PPP2R5B

protein phosphatase 2 regulatory subunit B'beta, the group of Armadillo like helical domain containing|Protein phosphatase 2 regulatory subunits

Basic information

Region (hg38): 11:64917553-64934475

Links

ENSG00000068971 ∙ NCBI:5526 ∙ OMIM:601644 ∙ HGNC:9310 ∙ Uniprot:Q15173 ∙ 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 PPP2R5B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PPP2R5B 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				9	3	12
missense			31	2		33
nonsense						0
start loss						0
frameshift						0
inframe indel			1			1
splice donor/acceptor (+/-2bp)						0
splice region				1	1	2
non coding			1	5	3	9
Total	0	0	33	16	6

Variants in PPP2R5B

This is a list of pathogenic ClinVar variants found in the PPP2R5B region.

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

Position	Type	Phenotype	Significance	ClinVar
11-64925753-C-T		PPP2R5B-related disorder	Uncertain significance (Jan 09, 2023)
11-64925766-C-T		not specified	Uncertain significance (Jul 26, 2024)
11-64925806-A-C			Likely benign (Sep 01, 2024)
11-64925833-C-A			Likely benign (Nov 25, 2023)
11-64925835-G-C		not specified	Uncertain significance (May 20, 2024)
11-64925843-C-T		not specified	Uncertain significance (Oct 20, 2021)
11-64925852-C-T		not specified	Uncertain significance (Dec 22, 2023)
11-64925861-C-T		not specified	Uncertain significance (Jul 30, 2023)
11-64925875-C-A		PPP2R5B-related disorder	Likely benign (Apr 04, 2024)
11-64925902-G-A			Likely benign (Jan 13, 2024)
11-64925902-G-C		not specified	Uncertain significance (Mar 11, 2022)
11-64925917-G-A			Benign/Likely benign (Aug 01, 2024)
11-64926692-G-C			Likely benign (Nov 30, 2021)
11-64926734-C-T			Likely benign (Nov 28, 2023)
11-64926737-G-A		PPP2R5B-related disorder	Likely benign (Apr 01, 2023)
11-64926781-T-C		not specified	Uncertain significance (Nov 03, 2022)
11-64926789-T-A			Uncertain significance (Apr 04, 2022)
11-64926797-C-G		PPP2R5B-related disorder	Likely benign (Apr 04, 2024)
11-64926822-C-T			Uncertain significance (Sep 22, 2023)
11-64926835-A-G		not specified	Uncertain significance (May 18, 2022)
11-64926866-G-A			Likely benign (Aug 05, 2023)
11-64926885-G-A		not specified	Uncertain significance (Dec 27, 2023)
11-64926885-G-C			Uncertain significance (Dec 07, 2023)
11-64927829-C-G			Uncertain significance (Sep 19, 2022)
11-64927831-G-A			Likely benign (Aug 27, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PPP2R5B	protein_coding	protein_coding	ENST00000164133	13	16921

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.984	0.0158	125740	0	8	125748	0.0000318

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.46	182	302	0.602	0.0000188	3219
Missense in Polyphen		70	124.49	0.56228		1262
Synonymous	0.363	117	122	0.958	0.00000698	988
Loss of Function	4.16	3	25.8	0.116	0.00000120	303

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000181	0.000181
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000264	0.0000264
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: As the regulatory component of the serine/threonine- protein phosphatase 2A (PP2A) holoenzyme, modulates substrate specificity, subcellular localization, and responsiveness to phosphorylation. The phosphorylated form mediates the interaction between PP2A and AKT1, leading to AKT1 dephosphorylation. {ECO:0000269|PubMed:21329884}.
• Pathway: PI3K-Akt signaling pathway - Homo sapiens (human);Dopaminergic synapse - Homo sapiens (human);Oocyte meiosis - Homo sapiens (human);mRNA surveillance pathway - Homo sapiens (human);AMPK signaling pathway - Homo sapiens (human);Adrenergic signaling in cardiomyocytes - Homo sapiens (human);Sphingolipid signaling pathway - Homo sapiens (human);Human papillomavirus infection - Homo sapiens (human);XBP1(S) activates chaperone genes;Focal Adhesion-PI3K-Akt-mTOR-signaling pathway;PI3K-Akt Signaling Pathway;Glycogen Metabolism;Degradation of beta-catenin by the destruction complex;RAF activation;Signaling by WNT;Signal Transduction;GPCR Dopamine D1like receptor;CTLA4 inhibitory signaling;Costimulation by the CD28 family;Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal;Amplification of signal from the kinetochores;Mitotic Spindle Checkpoint;Cell Cycle Checkpoints;Immune System;Adaptive Immune System;insulin Mam;RHO GTPases Activate Formins;Disassembly of the destruction complex and recruitment of AXIN to the membrane;RHO GTPase Effectors;Signaling by Rho GTPases;Hemostasis;Negative regulation of MAPK pathway;RAF/MAP kinase cascade;MAPK1/MAPK3 signaling;MAPK family signaling cascades;PIP3 activates AKT signaling;Beta-catenin phosphorylation cascade;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;M Phase;Cell Cycle;Resolution of Sister Chromatid Cohesion;Platelet sensitization by LDL;Platelet homeostasis;Cell Cycle, Mitotic;Intracellular signaling by second messengers;TCF dependent signaling in response to WNT;insulin (Consensus)

Recessive Scores

• pRec: 0.107

Intolerance Scores

• loftool: 0.175
• rvis_EVS: -0.54
• rvis_percentile_EVS: 20.26

Haploinsufficiency Scores

• pHI: 0.161
• hipred: Y
• hipred_score: 0.785
• ghis: 0.645

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.946

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ppp2r5b

Gene ontology

• Biological process: protein dephosphorylation;regulation of signaling receptor activity;positive regulation of neuron projection development;regulation of phosphatidylinositol 3-kinase signaling;positive regulation of protein complex assembly;regulation of protein autophosphorylation;IRE1-mediated unfolded protein response;regulation of phosphoprotein phosphatase activity;positive regulation of transcription by RNA polymerase II;regulation of peptidyl-tyrosine phosphorylation;positive regulation of DNA-binding transcription factor activity;positive regulation of neurotrophin TRK receptor signaling pathway;negative regulation of G0 to G1 transition;positive regulation of cell cycle arrest;cellular response to growth factor stimulus
• Cellular component: protein phosphatase type 2A complex;nucleus;cytoplasm;cytosol
• Molecular function: protein binding;protein phosphatase regulator activity;protein phosphatase activator activity