PPP3R1

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

Basic information

Region (hg38): 2:68178857-68256237

Links

ENSG00000221823 ∙ NCBI:5534 ∙ OMIM:601302 ∙ HGNC:9317 ∙ Uniprot:P63098 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Transcripts

Transcript IDs starting with ENST are treated as Ensembl, all others as RefSeq. Showing 4 of 4.

Transcript ID	Protein ID	Coding exons	MANE Select	MANE Plus Clinical
NM_000945.4	NP_000936.1	6	yes	-
ENST00000234310.8	ENSP00000234310.3	6	yes	-
ENST00000409377.1	ENSP00000387148.1	5	-	-
ENST00000409752.5	ENSP00000387216.1	6	-	-

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PPP3R1 gene.

• not_specified (2 variants)
• Neurodevelopmental_disorder (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PPP3R1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000945.4. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			1			1
missense			2			2
nonsense						0
start loss						0
frameshift			1			1
splice donor/acceptor (+/-2bp)			1			1
Total	0	0	5	0	0

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PPP3R1	protein_coding	protein_coding	ENST00000234310	6	77381

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
		124538	0	6	124544	0.0000241

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.89	10	84.8	0.118	0.00000380	1147
Missense in Polyphen		1	27.524	0.036332		385
Synonymous	1.02	23	30.1	0.764	0.00000151	283
Loss of Function	2.25	2	9.48	0.211	4.83e-7	123

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000105	0.000105
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000291	0.0000266
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:0000269|PubMed:26794871}.
• 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;TFs Regulate miRNAs related to cardiac hypertrophy;miR-targeted genes in lymphocytes - TarBase;Alzheimers Disease;Initiation of transcription and translation elongation at the HIV-1 LTR;MAPK Signaling Pathway;Wnt Signaling Pathway;Signaling by GPCR;Signaling by WNT;Signal Transduction;Calcineurin activates NFAT;Signaling by the B Cell Receptor (BCR);CLEC7A (Dectin-1) induces NFAT activation;CLEC7A (Dectin-1) signaling;C-type lectin receptors (CLRs);Activation of BAD and translocation to mitochondria ;Activation of BH3-only proteins;FCERI mediated Ca+2 mobilization;Fc epsilon receptor (FCERI) signaling;Intrinsic Pathway for Apoptosis;Innate Immune System;Immune System;Apoptosis;Programmed Cell Death;Adaptive Immune System;Downstream signaling events of B Cell Receptor (BCR);DARPP-32 events;Ca2+ pathway;Beta-catenin independent WNT signaling;Opioid Signalling;G alpha (i) signalling events;GPCR downstream signalling;CD4 T cell receptor signaling-JNK cascade;CD4 T cell receptor signaling (Consensus)

Intolerance Scores

• rvis_EVS: 0.08
• rvis_percentile_EVS: 59.43

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.486

Gene ontology

• Biological process: protein dephosphorylation;Wnt signaling pathway, calcium modulating pathway;calcineurin-NFAT signaling cascade;Fc-epsilon receptor signaling pathway;positive regulation of transcription by RNA polymerase II
• Cellular component: nucleoplasm;cytosol;calcineurin complex;sarcolemma
• Molecular function: calcium-dependent protein serine/threonine phosphatase activity;calcium ion binding;protein binding;calmodulin binding;cyclosporin A binding;phosphatase binding;protein domain specific binding