PPP4R1

protein phosphatase 4 regulatory subunit 1, the group of Armadillo like helical domain containing|Protein phosphatase 4 regulatory subunits

Basic information

Region (hg38): 18:9546791-9615240

Links

ENSG00000154845 ∙ NCBI:9989 ∙ OMIM:604908 ∙ HGNC:9320 ∙ Uniprot:Q8TF05 ∙ 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 PPP4R1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PPP4R1 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			72	1		73
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	72	1	0

Variants in PPP4R1

This is a list of pathogenic ClinVar variants found in the PPP4R1 region.

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

Position	Type	Phenotype	Significance	ClinVar
18-9547805-G-A		not specified	Uncertain significance (Apr 07, 2023)
18-9547814-A-G		not specified	Uncertain significance (Oct 05, 2023)
18-9547881-G-A		not specified	Uncertain significance (Apr 26, 2023)
18-9547900-G-C		not specified	Uncertain significance (Jan 03, 2024)
18-9547947-A-T		not specified	Uncertain significance (Nov 17, 2022)
18-9549217-C-T		not specified	Uncertain significance (Oct 02, 2023)
18-9549256-C-A		not specified	Uncertain significance (Sep 22, 2023)
18-9549257-T-C		not specified	Uncertain significance (Sep 25, 2024)
18-9549337-G-A		not specified	Uncertain significance (Dec 14, 2023)
18-9550062-A-G		not specified	Uncertain significance (Aug 16, 2021)
18-9550143-G-A		not specified	Uncertain significance (Jul 22, 2024)
18-9550180-C-T		not specified	Uncertain significance (Feb 19, 2025)
18-9550303-G-A		not specified	Uncertain significance (Jan 21, 2025)
18-9553343-C-T		not specified	Uncertain significance (Jan 14, 2025)
18-9557257-C-A		not specified	Uncertain significance (Mar 21, 2022)
18-9557267-T-A		not specified	Uncertain significance (Apr 04, 2023)
18-9557301-C-G		not specified	Uncertain significance (Apr 27, 2024)
18-9557352-T-C		not specified	Uncertain significance (Aug 15, 2023)
18-9559427-C-A		not specified	Uncertain significance (Oct 14, 2023)
18-9559447-G-A		not specified	Uncertain significance (Dec 05, 2022)
18-9559448-T-C		not specified	Uncertain significance (Sep 14, 2021)
18-9559451-C-G		not specified	Uncertain significance (Oct 06, 2021)
18-9559520-T-C		not specified	Uncertain significance (Sep 25, 2024)
18-9561999-T-C		not specified	Uncertain significance (Mar 31, 2023)
18-9562042-C-T		not specified	Uncertain significance (Nov 25, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PPP4R1	protein_coding	protein_coding	ENST00000400556	20	68450

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.000421	124780	0	14	124794	0.0000561

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.04	382	512	0.746	0.0000270	6261
Missense in Polyphen		110	185.72	0.59228		2233
Synonymous	1.03	169	187	0.904	0.0000106	1785
Loss of Function	5.68	6	48.8	0.123	0.00000275	589

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000646	0.0000646
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000556	0.0000556
Finnish	0.000139	0.000139
European (Non-Finnish)	0.0000628	0.0000618
Middle Eastern	0.0000556	0.0000556
South Asian	0.0000706	0.0000654
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Regulatory subunit of serine/threonine-protein phosphatase 4. May play a role in regulation of cell division in renal glomeruli. The PPP4C-PPP4R1 PP4 complex may play a role in dephosphorylation and regulation of HDAC3. {ECO:0000269|PubMed:15805470}.

Recessive Scores

• pRec: 0.109

Intolerance Scores

• loftool: 0.363
• rvis_EVS: 0.09
• rvis_percentile_EVS: 60.68

Haploinsufficiency Scores

• pHI: 0.217
• hipred: Y
• hipred_score: 0.736
• ghis: 0.464

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: H
• gene_indispensability_pred: E
• gene_indispensability_score: 0.691

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ppp4r1

Gene ontology

• Biological process: protein phosphorylation;protein dephosphorylation;signal transduction;regulation of phosphoprotein phosphatase activity
• Cellular component: protein phosphatase 4 complex
• Molecular function: phosphoprotein phosphatase activity;protein serine/threonine phosphatase activity;protein binding;protein phosphatase regulator activity