PPP1R7

protein-coding

protein phosphatase 1 regulatory subunit 7, the group of Protein phosphatase 1 regulatory subunits

Gene summary

This gene encodes a protein subunit that regulates the activity of the serine/threonine phosphatase, protein phosphatase-1. The encoded protein is required for completion of the mitotic cycle and for targeting protein phosphatase-1 to mitotic kinetochores. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Sep 2013]

MANE transcript

NM_002712.3

Inheritance

—

ClinVar variants

U:44B:2

Top phenotype

Autism spectrum disorder

gnomAD constraint

pLI —, LoF o/e 0.05

Max pathogenic AF

—

Genomic locus

chr2:241,149,576-241,183,652

External References & Databases

Ensembl (ENSG00000115685)

Transcript & Mutation Effects

hg38 • Region Span ~34.1 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 PPP1R7 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 40

not providedTotal: 1

Autism spectrum disorderTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_002712.3. 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			41 clinvar	1 clinvar		42
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	44	1	1	46

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 77 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_002712.3	RefSeq	NP_002703.1	10	MANE Select
ENST00000234038.11	Ensembl	ENSP00000234038.6	10	MANE Select
NM_001282409.1	RefSeq	NP_001269338.1	9	Standard
NM_001282410.1	RefSeq	NP_001269339.1	9	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

miR-targeted genes in epithelium - TarBase
miR-targeted genes in lymphocytes - TarBase
miR-targeted genes in muscle cell - TarBase
miR-targeted genes in squamous cell - TarBase

Biological Process

biological_process
positive regulation of protein dephosphorylation
regulation of phosphoprotein phosphatase activity

Molecular Function

protein binding
protein phosphatase regulator activity
enzyme regulator activity

Cellular Component

nucleus
chromosome
cytoplasm
extracellular exosome

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000234038
Coding exons: 10
Length: 34077
Individuals with no LoFs: 125745
Homozygous LoFs: 0
Heterozygous LoFs: 2
Defined: 125747
p: 0.00000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.86	138	215	0.643	0.0000130	2394
Missense (PolyPhen)		33	68.958	0.47855		868
Synonymous	0.592	84	91.2	0.921	0.00000584	665
Loss of Function	3.93	1	19.9	0.0503	0.00000100	234

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	0.000046	0.000046	rare
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: Regulatory subunit of protein phosphatase 1. {ECO:0000250}.;

Recessive Scores

pRec: 0.100

Intolerance Scores

RVIS EVS: -0.09
RVIS percentile EVS: 46.74

Essentials

Essential (CRISPR): N
Essential (CRISPR2): E
Essential (gene trap): E
Indispensability pred.: E
Indispensability score: 0.877

Gene Damage Prediction

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