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.

• not_specified (113 variants)

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. These statistics are base on transcript: NM_001042388.3. 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			112	1		113
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	112	1	0

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