PPP2R5C

protein phosphatase 2 regulatory subunit B'gamma, the group of Protein phosphatase 2 regulatory subunits|Armadillo like helical domain containing

Basic information

Region (hg38): 14:101761708-101927989

Links

ENSG00000078304 ∙ NCBI:5527 ∙ OMIM:601645 ∙ HGNC:9311 ∙ Uniprot:Q13362 ∙ 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 PPP2R5C gene.

• not provided (42 variants)
• Inborn genetic diseases (8 variants)
• Intellectual disability (1 variants)
• Macrocephaly-developmental delay syndrome (1 variants)
• See cases (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PPP2R5C 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				8	3	11
missense		2	13	3	1	19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			1	3	2	6
non coding			1	7	8	16
Total	0	2	14	18	12

Variants in PPP2R5C

This is a list of pathogenic ClinVar variants found in the PPP2R5C region.

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

Position	Type	Phenotype	Significance	ClinVar
14-101761898-C-T			Uncertain significance (Dec 06, 2022)
14-101761907-A-C			Uncertain significance (Oct 07, 2023)
14-101761915-G-C			Uncertain significance (Aug 16, 2022)
14-101762885-C-T			Benign (Apr 15, 2023)
14-101762940-A-G			Likely benign (Oct 01, 2023)
14-101818972-A-G			Uncertain significance (Jul 30, 2022)
14-101818979-T-C			Likely benign (May 20, 2023)
14-101818979-T-G			Likely benign (Apr 25, 2021)
14-101819008-A-G			Benign (Jun 15, 2023)
14-101819040-C-A		not specified	Uncertain significance (Oct 05, 2023)
14-101831721-G-A			Likely benign (Jan 01, 2023)
14-101856742-G-A			Uncertain significance (Jun 17, 2023)
14-101856756-T-C			Benign (Jan 22, 2024)
14-101856810-A-G			Likely benign (May 14, 2018)
14-101856841-C-T			Uncertain significance (Jul 01, 2022)
14-101856862-A-G		not specified	Uncertain significance (Aug 12, 2021)
14-101882153-G-A			Likely benign (May 10, 2022)
14-101882226-G-A			Likely benign (Jul 06, 2023)
14-101882229-G-A		PPP2R5C-related disorder	Likely benign (Jun 17, 2019)
14-101882230-G-A		Intellectual disability	Likely pathogenic (Jan 01, 2016)
14-101882239-CCAA-C			Uncertain significance (Sep 01, 2015)
14-101882264-A-G		See cases	Likely pathogenic (Apr 26, 2021)
14-101882276-C-T			Benign (Jan 13, 2024)
14-101882277-G-A			Uncertain significance (Jan 17, 2024)
14-101882291-A-G			Likely benign (May 20, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PPP2R5C	protein_coding	protein_coding	ENST00000422945	16	166192

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.971	0.0293	125729	0	18	125747	0.0000716

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.08	150	300	0.499	0.0000161	3669
Missense in Polyphen		32	101.99	0.31376		1324
Synonymous	0.687	98	107	0.915	0.00000609	980
Loss of Function	4.51	5	33.0	0.152	0.00000162	428

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000185	0.000185
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000266	0.0000264
Middle Eastern	0.00	0.00
South Asian	0.000392	0.000392
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: The B regulatory subunit might modulate substrate selectivity and catalytic activity, and also might direct the localization of the catalytic enzyme to a particular subcellular compartment. The PP2A-PPP2R5C holoenzyme may specifically dephosphorylate and activate TP53 and play a role in DNA damage- induced inhibition of cell proliferation. PP2A-PPP2R5C may also regulate the ERK signaling pathway through ERK dephosphorylation. {ECO:0000269|PubMed:16456541, ECO:0000269|PubMed:17245430}.
• Pathway: PI3K-Akt signaling pathway - Homo sapiens (human);Dopaminergic synapse - Homo sapiens (human);Oocyte meiosis - Homo sapiens (human);mRNA surveillance pathway - Homo sapiens (human);AMPK signaling pathway - Homo sapiens (human);Adrenergic signaling in cardiomyocytes - Homo sapiens (human);Sphingolipid signaling pathway - Homo sapiens (human);Human papillomavirus infection - Homo sapiens (human);miR-targeted genes in lymphocytes - TarBase;Focal Adhesion-PI3K-Akt-mTOR-signaling pathway;Wnt Signaling Pathway and Pluripotency;PI3K-Akt Signaling Pathway;Glycogen Metabolism;DNA Damage Response (only ATM dependent);Degradation of beta-catenin by the destruction complex;RAF activation;Signaling by WNT;Signal Transduction;Gene expression (Transcription);Generic Transcription Pathway;GPCR Dopamine D1like receptor;CTLA4 inhibitory signaling;Costimulation by the CD28 family;RNA Polymerase II Transcription;Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal;Amplification of signal from the kinetochores;Mitotic Spindle Checkpoint;Cell Cycle Checkpoints;Immune System;Adaptive Immune System;insulin Mam;RHO GTPases Activate Formins;Disassembly of the destruction complex and recruitment of AXIN to the membrane;RHO GTPase Effectors;Signaling by Rho GTPases;Hemostasis;Negative regulation of MAPK pathway;RAF/MAP kinase cascade;MAPK1/MAPK3 signaling;MAPK family signaling cascades;Regulation of TP53 Degradation;Regulation of TP53 Expression and Degradation;PIP3 activates AKT signaling;Beta-catenin phosphorylation cascade;Regulation of TP53 Activity;Transcriptional Regulation by TP53;PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling;Negative regulation of the PI3K/AKT network;Mitotic Prometaphase;Separation of Sister Chromatids;Mitotic Anaphase;Mitotic Metaphase and Anaphase;M Phase;Cell Cycle;Resolution of Sister Chromatid Cohesion;Platelet sensitization by LDL;Platelet homeostasis;Cell Cycle, Mitotic;Intracellular signaling by second messengers;TCF dependent signaling in response to WNT;insulin (Consensus)

Recessive Scores

• pRec: 0.127

Intolerance Scores

• loftool: 0.0814
• rvis_EVS: 0.02
• rvis_percentile_EVS: 55.45

Haploinsufficiency Scores

• pHI: 0.160
• hipred: Y
• hipred_score: 0.825
• ghis: 0.616

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.981

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ppp2r5c
• Phenotype: cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); normal 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); growth/size/body region phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); cellular phenotype; muscle phenotype

Gene ontology

• Biological process: protein dephosphorylation;signal transduction;negative regulation of cell population proliferation;regulation of phosphatidylinositol 3-kinase signaling;regulation of protein autophosphorylation;proteasome-mediated ubiquitin-dependent protein catabolic process;regulation of phosphoprotein phosphatase activity
• Cellular component: protein phosphatase type 2A complex;chromosome, centromeric region;nucleus;nucleoplasm;Golgi apparatus;cytosol
• Molecular function: protein binding;protein phosphatase regulator activity;protein phosphatase activator activity