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.

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.

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			16	2		18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			26			26
Total	0	0	42	2	0

Variants in PPP4R2

This is a list of pathogenic ClinVar variants found in the PPP4R2 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-73047262-C-T		not specified	Uncertain significance (Feb 03, 2022)
3-73059039-T-C		not specified	Uncertain significance (Aug 19, 2024)
3-73059062-T-A		not specified	Uncertain significance (Apr 22, 2022)
3-73062098-A-G		not specified	Uncertain significance (Sep 11, 2024)
3-73062124-A-C		not specified	Uncertain significance (Oct 20, 2023)
3-73062190-A-G		not specified	Uncertain significance (Oct 25, 2023)
3-73062229-C-T		not specified	Uncertain significance (Jun 13, 2023)
3-73062248-A-G		not specified	Uncertain significance (Oct 30, 2023)
3-73062250-C-G		not specified	Uncertain significance (Nov 07, 2022)
3-73062253-A-G		not specified	Uncertain significance (Mar 17, 2023)
3-73062268-G-T		not specified	Uncertain significance (Dec 06, 2021)
3-73062370-A-G		not specified	Uncertain significance (Aug 21, 2023)
3-73062376-G-C		not specified	Uncertain significance (Oct 20, 2024)
3-73062379-A-C		not specified	Uncertain significance (Jun 11, 2021)
3-73062401-C-T		not specified	Uncertain significance (Dec 28, 2022)
3-73062455-G-A		not specified	Uncertain significance (Oct 16, 2023)
3-73062470-G-A		not specified	Uncertain significance (Dec 28, 2023)
3-73062473-T-A		not specified	Uncertain significance (Nov 08, 2022)
3-73062480-T-A		not specified	Uncertain significance (Jul 05, 2022)
3-73062500-T-C		not specified	Uncertain significance (Dec 11, 2023)
3-73062512-G-A		not specified	Uncertain significance (Sep 27, 2022)
3-73062559-A-G		not specified	Uncertain significance (Dec 16, 2023)
3-73062575-C-G		not specified	Uncertain significance (Mar 31, 2024)
3-73062604-A-G		not specified	Uncertain significance (Oct 12, 2022)
3-73062608-C-G		not specified	Uncertain significance (Dec 07, 2023)

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