PPP2R2A

protein phosphatase 2 regulatory subunit Balpha, the group of Protein phosphatase 2 regulatory subunits|WD repeat domain containing

Basic information

Region (hg38): 8:26291507-26372680

Links

ENSG00000221914 ∙ NCBI:5520 ∙ OMIM:604941 ∙ HGNC:9304 ∙ Uniprot:P63151 ∙ 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 PPP2R2A gene.

• Hereditary breast ovarian cancer syndrome (16 variants)
• Inborn genetic diseases (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PPP2R2A 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	2	1	4
missense			4			4
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				7	5	12
Total	0	0	5	9	6

Variants in PPP2R2A

This is a list of pathogenic ClinVar variants found in the PPP2R2A region.

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

Position	Type	Phenotype	Significance	ClinVar
8-26293613-G-C		Hereditary breast ovarian cancer syndrome	Likely benign (Apr 19, 2022)
8-26293676-A-G		Hereditary breast ovarian cancer syndrome	Uncertain significance (Apr 19, 2022)
8-26293751-G-A		Hereditary breast ovarian cancer syndrome	Benign (Apr 19, 2022)
8-26293766-T-G		Hereditary breast ovarian cancer syndrome	Benign (Apr 19, 2022)
8-26293797-A-G		Hereditary breast ovarian cancer syndrome	Likely benign (Apr 19, 2022)
8-26354481-C-T		not specified	Uncertain significance (Oct 14, 2023)
8-26360273-A-G		not specified	Uncertain significance (Aug 30, 2022)
8-26360340-A-C		Hereditary breast ovarian cancer syndrome	Benign (Apr 19, 2022)
8-26360986-A-G		not specified	Uncertain significance (Jul 16, 2021)
8-26360992-A-G		not specified	Uncertain significance (Dec 13, 2023)
8-26361061-A-G		not specified	Uncertain significance (Jan 03, 2024)
8-26362748-T-G		not specified	Uncertain significance (Jan 09, 2024)
8-26362926-A-G		Hereditary breast ovarian cancer syndrome	Likely benign (Apr 19, 2022)
8-26363964-C-G		Hereditary breast ovarian cancer syndrome	Likely benign (Apr 19, 2022)
8-26366277-C-G		Hereditary breast ovarian cancer syndrome	Likely benign (Apr 19, 2022)
8-26366341-C-T		Hereditary breast ovarian cancer syndrome	Likely benign (Apr 19, 2022)
8-26366423-T-C		Hereditary breast ovarian cancer syndrome	Likely benign (Apr 19, 2022)
8-26370071-AT-A		Hereditary breast ovarian cancer syndrome	Likely benign (Apr 19, 2022)
8-26370083-A-C		Hereditary breast ovarian cancer syndrome	Benign (Apr 19, 2022)
8-26370124-A-G		Hereditary breast ovarian cancer syndrome	Benign (Apr 19, 2022)
8-26370187-C-T		not specified	Uncertain significance (Dec 16, 2022)
8-26370232-C-T		not specified	Uncertain significance (Dec 14, 2021)
8-26370302-C-T		Hereditary breast ovarian cancer syndrome	Likely benign (Apr 19, 2022)
8-26370316-A-G		not specified	Uncertain significance (Jan 16, 2024)
8-26370332-C-T		Hereditary breast ovarian cancer syndrome	Benign (Apr 19, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PPP2R2A	protein_coding	protein_coding	ENST00000315985	10	81190

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.995	0.00505	125733	0	4	125737	0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.36	95	242	0.392	0.0000118	3072
Missense in Polyphen		13	78.299	0.16603		1052
Synonymous	0.794	72	81.1	0.888	0.00000388	793
Loss of Function	4.21	2	24.5	0.0817	0.00000146	288

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000554	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000176	0.0000176
Middle Eastern	0.0000554	0.0000544
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);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);EGF-Ncore;Wnt Signaling Pathway and Pluripotency;PI3K-Akt Signaling Pathway;Glycogen Metabolism;Cyclin D associated events in G1;G1 Phase;Mitotic G1-G1/S phases;Cyclin A/B1/B2 associated events during G2/M transition;TGF_beta_Receptor;ErbB1 downstream signaling;G2/M Transition;Mitotic G2-G2/M phases;Initiation of Nuclear Envelope Reformation;Nuclear Envelope Reassembly;Mitotic Anaphase;Mitotic Metaphase and Anaphase;M Phase;Cell Cycle;Cell Cycle, Mitotic;TGF-beta receptor signaling (Consensus)

Intolerance Scores

• loftool: 0.402
• rvis_EVS: -0.34
• rvis_percentile_EVS: 30.07

Haploinsufficiency Scores

• hipred: Y
• hipred_score: 0.783
• ghis: 0.627

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.944

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ppp2r2a
• Phenotype: renal/urinary system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); homeostasis/metabolism phenotype; endocrine/exocrine gland phenotype

Gene ontology

• Biological process: G2/M transition of mitotic cell cycle;nuclear-transcribed mRNA catabolic process, nonsense-mediated decay;mitotic cell cycle;protein dephosphorylation;response to morphine;regulation of phosphoprotein phosphatase activity;peptidyl-serine dephosphorylation
• Cellular component: protein phosphatase type 2A complex;nucleoplasm;cytosol;glutamatergic synapse
• Molecular function: protein serine/threonine phosphatase activity;protein binding;protein phosphatase regulator activity;protein-containing complex binding;tau protein binding;protein phosphatase 2A binding