PPP1R2

protein phosphatase 1 regulatory inhibitor subunit 2, the group of Protein phosphatase 1 regulatory subunits

Basic information

Region (hg38): 3:195514428-195543386

Links

ENSG00000184203 ∙ NCBI:5504 ∙ OMIM:601792 ∙ HGNC:9288 ∙ Uniprot:P41236 ∙ 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 PPP1R2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PPP1R2 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			11	4		15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	11	4	0

Variants in PPP1R2

This is a list of pathogenic ClinVar variants found in the PPP1R2 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-195516906-C-T		not specified	Likely benign (Jun 26, 2024)
3-195516939-G-A		not specified	Uncertain significance (Jul 17, 2024)
3-195519030-C-T		not specified	Uncertain significance (Jan 21, 2025)
3-195523694-C-T		not specified	Likely benign (Jun 30, 2023)
3-195523707-A-T		not specified	Uncertain significance (Mar 07, 2025)
3-195523735-T-G		not specified	Uncertain significance (Sep 05, 2024)
3-195523752-G-A		not specified	Uncertain significance (Apr 12, 2023)
3-195523754-T-C		not specified	Uncertain significance (Jan 16, 2024)
3-195524831-A-G		not specified	Uncertain significance (Aug 12, 2024)
3-195524832-T-C		not specified	Likely benign (Jun 29, 2023)
3-195524870-C-G		not specified	Uncertain significance (Jun 30, 2024)
3-195524874-C-A		not specified	Uncertain significance (Oct 12, 2021)
3-195524876-T-C		not specified	Uncertain significance (Jul 09, 2024)
3-195524883-C-T		not specified	Uncertain significance (Oct 26, 2022)
3-195542926-C-T		not specified	Likely benign (Sep 27, 2021)
3-195542931-G-T		not specified	Uncertain significance (Jul 14, 2024)
3-195542955-G-A		not specified	Uncertain significance (Sep 03, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PPP1R2	protein_coding	protein_coding	ENST00000328432	6	28989

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0693	0.919	125733	0	6	125739	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.682	89	109	0.816	0.00000540	1358
Missense in Polyphen		11	21.98	0.50046		335
Synonymous	0.264	38	40.1	0.947	0.00000211	341
Loss of Function	2.19	4	12.3	0.326	6.99e-7	146

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000615	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000545	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000352	0.0000352
Middle Eastern	0.0000545	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Inhibitor of protein-phosphatase 1.

Recessive Scores

• pRec: 0.133

Intolerance Scores

• loftool: 0.312
• rvis_EVS: 0.26
• rvis_percentile_EVS: 70.06

Haploinsufficiency Scores

• hipred: Y
• hipred_score: 0.507
• ghis: 0.505

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.861

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ppp1r2
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span)

Gene ontology

• Biological process: glycogen metabolic process;generation of precursor metabolites and energy;regulation of signal transduction;negative regulation of phosphoprotein phosphatase activity;regulation of phosphoprotein phosphatase activity
• Molecular function: protein phosphatase inhibitor activity;protein serine/threonine phosphatase inhibitor activity;protein binding