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.

• not_specified (63 variants)

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. These statistics are base on transcript: NM_000006242.4. 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						0
missense			60	3		63
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	60	3	0

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