PPP1R17

protein-coding

protein phosphatase 1 regulatory subunit 17, the group of Protein phosphatase 1 regulatory subunits

Gene summary

The protein encoded by this gene is found primarily in cerebellar Purkinje cells, where it functions as a protein phosphatase inhibitor. The encoded protein is a substrate for cGMP-dependent protein kinase. An allele of this gene was discovered that increases susceptibility to hypercholesterolemia. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2010]

Previous symbols:

C7orf16

MANE transcript

NM_006658.5

Inheritance

—

ClinVar variants

U:21B:2

Top phenotype

Hypercholesterolemia, familial, 1

gnomAD constraint

pLI —, LoF o/e 0.76

Max pathogenic AF

—

Genomic locus

chr7:31,687,215-31,708,455

External References & Databases

Ensembl (ENSG00000106341)

Transcript & Mutation Effects

hg38 • Region Span ~21.2 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 PPP1R17 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 22

Hypercholesterolemia, familial, 1Total: 2

HypercholesterolemiaTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_006658.5. 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			21 clinvar	1 clinvar	1 clinvar	23
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	21	1	1	23

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 11 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_006658.5	RefSeq	NP_006649.2	4	MANE Select
ENST00000342032.8	Ensembl	ENSP00000340125.3	4	MANE Select
NM_001145123.3	RefSeq	NP_001138595.1	3	Standard
ENST00000409146.3	Ensembl	ENSP00000386459.3	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Long-term depression - Homo sapiens (human)

Biological Process

central nervous system development
regulation of phosphatase activity
negative regulation of phosphoprotein phosphatase activity
intracellular signal transduction

Molecular Function

protein serine/threonine phosphatase inhibitor activity

Cellular Component

cellular_component
nucleoplasm

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000342032
Coding exons: 4
Length: 21741
Individuals with no LoFs: 125645
Homozygous LoFs: 0
Heterozygous LoFs: 98
Defined: 125743
p: 0.000390

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.0203	85	84.5	1.01	0.00000414	1027
Missense (PolyPhen)		23	25.445	0.9039		319
Synonymous	0.0244	30	30.2	0.994	0.00000163	277
Loss of Function	0.558	5	6.54	0.764	2.74e-7	89

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00038	0.00037	rare
Latino/Admixed American	0.00066	0.00064	rare
Ashkenazi Jewish	0.0042	0.0042	notable
East Asian	0.000054	0.000054	rare
Finnish	0.000047	0.000046	rare
European (Non-Finnish)	0.00013	0.00013	rare
South Asian	0.00017	0.00016	rare
Other	0.0010	0.00098	notable

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Inhibits phosphatase activities of protein phosphatase 1 (PP1) and protein phosphatase 2A (PP2A) complexes. {ECO:0000250}.;

Recessive Scores

pRec: 0.194

Intolerance Scores

RVIS EVS: -0.03
RVIS percentile EVS: 51.66

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.114

Gene Damage Prediction

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