PPP1R10

protein-coding

protein phosphatase 1 regulatory subunit 10, the group of Protein phosphatase 1 regulatory subunits

Gene summary

This gene encodes a protein phosphatase 1 binding protein. The encoded protein plays a role in many cellular processes including cell cycle progression, DNA repair and apoptosis by regulating the activity of protein phosphatase 1. This gene lies within the major histocompatibility complex class I region on chromosome 6, and alternatively spliced transcript variants have been observed for this gene. [provided by RefSeq, Jul 2012]

MANE transcript

NM_002714.4

Inheritance

—

ClinVar variants

U:113B:13

Top phenotype

See cases

gnomAD constraint

pLI —, LoF o/e 0.06

Max pathogenic AF

—

Genomic locus

chr6:30,600,413-30,618,612

External References & Databases

Ensembl (ENSG00000204569)

Transcript & Mutation Effects

hg38 • Region Span ~18.2 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 PPP1R10 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 106

not providedTotal: 6

See casesTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_002714.4. 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 clinvar	2 clinvar	4
missense			106 clinvar	10 clinvar		116
nonsense			1 clinvar			1
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			4 clinvar			4
Total	0	0	113	11	2	126

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 24 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_002714.4	RefSeq	NP_002705.2	18	MANE Select
ENST00000376511.7	Ensembl	ENSP00000365694.2	18	MANE Select
NM_001376195.1	RefSeq	NP_001363124.1	18	Standard
ENST00000913675.1	Ensembl	ENSP00000583734.1	17	Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / Model	Organism	Observed Phenotype
ppp1r10	Danio rerio	Structure: eye Quality: decreased size abnormal

Gene / Model

Organism

Observed Phenotype

ppp1r10

Danio rerio

Structure: eye

Quality: decreased size

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

protein import into nucleus
negative regulation of cardiac muscle cell apoptotic process
positive regulation of telomere maintenance
negative regulation of phosphoprotein phosphatase activity
negative regulation of mitotic DNA damage checkpoint

Molecular Function

DNA binding
RNA binding
protein phosphatase inhibitor activity
protein binding
metal ion binding

Cellular Component

nuclear chromosome, telomeric region
chromatin
nucleus
nucleoplasm
nuclear body

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000376511
Coding exons: 18
Length: 18213
Individuals with no LoFs: 125743
Homozygous LoFs: 0
Heterozygous LoFs: 4
Defined: 125747
p: 0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.95	377	576	0.654	0.0000340	6028
Missense (PolyPhen)		51	117.03	0.43577		1494
Synonymous	0.268	202	207	0.976	0.0000121	1990
Loss of Function	6.19	3	50.4	0.0595	0.00000365	492

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000065	0.000062	rare
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0.00010	0.000099	rare
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000018	0.000018	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Scaffold protein which mediates the formation of the PTW/PP1 phosphatase complex by providing a binding platform to each component of the complex. The PTW/PP1 phosphatase complex plays a role in the control of chromatin structure and cell cycle progression during the transition from mitosis into interphase. Mediates interaction of WDR82 and PPP1CA. Inhibitor of PPP1CA and PPP1CC phosphatase activities. Has inhibitory activity on PPP1CA only when phosphorylated. Binds to mRNA, single-stranded DNA (ssDNA), poly(A) and poly(G) homopolymers (By similarity). {ECO:0000250, ECO:0000269|PubMed:9450550}.;

Recessive Scores

pRec: 0.110

Intolerance Scores

LoFtool: 0.114
RVIS EVS: -0.78
RVIS percentile EVS: 12.97

Essentials

Essential (CRISPR): E
Essential (CRISPR2): E
Essential (gene trap): E
Indispensability pred.: E
Indispensability score: 1.00

Gene Damage Prediction

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