PPP4R2

protein phosphatase 4 regulatory subunit 2, the group of Protein phosphatase 4 regulatory subunits

Basic information

Region (hg38): 3:72996803-73069198

Links

ENSG00000163605

∙ NCBI:151987 ∙ OMIM:613822 ∙ HGNC:18296 ∙ Uniprot:Q9NY27 ∙ 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 PPP4R2 gene.

not_specified (94 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PPP4R2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000174907.4. 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	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			40 clinvar	3 clinvar		43
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	40	3	0

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PPP4R2	protein_coding	protein_coding	ENST00000356692	9	72415

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.998	0.00165	125678	0	5	125683	0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.000893	206	206	1.00	0.00000978	2774
Missense in Polyphen		36	53.738	0.66992		789
Synonymous	-1.81	90	70.6	1.27	0.00000360	738
Loss of Function	4.00	0	18.7	0.00	9.92e-7	265

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.0000483	0.0000462
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.000109	0.000109
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Regulatory subunit of serine/threonine-protein phosphatase 4 (PP4). May regulate the activity of PPP4C at centrosomal microtubule organizing centers. Its interaction with the SMN complex leads to enhance the temporal localization of snRNPs, suggesting a role of PPP4C in maturation of spliceosomal snRNPs. The PPP4C-PPP4R2-PPP4R3A PP4 complex specifically dephosphorylates H2AFX phosphorylated on 'Ser-140' (gamma-H2AFX) generated during DNA replication and required for DNA double strand break repair. Mediates RPA2 dephosphorylation by recruiting PPP4C to RPA2 in a DNA damage-dependent manner. RPA2 dephosphorylation is required for the efficient RPA2-mediated recruitment of RAD51 to chromatin following double strand breaks, an essential step for DNA repair. {ECO:0000269|PubMed:10769191, ECO:0000269|PubMed:12668731, ECO:0000269|PubMed:18614045, ECO:0000269|PubMed:20154705}.;
Pathway: HDR through Homologous Recombination (HR) or Single Strand Annealing (SSA);DNA Repair;DNA Double-Strand Break Repair;Homology Directed Repair;Processing of DNA double-strand break ends (Consensus)

Recessive Scores

pRec: 0.0956

Intolerance Scores

loftool: 0.192
rvis_EVS: 0.22
rvis_percentile_EVS: 68.27

Haploinsufficiency Scores

pHI: 0.290
hipred: Y
hipred_score: 0.794
ghis: 0.499

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: K
gene_indispensability_pred: E
gene_indispensability_score: 0.761

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Ppp4r2
Phenotype: immune system phenotype; renal/urinary system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); hematopoietic system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan);

Gene ontology

Biological process: mRNA processing;cellular protein modification process;protein dephosphorylation;RNA splicing;regulation of double-strand break repair via homologous recombination;regulation of phosphoprotein phosphatase activity
Cellular component: nucleus;nucleoplasm;cytoplasm;centrosome;protein phosphatase 4 complex
Molecular function: protein binding;protein phosphatase regulator activity;protein binding, bridging