PPP1R1A

protein phosphatase 1 regulatory inhibitor subunit 1A, the group of Protein phosphatase 1 regulatory subunits

Basic information

Region (hg38): 12:54575387-54588659

Links

ENSG00000135447 ∙ NCBI:5502 ∙ OMIM:613246 ∙ HGNC:9286 ∙ Uniprot:Q13522 ∙ 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 PPP1R1A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PPP1R1A 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			12	1		13
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	12	1	0

Variants in PPP1R1A

This is a list of pathogenic ClinVar variants found in the PPP1R1A region.

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

Position	Type	Phenotype	Significance	ClinVar
12-54575599-C-T		not specified	Uncertain significance (Jul 19, 2022)
12-54576038-C-G		not specified	Uncertain significance (Feb 07, 2025)
12-54576057-C-G		not specified	Uncertain significance (Jun 18, 2021)
12-54576061-C-T		not specified	Uncertain significance (Jan 09, 2024)
12-54576066-G-A		not specified	Uncertain significance (Mar 15, 2024)
12-54576605-G-A		not specified	Uncertain significance (Apr 09, 2024)
12-54576639-G-A		not specified	Uncertain significance (May 08, 2024)
12-54576645-C-T		not specified	Uncertain significance (Apr 19, 2024)
12-54576690-G-A		not specified	Uncertain significance (Jan 27, 2022)
12-54577260-C-G		not specified	Uncertain significance (Sep 01, 2021)
12-54577261-C-G		not specified	Uncertain significance (May 24, 2023)
12-54577281-C-G		not specified	Uncertain significance (Apr 18, 2023)
12-54580992-T-A		not specified	Uncertain significance (Jan 26, 2023)
12-54580997-T-C		not specified	Uncertain significance (May 26, 2023)
12-54581054-G-A			Benign (Jul 06, 2018)
12-54581984-G-C		not specified	Uncertain significance (Jul 08, 2022)
12-54582006-AC-TG		Rosette-forming glioneuronal tumor	Uncertain significance (-)
12-54582012-C-T		not specified	Uncertain significance (Sep 22, 2023)
12-54582039-G-A		not specified	Likely benign (Dec 18, 2023)
12-54582069-C-T		Low-frequency hearing loss;Low-frequency sensorineural hearing impairment • not specified	Conflicting classifications of pathogenicity (Dec 14, 2024)
12-54582783-T-C		not specified	Uncertain significance (Mar 04, 2024)
12-54583233-C-T		not specified	Uncertain significance (Dec 10, 2024)
12-54584275-C-G		not specified	Uncertain significance (Jun 18, 2024)
12-54588415-G-A		not specified	Uncertain significance (Dec 02, 2022)
12-54588425-C-G		not specified	Uncertain significance (Dec 16, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PPP1R1A	protein_coding	protein_coding	ENST00000257905	7	13273

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0219	0.916	124645	0	9	124654	0.0000361

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.977	66	92.4	0.714	0.00000518	1080
Missense in Polyphen		28	38.255	0.73194		470
Synonymous	-0.628	36	31.5	1.14	0.00000160	330
Loss of Function	1.59	4	9.21	0.435	3.93e-7	119

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000599	0.0000556
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.0000599	0.0000556
South Asian	0.000261	0.000261
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Inhibitor of protein-phosphatase 1. This protein may be important in hormonal control of glycogen metabolism. Hormones that elevate intracellular cAMP increase I-1 activity in many tissues. I-1 activation may impose cAMP control over proteins that are not directly phosphorylated by PKA. Following a rise in intracellular calcium, I-1 is inactivated by calcineurin (or PP2B). Does not inhibit type-2 phosphatases.
• Pathway: Long-term potentiation - Homo sapiens (human);Adrenergic signaling in cardiomyocytes - Homo sapiens (human);Common Pathways Underlying Drug Addiction (Consensus)

Recessive Scores

• pRec: 0.115

Intolerance Scores

• loftool: 0.736
• rvis_EVS: 0.61
• rvis_percentile_EVS: 83.07

Haploinsufficiency Scores

• pHI: 0.454
• hipred: N
• hipred_score: 0.199

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0370

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ppp1r1a
• Phenotype: nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan)

Gene ontology

• Biological process: glycogen metabolic process;negative regulation of phosphoprotein phosphatase activity;intracellular signal transduction
• Cellular component: extracellular space;cytoplasm
• Molecular function: protein serine/threonine phosphatase inhibitor activity;protein binding