PPP1R3C

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

Basic information

Region (hg38): 10:91628442-91633071

Previous symbols: [ "PPP1R5" ]

Links

ENSG00000119938 ∙ NCBI:5507 ∙ OMIM:602999 ∙ HGNC:9293 ∙ Uniprot:Q9UQK1 ∙ 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 PPP1R3C gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PPP1R3C 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			20			20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	20	0	0

Variants in PPP1R3C

This is a list of pathogenic ClinVar variants found in the PPP1R3C region.

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

Position	Type	Phenotype	Significance	ClinVar
10-91629931-C-G		not specified	Uncertain significance (Nov 10, 2022)
10-91629949-T-C		not specified	Uncertain significance (Jan 03, 2022)
10-91630001-G-T		not specified	Uncertain significance (Dec 17, 2021)
10-91630066-G-C		not specified	Uncertain significance (Sep 26, 2023)
10-91630165-T-C		not specified	Uncertain significance (Jan 08, 2024)
10-91630238-T-C		not specified	Uncertain significance (Mar 03, 2022)
10-91630252-C-A		not specified	Uncertain significance (Apr 27, 2024)
10-91630286-C-T		not specified	Uncertain significance (Dec 22, 2023)
10-91630367-T-A		not specified	Uncertain significance (Mar 01, 2024)
10-91630372-G-C		not specified	Uncertain significance (Nov 03, 2023)
10-91630395-G-C		not specified	Uncertain significance (May 10, 2024)
10-91630423-T-C		Malignant tumor of prostate	Uncertain significance (-)
10-91630436-G-A		not specified	Uncertain significance (Nov 27, 2023)
10-91630496-G-A		not specified	Uncertain significance (Aug 17, 2022)
10-91630523-T-C		not specified	Uncertain significance (Jan 12, 2024)
10-91630526-G-A		not specified	Uncertain significance (Feb 05, 2024)
10-91630543-T-G		not specified	Uncertain significance (Mar 08, 2024)
10-91630556-C-A		not specified	Uncertain significance (Dec 16, 2023)
10-91630756-G-A		not specified	Uncertain significance (Nov 18, 2022)
10-91630766-A-G		not specified	Uncertain significance (Jul 26, 2022)
10-91630786-T-C		not specified	Uncertain significance (May 14, 2024)
10-91630795-C-T		not specified	Uncertain significance (May 17, 2023)
10-91630817-C-T		not specified	Uncertain significance (Oct 13, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PPP1R3C	protein_coding	protein_coding	ENST00000238994	2	4613

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00264	0.941	125709	0	39	125748	0.000155

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.107	166	170	0.977	0.00000983	2116
Missense in Polyphen		44	51.338	0.85706		660
Synonymous	-0.701	75	67.7	1.11	0.00000429	579
Loss of Function	1.66	6	12.3	0.488	8.32e-7	138

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000325	0.000325
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.000231	0.000231
European (Non-Finnish)	0.0000528	0.0000527
Middle Eastern	0.0000544	0.0000544
South Asian	0.000555	0.000555
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts as a glycogen-targeting subunit for PP1 and regulates its activity. Activates glycogen synthase, reduces glycogen phosphorylase activity and limits glycogen breakdown. Dramatically increases basal and insulin-stimulated glycogen synthesis upon overexpression in a variety of cell types. {ECO:0000250|UniProtKB:Q7TMB3, ECO:0000269|PubMed:8985175}.
• Pathway: Insulin resistance - Homo sapiens (human);Insulin signaling pathway - Homo sapiens (human);Exercise-induced Circadian Regulation;Metabolism of carbohydrates;Metabolism;Glycogen synthesis;Glycogen metabolism (Consensus)

Recessive Scores

• pRec: 0.159

Intolerance Scores

• loftool: 0.548
• rvis_EVS: 0.08
• rvis_percentile_EVS: 60.31

Haploinsufficiency Scores

• pHI: 0.345
• hipred: Y
• hipred_score: 0.754
• ghis: 0.436

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.942

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ppp1r3c
• Phenotype: muscle phenotype; cellular phenotype; homeostasis/metabolism phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan)

Gene ontology

• Biological process: glycogen metabolic process;glycogen biosynthetic process;protein dephosphorylation;regulation of phosphoprotein phosphatase activity
• Cellular component: cytosol
• Molecular function: protein serine/threonine phosphatase activity;protein binding;protein phosphatase regulator activity;protein phosphatase binding