PPP1R2

protein-coding

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

Gene summary

Protein phosphatase-1 (PP1) is one of the main eukaryotic serine/threonine phosphatases. The protein encoded by this gene binds to the catalytic subunit of PP1, strongly inhibiting its activity. Ten related pseudogenes have been found throughout the human genome. Several splice variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2015]

MANE transcript

NM_006241.8

Inheritance

—

ClinVar variants

U:23B:4

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.33

Max pathogenic AF

—

Genomic locus

chr3:195,514,428-195,543,386

External References & Databases

Ensembl (ENSG00000184203)

Transcript & Mutation Effects

hg38 • Region Span ~29.0 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 PPP1R2 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 23

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_006241.8. 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						0
missense			22 clinvar	4 clinvar		26
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	23	4	0	27

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 25 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_006241.8	RefSeq	NP_006232.1	6	MANE Select
ENST00000618156.5	Ensembl	ENSP00000484580.1	6	MANE Select
NM_001291504.2	RefSeq	NP_001278433.1	6	Standard
NM_001291505.2	RefSeq	NP_001278434.1	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

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

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000328432
Coding exons: 6
Length: 28989
Individuals with no LoFs: 125733
Homozygous LoFs: 0
Heterozygous LoFs: 6
Defined: 125739
p: 0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.682	89	109	0.816	0.00000540	1358
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000054	0.000054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000035	0.000035	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): E
Essential (CRISPR2): S
Essential (gene trap): E
Indispensability pred.: E
Indispensability score: 0.861

Gene Damage Prediction

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