PPP1R9B

protein phosphatase 1 regulatory subunit 9B, the group of Protein phosphatase 1 regulatory subunits|PDZ domain containing

Basic information

Region (hg38): 17:50133736-50150677

Previous symbols: [ "PPP1R6", "PPP1R9" ]

Links

ENSG00000108819 ∙ NCBI:84687 ∙ OMIM:603325 ∙ HGNC:9298 ∙ Uniprot:Q96SB3 ∙ 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 PPP1R9B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PPP1R9B 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				10	2	12
missense			8	6	2	16
nonsense						0
start loss						0
frameshift					2	2
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding					1	1
Total	0	0	8	16	7

Variants in PPP1R9B

This is a list of pathogenic ClinVar variants found in the PPP1R9B region.

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

Position	Type	Phenotype	Significance	ClinVar
17-50135573-T-G			Uncertain significance (Jan 01, 2018)
17-50135595-C-T			not provided (-)
17-50135607-A-C			Likely benign (Feb 01, 2023)
17-50136017-C-T		PPP1R9B-related disorder	Uncertain significance (Jan 22, 2024)
17-50136033-C-T			not provided (-)
17-50136072-C-A			not provided (-)
17-50139532-G-A			not provided (-)
17-50140208-C-T		PPP1R9B-related disorder	Likely benign (Jul 06, 2020)
17-50141355-G-T			Benign (Jun 26, 2018)
17-50143591-T-C			Benign (Jun 26, 2018)
17-50143633-G-A			not provided (-)
17-50143641-C-T			not provided (-)
17-50143714-G-A			not provided (-)
17-50149182-G-A			not provided (-)
17-50149243-G-A		PPP1R9B-related disorder	Likely benign (Jun 22, 2022)
17-50149377-T-C			not provided (-)
17-50149383-C-T			not provided (-)
17-50149402-G-A			not provided (-)
17-50149422-C-A		PPP1R9B-related disorder	Likely benign (Jun 01, 2021)
17-50149422-C-T			not provided (-)
17-50149425-C-G		PPP1R9B-related disorder	Benign (Apr 21, 2020)
17-50149437-T-C			not provided (-)
17-50149440-C-G			not provided (-)
17-50149443-C-T			not provided (-)
17-50149455-C-G			not provided (-)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PPP1R9B	protein_coding	protein_coding	ENST00000316878	12	16888

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.000247	121424	0	20	121444	0.0000823

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.02	206	369	0.558	0.0000205	5148
Missense in Polyphen		20	85.235	0.23464		1011
Synonymous	-0.417	169	162	1.04	0.00000998	1626
Loss of Function	4.74	1	28.2	0.0355	0.00000128	364

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00113	0.00113
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00113	0.00113
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Seems to act as a scaffold protein in multiple signaling pathways. Modulates excitatory synaptic transmission and dendritic spine morphology. Binds to actin filaments (F-actin) and shows cross-linking activity. Binds along the sides of the F-actin. May play an important role in linking the actin cytoskeleton to the plasma membrane at the synaptic junction. Believed to target protein phosphatase 1/PP1 to dendritic spines, which are rich in F-actin, and regulates its specificity toward ion channels and other substrates, such as AMPA-type and NMDA-type glutamate receptors. Plays a role in regulation of G-protein coupled receptor signaling, including dopamine D2 receptors and alpha- adrenergic receptors. May establish a signaling complex for dopaminergic neurotransmission through D2 receptors by linking receptors downstream signaling molecules and the actin cytoskeleton. Binds to ADRA1B and RGS2 and mediates regulation of ADRA1B signaling. May confer to Rac signaling specificity by binding to both, RacGEFs and Rac effector proteins. Probably regulates p70 S6 kinase activity by forming a complex with TIAM1 (By similarity). Required for hepatocyte growth factor (HGF)- induced cell migration. {ECO:0000250, ECO:0000269|PubMed:19151759}.

Recessive Scores

• pRec: 0.251

Haploinsufficiency Scores

• pHI: 0.444
• hipred: Y
• hipred_score: 0.662

Essentials

• gene_indispensability_pred: E
• gene_indispensability_score: 0.766

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ppp1r9b
• 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); skeleton phenotype; homeostasis/metabolism phenotype; cellular phenotype; growth/size/body region phenotype

Gene ontology

• Biological process: regulation of cell growth by extracellular stimulus;actin filament organization;cell cycle arrest;regulation of exit from mitosis;RNA splicing;cell migration;calcium-mediated signaling;negative regulation of cell growth;neuron projection development;negative regulation of phosphoprotein phosphatase activity;regulation of cell population proliferation;filopodium assembly;modulation of chemical synaptic transmission;cellular response to morphine;regulation of opioid receptor signaling pathway
• Cellular component: protein phosphatase type 1 complex;nucleoplasm;cytoplasm;plasma membrane;adherens junction;postsynaptic density;actin cytoskeleton;lamellipodium;filopodium;dendrite;ruffle membrane;dendritic spine
• Molecular function: protein phosphatase inhibitor activity;protein binding;protein phosphatase 1 binding;actin filament binding