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.

• not_specified (49 variants)
• Prostate_cancer (1 variants)

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. These statistics are base on transcript: NM_000005398.7. 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				1		1
missense			49			49
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	49	1	0

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
		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

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

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