PPP1R9A
protein-codingprotein phosphatase 1 regulatory subunit 9A, the group of Protein phosphatase 1 regulatory subunits|Sterile alpha motif domain containing|PDZ domain containing
Gene summary
This gene is imprinted, and located in a cluster of imprinted genes on chromosome 7q12. This gene is transcribed in both neuronal and multiple embryonic tissues, and it is maternally expressed mainly in embryonic skeletal muscle tissues and biallelically expressed in other embryonic tissues. The protein encoded by this gene includes a PDZ domain and a sterile alpha motif (SAM). It is a regulatory subunit of protein phosphatase I, and controls actin cytoskeleton reorganization. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2009]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~389.2 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to PPP1R9A variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001166160.2. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | 5 | 2 | 8 | ||
| missense | 175 | 11 | 4 | 190 | ||
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | ||||
| Total | 0 | 0 | 178 | 16 | 6 | 200 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001159632.1 | 19 | MANE Select | |
| Ensembl | ENSP00000405514.1 | 19 | MANE Select | |
| RefSeq | NP_001159633.1 | 18 | Standard | |
| RefSeq | NP_001159634.1 | 17 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- actin filament organization
- aging
- calcium-mediated signaling
- regulation of actin filament polymerization
- neuron projection development
Molecular Function
- protein binding
- protein C-terminus binding
- protein phosphatase 1 binding
- protein kinase binding
- protein domain specific binding
Cellular Component
- cytoplasm
- cytosol
- postsynaptic density
- actin cytoskeleton
- cell junction
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000433360
- Coding exons
- 19
- Length
- 389214
- Individuals with no LoFs
- 125714
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 34
- Defined
- 125748
- p
- 0.000135
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.22 | 611 | 702 | 0.870 | 0.0000347 | 9076 |
| Missense (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 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.000076 | 0.000062 | rare |
| Latino/Admixed American | 0.00016 | 0.00014 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00034 | 0.00033 | rare |
| Finnish | 0.00018 | 0.00018 | rare |
| European (Non-Finnish) | 0.000090 | 0.000088 | rare |
| South Asian | 0.00024 | 0.00023 | rare |
| Other | 0.00018 | 0.00016 | rare |
dbNSFP Gene Annotations
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
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.790
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |