PPP3CC

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

Basic information

Region (hg38): 8:22440818-22541142

Links

ENSG00000120910 ∙ NCBI:5533 ∙ OMIM:114107 ∙ HGNC:9316 ∙ Uniprot:P48454 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• schizophrenia (No Known Disease Relationship), mode of inheritance: Unknown

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PPP3CC gene.

• Inborn genetic diseases (17 variants)
• not provided (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PPP3CC 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			16	2		18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					2	2
Total	0	0	16	2	2

Variants in PPP3CC

This is a list of pathogenic ClinVar variants found in the PPP3CC region.

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

Position	Type	Phenotype	Significance	ClinVar
8-22441422-C-G		not specified	Uncertain significance (Dec 28, 2023)
8-22441431-C-T		not specified	Uncertain significance (Aug 08, 2022)
8-22441440-A-C		not specified	Uncertain significance (Jun 24, 2022)
8-22474994-A-C		not specified	Uncertain significance (Oct 17, 2023)
8-22474996-T-C		not specified	Uncertain significance (Dec 21, 2022)
8-22475031-A-C			Likely benign (Apr 06, 2018)
8-22475038-A-G		not specified	Uncertain significance (Apr 11, 2023)
8-22475058-C-G		not specified	Uncertain significance (Dec 15, 2022)
8-22475089-A-G		not specified	Uncertain significance (Feb 13, 2024)
8-22475095-G-T		not specified	Uncertain significance (Jul 26, 2022)
8-22475528-T-G		not specified	Uncertain significance (Feb 26, 2024)
8-22498011-A-G		not specified	Uncertain significance (Jan 23, 2023)
8-22513317-G-A		not specified	Uncertain significance (Jan 23, 2023)
8-22513381-C-T		not specified	Uncertain significance (Apr 07, 2022)
8-22513411-G-T		not specified	Uncertain significance (May 23, 2023)
8-22522541-T-A		not specified	Uncertain significance (Apr 28, 2023)
8-22527394-G-T		not specified	Uncertain significance (Feb 06, 2023)
8-22527417-T-G		not specified	Uncertain significance (Oct 26, 2022)
8-22528550-G-A		not specified	Uncertain significance (May 30, 2023)
8-22531335-G-A			Benign (Apr 06, 2018)
8-22532269-G-A		not specified	Uncertain significance (Dec 18, 2023)
8-22532282-T-C		Keratoconus	Uncertain significance (Feb 18, 2018)
8-22532937-G-A		not specified	Uncertain significance (Feb 23, 2023)
8-22539481-C-T		not specified	Uncertain significance (Nov 03, 2023)
8-22540648-G-A		not specified	Uncertain significance (Jan 31, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PPP3CC	protein_coding	protein_coding	ENST00000397775	15	100321

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.264	0.736	125721	0	26	125747	0.000103

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.32	222	284	0.780	0.0000148	3404
Missense in Polyphen		76	108.41	0.70107		1305
Synonymous	1.31	86	103	0.836	0.00000549	971
Loss of Function	3.86	7	29.7	0.236	0.00000157	359

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000909	0.0000908
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000177	0.000176
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000391	0.0000327
Other	0.000327	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Calcium-dependent, calmodulin-stimulated protein phosphatase which plays an essential role in the transduction of intracellular Ca(2+)-mediated signals. Dephosphorylates and activates transcription factor NFATC1. Dephosphorylates and inactivates transcription factor ELK1. Dephosphorylates DARPP32. {ECO:0000269|PubMed:19154138}.
• 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);Dopaminergic synapse - 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;Amyotrophic lateral sclerosis (ALS);Initiation of transcription and translation elongation at the HIV-1 LTR;G Protein Signaling Pathways;MAPK Signaling Pathway;Wnt Signaling Pathway;Signaling by GPCR;Signal Transduction;regulation of pgc-1a;nitric oxide signaling pathway;endocytotic role of ndk phosphins and dynamin;role of mef2d in t-cell apoptosis;effects of calcineurin in keratinocyte differentiation;nfat and hypertrophy of the heart ;signaling pathway from g-protein families;t cell receptor signaling pathway;bcr signaling pathway;Activation of BAD and translocation to mitochondria ;Activation of BH3-only proteins;Intrinsic Pathway for Apoptosis;Apoptosis;Programmed Cell Death;DARPP-32 events;fmlp induced chemokine gene expression in hmc-1 cells;BCR signaling pathway;Opioid Signalling;G alpha (i) signalling events;GPCR downstream signalling;CD4 T cell receptor signaling-JNK cascade;CD4 T cell receptor signaling (Consensus)

Recessive Scores

• pRec: 0.161

Intolerance Scores

• loftool: 0.612
• rvis_EVS: 0.53
• rvis_percentile_EVS: 80.82

Haploinsufficiency Scores

• pHI: 0.165
• hipred: Y
• hipred_score: 0.704
• ghis: 0.488

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.900

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ppp3cc
• Phenotype: reproductive system phenotype; cellular phenotype

Gene ontology

• Biological process: protein dephosphorylation;brain development;calcineurin-NFAT signaling cascade;calcineurin-mediated signaling;positive regulation of synaptic vesicle endocytosis
• Cellular component: cytoplasm;cytosol;calcineurin complex;glutamatergic synapse;presynaptic cytosol
• Molecular function: protein binding;calmodulin binding;calmodulin-dependent protein phosphatase activity;metal ion binding