PPP2R3B

protein phosphatase 2 regulatory subunit B''beta, the group of Pseudoautosomal region 1|Protein phosphatase 2 regulatory subunits|EF-hand domain containing

Basic information

Region (hg38): Y:333933-386955

Previous symbols: [ "PPP2R3L" ]

Links

ENSG00000292327

∙ NCBI:28227 ∙ OMIM:300339 ∙ HGNC:13417 ∙ Uniprot:Q9Y5P8 ∙ 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 PPP2R3B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PPP2R3B 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				2 clinvar		2
missense						0
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	0	2	0

Variants in PPP2R3B

This is a list of pathogenic ClinVar variants found in the PPP2R3B region.

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

Position	Type	Phenotype	Significance	ClinVar
Y-338615-G-A			Likely benign (Jun 01, 2022)	2659854

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PPP2R3B	protein_coding	protein_coding	ENST00000390665	13	52993

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.93e-8	0.958	125551	0	38	125589	0.000151

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.40	407	335	1.22	0.0000238	3695
Missense in Polyphen		104	101.37	1.0259		1098
Synonymous	-4.15	228	161	1.42	0.0000141	1099
Loss of Function	1.99	16	27.2	0.588	0.00000136	300

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000116	0.000116
Ashkenazi Jewish	0.0000998	0.0000992
East Asian	0.000275	0.000272
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.000143	0.000141
Middle Eastern	0.000275	0.000272
South Asian	0.000230	0.000229
Other	0.000493	0.000489

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);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);Wnt Signaling Pathway and Pluripotency;PI3K-Akt Signaling Pathway;Glycogen Metabolism;Inhibition of replication initiation of damaged DNA by RB1/E2F1;GPCR Dopamine D1like receptor;Cyclin D associated events in G1;G1 Phase;insulin Mam;E2F mediated regulation of DNA replication;Mitotic G1-G1/S phases;Cyclin A/B1/B2 associated events during G2/M transition;G2/M Transition;Mitotic G2-G2/M phases;G1/S Transition;Cell Cycle;Cell Cycle, Mitotic;Regulation of retinoblastoma protein;insulin (Consensus)

Intolerance Scores

loftool: 0.691
rvis_EVS: 0.34
rvis_percentile_EVS: 73.74

Haploinsufficiency Scores

pHI: 0.0708
hipred: Y
hipred_score: 0.519
ghis: 0.491

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.731

Gene Damage Prediction

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

Gene ontology

Biological process: protein dephosphorylation;cell cycle arrest;regulation of phosphoprotein phosphatase activity
Cellular component: protein phosphatase type 2A complex;nucleus;nucleoplasm
Molecular function: phosphoprotein phosphatase activity;protein serine/threonine phosphatase activity;calcium ion binding;protein binding;protein phosphatase regulator activity