTLA4 inhibitory signaling;Costimulation by the CD28 family;MASTL Facilitates Mitotic Progression;RNA Polymerase II Transcription;Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal;Amplification of signal from the kinetochores;Mitotic Spindle Checkpoint;Cell Cycle Checkpoints;Innate Immune System;Immune System;Metabolism;Cyclin D associated events in G1;G1 Phase;Adaptive Immune System;insulin Mam;RHO GTPases Activate Formins;E2F mediated regulation of DNA replication;Mitotic G1-G1/S phases;Nuclear Events (kinase and transcription factor activation);Disassembly of the destruction complex and recruitment of AXIN to the membrane;Cyclin A/B1/B2 associated events during G2/M transition;DARPP-32 events;Glycolysis;RHO GTPase Effectors;Signaling by Rho GTPases;ERKs are inactivated;Signaling by NTRK1 (TRKA);Signaling by NTRKs;ERK/MAPK targets;MAPK targets/ Nuclear events mediated by MAP kinases;MAP kinase activation;TRAF6 mediated induction of NFkB and MAP kinases upon TLR7/8 or 9 activation;Hemostasis;MyD88 dependent cascade initiated on endosome;Negative regulation of MAPK pathway;RAF/MAP kinase cascade;MAPK1/MAPK3 signaling;MAPK family signaling cascades;Regulation of TP53 Degradation;Regulation of TP53 Expression and Degradation;G2/M Transition;Mitotic G2-G2/M phases;PIP3 activates AKT signaling;G1/S Transition;Beta-catenin phosphorylation cascade;Mitotic Prophase;Regulation of TP53 Activity;Transcriptional Regulation by TP53;PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling;Negative regulation of the PI3K/AKT network;Mitotic Prometaphase;Separation of Sister Chromatids;Mitotic Anaphase;Mitotic Metaphase and Anaphase;Opioid Signalling;G alpha (i) signalling events;M Phase;Glucose metabolism;Cell Cycle;Resolution of Sister Chromatid Cohesion;TRIF(TICAM1)-mediated TLR4 signaling ;MyD88-independent TLR4 cascade ;Toll Like Receptor 4 (TLR4) Cascade;Signaling by Receptor Tyrosine Kinases;Integration of energy metabolism;Platelet sensitization by LDL;Platelet homeostasis;Cell Cycle, Mitotic;GPCR downstream signalling;Intracellular signaling by second messengers;MyD88:Mal cascade initiated on plasma membrane;Toll Like Receptor TLR1:TLR2 Cascade;Toll Like Receptor TLR6:TLR2 Cascade;Toll Like Receptor 2 (TLR2) Cascade;TCF dependent signaling in response to WNT;insulin (Consensus)

Recessive Scores

• pRec: 0.108

Intolerance Scores

• loftool: 0.491
• rvis_EVS: 0.09
• rvis_percentile_EVS: 60.57

Haploinsufficiency Scores

• pHI: 0.891
• hipred: Y
• hipred_score: 0.624
• ghis: 0.430

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.922

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Ppp2r1b
• Phenotype: hematopoietic system phenotype; reproductive system phenotype; immune system phenotype

Gene ontology

• Biological process: protein dephosphorylation;regulation of phosphoprotein phosphatase activity;apoptotic process involved in morphogenesis;positive regulation of extrinsic apoptotic signaling pathway in absence of ligand
• Cellular component: protein phosphatase type 2A complex;cytoplasm;membrane raft;extracellular exosome
• Molecular function: protein serine/threonine phosphatase activity;protein binding;protein phosphatase regulator activity