PPP2R3A

protein phosphatase 2 regulatory subunit B''alpha, the group of Protein phosphatase 2 regulatory subunits|EF-hand domain containing

Basic information

Region (hg38): 3:135965728-136147894

Previous symbols: [ "PPP2R3" ]

Links

ENSG00000073711 ∙ NCBI:5523 ∙ OMIM:604944 ∙ HGNC:9307 ∙ Uniprot:Q06190 ∙ 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 PPP2R3A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PPP2R3A 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	7	15
missense			68	9	12	89
nonsense					1	1
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)					1	1
splice region				2	2	4
non coding						0
Total	0	0	69	17	21

Variants in PPP2R3A

This is a list of pathogenic ClinVar variants found in the PPP2R3A region.

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

Position	Type	Phenotype	Significance	ClinVar
3-136001518-T-C		not specified	Uncertain significance (Oct 16, 2023)
3-136001636-G-T		PPP2R3A-related disorder	Likely benign (Sep 18, 2019)
3-136001661-C-G		not specified	Uncertain significance (Mar 31, 2022)
3-136001697-G-A		PPP2R3A-related disorder	Benign (Sep 25, 2019)
3-136001698-A-G		PPP2R3A-related disorder	Benign (Oct 30, 2019)
3-136001709-A-G		not specified	Likely benign (Jun 11, 2021)
3-136001730-G-A		PPP2R3A-related disorder	Likely benign (Mar 31, 2022)
3-136001821-A-G		PPP2R3A-related disorder	Likely benign (Apr 25, 2019)
3-136001822-C-A		not specified	Uncertain significance (Aug 29, 2022)
3-136001831-T-C		PPP2R3A-related disorder	Benign (Oct 30, 2019)
3-136002009-G-T		PPP2R3A-related disorder	Benign (Oct 17, 2019)
3-136002015-T-C		not specified	Uncertain significance (Oct 14, 2023)
3-136002033-A-C		not specified	Uncertain significance (Mar 06, 2023)
3-136002042-G-A		not specified	Uncertain significance (Jun 03, 2022)
3-136002046-A-G		not specified	Uncertain significance (Dec 15, 2023)
3-136002075-C-G		PPP2R3A-related disorder	Benign (Sep 18, 2019)
3-136002081-A-G		not specified	Uncertain significance (Dec 02, 2022)
3-136002082-C-T		not specified	Uncertain significance (Sep 07, 2022)
3-136002120-G-A		not specified	Uncertain significance (Mar 01, 2024)
3-136002189-A-G		not specified	Uncertain significance (Mar 27, 2023)
3-136002194-C-T		PPP2R3A-related disorder	Benign (Feb 20, 2019)
3-136002243-A-G		PPP2R3A-related disorder	Likely benign (Feb 28, 2019)
3-136002318-T-A		not specified	Uncertain significance (Feb 28, 2024)
3-136002327-G-C		not specified	Uncertain significance (Dec 19, 2022)
3-136002348-A-G		not specified	Uncertain significance (Dec 15, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PPP2R3A	protein_coding	protein_coding	ENST00000264977	13	182219

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.623	0.377	125288	11	448	125747	0.00183

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0389	591	588	1.00	0.0000287	7638
Missense in Polyphen		294	305.34	0.96285		4070
Synonymous	-0.145	217	214	1.01	0.0000110	2106
Loss of Function	5.00	10	47.0	0.213	0.00000239	632

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0250	0.0245
Ashkenazi Jewish	0.000100	0.0000992
East Asian	0.000109	0.000109
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000311	0.000308
Middle Eastern	0.000109	0.000109
South Asian	0.000230	0.000229
Other	0.000327	0.000326

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.
• Pathway: PI3K-Akt signaling pathway - Homo sapiens (human);Dopaminergic synapse - 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);Focal Adhesion-PI3K-Akt-mTOR-signaling pathway;Wnt Signaling Pathway and Pluripotency;PI3K-Akt Signaling Pathway;Glycogen Metabolism;GPCR Dopamine D1like receptor;insulin Mam;EGFR1;insulin (Consensus)

Recessive Scores

• pRec: 0.132

Intolerance Scores

• loftool: 0.870
• rvis_EVS: 0.37
• rvis_percentile_EVS: 74.78

Haploinsufficiency Scores

• pHI: 0.153
• hipred: Y
• hipred_score: 0.718
• ghis: 0.491

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.620

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ppp2r3a
• Phenotype: skeleton 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); growth/size/body region phenotype

Zebrafish Information Network

• Gene name: ppp2r3a
• Affected structure: cardiac muscle cell
• Phenotype tag: abnormal
• Phenotype quality: decreased amount

Gene ontology

• Biological process: protein dephosphorylation;regulation of phosphoprotein phosphatase activity;somite development
• Cellular component: protein phosphatase type 2A complex
• Molecular function: calcium ion binding;protein binding;protein phosphatase regulator activity