PPP1R3F

protein-coding

protein phosphatase 1 regulatory subunit 3F, the group of Protein phosphatase 1 regulatory subunits

Gene summary

This gene encodes a protein that has been identified as one of several type-1 protein phosphatase (PP1) regulatory subunits. One or two of these subunits, together with the well-conserved catalytic subunit, can form the PP1 holoenzyme, where the regulatory subunit functions to regulate substrate specificity and/or targeting to a particular cellular compartment. Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2010]

MANE transcript

NM_033215.5

Inheritance

ClinVar variants

P:1U:151B:33

Top phenotype

neurodevelopmental disorder

gnomAD constraint

pLI —, LoF o/e 0.73

Max pathogenic AF

—

Genomic locus

chrX:49,269,793-49,301,461

External References & Databases

Ensembl (ENSG00000049769)

Transcript & Mutation Effects

hg38 • Region Span ~31.7 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

neurodevelopmental disorderSTRONG

Inheritance Pattern: XL

Disease ID:MONDO:0700092

Submitter: PanelApp Australia

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to PPP1R3F variants in ClinVar

6 Conditions Cataloged

not specifiedTotal: 135

not providedTotal: 38

PPP1R3F-related conditionTotal: 7

PPP1R3F-related neurodevelopmental disorderTotal: 1

PPP1R3F Associated Neurodevelopmental DisorderTotal: 1

PPP1R3F-related disorderTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_033215.5. 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			2 clinvar	14 clinvar	2 clinvar	18
missense			146 clinvar	17 clinvar		163
nonsense						0
start loss						0
frameshift	1 clinvar		2 clinvar			3
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	1	0	151	31	2	185

Highest pathogenic variant AF is 0.00005294658

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 32 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_033215.5	RefSeq	NP_149992.3	4	MANE Select
ENST00000055335.11	Ensembl	ENSP00000055335.6	4	MANE Select
NM_001184745.2	RefSeq	NP_001171674.1	3	Standard
ENST00000376188.1	Ensembl	ENSP00000365359.1	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Insulin signaling pathway - Homo sapiens (human)

Biological Process

regulation of glycogen biosynthetic process
regulation of glycogen (starch) synthase activity

Molecular Function

protein phosphatase binding
glycogen binding

Cellular Component

membrane
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000055335
Coding exons: 4
Length: 31624
Individuals with no LoFs: 125719
Homozygous LoFs: 3
Heterozygous LoFs: 12
Defined: 125734
p: 0.0000597

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.213	284	294	0.965	0.0000251	4992
Missense (PolyPhen)		116	114.65	1.0118		1980
Synonymous	-0.424	140	134	1.05	0.0000123	1804
Loss of Function	0.846	8	11.0	0.725	7.01e-7	227

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00017	0.00012	rare
Latino/Admixed American	0.000074	0.000058	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000072	0.000054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00012	0.000079	rare
South Asian	0.000067	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Glycogen-targeting subunit for protein phosphatase 1 (PP1). {ECO:0000269|PubMed:21668450}.;

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.164

Gene Damage Prediction

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