PPP1R3F

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

Basic information

Region (hg38): X:49269793-49301461

Links

ENSG00000049769 ∙ NCBI:89801 ∙ ∙ HGNC:14944 ∙ Uniprot:Q6ZSY5 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PPP1R3F gene.

• not_specified (116 variants)
• not_provided (16 variants)
• PPP1R3F_Associated_Neurodevelopmental_Disorder (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PPP1R3F gene is commonly pathogenic or not. These statistics are base on transcript: NM_000033215.5. Only rare variants are included in the table.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				5	2	7
missense			114	9		123
nonsense						0
start loss						0
frameshift	1					1
splice donor/acceptor (+/-2bp)						0
Total	1	0	114	14	2

Highest pathogenic variant AF is 0.0000529466

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PPP1R3F	protein_coding	protein_coding	ENST00000055335	4	31624

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000415	0.643	125719	3	12	125734	0.0000597

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.213	284	294	0.965	0.0000251	4992
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000242	0.000197
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000722	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000118	0.0000791
Middle Eastern	0.0000722	0.0000544
South Asian	0.0000672	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Glycogen-targeting subunit for protein phosphatase 1 (PP1). {ECO:0000269|PubMed:21668450}.
• Pathway: Insulin signaling pathway - Homo sapiens (human) (Consensus)

Haploinsufficiency Scores

• pHI: 0.380
• hipred: N
• hipred_score: 0.180
• ghis: 0.557

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.164

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ppp1r3f

Gene ontology

• Biological process: regulation of glycogen biosynthetic process;regulation of glycogen (starch) synthase activity
• Cellular component: membrane;integral component of membrane
• Molecular function: protein phosphatase binding;glycogen binding