PPP1R3D

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

Basic information

Region (hg38): 20:59936663-59940305

Previous symbols: [ "PPP1R6" ]

Links

ENSG00000132825 ∙ NCBI:5509 ∙ OMIM:603326 ∙ HGNC:9294 ∙ Uniprot:O95685 ∙ 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 PPP1R3D gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PPP1R3D 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			40	2		42
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	40	2	0

Variants in PPP1R3D

This is a list of pathogenic ClinVar variants found in the PPP1R3D region.

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

Position	Type	Phenotype	Significance	ClinVar
20-59939058-C-T		not specified	Uncertain significance (Sep 22, 2022)
20-59939067-C-T		not specified	Uncertain significance (Apr 18, 2023)
20-59939072-G-A		not specified	Uncertain significance (Sep 16, 2021)
20-59939085-C-T		not specified	Uncertain significance (Jul 26, 2024)
20-59939088-G-A		not specified	Uncertain significance (Nov 19, 2022)
20-59939121-C-G		not specified	Uncertain significance (Aug 26, 2024)
20-59939171-T-C		not specified	Uncertain significance (Sep 08, 2024)
20-59939204-G-C		not specified	Uncertain significance (Apr 12, 2022)
20-59939253-C-T		not specified	Uncertain significance (Feb 22, 2025)
20-59939261-C-T		not specified	Uncertain significance (Oct 25, 2023)
20-59939262-G-A		not specified	Uncertain significance (Oct 03, 2024)
20-59939262-G-T		not specified	Uncertain significance (Nov 12, 2021)
20-59939332-G-C		not specified	Uncertain significance (Nov 13, 2024)
20-59939346-A-G		not specified	Likely benign (Sep 26, 2024)
20-59939378-G-A		not specified	Uncertain significance (Jan 17, 2025)
20-59939400-A-C		not specified	Uncertain significance (Dec 03, 2024)
20-59939541-C-T		not specified	Uncertain significance (Jul 05, 2023)
20-59939585-A-C		not specified	Uncertain significance (Feb 19, 2025)
20-59939632-C-A		not specified	Uncertain significance (May 11, 2022)
20-59939636-T-C		not specified	Likely benign (Dec 21, 2024)
20-59939664-C-T		not specified	Uncertain significance (Nov 13, 2024)
20-59939670-C-T		not specified	Uncertain significance (Oct 17, 2023)
20-59939687-C-T		not specified	Uncertain significance (Apr 07, 2022)
20-59939691-G-C		not specified	Uncertain significance (Sep 09, 2024)
20-59939696-G-A		not specified	Uncertain significance (Nov 14, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PPP1R3D	protein_coding	protein_coding	ENST00000370996	1	3459

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00470	0.700	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.583	154	176	0.876	0.0000129	1879
Missense in Polyphen		39	49.501	0.78786		469
Synonymous	0.883	76	86.4	0.879	0.00000700	677
Loss of Function	0.696	4	5.81	0.688	3.34e-7	63

LoF frequencies by population

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

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Seems to act as a glycogen-targeting subunit for PP1. PP1 is essential for cell division, and participates in the regulation of glycogen metabolism, muscle contractility and protein synthesis.
• Pathway: Insulin resistance - Homo sapiens (human);Insulin signaling pathway - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.105

Haploinsufficiency Scores

• pHI: 0.126
• hipred: N
• hipred_score: 0.490
• ghis: 0.399

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.858

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ppp1r3d

Gene ontology

• Biological process: glycogen metabolic process;regulation of glycogen biosynthetic process;regulation of glycogen catabolic process;protein dephosphorylation
• Cellular component: glycogen granule;intracellular membrane-bounded organelle
• Molecular function: protein serine/threonine phosphatase activity;enzyme binding