PPP1R9A

protein phosphatase 1 regulatory subunit 9A, the group of Protein phosphatase 1 regulatory subunits|Sterile alpha motif domain containing|PDZ domain containing

Basic information

Region (hg38): 7:94907201-95296415

Links

ENSG00000158528 ∙ NCBI:55607 ∙ OMIM:602468 ∙ HGNC:14946 ∙ Uniprot:Q9ULJ8 ∙ 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 PPP1R9A gene.

• Inborn genetic diseases (48 variants)
• not provided (9 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PPP1R9A 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					2	2
missense			45	6	4	55
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	45	6	6

Variants in PPP1R9A

This is a list of pathogenic ClinVar variants found in the PPP1R9A region.

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

Position	Type	Phenotype	Significance	ClinVar
7-94910147-A-G		not specified	Uncertain significance (Jan 26, 2023)
7-94910224-C-T		PPP1R9A-related disorder	Benign (Oct 28, 2019)
7-94910228-T-A			Benign (Nov 15, 2018)
7-94910238-A-T		not specified	Uncertain significance (Sep 30, 2021)
7-94910346-A-G		not specified	Likely benign (Dec 02, 2021)
7-94910413-G-A		not specified	Uncertain significance (Nov 09, 2021)
7-94910463-A-G		not specified	Uncertain significance (Nov 29, 2021)
7-94910506-C-T		PPP1R9A-related disorder	Likely benign (Apr 29, 2020)
7-94910544-A-C		not specified	Uncertain significance (Jan 09, 2024)
7-94910573-G-A		not specified	Uncertain significance (Jul 12, 2022)
7-94910694-G-C		not specified	Uncertain significance (Apr 05, 2023)
7-94910722-T-A		not specified	Uncertain significance (Oct 27, 2023)
7-94910844-C-A		not specified	Uncertain significance (Dec 06, 2022)
7-94910915-A-T			Likely benign (May 01, 2022)
7-94910925-C-T		not specified	Uncertain significance (Oct 03, 2022)
7-94910960-G-C		not specified	Uncertain significance (Sep 28, 2022)
7-94911044-C-G		not specified	Likely benign (Jun 16, 2023)
7-94911048-C-G		not specified	Uncertain significance (Aug 22, 2023)
7-94911104-A-G		PPP1R9A-related disorder	Benign (Feb 25, 2021)
7-94911122-C-T		not specified	Uncertain significance (Feb 17, 2024)
7-94911161-A-G		not specified	Uncertain significance (Apr 28, 2022)
7-94911168-T-C		not specified	Uncertain significance (Dec 15, 2022)
7-94911206-G-A		not specified	Uncertain significance (Jun 23, 2023)
7-94911215-G-A		PPP1R9A-related disorder	Benign (Jun 11, 2019)
7-94911239-G-T		not specified	Uncertain significance (Jul 20, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PPP1R9A	protein_coding	protein_coding	ENST00000433360	19	389214

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000108	1.00	125714	0	34	125748	0.000135

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.22	611	702	0.870	0.0000347	9076
Missense in Polyphen		188	286.83	0.65544		3803
Synonymous	1.44	229	258	0.886	0.0000134	2551
Loss of Function	4.95	21	63.6	0.330	0.00000351	776

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000231	0.000217
Ashkenazi Jewish	0.00	0.00
East Asian	0.000335	0.000326
Finnish	0.000185	0.000185
European (Non-Finnish)	0.0000903	0.0000879
Middle Eastern	0.000335	0.000326
South Asian	0.000238	0.000229
Other	0.000182	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Binds to actin filaments (F-actin) and shows cross- linking activity. Binds along the sides of the F-actin. May be involved in neurite formation. Inhibits protein phosphatase 1- alpha activity (By similarity). {ECO:0000250}.

Recessive Scores

• pRec: 0.128

Intolerance Scores

• loftool: 0.146
• rvis_EVS: 0.03
• rvis_percentile_EVS: 55.83

Haploinsufficiency Scores

• pHI: 0.437
• hipred: Y
• hipred_score: 0.648
• ghis: 0.529

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.790

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ppp1r9a
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); 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: actin filament organization;aging;calcium-mediated signaling;regulation of actin filament polymerization;neuron projection development;positive regulation of protein kinase activity;regulation of filopodium assembly;negative regulation of stress fiber assembly;regulation of synapse structural plasticity;regulation of synapse assembly;excitatory postsynaptic potential;positive regulation of dendritic spine development;regulation of dendritic spine morphogenesis;cellular response to toxic substance;postsynaptic actin cytoskeleton organization;negative regulation of long-term synaptic potentiation;positive regulation of long-term synaptic depression;negative regulation of spontaneous neurotransmitter secretion
• Cellular component: cytoplasm;cytosol;postsynaptic density;actin cytoskeleton;cell junction;filopodium;dendrite;cortical actin cytoskeleton;neuromuscular junction;neuronal cell body;dendritic spine neck;postsynaptic actin cytoskeleton;glutamatergic synapse;growth cone lamellipodium
• Molecular function: protein binding;protein C-terminus binding;protein phosphatase 1 binding;protein kinase binding;protein domain specific binding;protein homodimerization activity;ion channel binding;actin filament binding;GTPase binding