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): 7:94907202-95296415
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (153 variants)
- PPP1R9A-related_disorder (17 variants)
- not_provided (8 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. These statistics are base on transcript: NM_001166160.2. Only rare variants are included in the table.
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.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 7 | |||||
| missense | 147 | 11 | 162 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 147 | 16 | 6 |
Loading clinvar variants...
GnomAD
Source:
| 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:
- 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