PPP1R3B

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

Basic information

Region (hg38): 8:9136255-9151574

Links

ENSG00000173281 ∙ NCBI:79660 ∙ OMIM:610541 ∙ HGNC:14942 ∙ Uniprot:Q86XI6 ∙ 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 PPP1R3B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PPP1R3B 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						0
missense			18	1		19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	18	1	0

Variants in PPP1R3B

This is a list of pathogenic ClinVar variants found in the PPP1R3B region.

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

Position	Type	Phenotype	Significance	ClinVar
8-9140816-T-C		not specified	Uncertain significance (Dec 15, 2023)
8-9140936-G-T		not specified	Uncertain significance (Jan 31, 2024)
8-9140997-G-C		not specified	Uncertain significance (Jun 23, 2021)
8-9141009-C-G		not specified	Uncertain significance (Jun 10, 2022)
8-9141054-C-T		not specified	Uncertain significance (Jul 27, 2021)
8-9141134-G-A			Uncertain significance (Mar 05, 2018)
8-9141164-C-T		not specified	Uncertain significance (Aug 21, 2023)
8-9141174-C-A		not specified	Uncertain significance (Dec 03, 2021)
8-9141183-C-G		not specified	Uncertain significance (Mar 25, 2024)
8-9141227-T-G		not specified	Uncertain significance (Oct 03, 2022)
8-9141229-C-A		not specified	Uncertain significance (May 16, 2022)
8-9141258-G-A		not specified	Uncertain significance (Dec 21, 2023)
8-9141261-C-T		not specified	Likely benign (Jan 26, 2022)
8-9141293-T-C		not specified	Uncertain significance (Oct 05, 2023)
8-9141304-C-G		not specified	Uncertain significance (Oct 26, 2022)
8-9141398-G-A		not specified	Uncertain significance (Apr 06, 2023)
8-9141405-C-T		not specified	Uncertain significance (Jun 09, 2022)
8-9141565-C-A		not specified	Uncertain significance (Nov 30, 2022)
8-9141575-A-C		not specified	Uncertain significance (Jul 25, 2023)
8-9141613-C-T		not specified	Uncertain significance (Dec 21, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PPP1R3B	protein_coding	protein_coding	ENST00000310455	1	15320

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0650	0.877	125733	0	15	125748	0.0000596

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.11	198	159	1.25	0.00000988	1898
Missense in Polyphen		54	55.089	0.98023		689
Synonymous	-0.869	76	67.0	1.14	0.00000509	528
Loss of Function	1.60	3	7.82	0.384	4.07e-7	104

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000181	0.000181
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000529	0.0000527
Middle Eastern	0.000109	0.000109
South Asian	0.0000980	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts as a glycogen-targeting subunit for phosphatase PP1. Facilitates interaction of the PP1 with enzymes of the glycogen metabolism and regulates its activity. Suppresses the rate at which PP1 dephosphorylates (inactivates) glycogen phosphorylase and enhances the rate at which it activates glycogen synthase and therefore limits glycogen breakdown. Its activity is inhibited by PYGL, resulting in inhibition of the glycogen synthase and glycogen phosphorylase phosphatase activities of PP1. Dramatically increases basal and insulin-stimulated glycogen synthesis upon overexpression in hepatocytes (By similarity). {ECO:0000250}.
• Pathway: Insulin resistance - Homo sapiens (human);Insulin signaling pathway - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.133

Intolerance Scores

• loftool: 0.536
• rvis_EVS: 0.04
• rvis_percentile_EVS: 56.92

Haploinsufficiency Scores

• pHI: 0.179
• hipred: Y
• hipred_score: 0.568
• ghis: 0.458

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.293

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ppp1r3b
• Phenotype: reproductive system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); homeostasis/metabolism phenotype; growth/size/body region phenotype

Gene ontology

• Biological process: glycogen metabolic process;regulation of glycogen biosynthetic process;regulation of glycogen catabolic process;protein dephosphorylation;regulation of phosphoprotein phosphatase activity
• Cellular component: protein phosphatase type 1 complex;glycogen granule;intracellular membrane-bounded organelle
• Molecular function: protein binding;protein phosphatase regulator activity;enzyme binding;[phosphorylase] phosphatase activity