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.

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.

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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1	3	4
missense			58	4		62
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			1			1
non coding						0
Total	0	0	58	5	3

Variants in PPP1R3F

This is a list of pathogenic ClinVar variants found in the PPP1R3F region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
X-49269909-T-C		not specified	Likely benign (Apr 07, 2023)
X-49269927-G-A		not specified	Uncertain significance (Jun 22, 2021)
X-49269946-C-T		not specified	Uncertain significance (Feb 22, 2023)
X-49269958-C-T		not specified	Uncertain significance (Apr 07, 2023)
X-49269997-C-A		not specified	Uncertain significance (Apr 17, 2024)
X-49270036-C-G		not specified	Uncertain significance (Nov 07, 2022)
X-49270040-G-T		not specified	Uncertain significance (Dec 07, 2023)
X-49270071-G-A		not specified	Uncertain significance (Aug 04, 2021)
X-49270072-C-T		not specified	Uncertain significance (Feb 26, 2024)
X-49270077-G-C		not specified	Uncertain significance (Nov 18, 2022)
X-49270093-G-A		not specified	Uncertain significance (Apr 28, 2022)
X-49270143-G-A		not specified	Uncertain significance (Sep 15, 2021)
X-49270146-G-A		not specified	Uncertain significance (May 29, 2024)
X-49270186-C-G		not specified	Uncertain significance (Oct 13, 2023)
X-49270192-C-T		not specified	Uncertain significance (Jun 12, 2023)
X-49270193-C-T			Benign (Jun 10, 2019)
X-49270242-C-T		not specified	Uncertain significance (Apr 07, 2023)
X-49270243-C-T		not specified	Uncertain significance (Feb 02, 2024)
X-49270255-A-G			Uncertain significance (Nov 03, 2023)
X-49270267-G-A		not specified	Uncertain significance (Aug 08, 2022)
X-49270314-C-T		not specified	Uncertain significance (Apr 24, 2024)
X-49270329-G-A		not specified	Uncertain significance (Mar 19, 2024)
X-49270402-C-T		not specified	Uncertain significance (Sep 27, 2022)
X-49270476-C-G		not specified	Uncertain significance (Feb 27, 2024)
X-49270491-G-A		not specified	Uncertain significance (Apr 07, 2023)

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