PPP3CB

protein-coding

protein phosphatase 3 catalytic subunit beta, the group of Protein phosphatase catalytic subunits

Gene summary

Enables several functions, including calmodulin binding activity; calmodulin-dependent protein phosphatase activity; and protein phosphatase 2B binding activity. Involved in several processes, including calcineurin-NFAT signaling cascade; positive regulation of lysosome organization; and positive regulation of protein localization to nucleus. Located in cytosol. Part of calcineurin complex. Implicated in aortic valve stenosis. Biomarker of focal segmental glomerulosclerosis and schizophrenia. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

CALNB

MANE transcript

NM_021132.4

Inheritance

—

ClinVar variants

U:28

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0

Max pathogenic AF

—

Genomic locus

chr10:73,436,433-73,496,024

External References & Databases

Ensembl (ENSG00000107758)

Transcript & Mutation Effects

hg38 • Region Span ~59.6 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to PPP3CB variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 23

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_021132.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar			1
missense			23 clinvar			23
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			4 clinvar			4
Total	0	0	28	0	0	28

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 64 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_021132.4	RefSeq	NP_066955.1	14	MANE Select
ENST00000360663.10	Ensembl	ENSP00000353881.5	14	MANE Select
NM_001142353.3	RefSeq	NP_001135825.1	14	Standard
NM_001142354.3	RefSeq	NP_001135826.1	13	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

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)

Biological Process

negative regulation of T cell mediated cytotoxicity
lymphangiogenesis
protein phosphorylation
protein dephosphorylation
signal transduction

Molecular Function

protein serine/threonine phosphatase activity
calcium ion binding
protein binding
calmodulin binding
drug binding

Cellular Component

nucleoplasm
cytoplasm
cytosol
plasma membrane
calcineurin complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000394829
Coding exons: 14
Length: 59597
Individuals with no LoFs: 125540
Homozygous LoFs: 0
Heterozygous LoFs: 1
Defined: 125541
p: 0.00000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	3.79	100	278	0.360	0.0000138	3431
Missense (PolyPhen)		10	89.336	0.11194		1115
Synonymous	0.271	95	98.4	0.965	0.00000509	984
Loss of Function	5.11	0	30.4	0.00	0.00000174	367

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.0000088	0.0000088	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Calcium-dependent, calmodulin-stimulated protein phosphatase which plays an essential role in the transduction of intracellular Ca(2+)-mediated signals (PubMed:19154138, PubMed:26794871). Dephosphorylates and activates transcription factor NFATC1 (PubMed:19154138). Dephosphorylates and inactivates transcription factor ELK1 (PubMed:19154138). Dephosphorylates DARPP32 (PubMed:19154138). {ECO:0000269|PubMed:19154138, ECO:0000269|PubMed:26794871}.;

Recessive Scores

pRec: 0.185

Intolerance Scores

LoFtool: 0.156
RVIS EVS: -0.14
RVIS percentile EVS: 42.88

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.988

Gene Damage Prediction

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