PPP2R5E

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

Basic information

Region (hg38): 14:63371363-63543377

Links

ENSG00000154001 ∙ NCBI:5529 ∙ OMIM:601647 ∙ HGNC:9313 ∙ Uniprot:Q16537 ∙ 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 PPP2R5E gene.

• not provided (3 variants)
• Inborn genetic diseases (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PPP2R5E 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					3	3
missense			2			2
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	2	0	3

Variants in PPP2R5E

This is a list of pathogenic ClinVar variants found in the PPP2R5E region.

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

Position	Type	Phenotype	Significance	ClinVar
14-63384503-G-A			Benign (Dec 04, 2017)
14-63389678-T-C			Benign (Jun 15, 2018)
14-63396661-A-C			Uncertain significance (-)
14-63415211-G-T			Benign (Jun 15, 2018)
14-63453753-A-G		not specified	Uncertain significance (Sep 29, 2022)
14-63539640-C-T		not specified	Uncertain significance (Feb 11, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PPP2R5E	protein_coding	protein_coding	ENST00000337537	13	172018

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.0000339	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.83	78	248	0.315	0.0000129	3082
Missense in Polyphen		12	93.215	0.12874		1280
Synonymous	-1.13	100	86.6	1.15	0.00000460	827
Loss of Function	5.00	0	29.1	0.00	0.00000151	355

LoF frequencies by population

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

dbNSFP

Source: dbNSFP

• Function: FUNCTION: The B regulatory subunit might modulate substrate selectivity and catalytic activity, and also might direct the localization of the catalytic enzyme to a particular subcellular compartment.
• 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);Focal Adhesion-PI3K-Akt-mTOR-signaling pathway;Wnt Signaling Pathway and Pluripotency;PI3K-Akt Signaling Pathway;Glycogen Metabolism;DNA Damage Response (only ATM dependent);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: 0.149

Intolerance Scores

• loftool: 0.0350
• rvis_EVS: -0.41
• rvis_percentile_EVS: 26.23

Haploinsufficiency Scores

• pHI: 0.557
• hipred: Y
• hipred_score: 0.830
• ghis: 0.702

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.985

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ppp2r5e

Gene ontology

• Biological process: protein dephosphorylation;signal transduction;regulation of protein autophosphorylation;regulation of phosphoprotein phosphatase activity
• Cellular component: protein phosphatase type 2A complex;nucleus;cytoplasm;cytosol
• Molecular function: protein binding;protein phosphatase regulator activity;protein phosphatase activator activity