PPP2R2C

protein phosphatase 2 regulatory subunit Bgamma, the group of Protein phosphatase 2 regulatory subunits|WD repeat domain containing

Basic information

Region (hg38): 4:6320578-6563600

Links

ENSG00000074211 ∙ NCBI:5522 ∙ OMIM:605997 ∙ HGNC:9306 ∙ Uniprot:Q9Y2T4 ∙ 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 PPP2R2C gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PPP2R2C 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					1	1
missense			12			12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			2		1	3
Total	0	0	14	0	2

Variants in PPP2R2C

This is a list of pathogenic ClinVar variants found in the PPP2R2C region.

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

Position	Type	Phenotype	Significance	ClinVar
4-6323309-A-G		not specified	Uncertain significance (Oct 10, 2023)
4-6323393-G-A		not specified	Uncertain significance (May 09, 2023)
4-6323431-A-C		not specified	Uncertain significance (Nov 11, 2024)
4-6323445-G-A		not specified	Uncertain significance (Jan 03, 2024)
4-6323463-C-T		not specified	Uncertain significance (Nov 04, 2022)
4-6323471-C-T		not specified	Uncertain significance (Nov 13, 2024)
4-6323493-G-A		not specified	Uncertain significance (Dec 08, 2021)
4-6323546-C-T		not specified	Uncertain significance (Mar 16, 2022)
4-6333636-T-C		not specified	Uncertain significance (Jan 03, 2024)
4-6347836-C-T			Benign (Apr 30, 2018)
4-6348005-C-G		not specified	Uncertain significance (Apr 26, 2023)
4-6372536-G-A			Benign (Oct 10, 2018)
4-6375842-G-T		not specified	Uncertain significance (Jul 13, 2021)
4-6375889-C-T		not specified	Uncertain significance (Aug 12, 2024)
4-6378502-A-G		not specified	Uncertain significance (Sep 29, 2023)
4-6381080-T-C		not specified	Uncertain significance (Dec 21, 2023)
4-6381780-G-A		not specified	Uncertain significance (Jun 16, 2024)
4-6381782-G-T		not specified	Uncertain significance (May 17, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PPP2R2C	protein_coding	protein_coding	ENST00000335585	9	243023

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.900	0.100	124815	0	1	124816	0.00000401

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.53	123	293	0.420	0.0000191	2998
Missense in Polyphen		22	105.84	0.20786		1072
Synonymous	-0.621	131	122	1.07	0.00000885	829
Loss of Function	3.60	3	20.6	0.145	0.00000107	231

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.000100	0.000100
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: 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);Tight junction - Homo sapiens (human);mRNA surveillance pathway - Homo sapiens (human);AMPK signaling pathway - Homo sapiens (human);Adrenergic signaling in cardiomyocytes - Homo sapiens (human);Hippo signaling pathway - Homo sapiens (human);Chagas disease (American trypanosomiasis) - Homo sapiens (human);Sphingolipid signaling pathway - Homo sapiens (human);Hepatitis C - Homo sapiens (human);Human papillomavirus infection - Homo sapiens (human);Focal Adhesion-PI3K-Akt-mTOR-signaling pathway;Wnt Signaling Pathway and Pluripotency;PI3K-Akt Signaling Pathway;Glycogen Metabolism;GPCR Dopamine D1like receptor;insulin Mam;insulin (Consensus)

Recessive Scores

• pRec: 0.137

Intolerance Scores

• loftool: 0.194
• rvis_EVS: -0.67
• rvis_percentile_EVS: 15.62

Haploinsufficiency Scores

• pHI: 0.715
• hipred: Y
• hipred_score: 0.819
• ghis: 0.692

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.357

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ppp2r2c

Gene ontology

• Biological process: mitotic cell cycle;regulation of phosphoprotein phosphatase activity;peptidyl-serine dephosphorylation
• Cellular component: protein phosphatase type 2A complex;cytosol
• Molecular function: protein serine/threonine phosphatase activity;protein binding;protein phosphatase regulator activity