PPP3R2

protein phosphatase 3 regulatory subunit B, beta, the group of Protein phosphatase 3 regulatory subunits|EF-hand domain containing

Basic information

Region (hg38): 9:101591604-101595021

Links

ENSG00000188386 ∙ NCBI:5535 ∙ OMIM:613821 ∙ HGNC:9318 ∙ Uniprot:Q96LZ3 ∙ 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 PPP3R2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PPP3R2 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						0
missense			10			10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1			1
Total	0	0	11	0	0

Variants in PPP3R2

This is a list of pathogenic ClinVar variants found in the PPP3R2 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-101594414-C-T		not specified	Uncertain significance (Dec 01, 2022)
9-101594473-A-G		not specified	Uncertain significance (Feb 17, 2023)
9-101594522-C-A		not specified	Uncertain significance (Jan 04, 2022)
9-101594675-T-A		not specified	Uncertain significance (Oct 24, 2023)
9-101594726-C-T		not specified	Uncertain significance (Aug 17, 2022)
9-101594735-C-T		not specified	Uncertain significance (Aug 16, 2021)
9-101594767-T-G		not specified	Uncertain significance (Oct 12, 2022)
9-101594773-C-A		not specified	Uncertain significance (Apr 20, 2024)
9-101594777-G-C		not specified	Uncertain significance (Oct 12, 2021)
9-101594782-G-C		not specified	Uncertain significance (Jun 11, 2021)
9-101594836-T-C		not specified	Uncertain significance (Oct 29, 2021)
9-101594926-G-C		not specified	Uncertain significance (Aug 02, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PPP3R2	protein_coding	protein_coding	ENST00000374806	1	3387

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00107	0.392	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.000593	108	108	1.00	0.00000665	1170
Missense in Polyphen		32	27.999	1.1429		336
Synonymous	0.992	43	52.1	0.825	0.00000417	322
Loss of Function	-0.307	4	3.39	1.18	2.27e-7	38

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: Regulatory subunit of calcineurin, a calcium-dependent, calmodulin stimulated protein phosphatase. Confers calcium sensitivity. {ECO:0000250|UniProtKB:P63098}.
• Pathway: Oxytocin signaling pathway - Homo sapiens (human);T cell receptor signaling pathway - Homo sapiens (human);B cell receptor signaling pathway - Homo sapiens (human);Kaposi,s sarcoma-associated herpesvirus infection - Homo sapiens (human);VEGF signaling pathway - Homo sapiens (human);Long-term potentiation - Homo sapiens (human);Glutamatergic synapse - Homo sapiens (human);Oocyte meiosis - Homo sapiens (human);Alzheimer,s disease - Homo sapiens (human);Amyotrophic lateral sclerosis (ALS) - Homo sapiens (human);HTLV-I infection - Homo sapiens (human);Axon guidance - Homo sapiens (human);Glucagon signaling pathway - Homo sapiens (human);Calcium signaling pathway - Homo sapiens (human);C-type lectin receptor signaling pathway - Homo sapiens (human);Renin secretion - Homo sapiens (human);Tuberculosis - Homo sapiens (human);Th17 cell differentiation - Homo sapiens (human);Th1 and Th2 cell differentiation - Homo sapiens (human);MAPK signaling pathway - Homo sapiens (human);Natural killer cell mediated cytotoxicity - Homo sapiens (human);Amphetamine addiction - Homo sapiens (human);Osteoclast differentiation - Homo sapiens (human);Wnt signaling pathway - Homo sapiens (human);cGMP-PKG signaling pathway - Homo sapiens (human);Cellular senescence - Homo sapiens (human);Tacrolimus/Cyclosporine Pathway, Pharmacodynamics;Energy Metabolism;Alzheimers Disease;Initiation of transcription and translation elongation at the HIV-1 LTR;MAPK Signaling Pathway;Wnt Signaling Pathway (Consensus)

Intolerance Scores

• loftool: 0.688
• rvis_EVS: -0.01
• rvis_percentile_EVS: 53.19

Haploinsufficiency Scores

• pHI: 0.180
• hipred: N
• hipred_score: 0.357
• ghis: 0.394

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ppp3r2
• Phenotype: cellular phenotype; reproductive system phenotype; skeleton phenotype; limbs/digits/tail phenotype

Gene ontology

• Molecular function: calcium ion binding;protein binding