PPP2R1B

protein-coding

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

Gene summary

This gene encodes a constant regulatory subunit of protein phosphatase 2. 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 constant regulatory subunit A serves as a scaffolding molecule to coordinate the assembly of the catalytic subunit and a variable regulatory B subunit. This gene encodes a beta isoform of the constant regulatory subunit A. Mutations in this gene have been associated with some lung and colon cancers. Alternatively spliced transcript variants have been described. [provided by RefSeq, Apr 2010]

MANE transcript

NM_002716.5

Inheritance

—

ClinVar variants

P:1U:96B:3

Top phenotype

PPP2R1B-related disorder

gnomAD constraint

pLI —, LoF o/e 0.77

Max pathogenic AF

—

Genomic locus

chr11:111,726,908-111,766,389

External References & Databases

Ensembl (ENSG00000137713)

Transcript & Mutation Effects

hg38 • Region Span ~39.5 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to PPP2R1B variants in ClinVar

4 Conditions Cataloged

not specifiedTotal: 81

PPP2R1B-related disorderTotal: 3

not providedTotal: 2

Lung carcinomaTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_002716.5. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			4 clinvar	1 clinvar		5
missense	1 clinvar		88 clinvar	2 clinvar		91
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			4 clinvar			4
Total	1	0	96	3	0	100

Highest pathogenic variant AF is 0.010499544

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 58 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_002716.5	RefSeq	NP_002707.3	15	MANE Select
ENST00000527614.6	Ensembl	ENSP00000437193.1	15	MANE Select
NM_001177562.2	RefSeq	NP_001171033.1	14	Standard
NM_001177563.2	RefSeq	NP_001171034.1	13	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

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)

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

Molecular Function

protein serine/threonine phosphatase activity
protein binding
protein phosphatase regulator activity

Cellular Component

protein phosphatase type 2A complex
cytoplasm
membrane raft
extracellular exosome

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000311129
Coding exons: 16
Length: 39520
Individuals with no LoFs: 125467
Homozygous LoFs: 2
Heterozygous LoFs: 279
Defined: 125748
p: 0.00112

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.07	311	369	0.843	0.0000194	4323
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00031	0.00031	rare
Latino/Admixed American	0.0015	0.0015	notable
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0.00022	0.00022	rare
Finnish	0.00060	0.00055	rare
European (Non-Finnish)	0.0014	0.0014	notable
South Asian	0.0013	0.0013	notable
Other	0.0022	0.0020	notable

dbNSFP Gene Annotations

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.;

Recessive Scores

pRec: 0.108

Intolerance Scores

LoFtool: 0.491
RVIS EVS: 0.09
RVIS percentile EVS: 60.57

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.922

Gene Damage Prediction

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